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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Li, N;Liu, Y | 10.1007/s11426-011-4285-z | null | 16 DONGHUANGCHENGGEN NORTH ST, BEIJING 100717, PEOPLES R CHINA | 4z4116y2i4w55345n4i1d6t3z3nv4u188k6f | Influences of a periodic signal on a noisy synthetic gene network | Beijing Inst Technol | null | Li, N (corresponding author), Beijing Inst Technol, Sch Chem Engn & Environm, Beijing 100081, Peoples R China. | null | Li Nan;Liu Yan | Chemistry, Multidisciplinary | National Natural Science Foundation of China [20905009, 21003010]; Logistics Management & Engineering Platform of Beijing Area Logistics System & Technology Major Laboratory; Beijing Institute of Technology [2009Y1017] | WOS | Li, N | Beijing Inst Technol, Beijing, Peoples R China;Beijing Wuzi Univ, Beijing, Peoples R China | 54 | a;gene;influences;network;Noisy;of;on;periodic;signal;synthetic | 1 | null | SCIENCE PRESS | Beijing Inst Technol, Sch Chem Engn & Environm, Beijing 100081, Peoples R China;Beijing Wuzi Univ, Sch Logist, Beijing 101149, Peoples R China | Article | Beijing Inst Technol | BEIJING | null | null | Beijing Inst Technol;Beijing Wuzi Univ | Beijing Institute of Technology;Logistics Management & Engineering Platform of Beijing Area Logistics System & Technology Major Laboratory;National Natural Science Foundation of China | Li, N (corresponding author), Beijing Inst Technol, Sch Chem Engn & Environm, Beijing 100081, Peoples R China. | 997 | Li Nan;Liu Yan | 18 | 2 | 291,057,600,018 | Beijing Institute of Technology [2009Y1017];Logistics Management & Engineering Platform of Beijing Area Logistics System & Technology Major Laboratory;National Natural Science Foundation of China [20905009, 21003010] | China | SCIENCE CHINA-CHEMISTRY | China | null | null | Beijing Inst Technol, Sch Chem Engn & Environm, Beijing 100081, Peoples R China | 1674-7291 | Li, N;Liu, Y | JUN | leen04@163.com | influences;noisy synthetic gene network;periodic signal | 2 | J | Chemistry | amplification;cellular signal;COHERENCE RESONANCE;distance;DYNAMICS;effect;Effects;elicited;explicit internal signal stochastic resonance;fluctuation;fluctuations;frequency;gene network;Hopf bifurcation point;implicit internal signal stochastic resonance;influences;modulation;noise;noisy synthetic gene network;OSCILLATIONS;parameter;periodic signal;signal;stochastic resonance;switch process;synthetic gene network;SYSTEM;two interesting phenomena | Liu, Y | AMPLIFICATION;DYNAMICS;fluctuation;FLUCTUATIONS;OSCILLATIONS;periodic signal;stochastic resonance;Synthetic gene network;SYSTEM | 992 | [Liu Yan; Li Nan] Beijing Inst Technol, Sch Chem Engn & Environm, Beijing 100081, Peoples R China. [Liu Yan] Beijing Wuzi Univ, Sch Logist, Beijing 101149, Peoples R China. | This work was supported by the National Natural Science Foundation of China (20905009 and 21003010), the Logistics Management & Engineering Platform of Beijing Area Logistics System & Technology Major Laboratory, and Excellent Young Scholars Research Fund of Beijing Institute of Technology (2009Y1017). | cellular signal;coherence resonance;distance;effect;effects;elicited;explicit internal signal stochastic resonance;frequency;gene network;Hopf bifurcation point;implicit internal signal stochastic resonance;modulation;noise;parameter;periodic signal;signal;switch process;synthetic gene network;two interesting phenomena | 10.1002/1439-7641(20020315)3:3<285::AID-CPHC285>3.0.CO;2-A;10.1016/0012-1606(89)90276-5;10.1016/S0006-3495(00)76531-3;10.1016/S0009-2614(00)00343-2;10.1016/S0092-8674(01)00281-1;10.1016/S0168-9525(98)01659-X;10.1021/jp066773c;10.1021/jp901610x;10.1021/jp909858c;10.1021/nl9004546;10.1038/373033a0;10.1038/376236a0;10.1038/377209a0;10.1038/46279;10.1038/nature03508;10.1063/1.1398314;10.1063/1.166336;10.1063/1.1691737;10.1063/1.2920175;10.1063/1.2978183;10.1073/pnas.022642299;10.1073/pnas.0306484101;10.1073/pnas.110057697;10.1073/pnas.85.16.5819;10.1088/0305-4470/14/11/006;10.1093/bioinformatics/bti392;10.1101/gad.4.10.1823;10.1103/PhysRevA.39.4854;10.1103/PhysRevA.44.8032;10.1103/PhysRevE.62.1869;10.1103/PhysRevE.70.041907;10.1103/PhysRevE.71.041101;10.1103/PhysRevE.73.056123;10.1103/PhysRevE.75.031916;10.1103/PhysRevE.77.026205;10.1103/PhysRevE.81.011106;10.1103/PhysRevLett.71.807;10.1103/PhysRevLett.78.775;10.1103/PhysRevLett.81.2854;10.1103/PhysRevLett.81.5048;10.1103/PhysRevLett.84.5447;10.1103/PhysRevLett.88.148101;10.1103/PhysRevLett.88.230602;10.1103/PhysRevLett.93.154101;10.1103/PhysRevLett.94.038102;10.1103/PhysRevLett.97.016802;10.1152/jn.1996.76.5.3002 | Beijing Inst Technol | Li, N;Liu, Y | Liu, Y: Beijing Inst Technol, Sch Chem Engn & Environm, Beijing 100081, Peoples R China | null | 2009Y1017;20905009;21003010 | 47 | null | China | Beijing Inst Technol;Beijing Wuzi Univ | Liu Yan | null | AMPLIFICATION;DYNAMICS;FLUCTUATIONS;OSCILLATIONS;STOCHASTIC RESONANCE;SYSTEM | Liu Yan; Li Nan; | null | Beijing Inst Technol, Sch Chem Engn & Environm, Beijing 100081, Peoples R China;Beijing Wuzi Univ, Sch Logist, Beijing 101149, Peoples R China | Beijing Inst Technol, Sch Chem Engn & Environm, Beijing 100081, Peoples R China;Beijing Wuzi Univ, Sch Logist, Beijing 101149, Peoples R China | 1869-1870 | fluctuation;periodic signal;stochastic resonance;Synthetic gene network | 6 | 1981;1988;1989;1990;1991;1993;1995;1996;1997;1998;1999;2000;2001;2002;2004;2005;2006;2007;2008;2009;2010 | 0 | Beijing Inst Technol, Sch Chem Engn & Environm, Beijing 100081, Peoples R China | Sci. China-Chem. | Li Nan | SCIENCE PRESS | ";,;:;a;also;amplifying;and;be;been;bifurcation;both;by;can;cellular;coherence;coupled;destroyed;distance;effect;effects;elicited;even;explicit;frequency;from;furthermore;gene;have;Hopf;implicit;induced;inhibited;interesting;internal;investigated;is;locked;modulation;network;noise;occur;occurs;of;on;or;parameter;periodic;phenomena;point;process;resonance;signal;stochastic;switch;synthetic;the;to;tuning;two;when;with | Beijing Inst Technol | The effects of noise and a periodic signal on a synthetic gene network have been investigated. By tuning the distance of a parameter from the Hopf bifurcation point, both implicit internal signal stochastic resonance and explicit internal signal stochastic resonance can be induced by noise. Furthermore, a switch process can also be elicited. When a periodic signal is coupled to the gene network, two interesting phenomena occur with the modulation of the frequency of the signal: the effect of noise amplifying cellular signal can be inhibited or even destroyed, and "locked" coherence resonance occurs. | null | AMPLIFICATION;DYNAMICS;FLUCTUATIONS;OSCILLATIONS;STOCHASTIC RESONANCE;SYSTEM | 0 | null | fluctuation;periodic signal;stochastic resonance;Synthetic gene network | 6 | AMPLIFICATION;DYNAMICS;FLUCTUATIONS;OSCILLATIONS;periodic signal;stochastic resonance;synthetic gene networks;SYSTEM | WOS:000291057600018 | Beijing Inst Technol, Beijing, Peoples R China;Beijing Wuzi Univ, Beijing, Peoples R China | China | 2,011 | null | null | null | null | English | null | BIOINFORMATICS;BIOPHYS J;CELL;CHAOS;CHEM PHYS LETT;CHEMPHYSCHEM;DEV BIOL;GENE DEV;J CHEM PHYS;J NEUROPHYSIOL;J PHYS A-MATH GEN;J PHYS CHEM B;J PHYS CHEM C;NANO LETT;NATURE;P NATL ACAD SCI USA;PHYS REV A;PHYS REV E;PHYS REV LETT;TRENDS GENET | Li Nan;Liu Yan | 2024-03-11
ER | Ahmad, K;Baptista, M S;Benzi, R;Berg, O G;Bulter, T;Chen, L N;Collins, J J;Fiering, S;Fulinski, A;Fung, E;Gang, H;Ghosh, P;Gong, Y B;Guerra, D N;Hasty, J;Hoffmann, P;Hou, Z H;Hänggi, P;Jia, Y;Jiang, Y;Jung, P;Koseska, A;Lai, Y C;Lang, X F;Li, Q S;Lindner, J F;Liu, Q;Mcadams, H H;Mcmillen, D;Mcnamara, B;Olemskoi, A I;Paulsson, J;Pei, X;Pikovsky, A S;Russell, D F;Tong, N H;Vanroon, M A;Wang, H L;Weintraub, H;Wiesenfeld, K;Wijgerde, M;Xiao, T J;Zakharova, A;Zhong, S;Zhou, C S;Zhou, T S | 769ZU | Beijing, Peoples R China | 0 | null | 2 | null | null | Li Nan;Liu Yan | SCI CHINA CHEM | Beijing, Peoples R China |
di Bernardo, D;di Bernardo, M;Menolascina, F | 10.1016/j.automatica.2011.01.073 | null | THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND | 2r374w6n364h4a162y163e1a3x4q6k3e20o3k4x | Analysis, design and implementation of a novel scheme for in-vivo control of synthetic gene regulatory networks | Univ Naples Federico II | null | di Bernardo, M (corresponding author), Univ Naples Federico II, Dept Syst & Comp Engn, Naples, Italy. | SI | di Bernardo, Diego;di Bernardo, Mario;Menolascina, Filippo | Automation & Control Systems;Engineering, Electrical & Electronic | null | WOS | di Bernardo, M | Telethon Inst Genet & Med, Naples, Italy;Univ Bristol, Avon, England;Univ Naples Federico II, Naples, Italy | 47 | ,;a;Analysis;and;control;design;for;gene;implementation;in-vivo;networks;novel;of;regulatory;scheme;synthetic | 2 | di Bernardo, Diego;di Bernardo, Mario;Menolascina, Filippo | PERGAMON-ELSEVIER SCIENCE LTD | Telethon Inst Genet & Med, Syst & Synthet Biol Lab, Naples, Italy;Univ Bristol, Dept Engn Math, Bristol BS8 1TH, Avon, England;Univ Naples Federico II, Dept Comp Sci & Syst, Naples, Italy;Univ Naples Federico II, Dept Syst & Comp Engn, Naples, Italy | Article | Univ Naples Federico II | OXFORD | null | null | Telethon Inst Genet & Med;Univ Bristol;Univ Naples Federico II | null | di Bernardo, M (corresponding author), Univ Naples Federico II, Dept Syst & Comp Engn, Naples, Italy. | 1270 | di Bernardo, Diego;di Bernardo, Mario;Menolascina, Filippo | 12 | 4 | 291,456,100,023 | null | Italy;UK | AUTOMATICA | Italy | null | null | Univ Naples Federico II, Dept Syst & Comp Engn, Naples, Italy | 0005-1098 | di Bernardo, D;di Bernardo, M;Menolascina, F | JUN | dibernardo@tigem.it;mario.dibernardo@unina.it;menolascina@tigem.it | analysis;in-vivo control;novel scheme;synthetic gene regulatory networks | 3 | J | Automation & Control Systems;Engineering | analysis;C 2011 Elsevier Ltd;control design;control strategy;developed network;DYNAMICS;effective switching control strategy;experimental observations;Fluorescence microscopy;gene regulatory networks;good;in vivo control;in-vivo control;IRMA;MICROFLUIDICS;microfluidics devices;model predictions;novel scheme;preliminary experimental results;proof-of-concept;rights reserved;S. Cerevisiae;simple;suitable benchmark problem;synthetic biology;synthetic gene networks;synthetic gene regulatory networks;testbed circuit;use;vivo | Menolascina, F | gene regulatory networks;in vivo control;MICROFLUIDICS;Synthetic biology | 1265 | [Menolascina, Filippo; di Bernardo, Mario; di Bernardo, Diego] Univ Naples Federico II, Dept Syst & Comp Engn, Naples, Italy. [Menolascina, Filippo; di Bernardo, Diego] Telethon Inst Genet & Med, Syst & Synthet Biol Lab, Naples, Italy. [di Bernardo, Mario] Univ Bristol, Dept Engn Math, Bristol BS8 1TH, Avon, England. [di Bernardo, Diego] Univ Naples Federico II, Dept Comp Sci & Syst, Naples, Italy. | null | control design;control strategy;developed network;dynamics;effective switching control strategy;experimental observations;fluorescence microscopy;good;IRMA;microfluidics devices;model predictions;preliminary experimental results;proof-of-concept;S. Cerevisiae;simple;suitable benchmark problem;synthetic gene networks;testbed circuit;use;vivo | 10.1016/j.cell.2009.01.055;10.1016/S0092-8674(00)80740-0;10.1016/S0166-5316(97)00008-4;10.1038/nature07211;10.1038/nature07616;10.1038/nchembio0108-13;10.1038/nmeth1008;10.1038/nrg2697;10.1080/00207720903144560;10.1098/rsif.2009.0083.focus;10.1371/journal.pcbi.1000104 | Univ Naples Federico II | di Bernardo, D;di Bernardo, M;Menolascina, F | Menolascina, F: Univ Naples Federico II, Dept Syst & Comp Engn, Naples, Italy | di Bernardo, Diego;di Bernardo, Mario | null | 15 | null | Italy | Telethon Inst Genet & Med;Univ Bristol;Univ Naples Federico II | Menolascina, Filippo | null | null | Menolascina, Filippo; di Bernardo, Mario; di Bernardo, Diego; | null | Telethon Inst Genet & Med, Syst & Synthet Biol Lab, Naples, Italy;Univ Bristol, Dept Engn Math, Bristol BS8 1TH, Avon, England;Univ Naples Federico II, Dept Comp Sci & Syst, Naples, Italy;Univ Naples Federico II, Dept Syst & Comp Engn, Naples, Italy | Telethon Inst Genet & Med, Syst & Synthet Biol Lab, Naples, Italy;Univ Bristol, Dept Engn Math, Bristol BS8 1TH, Avon, England;Univ Naples Federico II, Dept Comp Sci & Syst, Naples, Italy;Univ Naples Federico II, Dept Syst & Comp Engn, Naples, Italy | 1873-2836 | gene regulatory networks;in vivo control;Microfluidics;Synthetic biology | 6 | 1957;1991;1997;1999;2007;2008;2009;2010 | 44 | Univ Naples Federico II, Dept Syst & Comp Engn, Naples, Italy | Automatica | di Bernardo, Diego | PERGAMON-ELSEVIER SCIENCE LTD | ,;a;an;and;are;as;based;benchmark;between;but;cerevisiae;circuit;concerned;control;design;developed;devices;dynamics;effective;experimental;fluorescence;for;gene;given;good;implementation;in;IRMA;is;matching;microfluidics;microscopy;model;network;networks;observations;of;on;paper;predictions;preliminary;presented;problem;proof-of-concept;proposed;recently;regulate;results;S.;showing;simple;strategy;suitable;switching;synthetic;testbed;the;this;to;use;vivo;which;with | Univ Naples Federico II | This paper is concerned with the design and implementation of a simple but effective switching control strategy to regulate the dynamics of synthetic gene networks. The testbed circuit is IRMA, a recently developed network in S. Cerevisiae which is proposed as a suitable benchmark problem for control design. The proof-of-concept of an implementation of the control strategy in vivo is presented which is based on the use of microfluidics devices and fluorescence microscopy. Preliminary experimental results are given showing the good matching between the model predictions and the experimental observations. | AAF-5881-2021;AAL-9311-2021;I-2805-2012;I-9440-2012 | null | 0 | null | gene regulatory networks;in vivo control;Microfluidics;Synthetic biology | 6 | gene regulatory networks;in vivo control;MICROFLUIDICS;Synthetic biology | WOS:000291456100023 | Telethon Inst Genet & Med, Naples, Italy;Univ Bristol, Avon, England;Univ Naples Federico II, Naples, Italy | Italy;UK | 2,011 | null | 0000-0002-1911-7407;0000-0002-2171-4745;0000-0002-4937-7912 | null | null | English | null | CELL;Chemical Engineering Progress;INT J SYST SCI;J R SOC INTERFACE;Microbiology;NAT CHEM BIOL;NAT METHODS;NAT REV GENET;NATURE;PERFORM EVALUATION;PLOS COMPUT BIOL;Principles of Power Electron | di Bernardo, Diego;di Bernardo, Mario;Menolascina, Filippo | 2024-03-11
ER | [Anonymous];Bagheri, N;Bennett, M R;Cantone, I;Cosma, M P;Dougherty, E R;Goodman, C;Gordon, A;Gulati, S;Kassakian J.;Mascolo, S;Mukherji, S;Smith O. J.;Tigges, M;Willey J. | 775JR | Naples, Italy | 44 | null | 3 | null | null | di Bernardo, Diego;di Bernardo, Mario;Menolascina, Filippo | AUTOMATICA | Avon, England;Naples, Italy |
Fussenegger, M;Weber, W | 10.1016/j.cbpa.2011.03.003 | null | THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, OXON, ENGLAND | 272mnt2c6p4o2z30642s86l27641g5c4g175b | Molecular diversity-the toolbox for synthetic gene switches and networks | Swiss Fed Inst Technol | null | Fussenegger, M (corresponding author), Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Mattenstr 26, CH-4058 Basel, Switzerland. | null | Fussenegger, Martin;Weber, Wilfried | Biochemistry & Molecular Biology;Biophysics | Excellence Initiative of the German Federal and State Governments [EXC 294]; Swiss National Science Foundation [31003A0-126022]; EC | WOS | Fussenegger, M | Swiss Fed Inst Technol, Basel, Switzerland;Univ Basel, Basel, Switzerland;Univ Freiburg, Freiburg, Germany | 15 | and;diversity-the;for;gene;molecular;networks;switches;synthetic;Toolbox | 2 | Weber, Wilfried | ELSEVIER SCI LTD | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, CH-4058 Basel, Switzerland;Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Mattenstr 26, CH-4058 Basel, Switzerland;Univ Basel, Fac Sci, CH-4058 Basel, Switzerland;Univ Freiburg, Ctr Biol Signalling Studies BIOSS, D-79108 Freiburg, Germany;Univ Freiburg, Fac Biol, D-79104 Freiburg, Germany | Review | Swiss Fed Inst Technol | OXFORD | null | null | Swiss Fed Inst Technol;Univ Basel;Univ Freiburg | EC;Excellence Initiative of the German Federal and State Governments;Swiss National Science Foundation | Fussenegger, M (corresponding author), Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Mattenstr 26, CH-4058 Basel, Switzerland. | 420 | Fussenegger, Martin;Weber, Wilfried | 21 | 4 | 292,434,900,011 | EC;Excellence Initiative of the German Federal and State Governments [EXC 294];Swiss National Science Foundation [31003A0-126022] | Germany;Switzerland | CURRENT OPINION IN CHEMICAL BIOLOGY | Switzerland | null | null | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, CH-4058 Basel, Switzerland | 1367-5931 | Fussenegger, M;Weber, W | JUN | fussenegger@bsse.ethz.ch | molecular diversity-the toolbox;networks;synthetic gene switches | 2 | J | Biochemistry & Molecular Biology;Biophysics | BIOLOGY;characterization;chemicals;circuit;compatible genetic switches;complex expression dynamics;DESIGN;development;endogenous metabolites driving prosthetic circuits;exogenous stimuli;fundamental control components;GENE;gene control components;induction;MAMMALIAN-CELLS;metabolic disorders;Mice;modular design;molecular diversity;molecular diversity-the toolbox;networks;ongoing metagenomic discovery;oscillating transgene expression profiles;OSCILLATOR;overview;paradigm;physical cues;PROTEIN INTERACTIONS;rapid development;recent advances;resolved band-detect functions;self-sufficient manner;SPACE;synthetic biology;synthetic control devices;synthetic gene;synthetic gene switches;systems;time;TRANSGENE EXPRESSION;transgene expression dynamics;trigger-inducible mammalian expression devices;unexplored sequence space | Weber, W | BIOLOGY;CIRCUIT;DESIGN;INDUCTION;MAMMALIAN-CELLS;MICE;OSCILLATOR;PROTEIN INTERACTIONS;SYSTEMS;TRANSGENE EXPRESSION | 414 | [Weber, Wilfried; Fussenegger, Martin] Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, CH-4058 Basel, Switzerland. [Weber, Wilfried] Univ Freiburg, Fac Biol, D-79104 Freiburg, Germany. [Weber, Wilfried] Univ Freiburg, Ctr Biol Signalling Studies BIOSS, D-79108 Freiburg, Germany. [Fussenegger, Martin] Univ Basel, Fac Sci, CH-4058 Basel, Switzerland. | Work by the group of WW was supported partly by the Excellence Initiative of the German Federal and State Governments (EXC 294). Work by the group of ME was supported partly by the Swiss National Science Foundation (grant no. 31003A0-126022) and partly by the EC Framework 7 (Persist). | characterization;chemicals;compatible genetic switches;complex expression dynamics;development;endogenous metabolites driving prosthetic circuits;exogenous stimuli;fundamental control components;gene;gene control components;metabolic disorders;modular design;molecular diversity;ongoing metagenomic discovery;oscillating transgene expression profiles;overview;paradigm;physical cues;rapid development;recent advances;resolved band-detect functions;self-sufficient manner;space;synthetic biology;synthetic control devices;synthetic gene;time;transgene expression dynamics;trigger-inducible mammalian expression devices;unexplored sequence space | 10.1002/jgm.314;10.1002/jgm.903;10.1016/0092-8674(88)90182-1;10.1016/j.copbio.2007.07.013;10.1016/j.copbio.2008.10.014;10.1016/j.copbio.2009.08.007;10.1016/j.gde.2010.09.003;10.1016/j.jconrel.2010.11.016;10.1038/463288a;10.1038/81208;10.1038/msb4100073;10.1038/nature04228;10.1038/nature07616;10.1038/nbt.1568;10.1038/nbt.1569;10.1038/nbt.1617;10.1038/nbt731;10.1038/nbt980;10.1038/nm0996-1028;10.1038/NMETH.1524;10.1073/pnas.0500345102;10.1073/pnas.0606398104;10.1073/pnas.0800663105;10.1073/pnas.0901501106;10.1073/pnas.1005615107;10.1073/pnas.89.12.5547;10.1093/nar/gkm652;10.1093/nar/gkq671;10.1126/science.1155761;10.1128/MMBR.69.2.326-356.2005 | Swiss Fed Inst Technol | Fussenegger, M;Weber, W | Weber, W: Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, CH-4058 Basel, Switzerland | Weber, Wilfried | 31003A0-126022;EXC 294 | 31 | null | Switzerland | Swiss Fed Inst Technol;Univ Basel;Univ Freiburg | Weber, Wilfried | null | BIOLOGY;CIRCUIT;DESIGN;INDUCTION;MAMMALIAN-CELLS;MICE;OSCILLATOR;PROTEIN INTERACTIONS;SYSTEMS;TRANSGENE EXPRESSION | Weber, Wilfried; Fussenegger, Martin; | null | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, CH-4058 Basel, Switzerland;Univ Basel, Fac Sci, CH-4058 Basel, Switzerland;Univ Freiburg, Ctr Biol Signalling Studies BIOSS, D-79108 Freiburg, Germany;Univ Freiburg, Fac Biol, D-79104 Freiburg, Germany | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, CH-4058 Basel, Switzerland;Univ Basel, Fac Sci, CH-4058 Basel, Switzerland;Univ Freiburg, Ctr Biol Signalling Studies BIOSS, D-79108 Freiburg, Germany;Univ Freiburg, Fac Biol, D-79104 Freiburg, Germany | 1879-0402 | null | 3 | 1988;1992;1996;2000;2002;2004;2005;2006;2007;2008;2009;2010;2011 | 49 | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Mattenstr 26, CH-4058 Basel, Switzerland | Curr. Opin. Chem. Biol. | Fussenegger, Martin | ELSEVIER SCI LTD | a;advances;also;an;and;are;as;assembled;band-detect;be;biology;by;can;characterization;chemicals;circuits;compatible;complex;components;constantly;control;controlled;cues;design;development;devices;discovery;disorders;diversity;driving;dynamics;either;endogenous;exogenous;expression;fuels;functions;fundamental;further;gene;genetic;here;highly;how;in;increasing;is;mammalian;manner;metabolic;metabolites;metagenomic;modular;molecular;naturally;networks;occurring;of;offer;on;ongoing;or;oscillating;overview;paradigm;physical;precisely;profiles;programmed;prosthetic;provide;rapid;recent;resolved;responsive;self-sufficient;sequence;show;space;stimuli;such;switches;synthetic;temporally;that;the;time;to;transgene;treat;trigger-inducible;unexplored;used;we | Swiss Fed Inst Technol | The rapid development of synthetic biology is a paradigm of how the molecular diversity of naturally occurring gene control components can be used to design synthetic control devices and gene networks that provide precisely programmed transgene expression dynamics in space and time. Here we offer an overview on recent advances in the modular design of trigger-inducible mammalian expression devices that are either responsive by exogenous stimuli such as chemicals and physical cues or controlled by endogenous metabolites driving prosthetic circuits to treat metabolic disorders in a self-sufficient manner. Compatible genetic switches can also be assembled to synthetic gene networks that show highly complex expression dynamics such as temporally resolved band-detect functions or oscillating transgene expression profiles. The ongoing metagenomic discovery and characterization of the unexplored sequence space is constantly increasing the molecular diversity in fundamental control components that fuels the further development of synthetic biology. | B-4732-2012 | BIOLOGY;CIRCUITS;DESIGN;INDUCTION;PROTEIN INTERACTIONS;MAMMALIAN-CELLS;MICE;OSCILLATIONS;SYSTEM;TRANSGENE EXPRESSION | 0 | null | null | 7 | BIOLOGY;CIRCUITS;DESIGN;INDUCTION;PROTEIN INTERACTIONS;MAMMALIAN-CELLS;MICE;OSCILLATIONS;SYSTEM;TRANSGENE EXPRESSION | WOS:000292434900011 | Swiss Fed Inst Technol, Basel, Switzerland;Univ Basel, Basel, Switzerland;Univ Freiburg, Freiburg, Germany | Germany;Switzerland | 2,011 | null | 0000-0003-4340-4446 | null | null | English | null | CELL;CURR OPIN BIOTECH;CURR OPIN GENET DEV;J CONTROL RELEASE;J GENE MED;MICROBIOL MOL BIOL R;MOL SYST BIOL;NAT BIOTECHNOL;NAT MED;NAT METHODS;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;SCIENCE | Fussenegger, Martin;Weber, Wilfried | 2024-03-11
ER | Andrianantoandro, E;Aubel, D;Coleman, J R;Driever, W;Fussenegger, M;Gitzinger, M;Gossen, M;Greber, D;Hartenbach, S;Kemmer, C;Kennedy, M J;Kollmann, M;Kramer, B P;Kwok, R;Lee, S K;Marchisio, M A;Nov, D;Ramos, J L;Rivera, V M;Salis, H M;Tigges, M;Toettcher, J E;Weber, W;Yazawa, M | 788HB | Basel, Switzerland | 52 | null | 3 | null | 21,470,897 | Fussenegger, Martin;Weber, Wilfried | CURR OPIN CHEM BIOL | Basel, Switzerland;Freiburg, Germany |
Bulsara, A R;Dari, A;Ditto, W;Kia, B;Wang, X | 10.1103/PhysRevE.83.041909 | 041909 | ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA | 1o5m373e41fh1e1d2je4l5h6431t6x3s2m1h | Noise-aided computation within a synthetic gene network through morphable and robust logic gates | Arizona State Univ | null | Dari, A (corresponding author), Arizona State Univ, Sch Biol & Hlth Syst Engn, Tempe, AZ 85287 USA. | null | Bulsara, Adi R;Dari, Anna;Ditto, William;Kia, Behnam;Wang, Xiao | Physics, Fluids & Plasmas;Physics, Mathematical | Office of Naval Research [N000140211019, N0000148WX20330AA] | WOS | Dari, A | Arizona State Univ, Tempe, AZ USA;SPAWAR Pacific Code, San Diego, CA USA | 83 | a;and;computation;gates;gene;logic;morphable;network;noise-Aided;robust;synthetic;through;within | 1 | Ditto, William;Wang, Xiao | AMER PHYSICAL SOC | Arizona State Univ, Sch Biol & Hlth Syst Engn, Tempe, AZ 85287 USA;Arizona State Univ, Sch Elect Comp & Energy Engn, Tempe, AZ 85287 USA;SPAWAR Pacific Code 71000, San Diego, CA 92152 USA | Article | Arizona State Univ | COLLEGE PK | null | null | Arizona State Univ;SPAWAR Pacific Code 71000 | Office of Naval Research | Dari, A (corresponding author), Arizona State Univ, Sch Biol & Hlth Syst Engn, Tempe, AZ 85287 USA. | null | Bulsara, Adi R;Dari, Anna;Ditto, William;Kia, Behnam;Wang, Xiao | 23 | 3 | 289,354,500,008 | Office of Naval Research [N000140211019, N0000148WX20330AA] | USA | PHYSICAL REVIEW E | USA | null | null | Arizona State Univ, Sch Biol & Hlth Syst Engn, Tempe, AZ 85287 USA | 1539-3755 | Bulsara, A R;Dari, A;Ditto, W;Kia, B;Wang, X | APR 11 | null | morphable;noise-aided computation;robust logic gates;synthetic gene network | 5 | J | Physics | actual function;application;article;bacteriophage lambda;BACTERIOPHAGE-LAMBDA;biological logic gate;circuit;CONSTRUCTION;CRO;DESIGN;expression;external;external control parameter;full system characterization;Gate;Genetic circuits;Genetic networks;important goal;internal noise;intriguing possibilities;logic gate performance;logical stochastic resonance paradigm;MODEL;morphable;NETWORK;noise;noise-aided computation;noisy background;nonlinearity;numerical simulations;operations;performing assigned operations;realization;reconfigurable logic gate;REPRESSOR;robust logic gates;ROBUSTNESS;ROLES;stability;synthetic biology;synthetic gene network;tunable genetic;varying internal system parameters;via | Dari, A | BACTERIOPHAGE-LAMBDA;CIRCUIT;CONSTRUCTION;CRO;DESIGN;EXPRESSION;MODEL;REPRESSOR;ROLES;STABILITY | null | [Dari, Anna; Kia, Behnam; Wang, Xiao; Ditto, William] Arizona State Univ, Sch Biol & Hlth Syst Engn, Tempe, AZ 85287 USA. [Kia, Behnam] Arizona State Univ, Sch Elect Comp & Energy Engn, Tempe, AZ 85287 USA. [Bulsara, Adi R.] SPAWAR Pacific Code 71000, San Diego, CA 92152 USA. | We gratefully acknowledge support from the Office of Naval Research under Grants No. N000140211019 and No. N0000148WX20330AA. A. R. B. acknowledges fruitful conversations with Professor Bart Kosko. | actual function;application;article;bacteriophage lambda;biological logic gate;external;external control parameter;full system characterization;gate;genetic circuits;genetic networks;important goal;internal noise;intriguing possibilities;logic gate performance;logical stochastic resonance paradigm;network;noise;noisy background;nonlinearity;numerical simulations;operations;performing assigned operations;realization;reconfigurable logic gate;robustness;synthetic biology;synthetic gene network;tunable genetic;varying internal system parameters;via | 10.1002/bit.20371;10.1002/bit.21463;10.1006/jtbi.2000.1068;10.1007/BF00198768;10.1016/0022-2836(80)90303-4;10.1016/0092-8674(80)90383-9;10.1016/j.chemphys.2010.06.015;10.1021/nl9034175;10.1038/294217a0;10.1038/35002125;10.1038/35002131;10.1038/35014651;10.1038/373033a0;10.1038/msb.2008.31;10.1038/nature01257;10.1038/nature01258;10.1038/nature09326;10.1038/nbt.1536;10.1038/nbt1413;10.1038/ng881;10.1038/nrg2697;10.1063/1.1345702;10.1063/1.881491;10.1073/pnas.040411297;10.1073/pnas.0408507102;10.1073/pnas.0809901106;10.1073/pnas.0810399106;10.1073/pnas.1332628100;10.1073/pnas.151588598;10.1073/pnas.79.4.1129;10.1073/pnas.94.3.814;10.1074/jbc.M006264200;10.1088/1478-3975/5/3/036006;10.1093/emboj/20.10.2528;10.1093/nar/gkq091;10.1101/gad.1586107;10.1103/PhysRevLett.102.104101;10.1103/RevModPhys.70.223;10.1126/science.1070919;10.1126/science.1151153;10.1126/science.1190719;10.1126/science.7624793;10.1146/annurev.bioeng.5.040202.121553;10.1186/1754-1611-4-4 | Arizona State Univ | Bulsara, A R;Dari, A;Ditto, W;Kia, B;Wang, X | Dari, A: Arizona State Univ, Sch Biol & Hlth Syst Engn, Tempe, AZ 85287 USA | Ditto, William;Wang, Xiao | N0000148WX20330AA;N000140211019 | 51 | null | USA | Arizona State Univ;SPAWAR Pacific Code 71000 | Dari, Anna | null | BACTERIOPHAGE-LAMBDA;CIRCUIT;CONSTRUCTION;CRO;DESIGN;EXPRESSION;MODEL;REPRESSOR;ROLES;STABILITY | Dari, Anna; Kia, Behnam; Wang, Xiao; Bulsara, Adi R.; Ditto, William; | null | Arizona State Univ, Sch Biol & Hlth Syst Engn, Tempe, AZ 85287 USA;Arizona State Univ, Sch Elect Comp & Energy Engn, Tempe, AZ 85287 USA;SPAWAR Pacific Code 71000, San Diego, CA 92152 USA | Arizona State Univ, Sch Biol & Hlth Syst Engn, Tempe, AZ 85287 USA;Arizona State Univ, Sch Elect Comp & Energy Engn, Tempe, AZ 85287 USA;SPAWAR Pacific Code 71000, San Diego, CA 92152 USA | 1550-2376 | null | 4 | 1974;1980;1981;1982;1983;1984;1989;1992;1995;1996;1997;1998;2000;2001;2002;2003;2005;2007;2008;2009;2010 | 38 | Arizona State Univ, Sch Biol & Hlth Syst Engn, Tempe, AZ 85287 USA | Phys. Rev. E | Ditto, William | AMER PHYSICAL SOC | ";,;a;actual;afford;after;an;and;application;are;article;assigned;background;bacteriophage;be;been;biological;biology;build;built;can;capable;changed;characterization;circuits;control;derived;emulate;engineered;exploit;external;for;from;full;function;gate;gene;genetic;goal;has;illustrated;important;in;internal;intriguing;is;lambda;logic;logical;morph;network;networks;noise;noisy;nonlinearity;numerical;of;operations;or;paradigm;parameter;parameters;performance;performing;possibilities;presence;realization;reconfigurable;regulatory;reported;resonance;robust;robustness;simulations;stochastic;studied;such;synthetic;system;that;the;this;through;to;tunable;underpins;usually;varying;via;we;wherein;which;with;work | Arizona State Univ | An important goal for synthetic biology is to build robust and tunable genetic regulatory networks that are capable of performing assigned operations, usually in the presence of noise. In this work, a synthetic gene network derived from the bacteriophage lambda underpins a reconfigurable logic gate wherein we exploit noise and nonlinearity through the application of the logical stochastic resonance paradigm. This biological logic gate can emulate or "morph" the AND and OR operations through varying internal system parameters in a noisy background. Such genetic circuits can afford intriguing possibilities in the realization of engineered genetic networks in which the actual function of the gate can be changed after the network has been built, via an external control parameter. In this article, the full system characterization is reported, with the logic gate performance studied in the presence of external and internal noise. The robustness of the gate, to noise, is studied and illustrated through numerical simulations. | A-8414-2008;AAK-9827-2020 | BACTERIOPHAGE-LAMBDA;CIRCUITS;CONSTRUCTION;CRO;DESIGN;EXPRESSION;MODEL;REPRESSOR;ROLES;STABILITY | 2 | null | null | 12 | BACTERIOPHAGE-LAMBDA;CIRCUITS;CONSTRUCTION;CRO;DESIGN;EXPRESSION;MODEL;REPRESSOR;ROLES;STABILITY | WOS:000289354500008 | Arizona State Univ, Tempe, AZ USA;SPAWAR Pacific Code, San Diego, CA USA | USA | 2,011 | null | 0000-0002-4056-0155;0000-0002-7416-8012 | null | null | English | null | ANNU REV BIOMED ENG;BACTERIOPHAGES;BIOL CYBERN;BIOTECHNOL BIOENG;CELL;CHAOS;CHEM PHYS;EMBO J;GENE DEV;GENES;HDB STOCHASTIC METHO;J BIOL CHEM;J Biol Eng;J MOL BIOL;J THEOR BIOL;Methods Enzymol;MOL SYST BIOL;NANO LETT;NAT BIOTECHNOL;NAT GENET;NAT REV GENET;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;P NATL ACAD SCI-BIOL;PHYS BIOL;PHYS REV LETT;PHYS TODAY;REV MOD PHYS;SCIENCE;STOCHASTIC MODELS BI;The Fokker-Planck Equation | Bulsara, Adi R;Dari, Anna;Ditto, William;Kia, Behnam;Wang, Xiao | 2024-03-11
ER | [Anonymous];Ackers, G K;Ajo-Franklin, C M;Bashor, C J;Becskei, A;Bulsara, A R;Calendar R.L.;Canton, B;Cherry, J L;Eldar, A;Ellis, T;Elowitz, M B;Gammaitoni, L;Gardiner C. W.;Gardner, T S;Gibson, D G;Goel N.S.;Guerra, D N;Hasty, J;Hooshangi, S;Isaacs, F J;Johnson A, D;Johnson, A D;Karig, D;Kierzek, A M;Kærn, M;Lu, T;Mcadams, H H;Meyer, B J;Morelli, M J;Mukherji, S;Murali, K;Murphy, K F;Nevozhay, D;Nistala Goutam, J;Ptashne M.;Ptashne, M;Rao, C V;Risken, H;Shahrezaei, V;Shen-Orr, S S;Thattai, M;Weber, W;Wiesenfeld, K | 747XL | Tempe, AZ USA | 38 | null | 2 | 1 | 21,599,203 | Bulsara, Adi R;Dari, Anna;Ditto, William;Kia, Behnam;Wang, Xiao | PHYS REV E | San Diego, CA USA;Tempe, AZ USA |
Axelsson, E;Boutros, M;Fischer, B;Horn, T;Huber, W;Sandmann, T | 10.1038/NMETH.1581 | null | MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND | 71x5y1r13604nj4z544z6p2r593k353q4p3y1i | Mapping of signaling networks through synthetic genetic interaction analysis by RNAi | Deutsch Krebsforschungszentrum | null | Boutros, M (corresponding author), Deutsch Krebsforschungszentrum, Div Signaling & Funct Genom, German Canc Res Ctr, D-6900 Heidelberg, Germany. | null | Axelsson, Elin;Boutros, Michael;Fischer, Bernd;Horn, Thomas;Huber, Wolfgang;Sandmann, Thomas | Biochemical Research Methods | Studienstiftung; CellNetworks Cluster of Excellence; Human Frontiers Sciences Program; EU | WOS | Boutros, M | Deutsch Krebsforschungszentrum, Heidelberg, Germany;European Mol Biol Lab, Heidelberg, Germany;Univ Heidelberg, Heidelberg, Germany | 8 | Analysis;by;genetic;Interaction;Mapping;networks;of;RNAi;Signaling;synthetic;through | 1 | Axelsson, Elin;Boutros, Michael;Fischer, Bernd;Huber, Wolfgang;Sandmann, Thomas | NATURE PUBLISHING GROUP | Deutsch Krebsforschungszentrum, Div Signaling & Funct Genom, German Canc Res Ctr, D-6900 Heidelberg, Germany;European Mol Biol Lab, Genome Biol Unit, Heidelberg, Germany;Univ Heidelberg, Dept Cell & Mol Biol, Fac Med Mannheim, Heidelberg, Germany;Univ Heidelberg, Hartmut Hoffmann Berling Int Grad Sch Mol & Cellu, Heidelberg, Germany | Article | Deutsch Krebsforschungszentrum | LONDON | null | null | Deutsch Krebsforschungszentrum;European Mol Biol Lab;Univ Heidelberg | CellNetworks Cluster of Excellence;EU;Human Frontiers Sciences Program;Studienstiftung | Boutros, M (corresponding author), Deutsch Krebsforschungszentrum, Div Signaling & Funct Genom, German Canc Res Ctr, D-6900 Heidelberg, Germany. | U91 | Axelsson, Elin;Boutros, Michael;Fischer, Bernd;Horn, Thomas;Huber, Wolfgang;Sandmann, Thomas | 17 | 4 | 288,940,300,022 | CellNetworks Cluster of Excellence;EU;Human Frontiers Sciences Program;Studienstiftung | Germany | NATURE METHODS | Germany | null | null | Deutsch Krebsforschungszentrum, Div Signaling & Funct Genom, German Canc Res Ctr, D-6900 Heidelberg, Germany | 1548-7091 | Axelsson, E;Boutros, M;Fischer, B;Horn, T;Huber, W;Sandmann, T | APR | m.boutros@dkfz.de;whuber@embl.de | mapping;RNAi;signaling networks;synthetic genetic interaction analysis | 6 | J | Biochemistry & Molecular Biology | 600 interactions affecting different quantitative phenotypes;70,000 pairwise perturbations;analysis;BACTERIA;biological systems;cellular networks;collections;comparable approaches;complex;components;computational analysis;connectivity;conserved regulator;deletion strains;DESIGN;DROSOPHILA CELLS;Drosophila melanogaster cells;gene function;genetic interactions;high level;higher organisms;interaction matrix;large-scale genetic interaction mapping;limited repertoire;mapping;matrices;method;performing;PROTEIN;quantitative interaction profiles;Ras-MAPK signaling;RECEPTOR TYROSINE KINASE;revealing gene function;RNAi;robust manner;scalable approach;SCREEN;signaling factors;signaling networks;signaling pathways;studies;synthetic genetic interaction analysis;synthetic genetic interaction networks;taken advantage;tissue culture cells;yeast | Horn, T | COMPLEX;DESIGN;DROSOPHILA CELLS;PROTEIN;RECEPTOR TYROSINE KINASE;SCREEN;YEAST | 341 | [Horn, Thomas; Sandmann, Thomas; Boutros, Michael] Deutsch Krebsforschungszentrum, Div Signaling & Funct Genom, German Canc Res Ctr, D-6900 Heidelberg, Germany. [Horn, Thomas; Sandmann, Thomas; Boutros, Michael] Univ Heidelberg, Dept Cell & Mol Biol, Fac Med Mannheim, Heidelberg, Germany. [Horn, Thomas] Univ Heidelberg, Hartmut Hoffmann Berling Int Grad Sch Mol & Cellu, Heidelberg, Germany. [Fischer, Bernd; Axelsson, Elin; Huber, Wolfgang] European Mol Biol Lab, Genome Biol Unit, Heidelberg, Germany. | We thank A.-C. Gavin, A. Teleman and F. Markowetz for helpful comments on the manuscript, N. Perrimon (Harvard Medical School), W. Du (University of Chicago) and S. Hou (National Cancer Institute-Frederick) for sharing reagents and fly stocks, members of the Drosophila Genomics Resource Center for providing plasmids, members of the Bloomington Drosophila stock center for fly stocks and the information technology Service Units of the European Molecular Biology Laboratory and the German Cancer Research Center, for technical support; and A. Kiger and R. Gentleman for helpful discussions. The work was supported in part by a fellowship of the Studienstiftung (T.H.), the CellNetworks Cluster of Excellence (T.S.), a program grant of the Human Frontiers Sciences Program (W.H. and M.B.) and the EU FP7 project CancerPathways (W.H. and M.B.). | 600 interactions affecting different quantitative phenotypes;70,000 pairwise perturbations;analysis;bacteria;biological systems;cellular networks;collections;comparable approaches;components;computational analysis;connectivity;conserved regulator;deletion strains;Drosophila melanogaster cells;gene function;genetic interactions;high level;higher organisms;interaction matrix;large-scale genetic interaction mapping;limited repertoire;matrices;method;performing;quantitative interaction profiles;Ras-MAPK signaling;revealing gene function;RNAi;robust manner;scalable approach;signaling factors;signaling pathways;studies;synthetic genetic interaction networks;taken advantage;tissue culture cells;yeast | 10.1007/978-1-59745-583-1_8;10.1016/j.cell.2009.05.006;10.1016/j.chembiol.2010.06.008;10.1016/j.devcel.2004.06.007;10.1016/j.molcel.2010.08.002;10.1016/j.tcb.2006.08.006;10.1016/S0960-9822(03)00535-9;10.1038/msb.2010.27;10.1038/nature05280;10.1038/nature05649;10.1038/nature08494;10.1038/nbt.1549;10.1038/ng1844;10.1038/NMETH.1534;10.1073/pnas.0712255105;10.1073/pnas.0810388105;10.1073/pnas.1530509100;10.1074/mcp.M800266-MCP200;10.1093/bioinformatics/btn472;10.1093/nar/24.21.4362;10.1093/nar/gkn788;10.1098/rsnr.1976.0005;10.1101/gad.10.3.272;10.1126/science.1091266;10.1126/science.1091317;10.1126/science.1158739;10.1126/science.1180823;10.1126/science.1189015;10.1128/MCB.22.6.1792-1803.2002;10.1186/1471-2105-9-465;10.1186/1471-2164-9-461;10.1186/gb-2009-10-2-r20;10.1186/gb-2010-11-6-r61;10.1186/jbiol58;10.2202/1544-6115.1027, 10.2202/1544-6115.1027] | Deutsch Krebsforschungszentrum | Axelsson, E;Boutros, M;Fischer, B;Horn, T;Huber, W;Sandmann, T | Horn, T: Deutsch Krebsforschungszentrum, Div Signaling & Funct Genom, German Canc Res Ctr, D-6900 Heidelberg, Germany | Boutros, Michael;Fischer, Bernd | null | 39 | null | Germany | Deutsch Krebsforschungszentrum;European Mol Biol Lab;Univ Heidelberg | Horn, Thomas | null | COMPLEX;DESIGN;DROSOPHILA CELLS;PROTEIN;RECEPTOR TYROSINE KINASE;SCREEN;YEAST | Horn, Thomas; Sandmann, Thomas; Fischer, Bernd; Axelsson, Elin; Huber, Wolfgang; Boutros, Michael; | null | Deutsch Krebsforschungszentrum, Div Signaling & Funct Genom, German Canc Res Ctr, D-6900 Heidelberg, Germany;European Mol Biol Lab, Genome Biol Unit, Heidelberg, Germany;Univ Heidelberg, Dept Cell & Mol Biol, Fac Med Mannheim, Heidelberg, Germany;Univ Heidelberg, Hartmut Hoffmann Berling Int Grad Sch Mol & Cellu, Heidelberg, Germany | Deutsch Krebsforschungszentrum, Div Signaling & Funct Genom, German Canc Res Ctr, D-6900 Heidelberg, Germany;European Mol Biol Lab, Genome Biol Unit, Heidelberg, Germany;Univ Heidelberg, Dept Cell & Mol Biol, Fac Med Mannheim, Heidelberg, Germany;Univ Heidelberg, Hartmut Hoffmann Berling Int Grad Sch Mol & Cellu, Heidelberg, Germany | null | null | 4 | 1976;1994;1996;1999;2002;2003;2004;2006;2007;2008;2009;2010 | 137 | Deutsch Krebsforschungszentrum, Div Signaling & Funct Genom, German Canc Res Ctr, D-6900 Heidelberg, Germany | Nat. Methods | Boutros, Michael | NATURE PUBLISHING GROUP | ,;600;70,000;>;a;achieve;advantage;affecting;allowed;analysis;and;approach;approaches;bacteria;been;biological;by;can;cells;cellular;collections;comparable;complexity;components;computational;connectivity;conserved;construct;culture;deletion;different;difficult;Drosophila;factors;for;function;gene;genetic;have;here;high;higher;how;identified;identify;implement;in;infer;interaction;interactions;is;large-scale;level;limited;manner;mapping;matrices;matrix;melanogaster;method;more;networks;of;organisms;pairwise;pathways;performing;perturbations;phenotypes;profiles;quantitative;Ras-MAPK;reconstruct;regulator;repertoire;report;reveal;revealing;RNAi;robust;scalable;signaling;strains;studies;synthetic;systems;taken;than;the;this;through;tissue;to;us;versatile;we;with;yeast;yet | Deutsch Krebsforschungszentrum | The analysis of synthetic genetic interaction networks can reveal how biological systems achieve a high level of complexity with a limited repertoire of components. Studies in yeast and bacteria have taken advantage of collections of deletion strains to construct matrices of quantitative interaction profiles and infer gene function. Yet comparable approaches in higher organisms have been difficult to implement in a robust manner. Here we report a method to identify genetic interactions in tissue culture cells through RNAi. By performing more than 70,000 pairwise perturbations of signaling factors, we identified > 600 interactions affecting different quantitative phenotypes of Drosophila melanogaster cells. Computational analysis of this interaction matrix allowed us to reconstruct signaling pathways and identify a conserved regulator of Ras-MAPK signaling. Large-scale genetic interaction mapping by RNAi is a versatile, scalable approach for revealing gene function and the connectivity of cellular networks. | C-3566-2008;E-7461-2011 | COMPLEX;DESIGN;DROSOPHILA CELLS;PROTEIN;RECEPTOR TYROSINE KINASES;SCREEN;YEAST | 0 | null | null | 9 | YEAST;COMPLEX;DESIGN;DROSOPHILA CELLS;PROTEIN;RECEPTOR TYROSINE KINASES;SCREEN | WOS:000288940300022 | Deutsch Krebsforschungszentrum, Heidelberg, Germany;European Mol Biol Lab, Heidelberg, Germany;Univ Heidelberg, Heidelberg, Germany | Germany | 2,011 | null | 0000-0001-9437-2099;0000-0002-0474-2218;0000-0002-6601-8890;0000-0002-9458-817X;0000-0003-4382-1880 | null | null | English | null | BIOINFORMATICS;BMC BIOINFORMATICS;BMC GENOMICS;CELL;CHEM BIOL;CURR BIOL;DEV CELL;DEVELOPMENT;DROSOPH INF SERV;GENE DEV;GENOME BIOL;J Biol;J BIOL CHEM;MOL CELL;MOL CELL BIOL;MOL CELL PROTEOMICS;MOL SYST BIOL;NAT BIOTECHNOL;NAT GENET;NAT METHODS;NATURE;NOTES REC ROY SOC;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;SCIENCE;Stat Appl Genet Mol Biol;STAT SINICA;TRENDS CELL BIOL | Axelsson, Elin;Boutros, Michael;Fischer, Bernd;Horn, Thomas;Huber, Wolfgang;Sandmann, Thomas | 2024-03-11
ER | Arvidsson, S;Bakal, C;Baryshnikova, A;Battle, A;Boutros, M;Brückner, K;Byrne Alexandra, B;Casey, F P;Chen, H W;Collins, S R;Costanzo, M;Dowell, R D;Farha, M A;Friedman, A;Goudreault, M;Han, K H;Horn, T;Lehner, B;Lehár, J;Luo, J;Lönnstedt, I;Mani, R;Manolio, T A;Mcpherson, P S;Norton, B;Ory, S;Reich, A;Ribeiro, P S;Ridley, A J;Shao, H F;Sims, D;Smyth Gk.;Steinbrink Sandra;Storey, J D;Tong, A H Y;Tweedie, S;Wassarman, D A;Weng L.;Yu, J K | 742KE | Heidelberg, Germany | 167 | null | 3 | null | 21,378,980 | Axelsson, Elin;Boutros, Michael;Fischer, Bernd;Horn, Thomas;Huber, Wolfgang;Sandmann, Thomas | NAT METHODS | Heidelberg, Germany |
Aihara, K;Ando, H;Sinha, S;Storni, R | 10.1209/0295-5075/93/50001 | 50001 | TEMPLE CIRCUS, TEMPLE WAY, BRISTOL BS1 6BE, ENGLAND | 1l4lq2q271p1x3k58b2lk4036482ol2v64x | Synthetic gene networks as potential flexible parallel logic gates | RIKEN | null | Ando, H (corresponding author), RIKEN, Brain Sci Inst, 2-1 Hirosawa, Wako, Saitama 3510198, Japan. | null | Aihara, Kazuyuki;Ando, Hiroyasu;Sinha, Sudeshna;Storni, Remo | Physics, Multidisciplinary | KAKENHI [21800089]; Grants-in-Aid for Scientific Research [21800089] Funding Source: KAKEN | WOS | Ando, H | Aihara Innovat Math Modelling Project, Tokyo, Japan;Indian Inst Sci Educ & Res IISER Mohali, Chandigarh, India;RIKEN, Saitama, Japan;Univ Tokyo, Tokyo, Japan | 93 | as;flexible;gates;gene;logic;networks;parallel;Potential;synthetic | 2 | Sinha, Sudeshna | IOP PUBLISHING LTD | Aihara Innovat Math Modelling Project, FIRST, Tokyo, Japan;Indian Inst Sci Educ & Res IISER Mohali, Chandigarh 160019, India;RIKEN, Brain Sci Inst, 2-1 Hirosawa, Wako, Saitama 3510198, Japan;RIKEN, Brain Sci Inst, Wako, Saitama 3510198, Japan;Univ Tokyo, Inst Ind Sci, Meguro Ku, Tokyo 1538505, Japan | Article | RIKEN | BRISTOL | null | null | Aihara Innovat Math Modelling Project;Brain Sci Inst;Indian Inst Sci Educ & Res IISER Mohali;RIKEN;Univ Tokyo | Grants-in-Aid for Scientific Research;KAKENHI | Ando, H (corresponding author), RIKEN, Brain Sci Inst, 2-1 Hirosawa, Wako, Saitama 3510198, Japan. | null | Aihara, Kazuyuki;Ando, Hiroyasu;Sinha, Sudeshna;Storni, Remo | 16 | 4 | 288,322,900,001 | Grants-in-Aid for Scientific Research [21800089] Funding Source: KAKEN;KAKENHI [21800089] | India;Japan | EPL | Japan | null | null | RIKEN, Brain Sci Inst, Wako, Saitama 3510198, Japan | 0295-5075 | Aihara, K;Ando, H;Sinha, S;Storni, R | MAR | hiroyasu_ando@brain.riken.jp | potential flexible parallel logic gates;synthetic gene networks | 4 | J | Physics | 2011;biological system;copyright (c) EPLA;flexible parallel processing potential;function;gene network;instance toggle;logic functionality;logic operation;noise;noise level;optimal window;potential flexible parallel logic gates;reliability;robust logic gate;SWITCHES;synthetic gene network;synthetic gene networks;two complementary gate operations;two-dimensional model;XOR gates | Ando, H | NOISE;SWITCHES | null | [Ando, Hiroyasu] RIKEN, Brain Sci Inst, Wako, Saitama 3510198, Japan. [Sinha, Sudeshna] Indian Inst Sci Educ & Res IISER Mohali, Chandigarh 160019, India. [Storni, Remo; Aihara, Kazuyuki] Univ Tokyo, Inst Ind Sci, Meguro Ku, Tokyo 1538505, Japan. [Aihara, Kazuyuki] Aihara Innovat Math Modelling Project, FIRST, Tokyo, Japan. | This work is partly supported by KAKENHI 21800089. | 2011;biological system;copyright (c) EPLA;flexible parallel processing potential;function;gene network;instance toggle;logic functionality;logic operation;noise;noise level;optimal window;reliability;robust logic gate;synthetic gene network;two complementary gate operations;two-dimensional model;XOR gates | 10.1016/j.physleta.2010.03.026;10.1021/nl9034175;10.1038/35002131;10.1063/1.1345702;10.1063/1.3245318;10.1063/1.3302457;10.1073/pnas.040411297;10.1103/PhysRevLett.102.104101;10.1186/1752-0509-1-50;10.1209/0295-5075/86/60003 | RIKEN | Aihara, K;Ando, H;Sinha, S;Storni, R | Ando, H: RIKEN, Brain Sci Inst, Wako, Saitama 3510198, Japan | null | 21800089 | 15 | null | Japan | Aihara Innovat Math Modelling Project;Indian Inst Sci Educ & Res IISER Mohali;RIKEN;Univ Tokyo | Ando, Hiroyasu | null | NOISE;SWITCHES | Ando, Hiroyasu; Sinha, Sudeshna; Storni, Remo; Aihara, Kazuyuki; | null | Aihara Innovat Math Modelling Project, FIRST, Tokyo, Japan;Indian Inst Sci Educ & Res IISER Mohali, Chandigarh 160019, India;RIKEN, Brain Sci Inst, Wako, Saitama 3510198, Japan;Univ Tokyo, Inst Ind Sci, Meguro Ku, Tokyo 1538505, Japan | Aihara Innovat Math Modelling Project, FIRST, Tokyo, Japan;Indian Inst Sci Educ & Res IISER Mohali, Chandigarh 160019, India;RIKEN, Brain Sci Inst, Wako, Saitama 3510198, Japan;Univ Tokyo, Inst Ind Sci, Meguro Ku, Tokyo 1538505, Japan | 1286-4854 | null | 5 | 1989;1991;1993;2000;2001;2007;2009;2010;2011 | 46 | RIKEN, Brain Sci Inst, 2-1 Hirosawa, Wako, Saitama 3510198, Japan | EPL | Aihara, Kazuyuki | IOP PUBLISHING LTD | (c);,;2011;a;achieved;also;an;and;as;be;between;biological;can;complementary;consider;Copyright;enhances;EPLA;flexible;for;function;functionality;further;gate;gates;gene;how;in;indicates;instance;interestingly;level;logic;model;network;noise;of;operation;operations;optimal;or;parallel;potential;processing;reliability;robust;show;simultaneously;switch;synthetic;system;the;this;to;toggle;two;two-dimensional;used;we;where;window;XOR | RIKEN | We show how a synthetic gene network can function, in an optimal window of noise, as a robust logic gate. Interestingly, noise enhances the reliability of the logic operation. Further, the noise level can also be used to switch logic functionality, for instance toggle between AND, OR and XOR gates. We also consider a two-dimensional model of a gene network, where we show how two complementary gate operations can be achieved simultaneously. This indicates the flexible parallel processing potential of this biological system. Copyright (c) EPLA, 2011 | null | NOISE;SWITCH | 2 | null | null | 6 | NOISE;SWITCH | WOS:000288322900001 | Aihara Innovat Math Modelling Project, Tokyo, Japan;Indian Inst Sci Educ & Res IISER Mohali, Chandigarh, India;RIKEN, Saitama, Japan;Univ Tokyo, Tokyo, Japan | India;Japan | 2,011 | null | 0000-0002-1364-5276 | null | null | English | null | APPL PHYS LETT;BMC SYST BIOL;CHAOS;COMPUTER ARCHITECTUR;COMPUTER SYSTEM ARCH;EPL;EPL-EUROPHYS LETT;F PLANCK EQUATION ME;MOD BIOM NETW CELLS;NANO LETT;NATURE;P NATL ACAD SCI USA;PHYS LETT A;PHYS REV LETT | Aihara, Kazuyuki;Ando, Hiroyasu;Sinha, Sudeshna;Storni, Remo | 2024-03-11
ER | Anna, D;Bartee;Chen L.;Fierens, P I;Gardner, T S;Guerra, D N;Hasty, J;Mano Mm.;Murali, K;Risken, H;Sinha, S;Wang, J W;Worschech, L | 734GP | Saitama, Japan | 47 | null | 4 | null | null | Aihara, Kazuyuki;Ando, Hiroyasu;Sinha, Sudeshna;Storni, Remo | EPL-EUROPHYS LETT | Chandigarh, India;Saitama, Japan;Tokyo, Japan |
Chen, A M | 10.1007/s11071-010-9832-1 | null | VAN GODEWIJCKSTRAAT 30, 3311 GZ DORDRECHT, NETHERLANDS | 4v3j36z2i2e4b6i5e6ug2r1l6o5lt28705f2m | Modeling a synthetic biological chaotic system: relaxation oscillators coupled by quorum sensing | Henan Univ | null | Chen, AM (corresponding author), Henan Univ, Inst Appl Math, Kaifeng 475004, Peoples R China. | null | Chen, Aimin | Engineering, Mechanical;Mechanics | Natural Science Foundation of the People's Republic of China [30973980, 60704045]; Research Fund of Youth Scholars for the Doctoral Program of Higher Education of China [20070558053] | WOS | Chen, A M | Henan Univ, Kaifeng, Peoples R China | 63 | :;a;biological;by;chaotic;coupled;modeling;Oscillators;Quorum;relaxation;Sensing;synthetic;system | 1 | null | SPRINGER | Henan Univ, Inst Appl Math, Kaifeng 475004, Peoples R China;Henan Univ, Sch Math & Informat Sci, Kaifeng 475004, Peoples R China | Article | Henan Univ | DORDRECHT | null | null | Henan Univ | Natural Science Foundation of the People's Republic of China;Research Fund of Youth Scholars for the Doctoral Program of Higher Education of China | Chen, AM (corresponding author), Henan Univ, Inst Appl Math, Kaifeng 475004, Peoples R China. | 718 | Chen, Aimin | 20 | 2 | 287,506,300,017 | Natural Science Foundation of the People's Republic of China [30973980, 60704045];Research Fund of Youth Scholars for the Doctoral Program of Higher Education of China [20070558053] | China | NONLINEAR DYNAMICS | China | null | null | Henan Univ, Inst Appl Math, Kaifeng 475004, Peoples R China | 0924-090X | Chen, A M | MAR | aimchenhenu@yahoo.com.cn | Quorum Sensing;relaxation oscillators;synthetic biological chaotic system | 1 | J | Engineering;Mechanics | bifurcation;biological systems;CHAOS;chaotic biological system;chaotic system;CIRCADIAN-RHYTHMS;CIRCUITS;CONSTRUCTION;detailed dynamical behaviors;DROSOPHILA;DYNAMICS;feedback loops;gene networks;investigating synthetic genetic relaxation oscillators;Lyapunov exponents spectrum;mapping;Poincar;quorum sensing;relaxation oscillators;synthetic biological chaotic system;synthetic genetic networks | Chen, A M | Biological systems;CHAOS;CIRCADIAN-RHYTHMS;CIRCUITS;CONSTRUCTION;DROSOPHILA;DYNAMICS;FEEDBACK LOOPS;gene networks;quorum sensing;Synthetic genetic networks | 711 | [Chen, Aimin] Henan Univ, Inst Appl Math, Kaifeng 475004, Peoples R China. [Chen, Aimin] Henan Univ, Sch Math & Informat Sci, Kaifeng 475004, Peoples R China. | We acknowledge the support from the Natural Science Foundation (No. 30973980) of the People's Republic of China, the Natural Science Foundation (No. 60704045) of the People's Republic of China and the Research Fund of Youth Scholars for the Doctoral Program of Higher Education of China (No. 20070558053). | bifurcation;biological systems;chaos;chaotic biological system;chaotic system;detailed dynamical behaviors;investigating synthetic genetic relaxation oscillators;Lyapunov exponents spectrum;mapping;Poincar;quorum sensing | 10.1006/jtbi.1995.0014;10.1006/jtbi.1998.0790;10.1006/jtbi.1999.0924;10.1006/jtbi.2000.1068;10.1016/0092-8240(94)00036-C;10.1016/0167-2789(96)00086-3;10.1016/j.jtbi.2009.11.007;10.1016/S0006-3495(99)77078-5;10.1016/S0022-2836(61)80072-7;10.1016/S1369-5274(99)00025-9;10.1038/252546a0;10.1038/343653a0;10.1038/35002125;10.1038/35002131;10.1038/35002258;10.1038/35014651;10.1038/nature04473;10.1038/nature07389;10.1038/nature08753;10.1038/nbt.1536;10.1063/1.1345702;10.1073/pnas.022642299;10.1103/PhysRevE.78.031904;10.1103/PhysRevE.79.041903;10.1103/PhysRevLett.64.1196;10.1103/PhysRevLett.99.148103;10.1126/science.1088926;10.1126/science.1172005;10.1126/science.2382131;10.1126/science.286.5440.766;10.1126/science.7313693;10.1142/S0218127491000415;10.1146/annurev.micro.50.1.727;10.1152/ajpcell.1998.274.2.C531;10.1152/ajpcell.1999.277.4.C777;10.1152/ajpheart.1989.257.2.H693;10.1152/ajprenal.1991.261.3.F400;10.1177/074873098128999934;10.1177/074873099129000948 | Henan Univ | Chen, A M | Chen, A M: Henan Univ, Inst Appl Math, Kaifeng 475004, Peoples R China | null | 20070558053;30973980;60704045 | 48 | null | China | Henan Univ | Chen, Aimin | null | CIRCADIAN-RHYTHMS;CIRCUITS;CONSTRUCTION;DROSOPHILA;DYNAMICS;FEEDBACK LOOPS;GENE NETWORKS | Chen, Aimin; | null | Henan Univ, Inst Appl Math, Kaifeng 475004, Peoples R China;Henan Univ, Sch Math & Informat Sci, Kaifeng 475004, Peoples R China | Henan Univ, Inst Appl Math, Kaifeng 475004, Peoples R China;Henan Univ, Sch Math & Informat Sci, Kaifeng 475004, Peoples R China | 1573-269X | Biological systems;Chaos;quorum sensing;Synthetic genetic networks | 4 | 1961;1974;1975;1978;1981;1988;1989;1990;1991;1994;1995;1996;1998;1999;2000;2001;2002;2006;2007;2008;2009;2010 | 13 | Henan Univ, Inst Appl Math, Kaifeng 475004, Peoples R China | Nonlinear Dyn. | Chen, Aimin | SPRINGER | ,;a;and;are;behaviors;bifurcation;biological;by;chaos;chaotic;coupled;detailed;dynamical;exists;exponents;genetic;in;including;investigated;investigating;Lyapunov;mapping;of;oscillators;paper;Poincar;quorum;relaxation;reports;sensing;spectrum;synthetic;system;systems;the;this;through | Henan Univ | Chaos exists in biological systems. Through investigating synthetic genetic relaxation oscillators coupled by quorum sensing, this paper reports a chaotic system. The detailed dynamical behaviors of this chaotic biological system are investigated, including Lyapunov exponents spectrum, bifurcation, and Poincar, mapping. | null | CIRCADIAN-RHYTHMS;CIRCUITS;CONSTRUCTION;DROSOPHILA;DYNAMICS;FEEDBACK LOOPS;GENE NETWORKS | 0 | null | Biological systems;Chaos;quorum sensing;Synthetic genetic networks | 8 | BIOLOGICAL-SYSTEMS;CHAOS;CIRCADIAN-RHYTHMS;CIRCUITS;CONSTRUCTION;DROSOPHILA;DYNAMICS;FEEDBACK LOOPS;gene networks;quorum sensing;Synthetic genetic networks | WOS:000287506300017 | Henan Univ, Kaifeng, Peoples R China | China | 2,011 | null | null | null | null | English | null | ADV NEURAL INFORM PR;AM J PHYSIOL;AM J PHYSIOL-CELL PH;ANNU REV MICROBIOL;B MATH BIOL;BIOPHYS J;CARDIAC ELECTROPHYSI;CHAOS;CHAOS BIOL SYSTEMS;CURR OPIN MICROBIOL;Current Protocols in Molecular Biology;EXPLORING CHAOS GUID;From Clocks to Chaos;INT J BIFURCAT CHAOS;J BIOL RHYTHM;J MOL BIOL;J THEOR BIOL;MOL CLONING;NAT BIOTECHNOL;NATURE;P NATL ACAD SCI USA;PHYS REV E;PHYS REV LETT;PHYSICA D;PROG THEOR BIOL;SCIENCE | Chen, Aimin | 2024-03-11
ER | Ausubel F. M.;Barkai, N;Bassler, B L;Becskei, A;Bialek, W;Cherry, J L;Chialvo, D R;Courtemanche, M;Danino, T;Dickson, R C;Ellis, T;Elowitz, M B;Friedland, A E;Fuqua, C;Gardner, T S;Glass L.;Glossop, N R J;Guevara Mr.;Guevara, M R;Guido, N J;Hall, N;Hasty, J;Hayashi, H;Jacob, F;Keller, A D;Koseska, A;Leloup, J C;Mcmillen, D;Mestl, T;Olsen, L F;Ott, E;Sambrook J.;Savageau, M A;Segundo, J P;Smolen, P;Stricker, J;Thomas, R;Tyson, J J;Ullner, E;Weiss, R;Wolf, D M;Yip, K P;Zhang, J J | 723KV | Kaifeng, Peoples R China | 13 | null | 1 | null | null | Chen, Aimin | NONLINEAR DYNAM | Kaifeng, Peoples R China |
Chang, C H;Chen, B S;Lee, H C;Wang, Y C;Wu, C H | 10.1016/j.mbs.2010.12.007 | null | 360 PARK AVE SOUTH, NEW YORK, NY 10010-1710 USA | 593i1hj4t6a74464j172n2d1q5f235x4b92c | Robust model matching design methodology for a stochastic synthetic gene network | Natl Tsing Hua Univ | null | Chen, BS (corresponding author), Natl Tsing Hua Univ, Dept Elect Engn, Lab Control & Syst Biol, Hsinchu 30013, Taiwan. | null | Chang, Chia-Hung;Chen, Bor-Sen;Lee, Hsiao-Ching;Wang, Yu-Chao;Wu, Chih-Hung | Biology;Mathematical & Computational Biology | National Tsing Hua University [98N2565E1]; National Science Council of Taiwan [NSC 98-2221-E-007-113-MY3, NSC 99-2745-E-007-001-ASP] | WOS | Chen, B S | Natl Chiao Tung Univ, Hsinchu, Taiwan;Natl Tsing Hua Univ, Hsinchu, Taiwan | 230 | a;design;for;gene;matching;methodology;model;network;robust;stochastic;synthetic | 1 | Wang, Yu-Chao | ELSEVIER SCIENCE INC | Natl Chiao Tung Univ, Dept Biol Sci & Technol, Hsinchu 30068, Taiwan;Natl Tsing Hua Univ, Dept Elect Engn, Lab Control & Syst Biol, Hsinchu 30013, Taiwan | Article | Natl Tsing Hua Univ | NEW YORK | null | null | Natl Chiao Tung Univ;Natl Tsing Hua Univ | National Science Council of Taiwan;National Tsing Hua University | Chen, BS (corresponding author), Natl Tsing Hua Univ, Dept Elect Engn, Lab Control & Syst Biol, Hsinchu 30013, Taiwan. | 36 | Chang, Chia-Hung;Chen, Bor-Sen;Lee, Hsiao-Ching;Wang, Yu-Chao;Wu, Chih-Hung | 4 | 2 | 288,630,100,003 | National Science Council of Taiwan [NSC 98-2221-E-007-113-MY3, NSC 99-2745-E-007-001-ASP];National Tsing Hua University [98N2565E1] | Taiwan | MATHEMATICAL BIOSCIENCES | Taiwan | null | null | Natl Tsing Hua Univ, Dept Elect Engn, Lab Control & Syst Biol, Hsinchu 30013, Taiwan | 0025-5564 | Chang, C H;Chen, B S;Lee, H C;Wang, Y C;Wu, C H | MAR | bschen@ee.nthu.edu.tw | robust model matching design methodology;stochastic synthetic gene network | 5 | J | Life Sciences & Biomedicine - Other Topics;Mathematical & Computational Biology | behavior;C 2010 Elsevier Inc;CONSTRUCTION;decade;design procedure;desired behavior;desired behaviors;desired reference matching purpose;environmental disturbances;ESCHERICHIA-COLI;expression;External disturbances;extrinsic disturbances;Global linearization;global linearization technique;Hamilton-Jacobi inequality (HJI);host cell;INTERPOLATION;intrinsic parameter fluctuations;intrinsic parameter uncertainties;intrinsic parameter variations;linear matrix inequalities (LMIs);LMI;LMI toolbox;MATLAB;noise;non-linear stochastic gene network;non-linear stochastic robust matching design;non-linear stochastic robust matching design methodology;potential;promising applications;proposed matching design methodology;real environment;result;rights reserved;Robust model matching design;robust model matching design methodology;robust model matching performance;robust synthetic gene network;silico design examples;SINGLE-CELL;spite;stochastic parameter fluctuations;Stochastic synthetic gene network;study;synthetic biology;synthetic gene networks;systems biology;toggle switch;two | Chen, B S | BEHAVIOR;CONSTRUCTION;ESCHERICHIA-COLI;EXPRESSION;External disturbances;Global linearization;INTERPOLATION;Intrinsic parameter fluctuations;LMI;NOISE;Robust model matching design;SINGLE-CELL;Stochastic synthetic gene network;systems biology;toggle switch | 23 | [Chen, Bor-Sen; Chang, Chia-Hung; Wang, Yu-Chao; Wu, Chih-Hung] Natl Tsing Hua Univ, Dept Elect Engn, Lab Control & Syst Biol, Hsinchu 30013, Taiwan. [Lee, Hsiao-Ching] Natl Chiao Tung Univ, Dept Biol Sci & Technol, Hsinchu 30068, Taiwan. | The study is supported by National Tsing Hua University under grant 98N2565E1 and by the National Science Council of Taiwan under grants NSC 98-2221-E-007-113-MY3 and NSC 99-2745-E-007-001-ASP. | decade;design procedure;desired behavior;desired behaviors;desired reference matching purpose;environmental disturbances;external disturbances;extrinsic disturbances;global linearization technique;Hamilton-Jacobi inequality (HJI);host cell;intrinsic parameter fluctuations;intrinsic parameter uncertainties;intrinsic parameter variations;linear matrix inequalities (LMIs);LMI toolbox;MATLAB;non-linear stochastic gene network;non-linear stochastic robust matching design;non-linear stochastic robust matching design methodology;potential;promising applications;proposed matching design methodology;real environment;result;robust model matching performance;robust synthetic gene network;silico design examples;spite;stochastic parameter fluctuations;study;synthetic biology;synthetic gene networks;two | 10.1016/j.jbiotec.2007.05.014;10.1016/j.jmb.2005.10.076;10.1016/j.sbi.2006.06.011;10.1016/j.tibtech.2005.12.003;10.1016/S0025-5564(02)00162-1;10.1016/S0092-8674(03)00346-5;10.1038/229542a0;10.1038/35002125;10.1038/35002131;10.1038/35093556;10.1038/448032a;10.1038/msb4100073;10.1038/msb4100187;10.1038/nature01546;10.1038/nature04342;10.1038/nature04473;10.1038/nature07521;10.1038/nbt.1536;10.1038/nbt0708-771;10.1038/nbt1413;10.1038/nrg1471;10.1038/nrg2591;10.1038/nrg2775;10.1049/sb:20045006;10.1073/pnas.0408507102;10.1073/pnas.1332628100;10.1093/bioinformatics/btm362;10.1093/bioinformatics/btp310;10.1093/nar/gkq091;10.1103/PhysRevLett.84.2529;10.1109/TBCAS.2007.907060;10.1109/TCSI.2008.2007059;10.1109/TFUZZ.2010.2070842;10.1109/TSMCB.2007.906975;10.1109/TSP.2004.840724;10.1126/science.1069492;10.1126/science.1069981;10.1126/science.1070919;10.1126/science.1104635;10.1126/science.1106914;10.1137/S0363012903423727;10.1146/annurev.genet.36.061102.093104;10.1186/1471-2105-3-38;10.1186/1471-2105-7-52;10.1186/1471-2105-8-12;10.1186/1752-0509-1-6;10.1186/1752-0509-3-66;10.1371/journal.pone.0002030;10.1529/biophysj.104.044131;10.2307/2006273 | Natl Tsing Hua Univ | Chang, C H;Chen, B S;Lee, H C;Wang, Y C;Wu, C H | Chen, B S: Natl Tsing Hua Univ, Dept Elect Engn, Lab Control & Syst Biol, Hsinchu 30013, Taiwan | Chen, Bor-Sen | 98N2565E1;NSC 98-2221-E-007-113-MY3;NSC 99-2745-E-007-001-ASP | 57 | null | Taiwan | Natl Chiao Tung Univ;Natl Tsing Hua Univ | Chen, Bor-Sen | null | BEHAVIOR;CONSTRUCTION;ESCHERICHIA-COLI;EXPRESSION;INTERPOLATION;NOISE;SINGLE-CELL;SYSTEMS BIOLOGY;TOGGLE SWITCH | Chen, Bor-Sen; Chang, Chia-Hung; Wang, Yu-Chao; Wu, Chih-Hung; Lee, Hsiao-Ching; | null | Natl Chiao Tung Univ, Dept Biol Sci & Technol, Hsinchu 30068, Taiwan;Natl Tsing Hua Univ, Dept Elect Engn, Lab Control & Syst Biol, Hsinchu 30013, Taiwan | Natl Chiao Tung Univ, Dept Biol Sci & Technol, Hsinchu 30068, Taiwan;Natl Tsing Hua Univ, Dept Elect Engn, Lab Control & Syst Biol, Hsinchu 30013, Taiwan | 1879-3134 | External disturbances;Global linearization;Intrinsic parameter fluctuations;LMI;Robust model matching design;Stochastic synthetic gene network | 1 | 1971;1978;1990;1994;1995;2000;2001;2002;2003;2004;2005;2006;2007;2008;2009;2010 | 11 | Natl Tsing Hua Univ, Dept Elect Engn, Lab Control & Syst Biol, Hsinchu 30013, Taiwan | Math. Biosci. | Lee, Hsiao-Ching | ELSEVIER SCIENCE INC | (HJI);(LMIs);,;a;achieve;and;applications;are;as;attenuate;avoid;be;behavior;behaviors;biology;by;can;cannot;cell;confirm;decade;design;designed;desired;disturbances;due;efficiently;environment;environmental;examples;external;extrinsic;finally;fluctuations;gene;given;global;Hamilton-Jacobi;has;help;host;however;illustrate;in;inequalities;inequality;intrinsic;introduced;is;its;last;linear;linearization;LMI;maintain;many;matching;MATLAB;matrix;methodology;mimic;model;modeled;network;networks;non-linear;of;order;parameter;performance;potential;procedure;promising;properly;proposed;purpose;real;reference;result;robust;set;shown;silico;simplify;solving;spite;stochastic;study;synthetic;technique;the;their;then;this;to;toolbox;two;uncertainties;used;variations;with;withstand;work | Natl Tsing Hua Univ | Synthetic biology has shown its potential and promising applications in the last decade. However, many synthetic gene networks cannot work properly and maintain their desired behaviors due to intrinsic parameter variations and extrinsic disturbances. In this study, the intrinsic parameter uncertainties and external disturbances are modeled in a non-linear stochastic gene network to mimic the real environment in the host cell. Then a non-linear stochastic robust matching design methodology is introduced to withstand the intrinsic parameter fluctuations and to attenuate the extrinsic disturbances in order to achieve a desired reference matching purpose. To avoid solving the Hamilton-Jacobi inequality (HJI) in the non-linear stochastic robust matching design, global linearization technique is used to simplify the design procedure by solving a set of linear matrix inequalities (LMIs). As a result, the proposed matching design methodology of the robust synthetic gene network can be efficiently designed with the help of LMI toolbox in Matlab. Finally, two in silico design examples of the robust synthetic gene network are given to illustrate the design procedure and to confirm the robust model matching performance to achieve the desired behavior in spite of stochastic parameter fluctuations and environmental disturbances in the host cell. | D-9114-2017 | BEHAVIOR;CONSTRUCTION;ESCHERICHIA-COLI;EXPRESSION;INTERPOLATION;NOISE;SINGLE-CELL;SYSTEMS BIOLOGY;TOGGLE SWITCH | 0 | null | External disturbances;Global linearization;Intrinsic parameter fluctuations;LMI;Robust model matching design;Stochastic synthetic gene network | 14 | ESCHERICHIA-COLI;BEHAVIOR;CONSTRUCTION;EXPRESSION;External disturbances;Global linearization;INTERPOLATION;Intrinsic parameter fluctuations;LMI;NOISE;Robust model matching design;SINGLE-CELL;Stochastic synthetic gene network;systems biology;toggle switch | WOS:000288630100003 | Natl Chiao Tung Univ, Hsinchu, Taiwan;Natl Tsing Hua Univ, Hsinchu, Taiwan | Taiwan | 2,011 | null | 0000-0002-1574-1691 | null | null | English | null | ANNU REV GENET;BIOINFORMATICS;BIOPHYS J;BMC BIOINFORMATICS;BMC SYST BIOL;CELL;COMPUTER CONTROLLED;CURR OPIN STRUC BIOL;IEEE T BIOMED CIRC S;IEEE T CIRCUITS-I;IEEE T FUZZY SYST;IEEE T SIGNAL PROCES;IEEE T SYST MAN CY B;INTRO SYSTEMS BIOL D;J BIOTECHNOL;J MOL BIOL;Linear MatrixInequalities in System and Control Theory;Linear Stochastic Control Systems;LMI Control Toolbox;MATH BIOSCI;MATH COMPUT;MOL SYST BIOL;NAT BIOTECHNOL;NAT REV GENET;NATURE;New Atlantis;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PHYS REV LETT;PLOS ONE;SCIENCE;SIAM J CONTROL OPTIM;Systems Biology;TRENDS BIOTECHNOL | Chang, Chia-Hung;Chen, Bor-Sen;Lee, Hsiao-Ching;Wang, Yu-Chao;Wu, Chih-Hung | 2024-03-11
ER | Alon, U;Anderson, J C;Andrianantoandro, E;Arkin, A;Astrom K.J.;Atkinson, M R;Ball, P;Batt, G;Blake, W J;Boyd S.;Canton, B;Carlson, J M;Chen G.;Chen, B S;Chin, J W;Copeland, N G;Court, D L;Cox, R S;Csete, M E;Ellis, T;Elowitz, M B;Endy, D;Feng, X J;Gahinet P.;Gardner, T S;Gertz, J;Gordon, W J;Greber, D;Guido, N J;Hammer, K;Hood, L;Hooshangi, S;Isaacs, F J;Khalil, A S;Kinkhabwala, A;Kitano, H;Kuepfer, L;Li, C G;Ma, L;Murphy, K F;Rosenfeld, N;Savageau, M A;Segal, E;Sontag E. D.;Tucker Jonathan, B;Voit E. O.;Voit, E O;Zhang, W H | 738HE | Hsinchu, Taiwan | 13 | null | 2 | null | 21,215,760 | Chang, Chia-Hung;Chen, Bor-Sen;Lee, Hsiao-Ching;Wang, Yu-Chao;Wu, Chih-Hung | MATH BIOSCI | Hsinchu, Taiwan |
di Bernardo, M;Grierson, C S;Purcell, O;Savery, N J | 10.1371/journal.pone.0016140 | e16140 | 185 BERRY ST, STE 1300, SAN FRANCISCO, CA 94107 USA | 1p2438y3234612s3v2f5j2q715a2r602y19531p | A Multi-Functional Synthetic Gene Network: A Frequency Multiplier, Oscillator and Switch | Univ Bristol | null | Purcell, O (corresponding author), Univ Bristol, Bristol Ctr Complex Sci, Dept Engn Math, Bristol, Avon, England. | null | di Bernardo, Mario;Grierson, Claire S;Purcell, Oliver;Savery, Nigel J | Multidisciplinary Sciences | Engineering and Physical Sciences Research Council (EPSRC) | WOS | Purcell, O | Univ Bristol, Avon, England;Univ Naples Federico, Naples, Italy | 6 | ,;:;a;and;Frequency;gene;Multi-Functional;Multiplier;network;Oscillator;Switch;synthetic | 2 | di Bernardo, Mario;Savery, Nigel | PUBLIC LIBRARY SCIENCE | Univ Bristol, Bristol Ctr Complex Sci, Dept Engn Math, Bristol, Avon, England;Univ Bristol, Sch Biochem, Bristol, Avon, England;Univ Bristol, Sch Biol Sci, Bristol, Avon, England;Univ Naples Federico 2, Dept Syst & Comp Engn, Naples, Italy | Article | Univ Bristol | SAN FRANCISCO | null | null | Univ Bristol;Univ Naples Federico 2 | Engineering and Physical Sciences Research Council (EPSRC) | Purcell, O (corresponding author), Univ Bristol, Bristol Ctr Complex Sci, Dept Engn Math, Bristol, Avon, England. | null | di Bernardo, Mario;Grierson, Claire S;Purcell, Oliver;Savery, Nigel J | 19 | 4 | 287,482,300,015 | Engineering and Physical Sciences Research Council (EPSRC) | Italy;UK | PLOS ONE | UK | null | null | Univ Bristol, Bristol Ctr Complex Sci, Dept Engn Math, Bristol, Avon, England | 1932-6203 | di Bernardo, M;Grierson, C S;Purcell, O;Savery, N J | FEB 17 | enoep@bristol.ac.uk | Frequency Multiplier;Multi-Functional Synthetic Gene Network;Oscillator;Switch | 4 | J | Science & Technology - Other Topics | analysis;available genetic oscillators;behavior;bifurcation structure;BIOLOGY;capabilities;cells;different responses;efficient coordination;ESCHERICHIA-COLI;expression;frequency multiplication;Frequency Multiplier;functioning;half;input;input frequency;MAMMALIAN OSCILLATOR;Multi-Functional Synthetic Gene Network;multi-functionality;NETWORK;neuronal networks;novel;OSCILLATOR;output;pattern;produces oscillations;programmable multi-functionality;proteins;significant theoretical addition;SWITCH;synthetic gene;synthetic gene networks;takes oscillatory transcription factor concentrations;temporal nature;toggle switch | Purcell, O | BEHAVIOR;BIOLOGY;CELLS;ESCHERICHIA-COLI;EXPRESSION;MAMMALIAN OSCILLATOR;PATTERN;Proteins;toggle switch | null | [Purcell, Oliver; di Bernardo, Mario] Univ Bristol, Bristol Ctr Complex Sci, Dept Engn Math, Bristol, Avon, England. [di Bernardo, Mario] Univ Naples Federico 2, Dept Syst & Comp Engn, Naples, Italy. [Grierson, Claire S.] Univ Bristol, Sch Biol Sci, Bristol, Avon, England. [Savery, Nigel J.] Univ Bristol, Sch Biochem, Bristol, Avon, England. | Funding was provided by the Engineering and Physical Sciences Research Council (EPSRC). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. | analysis;available genetic oscillators;bifurcation structure;capabilities;different responses;efficient coordination;frequency multiplication;frequency multiplier;functioning;half;input;input frequency;multi-functionality;network;neuronal networks;novel;oscillator;output;produces oscillations;programmable multi-functionality;significant theoretical addition;switch;synthetic gene;synthetic gene networks;takes oscillatory transcription factor concentrations;temporal nature | 10.1007/s003590050085;10.1016/j.cbpa.2009.09.026;10.1016/j.cell.2007.05.045;10.1016/j.jmb.2005.06.082;10.1016/j.jtbi.2009.07.040;10.1016/S0092-8674(03)00346-5;10.1038/35002125;10.1038/35002131;10.1038/msb.2010.2;10.1038/msb4100053;10.1038/nature03508;10.1038/nature07389;10.1038/nature07616;10.1038/nbt.1591;10.1038/nbt980;10.1038/nrg2775;10.1038/nrm2698;10.1073/pnas.0901246106;10.1093/nar/25.6.1203;10.1093/nar/gkn449;10.1093/nar/gkn545;10.1093/nar/gkq121;10.1098/rsif.2008.0046.focus;10.1098/rsif.2010.0183;10.1128/JB.187.15.5496-5499.2005;10.1146/annurev.neuro.12.1.185;10.1146/annurev.neuro.31.060407.125552;10.1146/annurev.physchem.012809.103457;10.1371/journal.pone.0002030;10.1371/journal.pone.0012314;10.1523/JNEUROSCI.22-05-01985.2002 | Univ Bristol | di Bernardo, M;Grierson, C S;Purcell, O;Savery, N J | Purcell, O: Univ Bristol, Bristol Ctr Complex Sci, Dept Engn Math, Bristol, Avon, England | di Bernardo, Mario | null | 35 | null | UK | Univ Bristol;Univ Naples Federico 2 | Purcell, Oliver | Green Submitted, Green Published, gold | BEHAVIOR;BIOLOGY;CELLS;ESCHERICHIA-COLI;EXPRESSION;MAMMALIAN OSCILLATOR;PATTERN;PROTEINS;TOGGLE SWITCH | Purcell, Oliver; di Bernardo, Mario; Grierson, Claire S.; Savery, Nigel J.; | null | Univ Bristol, Bristol Ctr Complex Sci, Dept Engn Math, Bristol, Avon, England;Univ Bristol, Sch Biochem, Bristol, Avon, England;Univ Bristol, Sch Biol Sci, Bristol, Avon, England;Univ Naples Federico 2, Dept Syst & Comp Engn, Naples, Italy | Univ Bristol, Bristol Ctr Complex Sci, Dept Engn Math, Bristol, Avon, England;Univ Bristol, Sch Biochem, Bristol, Avon, England;Univ Bristol, Sch Biol Sci, Bristol, Avon, England;Univ Naples Federico 2, Dept Syst & Comp Engn, Naples, Italy | null | null | 2 | 1985;1989;1997;2000;2002;2003;2004;2005;2006;2007;2008;2009;2010 | 24 | Univ Bristol, Bristol Ctr Complex Sci, Dept Engn Math, Bristol, Avon, England | PLoS One | Savery, Nigel J | PUBLIC LIBRARY SCIENCE | ,;;;a;able;addition;allow;also;an;analysis;and;as;available;bifurcation;capabilities;concentrations;coordination;currently;depending;design;different;efficient;extends;factor;for;frequency;from;function;functioning;gene;genetic;half;in;input;is;it;multi-functionality;multiplication;multiplier;nature;network;networks;neuronal;novel;observed;of;often;on;or;oscillations;oscillator;oscillators;oscillatory;output;performs;present;produced;produces;programmable;represents;responses;reveals;significant;structure;such;suggested;switch;synthetic;takes;temporal;that;the;theoretical;this;those;to;transcription;we;where;with | Univ Bristol | We present the design and analysis of a synthetic gene network that performs frequency multiplication. It takes oscillatory transcription factor concentrations, such as those produced from the currently available genetic oscillators, as an input, and produces oscillations with half the input frequency as an output. Analysis of the bifurcation structure also reveals novel, programmable multi-functionality; in addition to functioning as a frequency multiplier, the network is able to function as a switch or an oscillator, depending on the temporal nature of the input. Multi-functionality is often observed in neuronal networks, where it is suggested to allow for the efficient coordination of different responses. This network represents a significant theoretical addition that extends the capabilities of synthetic gene networks. | AAL-9311-2021;I-2805-2012 | BEHAVIOR;BIOLOGY;CELLS;ESCHERICHIA-COLI;EXPRESSION;MAMMALIAN OSCILLATOR;PATTERNS;PROTEIN;TOGGLE SWITCH | 1 | null | null | 12 | ESCHERICHIA-COLI;BEHAVIOR;BIOLOGY;CELLS;EXPRESSION;MAMMALIAN OSCILLATOR;PATTERNS;PROTEIN;toggle switch | WOS:000287482300015 | Univ Bristol, Avon, England;Univ Naples Federico, Naples, Italy | Italy;UK | 2,011 | null | 0000-0002-0803-4075;0000-0002-2171-4745 | null | null | English | null | ANNU REV NEUROSCI;ANNU REV PHYS CHEM;CELL;CURR OPIN CHEM BIOL;ELEMENTS APPL BIFURC;INTRO SYSTEMS BIOL D;J BACTERIOL;J COMP PHYSIOL A;J MOL BIOL;J NEUROSCI;J R SOC INTERFACE;J THEOR BIOL;MOL SYST BIOL;NAT BIOTECHNOL;NAT REV GENET;NAT REV MOL CELL BIO;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PLOS ONE | di Bernardo, Mario;Grierson, Claire S;Purcell, Oliver;Savery, Nigel J | 2024-03-11
ER | [Anonymous];Alon, U;Atkinson, M R;Briggman, K L;Conrad, E;Deans, T L;Deiters, A;Doedel, E;Elowitz, M B;Fung, E;Gardner, T S;Getting P.A.;Getting, P A;Giesecke, A V;Gommans, W M;Guantes, R;Khalil, A S;Kinkhabwala, A;Kramer, B P;Lee, J Y;Lou, C B;Lu, T K;Lutz, R;Neupert, J;Park, K S;Polynikis, A;Popescu, I R;Purcell, O;Purnick, P E M;Soffe, S R;Sohka, T;Stricker, J;Tigges, M;Tyson, J J | 723BX | Avon, England | 24 | null | 2 | null | 21,359,152 | di Bernardo, Mario;Grierson, Claire S;Purcell, Oliver;Savery, Nigel J | PLOS ONE | Avon, England;Naples, Italy |
Marchisio, M A;Stelling, J | 10.1371/journal.pcbi.1001083 | e1001083 | 1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USA | 1y4b5t6e3k3i6d5k2c50486m5s5i3w2o22bv6l | Automatic Design of Digital Synthetic Gene Circuits | Swiss Fed Inst Technol | null | Marchisio, MA (corresponding author), Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland. | null | Marchisio, Mario A;Stelling, Joerg | Biochemical Research Methods;Mathematical & Computational Biology | EU [043338, 043379] | WOS | Marchisio, M A | Swiss Fed Inst Technol, Basel, Switzerland | 7 | automatic;circuits;design;Digital;gene;of;synthetic | 1 | Marchisio, Mario Andrea | PUBLIC LIBRARY SCIENCE | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland;Swiss Fed Inst Technol, Swiss Inst Bioinformat, Basel, Switzerland | Article | Swiss Fed Inst Technol | SAN FRANCISCO | null | null | Swiss Fed Inst Technol | EU | Marchisio, MA (corresponding author), Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland. | null | Marchisio, Mario A | 20 | 2 | 287,698,700,018 | EU [043338, 043379] | Switzerland | PLOS COMPUTATIONAL BIOLOGY | Switzerland | null | null | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland | null | Marchisio, M A;Stelling, J | FEB | joerg.stelling@bsse.ethz.ch | automatic Design;Digital Synthetic Gene Circuits | 2 | J | Biochemistry & Molecular Biology;Mathematical & Computational Biology | action;automatic circuit design;automatic Design;BINDING;biological Boolean gates;brute-force approaches run optimization algorithms;chemicals;circuit's input-output relations;CIRCUITS;corresponding tool;de novo computational design;devising new circuits;Digital Synthetic Gene Circuits;direct rational methods;existing solutions;expression;Faithful;focusing;four inputs;given truth;hard task;kinetic parameter values;lacking;logic behavior;logic gates;MAMMALIAN-CELLS;method;need;NETWORK;networks;optimization;parametric perturbations;potential;promoters;ranks several possible circuit schemes;regulators;regulatory factors;RIBOREGULATORS;ribosome binding sites;RIBOSWITCH;same function;silico automatic design;simpler designs;simulations;stochastic noise;structure;synthetic gene;systems biology;transcriptional regulation;unequivocal truth table representation;well-defined target functions | Marchisio, M A | BINDING;EXPRESSION;logic gates;MAMMALIAN-CELLS;NETWORKS;REGULATORS;RIBOREGULATORS;RIBOSWITCH;systems biology;Transcriptional regulation | null | [Marchisio, Mario A.] Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland. Swiss Fed Inst Technol, Swiss Inst Bioinformat, Basel, Switzerland. | We gratefully acknowledge financial support by the EU FP6 projects EMERGENCE (contract 043338) and COBIOS (contract 043379). The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. | action;automatic circuit design;biological Boolean gates;brute-force approaches run optimization algorithms;chemicals;circuit's input-output relations;circuits;corresponding tool;de novo computational design;devising new circuits;digital synthetic gene circuits;direct rational methods;existing solutions;faithful;focusing;four inputs;given truth;hard task;kinetic parameter values;lacking;logic behavior;method;need;network;optimization;parametric perturbations;potential;promoters;ranks several possible circuit schemes;regulatory factors;ribosome binding sites;same function;silico automatic design;simpler designs;simulations;stochastic noise;structure;synthetic gene;unequivocal truth table representation;well-defined target functions | 10.1002/bit.20142;10.1002/cbic.200700057;10.1006/jmbi.1999.3306;10.1007/B117060;10.1016/j.copbio.2009.08.002;10.1016/j.copbio.2009.08.007;10.1016/j.febslet.2008.01.060;10.1016/j.gde.2005.02.006;10.1016/j.gde.2005.02.007;10.1016/j.jmb.2003.09.049;10.1016/j.jmb.2005.10.076;10.1016/j.jmb.2005.12.003;10.1016/j.physd.2008.01.027;10.1021/bi051008u;10.1021/ja0710149;10.1038/35002125;10.1038/msb4100010;10.1038/msb4100173;10.1038/nature01145;10.1038/nature04342;10.1038/nbt.1536;10.1038/nbt.1568;10.1038/nbt1069;10.1038/nbt1208;10.1038/nbt1253;10.1038/nbt1307;10.1038/nbt862;10.1038/nbt986;10.1038/nmeth1008;10.1038/nrg2172;10.1038/nrg2775;10.1039/b822268c;10.1049/iet-stb:20070013;10.1073/pnas.0304532101;10.1080/10409230590918702;10.1093/bioinformatics/btg015;10.1093/bioinformatics/btg128;10.1093/bioinformatics/bti799;10.1093/bioinformatics/btl485;10.1093/bioinformatics/btm237;10.1093/bioinformatics/btn330;10.1093/bioinformatics/btp029;10.1093/nar/gkp079;10.1103/PhysRevE.70.031909;10.1109/ISCAS.2009.5117747;10.1109/TCE.1953.6371932];10.1126/science.1100829;10.1126/science.1130716;10.1126/science.1132493;10.1126/science.1152621;10.1126/science.1160311;10.1186/1752-0509-2-24;10.1186/1754-1611-3-19;10.1371/journal.pbio.0020328;10.1371/journal.pcbi.1000363;10.1371/journal.pone.0005553;[10.1038/NMETH.1318, 10.1038/nmeth.1318] | Swiss Fed Inst Technol | Marchisio, M A;Stelling, J | Marchisio, M A: Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland | Marchisio, Mario Andrea;Stelling, Joerg | 043338;043379 | 63 | null | Switzerland | Swiss Fed Inst Technol | Marchisio, Mario A | Green Published, gold, Green Submitted | BINDING;EXPRESSION;LOGIC GATES;MAMMALIAN-CELLS;NETWORKS;REGULATORS;RIBOREGULATORS;RIBOSWITCH;SYSTEMS BIOLOGY;TRANSCRIPTIONAL REGULATION | Marchisio, Mario A.; Stelling, Joerg; | null | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland;Swiss Fed Inst Technol, Swiss Inst Bioinformat, Basel, Switzerland | 1553-7358 | null | 2 | 1953;1999;2000;2002;2003;2004;2005;2006;2007;2008;2009;2010 | 68 | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland | PLoS Comput. Biol. | Stelling, Joerg | PUBLIC LIBRARY SCIENCE | ,;a;achieve;action;addition;algorithm;algorithms;already;and;any;approaches;are;automatic;behavior;binding;biological;Boolean;both;brute-force;by;chemicals;circuit;circuit's;circuits;comparison;computational;corresponding;de;design;designs;developed;devising;digital;direct;even;existing;expect;factors;faithful;focusing;for;four;function;functions;gates;gene;generates;given;hard;help;however;implemented;in;input-output;inputs;is;kinetic;lacking;logic;method;methodology;methods;more;need;network;new;noise;novo;of;on;optimization;our;parameter;parametric;perturbations;possible;potential;promoters;ranks;rational;regulatory;relations;representation;reproduced;reveals;Ribosome;run;same;schemes;several;show;silico;simpler;simplifying;simulations;sites;solutions;specifies;stochastic;structure;synthetic;table;target;task;that;the;therefore;to;tool;truth;under;unequivocal;up;values;we;well-defined;with;without | Swiss Fed Inst Technol | De novo computational design of synthetic gene circuits that achieve well-defined target functions is a hard task. Existing, brute-force approaches run optimization algorithms on the structure and on the kinetic parameter values of the network. However, more direct rational methods for automatic circuit design are lacking. Focusing on digital synthetic gene circuits, we developed a methodology and a corresponding tool for in silico automatic design. For a given truth table that specifies a circuit's input-output relations, our algorithm generates and ranks several possible circuit schemes without the need for any optimization. Logic behavior is reproduced by the action of regulatory factors and chemicals on the promoters and on the ribosome binding sites of biological Boolean gates. Simulations of circuits with up to four inputs show a faithful and unequivocal truth table representation, even under parametric perturbations and stochastic noise. A comparison with already implemented circuits, in addition, reveals the potential for simpler designs with the same function. Therefore, we expect the method to help both in devising new circuits and in simplifying existing solutions. | ABE-8451-2020;F-7499-2010 | BINDING;EXPRESSION;LOGIC GATES;MAMMALIAN-CELLS;NETWORKS;TRANSCRIPTIONAL REGULATION;REGULATORS;RIBOREGULATORS;RIBOSWITCHES;SYSTEMS BIOLOGY | 0 | null | null | 13 | BINDING;EXPRESSION;logic gates;MAMMALIAN-CELLS;NETWORKS;Transcriptional regulation;REGULATOR;RIBOREGULATORS;RIBOSWITCH;systems biology | WOS:000287698700018 | Swiss Fed Inst Technol, Basel, Switzerland | Switzerland | 2,011 | null | 0000-0002-5102-1069 | null | null | English | null | 026 CALTECH DISTR GR;BIOCHEMISTRY-US;BIOINFORMATICS;BIOTECHNOL BIOENG;BMC SYST BIOL;CHEMBIOCHEM;CRIT REV BIOCHEM MOL;CURR OPIN BIOTECH;CURR OPIN GENET DEV;DESIGN SIMULATION TO;FEBS LETT;I;IEEE INT SYMP CIRC S;IET Synthetic Biology;INTRO SYSTEMS BIOL;J AM CHEM SOC;J Biol Eng;J MOL BIOL;LESSONS ELECT CIRCUI;Logic synthesis and verification algorithms;MOL BIOSYST;MOL SYST BIOL;NAT BIOTECHNOL;NAT METHODS;NAT REV GENET;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PHYS REV E;PHYSICA D;PLOS BIOL;PLOS COMPUT BIOL;PLOS ONE;SCIENCE | Marchisio, Mario A | 2024-03-11
ER | Alon, U;Anderson, J C;Bayer, T S;Beisel, C L;Benenson, Y;Bintu, L;Breaker, R R;Chandran Deepak;Dasika, M S;Desai, T A;Eichenberger, P;Ellis, T;Elowitz, M B;Endy, D;Engler, C;Franch, T;François, P;Frezza, B M;Gibson, D G;Gibson, M A;Ginkel, M;Goler, J A;Gordon, A;Hachtel G. D.;Hoops, S;Hucka, M;Isaacs, F J;Kahan, M;Kalir, S;Karnaugh M.;Kashtan, N;Khalil, A S;Kramer, B P;Kuphaldt T.;Majdalani, N;Mandal, M;Mangan, S;Marchisio, M A;Mirschel, S;Rieder, R;Rinaudo, K;Rodrigo, G;Salis, H M;Samoilov, M S;Schmidt, H;Seelig, G;Serganov, A;Silva-Rocha, R;Stojanovic, M N;Streichert, F;Sudarsan, N;Terzer M.;Tian, J D;Weiss, R;Wickiser, J K;Win, M N;Winkler, W | 726DJ | Basel, Switzerland | 75 | null | 1 | null | 21,399,700 | Marchisio, Mario A;Stelling, Joerg | PLOS COMPUT BIOL | Basel, Switzerland |
Bagh, S;McMillen, D R | 10.1007/s11047-009-9167-3 | null | VAN GODEWIJCKSTRAAT 30, 3311 GZ DORDRECHT, NETHERLANDS | 483f372n5i3b5p6f163s4p1f6y1s1d2j2z1h3824 | A synthetic genetic circuit whose signal-response curve is temperature-tunable from band-detection to sigmoidal behaviour | Univ Toronto | null | McMillen, DR (corresponding author), Univ Toronto, Dept Chem & Phys Sci, Inst Opt Sci, 3359 Mississauga Rd N, Mississauga, ON L5L 1C6, Canada. | SI | Bagh, Sangram;McMillen, David R | Computer Science, Artificial Intelligence;Computer Science, Interdisciplinary Applications;Computer Science, Theory & Methods | Natural Sciences and Engineering Research Council (NSERC) of Canada; Canada Foundation for Innovation (CFI); Ontario Photonics Consortium (OPC); Canadian Institutes for Health Research (CIHR); Ontario Research Fund (ORF) | WOS | McMillen, D R | Univ Toronto, Mississauga ON, Canada | 9 | a;band-detection;behaviour;circuit;curve;From;genetic;is;sigmoidal;signal-response;synthetic;temperature-tunable;to;whose | 1 | McMillen, David | SPRINGER | Univ Toronto, Dept Chem & Phys Sci, Inst Opt Sci, 3359 Mississauga Rd N, Mississauga, ON L5L 1C6, Canada;Univ Toronto, Dept Chem & Phys Sci, Inst Opt Sci, Mississauga, ON L5L 1C6, Canada | Article | Univ Toronto | DORDRECHT | null | null | Univ Toronto | Canada Foundation for Innovation (CFI);Canadian Institutes for Health Research (CIHR);Natural Sciences and Engineering Research Council (NSERC) of Canada;Ontario Photonics Consortium (OPC);Ontario Research Fund (ORF) | McMillen, DR (corresponding author), Univ Toronto, Dept Chem & Phys Sci, Inst Opt Sci, 3359 Mississauga Rd N, Mississauga, ON L5L 1C6, Canada. | 1006 | Bagh, Sangram;McMillen, David R | 5 | 1 | 286,534,400,013 | Canada Foundation for Innovation (CFI);Canadian Institutes for Health Research (CIHR);Natural Sciences and Engineering Research Council (NSERC) of Canada;Ontario Photonics Consortium (OPC);Ontario Research Fund (ORF) | Canada | NATURAL COMPUTING | Canada | null | null | Univ Toronto, Dept Chem & Phys Sci, Inst Opt Sci, Mississauga, ON L5L 1C6, Canada | 1567-7818 | Bagh, S;McMillen, D R | DEC | david.mcmillen@utoronto.ca | band-detection;sigmoidal behaviour;signal-response curve;synthetic;temperature-tunable | 2 | J | Computer Science | ability;band;band detection (strongest response;band-detection;band-detection response;CELL-CELL COMMUNICATION;cells;Cellular computing;Change;circuit;CONSTRUCTION;couple;Escherichia coli;ESCHERICHIA-COLI;essential qualitative behaviours;EXACT STOCHASTIC SIMULATION;expression;genetic alterations;Genetic networks;Genetic signal processing;host cell;important element;information processing systems;input concentrations);investigation;key goal;LAMBDA;mathematical model;minimal effort;natural genetic circuits;NETWORK;noise;output;process;programming new cellular functions;range;replacement;REPRESSOR;response curves;serve;sigmoidal behaviour;sigmoidal response;Signal-response;signal-response behaviours;signal-response characteristics;signal-response curve;single system;switch-like sigmoidal response;synthetic;synthetic biology;synthetic gene circuits;synthetic gene system;synthetic systems;SYSTEM;systems;temperature;temperature-tunable;toggle switch;useful modular component | Bagh, S | CELL-CELL COMMUNICATION;Cellular computing;CONSTRUCTION;Escherichia coli;ESCHERICHIA-COLI;EXACT STOCHASTIC SIMULATION;EXPRESSION;Genetic networks;Genetic signal processing;LAMBDA;NETWORK;NOISE;REPRESSOR;Signal-response;Synthetic biology;toggle switch | 991 | [Bagh, Sangram; McMillen, David R.] Univ Toronto, Dept Chem & Phys Sci, Inst Opt Sci, Mississauga, ON L5L 1C6, Canada. | This work was funded by the Natural Sciences and Engineering Research Council (NSERC, Discovery grant) of Canada, the Canada Foundation for Innovation (CFI, New Opportunities and Infrastructure Operating Fund grants), the Ontario Photonics Consortium (OPC), the Canadian Institutes for Health Research (CIHR, Tools, Techniques, and Devices grant), and the Ontario Research Fund (ORF). | ability;band;band detection (strongest response;band-detection response;cells;change;circuit;couple;Escherichia coli;essential qualitative behaviours;genetic alterations;host cell;important element;information processing systems;input concentrations);investigation;key goal;mathematical model;minimal effort;natural genetic circuits;output;process;programming new cellular functions;range;replacement;response curves;serve;sigmoidal response;signal-response behaviours;signal-response characteristics;signal-response curve;single system;switch-like sigmoidal response;synthetic;synthetic biology;synthetic gene circuits;synthetic gene system;synthetic systems;system;systems;temperature;useful modular component | 10.1002/bit.21862;10.1007/s002030050601;10.1016/0022-2836(80)90302-2;10.1016/0092-8674(80)90383-9;10.1016/j.jbiotec.2005.08.030;10.1016/S0092-8674(03)00346-5;10.1021/j100540a008;10.1021/jp993732q;10.1023/A:1023307812034;10.1038/35002125;10.1038/35002131;10.1038/msb4100073;10.1038/msb4100173;10.1038/nature01257;10.1038/nature02257;10.1038/nature02491;10.1038/nature03461;10.1038/nbt0708-771;10.1038/nbt1162;10.1038/ng1807;10.1038/nrg1615;10.1038/nrg1637;10.1049/iet-stb:20070004;10.1063/1.1345702;10.1073/pnas.0400473101;10.1073/pnas.1332628100;10.1093/nar/25.6.1203;10.1103/PhysRevE.77.021919;10.1103/PhysRevLett.88.148101;10.1126/science.1067407;10.1126/science.1105891;10.1126/science.1109090;10.1126/science.1151153;10.1126/science.271.5253.1247;10.1128/AEM.59.10.3485-3487.1993;10.1128/JB.164.3.1366-1369.1985;10.1128/JVI.32.1.162-166.1979;10.1146/annurev.bioeng.5.040202.121553;10.1186/1471-2105-5-24;10.1529/biophysj.104.044131 | Univ Toronto | Bagh, S;McMillen, D R | Bagh, S: Univ Toronto, Dept Chem & Phys Sci, Inst Opt Sci, Mississauga, ON L5L 1C6, Canada | null | null | 45 | null | Canada | Univ Toronto | Bagh, Sangram | null | CELL-CELL COMMUNICATION;CONSTRUCTION;ESCHERICHIA-COLI;EXACT STOCHASTIC SIMULATION;EXPRESSION;LAMBDA;NETWORK;NOISE;REPRESSOR;TOGGLE SWITCH | Bagh, Sangram; McMillen, David R.; | null | Univ Toronto, Dept Chem & Phys Sci, Inst Opt Sci, Mississauga, ON L5L 1C6, Canada | Univ Toronto, Dept Chem & Phys Sci, Inst Opt Sci, Mississauga, ON L5L 1C6, Canada | 1572-9796 | Escherichia coli;Cellular computing;Genetic networks;Genetic signal processing;Signal-response;Synthetic biology | 4 | 1977;1979;1980;1985;1992;1993;1996;1997;1998;2000;2001;2002;2003;2004;2005;2006;2007;2008 | 2 | Univ Toronto, Dept Chem & Phys Sci, Inst Opt Sci, 3359 Mississauga Rd N, Mississauga, ON L5L 1C6, Canada | Nat. Comput. | McMillen, David R | SPRINGER | (strongest;,;:;a;ability;allows;also;alterations;altering;an;and;any;as;band;band-detection;be;been;behaviours;biology;by;captures;cell;cells;cellular;change;characteristics;circuit;circuits;coli;component;concentrations);couple;curve;curves;detection;developed;effort;element;Escherichia;essential;from;functions;gene;genetic;goal;has;here;host;implemented;important;in;information;input;inserted;into;investigation;is;its;key;mathematical;may;minimal;model;modular;natural;new;not;of;once;or;other;output;present;previously;process;processing;programming;provides;qualitative;range;replacement;response;serve;sigmoidal;signal-response;simply;single;switch-like;synthetic;system;systems;temperature;the;this;thus;to;tuned;useful;using;various;we;which;whose;with;within;without | Univ Toronto | Programming new cellular functions by using synthetic gene circuits is a key goal in synthetic biology, and an important element of this process is the ability to couple to the information processing systems of the host cell using synthetic systems with various signal-response characteristics. Here, we present a synthetic gene system in Escherichia coli whose signal-response curve may be tuned from band detection (strongest response within a band of input concentrations) to a switch-like sigmoidal response, simply by altering the temperature. This change from a band-detection response to a sigmoidal response has not previously been implemented. The system allows investigation of a range of signal-response behaviours with minimal effort: a single system, once inserted into the cells, provides a range of response curves without any genetic alterations or replacement with other systems. By altering its output, the system may couple to other synthetic or natural genetic circuits, and thus serve as a useful modular component. A mathematical model has also been developed which captures the essential qualitative behaviours of the circuit. | null | CELL-CELL COMMUNICATION;CONSTRUCTION;ESCHERICHIA-COLI;EXACT STOCHASTIC SIMULATION;EXPRESSION;LAMBDA;NETWORKS;NOISE;REPRESSOR;TOGGLE SWITCH | 0 | null | Cellular computing;Escherichia coli;Genetic networks;Genetic signal processing;Signal-response;Synthetic biology | 16 | ESCHERICHIA-COLI;CELL-CELL COMMUNICATION;Cellular computing;CONSTRUCTION;EXACT STOCHASTIC SIMULATION;EXPRESSION;Genetic networks;Genetic signal processing;LAMBDA;NETWORKS;NOISE;REPRESSOR;Signal-response;Synthetic biology;toggle switch | WOS:000286534400013 | Univ Toronto, Mississauga ON, Canada | Canada | 2,010 | null | 0000-0003-2676-5450 | null | null | English | null | ANNU REV BIOMED ENG;APPL ENVIRON MICROB;ARCH MICROBIOL;BIOPHYS J;BIOTECHNOL BIOENG;BMC BIOINFORMATICS;CELL;CELLULAR COMPUTING;CHAOS;IET Synthetic Biology;J BACTERIOL;J BIOTECHNOL;J MOL BIOL;J PHYS CHEM A;J PHYS CHEM-US;J VIROL;MOL SYST BIOL;NAT BIOTECHNOL;NAT COMPUT;NAT GENET;NAT REV GENET;Natural Computing;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PHYS REV E;PHYS REV LETT;SCIENCE;SYSTEM MODELING CELL | Bagh, Sangram;McMillen, David R | 2024-03-11
ER | Adalsteinsson, D;Anderson, J C;Andrianantoandro, E;Arkin, A;Atkinson, M R;Bagh, S;Bar-Even, A;Bashor, C J;Basu S.;Basu, S;Benner, S A;Chen, M T;Elowitz, M B;Feng, X J;Friedman, B E;Gardner, T S;Gerchman, Y;Gibson, M A;Gillespie, D T;Guet, C C;Hasty, J;Haynes K. A.;Iadevaia, S;Isaacs, F J;Kaern, M;Kærn, M;Lewis, M;Lieb, M;Lutz, R;Maurer, R;Mieschendahl, M;Paulsson, J;Pedraza, J M;Ptashne M.;Ptashne, M;Raser, J M;Trueba, F J;Villaverde, A;Weiss R.;Weiss, L E;Weiss, R;You, L C | 710SN | Mississauga ON, Canada | 2 | null | 1 | null | null | Bagh, Sangram;McMillen, David R | NAT COMPUT | Mississauga ON, Canada |
Chen, B S;Wu, C H | 10.1109/TFUZZ.2010.2070842 | null | 445 HOES LANE, PISCATAWAY, NJ 08855-4141 USA | 516y2n2wk4g3j6mp1l3m694bn4o5b6wl6h33 | Robust Optimal Reference-Tracking Design Method for Stochastic Synthetic Biology Systems: T-S Fuzzy Approach | Natl Tsing Hua Univ | null | Chen, BS (corresponding author), Natl Tsing Hua Univ, Dept Elect Engn, Lab Control & Syst Biol, Hsinchu 30013, Taiwan. | null | Chen, Bor-Sen;Wu, Chih-Hung | Computer Science, Artificial Intelligence;Engineering, Electrical & Electronic | National Science Council [NSC 98-2221-E-007-113-MY3]; National Tsing Hua University [98N2565E1] | WOS | Chen, B S | Natl Tsing Hua Univ, Hsinchu, Taiwan | 18 | :;approach;biology;design;for;Fuzzy;method;optimal;Reference-Tracking;robust;stochastic;synthetic;systems;T-S | 1 | null | IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC | Natl Tsing Hua Univ, Dept Elect Engn, Lab Control & Syst Biol, Hsinchu 30013, Taiwan;Natl Tsing Hua Univ, Dept Elect Engn, Lab Syst Biol, Hsinchu 30013, Taiwan | Article | Natl Tsing Hua Univ | PISCATAWAY | null | null | Natl Tsing Hua Univ | National Science Council;National Tsing Hua University | Chen, BS (corresponding author), Natl Tsing Hua Univ, Dept Elect Engn, Lab Control & Syst Biol, Hsinchu 30013, Taiwan. | 1159 | Chen, Bor-Sen;Wu, Chih-Hung | 22 | 1 | 284,855,200,010 | National Science Council [NSC 98-2221-E-007-113-MY3];National Tsing Hua University [98N2565E1] | Taiwan | IEEE TRANSACTIONS ON FUZZY SYSTEMS | Taiwan | null | null | Natl Tsing Hua Univ, Dept Elect Engn, Lab Syst Biol, Hsinchu 30013, Taiwan | 1063-6706 | Chen, B S;Wu, C H | DEC | bschen@ee.nthu.edu.tw;g883743@alumni.nthu.edu.tw | robust Optimal Reference-Tracking Design Method;Stochastic Synthetic Biology Systems;T-S Fuzzy Approach | 2 | J | Computer Science;Engineering | CONTROLLER-DESIGN;convex optimization techniques;design procedure;desired behaviors;desired reference model;development;difficult;DYNAMIC-SYSTEMS;Eigenvalue-shifted design method;environmental disturbances;ESCHERICHIA-COLI;expedient scheme;External disturbances;extracellular environments;extrinsic disturbances;four design specifications;gene networks;GENETIC REGULATORY SYSTEMS;H-INFINITY CONTROL;host cell;important topic;intrinsic parameter fluctuations;linear matrix inequality (LMI);linear matrix inequality (LMI)-constrained optimization method;MATRIX INEQUALITIES;nascent field;networks;new gene network;nonfunctioning;NONLINEAR INTERCONNECTED SYSTEMS;nonlinear stochastic minimum-error-tracking design problem;nonlinear stochastic systems;nonlinear synthetic gene networks;PIECEWISE LYAPUNOV FUNCTIONS;present;robust optimal nonlinear stochastic-tracking design;robust optimal reference tracking;robust Optimal Reference-Tracking Design Method;robust optimal reference-tracking design problem;robust optimal tracking;simple design procedure;spite;STABILIZATION;stochastic optimal reference-tracking design;stochastic optimal-tracking design method;Stochastic Synthetic Biology Systems;Stochastic synthetic gene network;study;synthetic biology;synthetic gene network;synthetic gene networks;synthetic gene oscillators;T-S Fuzzy Approach;Takagi-Sugeno (T-S) fuzzy method;Takagi-Sugeno (T-S) fuzzy model;uncertain interactions;unknown molecules;vivo | Chen, B S | CONTROLLER-DESIGN;DYNAMIC-SYSTEMS;Eigenvalue-shifted design method;ESCHERICHIA-COLI;GENETIC REGULATORY SYSTEMS;H-INFINITY CONTROL;linear matrix inequality (LMI);MATRIX INEQUALITIES;NETWORKS;NONLINEAR INTERCONNECTED SYSTEMS;PIECEWISE LYAPUNOV FUNCTIONS;STABILIZATION;stochastic optimal reference-tracking design;Synthetic gene network;Takagi-Sugeno (T-S) fuzzy model | 1144 | [Chen, Bor-Sen; Wu, Chih-Hung] Natl Tsing Hua Univ, Dept Elect Engn, Lab Syst Biol, Hsinchu 30013, Taiwan. | Manuscript received October 21, 2009; revised March 15, 2010; accepted July 14, 2010. Date of publication August 30, 2010; date of current version December 3, 2010. This work was supported by National Science Council under Contract NSC 98-2221-E-007-113-MY3 and by National Tsing Hua University under Contract 98N2565E1. | convex optimization techniques;design procedure;desired behaviors;desired reference model;development;difficult;eigenvalue-shifted design method;environmental disturbances;expedient scheme;external disturbances;extracellular environments;extrinsic disturbances;four design specifications;gene networks;host cell;important topic;intrinsic parameter fluctuations;linear matrix inequality (LMI)-constrained optimization method;nascent field;new gene network;nonfunctioning;nonlinear stochastic minimum-error-tracking design problem;nonlinear stochastic systems;nonlinear synthetic gene networks;present;robust optimal nonlinear stochastic-tracking design;robust optimal reference tracking;robust optimal reference-tracking design problem;robust optimal tracking;simple design procedure;spite;stochastic optimal-tracking design method;stochastic synthetic gene network;study;synthetic biology;synthetic gene networks;synthetic gene oscillators;Takagi-Sugeno (T-S) fuzzy method;uncertain interactions;unknown molecules;vivo | 10.1016/j.fss.2006.09.014;10.1016/j.sbi.2006.06.011;10.1021/bp000124f;10.1038/35002125;10.1038/75398;10.1038/msb4100073;10.1038/nature01257;10.1038/nbt0708-771;10.1038/nbt1413;10.1038/nrg1292;10.1049/sb:20045006;10.1073/pnas.0306484101;10.1073/pnas.0408507102;10.1089/10665270252833208;10.1093/bioinformatics/btm362;10.1093/bioinformatics/btp310;10.1109/91.481840;10.1109/91.728449;10.1109/91.797980;10.1109/91.855915;10.1109/91.919246;10.1109/TBCAS.2008.926728;10.1109/TCSI.2005.852492;10.1109/TFUZZ.2003.814861;10.1109/TFUZZ.2004.834811;10.1109/TFUZZ.2004.836067;10.1109/TFUZZ.2004.839662;10.1109/TFUZZ.2005.859309;10.1109/TFUZZ.2006.878252;10.1109/TFUZZ.2006.881446;10.1109/TFUZZ.2006.889964;10.1109/TFUZZ.2008.924355;10.1109/TSMC.1985.6313399;10.1109/TSMCB.2003.811500;10.1109/TSMCB.2007.896016;10.1109/TSMCB.2007.906975;10.1109/TSP.2004.840724;10.1137/S0363012903423727;10.1146/annurev.biochem.69.1.571;10.1186/1471-2105-8-12;10.1186/1752-0509-3-66 | Natl Tsing Hua Univ | Chen, B S;Wu, C H | Chen, B S: Natl Tsing Hua Univ, Dept Elect Engn, Lab Syst Biol, Hsinchu 30013, Taiwan | Chen, Bor-Sen | 98N2565E1;NSC 98-2221-E-007-113-MY3 | 50 | null | Taiwan | Natl Tsing Hua Univ | Chen, Bor-Sen | null | CONTROLLER-DESIGN;DYNAMIC-SYSTEMS;ESCHERICHIA-COLI;GENETIC REGULATORY SYSTEMS;H-INFINITY CONTROL;MATRIX INEQUALITIES;NETWORKS;NONLINEAR INTERCONNECTED SYSTEMS;PIECEWISE LYAPUNOV FUNCTIONS;STABILIZATION | Chen, Bor-Sen; Wu, Chih-Hung; | null | Natl Tsing Hua Univ, Dept Elect Engn, Lab Syst Biol, Hsinchu 30013, Taiwan | Natl Tsing Hua Univ, Dept Elect Engn, Lab Syst Biol, Hsinchu 30013, Taiwan | 1941-0034 | Eigenvalue-shifted design method;linear matrix inequality (LMI);stochastic optimal reference-tracking design;Synthetic gene network;Takagi-Sugeno (T-S) fuzzy model | 6 | 1985;1994;1995;1996;1997;1998;1999;2000;2001;2002;2003;2004;2005;2006;2007;2008;2009 | 57 | Natl Tsing Hua Univ, Dept Elect Engn, Lab Control & Syst Biol, Hsinchu 30013, Taiwan | IEEE Trans. Fuzzy Syst. | Wu, Chih-Hung | IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC | (LMI)-constrained;(T-S);,;a;achieve;also;an;and;are;as;at;be;behaviors;biology;by;can;cell;completely;convex;created;design;desired;developed;development;difficult;disturbances;due;eigenvalue-shifted;environmental;environments;expedient;external;extracellular;extrinsic;field;finally;fluctuations;for;four;further;fuzzy;gene;guarantee;hard;hence;host;how;however;important;improve;in;inequality;interactions;into;intra;intrinsic;introduced;is;linear;matrix;meet;method;minimum-error-tracking;model;modeled;molecules;most;nascent;network;networks;new;newly;nonfunctioning;nonlinear;of;on;optimal;optimal-tracking;optimization;order;oscillators;parameter;present;problem;procedure;proposed;reference;reference-tracking;robust;scheme;simple;simplify;solve;solved;some;specifications;spite;still;stochastic;stochastic-tracking;study;synthetic;systems;Takagi-Sugeno;techniques;that;the;these;this;to;topic;track;tracking;uncertain;under;unknown;using;vivo;which;with | Natl Tsing Hua Univ | At present, the development in the nascent field of synthetic gene networks is still difficult. Most newly created gene networks are nonfunctioning due to intrinsic parameter fluctuations, uncertain interactions with unknown molecules and external disturbances of intra and extracellular environments on the host cell. How to design a completely new gene network, that is to track some desired behaviors under these intrinsic and extrinsic disturbances on the host cell, is the most important topic in synthetic biology. In this study, the intrinsic parameter fluctuations, uncertain interactions with unknown molecules and environmental disturbances, are modeled into the nonlinear stochastic systems of synthetic gene networks in vivo. Four design specifications are introduced to guarantee the stochastic synthetic gene network, which can achieve robust optimal tracking of a desired reference model in spite of these intrinsic and extrinsic disturbances on the host cell. However, the robust optimal reference-tracking design problem of nonlinear synthetic gene networks is still hard to solve. In order to simplify the design procedure of the robust optimal nonlinear stochastic-tracking design for synthetic gene networks, the Takagi-Sugeno (T-S) fuzzy method is introduced to solve the nonlinear stochastic minimum-error-tracking design problem. Hence, the robust optimal reference-tracking design problem under four design specifications can be solved by the linear matrix inequality (LMI)-constrained optimization method using convex optimization techniques. Further, a simple design procedure is developed for synthetic gene networks to meet the four design specifications to achieve robust optimal reference tracking. Finally, an eigenvalue-shifted design method is also proposed as an expedient scheme to improve the stochastic optimal-tracking design method of synthetic gene oscillators. | D-9114-2017 | CONTROL DESIGN;DYNAMICAL-SYSTEMS;ESCHERICHIA-COLI;GENETIC REGULATORY SYSTEMS;H-INFINITY CONTROL;MATRIX INEQUALITIES;NETWORKS;NONLINEAR INTERCONNECTED SYSTEMS;PIECEWISE LYAPUNOV FUNCTIONS;STABILITY | 3 | null | Eigenvalue-shifted design method;linear matrix inequality (LMI);stochastic optimal reference-tracking design;Synthetic gene network;Takagi-Sugeno (T-S) fuzzy model | 16 | ESCHERICHIA-COLI;CONTROL DESIGN;dynamical systems;Eigenvalue-shifted design method;GENETIC REGULATORY SYSTEMS;H-INFINITY CONTROL;linear matrix inequality (LMI);MATRIX INEQUALITIES;NETWORKS;NONLINEAR INTERCONNECTED SYSTEMS;PIECEWISE LYAPUNOV FUNCTIONS;STABILITY;stochastic optimal reference-tracking design;synthetic gene networks;Takagi-Sugeno (T-S) fuzzy model | WOS:000284855200010 | Natl Tsing Hua Univ, Hsinchu, Taiwan | Taiwan | 2,010 | null | null | null | null | English | null | ANNU REV BIOCHEM;BIOINFORM BIOL INSIG;BIOINFORMATICS;BIOTECHNOL PROGR;BMC BIOINFORMATICS;BMC SYST BIOL;COMPUTER CONTROLLED;CURR OPIN STRUC BIOL;Dynamic Noncooperative Game Theory;Fuzzy control;FUZZY SET SYST;IEEE T BIOMED CIRC S;IEEE T CIRCUITS-I;IEEE T FUZZY SYST;IEEE T SIGNAL PROCES;IEEE T SYST MAN CY B;IEEE T SYST MAN CYB;INTRO SYSTEMS BIOL D;J COMPUT BIOL;Linear MatrixInequalities in System and Control Theory;Linear Stochastic Control Systems;MOL SYST BIOL;NAT BIOTECHNOL;NAT REV GENET;NATURE;P NATL ACAD SCI USA;ROBUST CONTROL TOOLB;SIAM J CONTROL OPTIM;Systems Biology | Chen, Bor-Sen;Wu, Chih-Hung | 2024-03-11
ER | Alon, U;Andrianantoandro, E;Arkin, A;Astrom K.;Balas G.;Basar T.;Batt, G;Boyd S.;Bulter, T;Canton, B;Chen G.;Chen, B S;Chin, J W;De Jong, H;Elowitz, M B;Farmer, W R;Feng, G;Hasty, J;Hooshangi, S;Hsiao, F H;Hwang, C L;Kuepfer, L;Li, T H S;Lin, C L;Lin, W W;Mcadams, H H;Passino K. M.;Sontag E. D.;Takagi, T;Tanaka T.;Tanaka, K;Tseng, C S;Tucker, M;Wang, C W;Wang, W J;Zhang, W H | 688NC | Hsinchu, Taiwan | 58 | null | 1 | null | null | Chen, Bor-Sen;Wu, Chih-Hung | IEEE T FUZZY SYST | Hsinchu, Taiwan |
Egorov, T A;Grishin, E V;Odintsova, T I;Pukhal'skiy, V A;Rogozhin, E A;Shiyan, A N;Slavokhotova, A A;Utkina, L L;Zhabon, E O | 10.1134/S1022795410120070 | null | 233 SPRING ST, NEW YORK, NY 10013-1578 USA | 67265412u1h696o3q1e715w6b32y3g2l301e0 | Heterologous expression of a synthetic gene encoding a novel hevein-type antimicrobial peptide of Leymus arenarius in Escherichia coli cells | Russian Acad Sci | null | Utkina, LL (corresponding author), Russian Acad Sci, Vavilov Inst Gen Genet, Moscow 119991, Russia. | null | Egorov, Ts A;Grishin, E V;Odintsova, T I;Pukhal'skiy, V A;Rogozhin, E A;Shiyan, A N;Slavokhotova, A A;Utkina, L L;Zhabon, E O | Genetics & Heredity | Russian Foundation for Basic Research [09-04-00250a, 08-04-00783a]; Presidium of the Russian Academy of Sciences | WOS | Utkina, L L | Russian Acad Agr Sci, Vladimir Oblast, Russia;Russian Acad Sci, Moscow, Russia | 46 | a;Antimicrobial;arenarius;Cells;coli;encoding;Escherichia;expression;gene;Heterologous;hevein-type;in;Leymus;novel;of;peptide;synthetic | 1 | Rogozhin, Eugene;Slavokhotova, Anna A;Utkina, Lyubov | MAIK NAUKA/INTERPERIODICA/SPRINGER | Russian Acad Agr Sci, Natl Res Inst Vet Virol & Microbiol, Pokrov 601120, Vladimir Oblast, Russia;Russian Acad Sci, Shemyakin & Ovchinnikov Inst Bioorgan Chem, Moscow 177997, Russia;Russian Acad Sci, Vavilov Inst Gen Genet, Moscow 119991, Russia | Article | Russian Acad Sci | NEW YORK | null | null | Russian Acad Agr Sci;Russian Acad Sci | Presidium of the Russian Academy of Sciences;Russian Foundation for Basic Research | Utkina, LL (corresponding author), Russian Acad Sci, Vavilov Inst Gen Genet, Moscow 119991, Russia. | 1454 | Egorov, Ts A;Grishin, E V;Odintsova, T I;Pukhal'skiy, V A;Rogozhin, E A;Shiyan, A N;Slavokhotova, A A;Utkina, L L | 5 | 3 | 285,378,600,007 | Presidium of the Russian Academy of Sciences;Russian Foundation for Basic Research [09-04-00250a, 08-04-00783a] | Russia | RUSSIAN JOURNAL OF GENETICS | Russia | null | null | Russian Acad Sci, Vavilov Inst Gen Genet, Moscow 119991, Russia | 1022-7954 | Egorov, T A;Grishin, E V;Odintsova, T I;Pukhal'skiy, V A;Rogozhin, E A;Shiyan, A N;Slavokhotova, A A;Utkina, L L;Zhabon, E O | DEC | lyuba_utk@mail.ru | Escherichia coli cells;heterologous expression;Leymus arenarius;novel hevein-type antimicrobial peptide;synthetic gene | 9 | J | Genetics & Heredity | amino acid;ANTIFUNGAL ACTIVITY;CHITIN-BINDING PROTEINS;chromatography;engineering pathogen-resistant crops;Escherichia coli cells;expression;fusion;GENE;genetic transformation;heterologous expression;high inhibitory activity;identity;LAMP-1a;Leymus arenarius;mass spectrometry;native LAMP-1a;novel antifungal peptide;novel hevein-type antimicrobial peptide;number;peptide;phytopathogenic fungi;PLANT DEFENSE;plants;possibilities;recombinant peptide;sand-elymus (Leymus arenarius) seeds;synthetic gene;target peptide;thioredoxin;vitro assays | Utkina, L L | ANTIFUNGAL ACTIVITY;CHITIN-BINDING PROTEINS;PLANT DEFENSE | 1449 | [Utkina, L. L.; Slavokhotova, A. A.; Shiyan, A. N.; Odintsova, T. I.; Pukhal'skiy, V. A.] Russian Acad Sci, Vavilov Inst Gen Genet, Moscow 119991, Russia. [Utkina, L. L.; Slavokhotova, A. A.; Shiyan, A. N.; Odintsova, T. I.; Pukhal'skiy, V. A.] Russian Acad Agr Sci, Natl Res Inst Vet Virol & Microbiol, Pokrov 601120, Vladimir Oblast, Russia. [Rogozhin, E. A.; Grishin, E. V.; Egorov, Ts A.] Russian Acad Sci, Shemyakin & Ovchinnikov Inst Bioorgan Chem, Moscow 177997, Russia. | The work was supported by the Russian Foundation for Basic Research (grants nos. 09-04-00250a and 08-04-00783a) and by the Programs of the Presidium of the Russian Academy of Sciences "Biological Diversity" and "Molecular and Cell Biology". | amino acid;chromatography;engineering pathogen-resistant crops;Escherichia coli cells;expression;fusion;gene;genetic transformation;high inhibitory activity;identity;LAMP-1a;mass spectrometry;native LAMP-1a;novel antifungal peptide;number;peptide;phytopathogenic fungi;plants;possibilities;recombinant peptide;sand-elymus (Leymus arenarius) seeds;synthetic gene;target peptide;thioredoxin;vitro assays | 10.1002/(SICI)1097-0282(1998)47:6<479::AID-BIP6>3.0.CO;2-K;10.1006/abbi.2001.2564;10.1006/prep.1999.1085;10.1007/BF00197797;10.1007/s00253-008-1648-2;10.1016/0014-5793(94)00753-5;10.1016/j.biochi.2008.06.007;10.1016/j.peptides.2005.03.007;10.1016/j.plaphy.2008.06.011;10.1016/S0014-5793(01)02456-5;10.1080/713608148;10.1094/MPMI.2000.13.1.54;10.1104/pp.010233;10.1111/j.1742-4658.2009.07135.x;10.1146/annurev.pp.44.060193.003111;10.2174/187221308783399261 | Russian Acad Sci | Egorov, T A;Grishin, E V;Odintsova, T I;Pukhal'skiy, V A;Rogozhin, E A;Shiyan, A N;Slavokhotova, A A;Utkina, L L;Zhabon, E O | Utkina, L L: Russian Acad Sci, Vavilov Inst Gen Genet, Moscow 119991, Russia | Rogozhin, Eugene;Slavokhotova, Anna A;Utkina, Lyubov | 08-04-00783a;09-04-00250a | 19 | null | Russia | Russian Acad Agr Sci;Russian Acad Sci | Utkina, L L | null | ANTIFUNGAL ACTIVITY;CHITIN-BINDING PROTEINS;PLANT DEFENSE | Utkina, L. L.; Zhabon, E. O.; Slavokhotova, A. A.; Rogozhin, E. A.; Shiyan, A. N.; Grishin, E. V.; Egorov, Ts A.; Odintsova, T. I.; Pukhal'skiy, V. A.; | null | Russian Acad Agr Sci, Natl Res Inst Vet Virol & Microbiol, Pokrov 601120, Vladimir Oblast, Russia;Russian Acad Sci, Shemyakin & Ovchinnikov Inst Bioorgan Chem, Moscow 177997, Russia;Russian Acad Sci, Vavilov Inst Gen Genet, Moscow 119991, Russia | Russian Acad Agr Sci, Natl Res Inst Vet Virol & Microbiol, Pokrov 601120, Vladimir Oblast, Russia;Russian Acad Sci, Shemyakin & Ovchinnikov Inst Bioorgan Chem, Moscow 177997, Russia;Russian Acad Sci, Vavilov Inst Gen Genet, Moscow 119991, Russia | null | null | 12 | 1991;1993;1994;1997;1998;1999;2000;2001;2003;2005;2007;2008;2009 | 15 | Russian Acad Sci, Vavilov Inst Gen Genet, Moscow 119991, Russia | Russ. J. Genet. | Pukhal'skiy, V A | MAIK NAUKA/INTERPERIODICA/SPRINGER | (Leymus;,;a;acid;activity;amino;and;antifungal;arenarius);as;assays;be;by;cells;chromatography;coli;confirmed;crops;displayed;encoding;engineering;Escherichia;expressed;expression;for;from;fungi;fusion;gene;genetic;high;identity;in;inhibitory;isolated;it;LAMP-1a;mass;native;novel;number;obtained;of;opens;pathogen-resistant;peptide;phytopathogenic;plants;possibilities;recombinant;respect;sand-elymus;seeds;sequencing;spectrometry;synthetic;target;the;thioredoxin;this;to;transformation;up;used;vitro;was;which;with | Russian Acad Sci | A novel antifungal peptide, LAMP-1a, was isolated from sand-elymus (Leymus arenarius) seeds. Expression of a synthetic gene encoding this peptide in Escherichia coli cells was obtained. The target peptide was expressed as a fusion with thioredoxin. Identity of the recombinant peptide to native LAMP-1a was confirmed by chromatography, mass spectrometry, and amino acid sequencing. LAMP-1a displayed a high inhibitory activity in respect of a number of phytopathogenic fungi in in vitro assays, which opens up possibilities for the gene encoding it to be used for genetic transformation of plants and for engineering pathogen-resistant crops. | AAO-7240-2020;E-5333-2014;I-2005-2014 | ANTIFUNGAL ACTIVITY;CHITIN-BINDING PROTEINS;PLANT DEFENSE | 0 | null | null | 6 | ANTIFUNGAL ACTIVITY;CHITIN-BINDING PROTEINS;PLANT DEFENSE | WOS:000285378600007 | Russian Acad Agr Sci, Vladimir Oblast, Russia;Russian Acad Sci, Moscow, Russia | Russia | 2,010 | null | 0000-0001-7025-3044;0000-0002-2284-0700;0000-0003-0659-9547 | null | null | English | null | ANNU REV PLANT PHYS;APPL MICROBIOL BIOT;ARCH BIOCHEM BIOPHYS;BIOCHIMIE;BIOPOLYMERS;CRIT REV PLANT SCI;FEBS J;FEBS LETT;MOL PLANT MICROBE IN;PEPTIDES;PLANT PHYSIOL;PLANT PHYSIOL BIOCH;PLANTA;PROTEIN EXPRES PURIF;RECENT PATENTS INFLA;Uspekhi Sovremennoi Biologii | Egorov, Ts A;Grishin, E V;Odintsova, T I;Pukhal'skiy, V A;Rogozhin, E A;Shiyan, A N;Slavokhotova, A A;Utkina, L L | 2024-03-11
ER | Almeida, M S;Beintema, J J;Broekaert, W F;Degray, G;Egorov, T A;García-Olmedo, F;Hui, L D;Kovalskaya, N;Kristensen, A K;Odintsova, T I;Raikhel, N V;Sels, J;Sotchenkov D. V.;Thevissen, K;Vanparijs, J;Vassilevski, A A;Vijayan, S | 695NQ | Moscow, Russia | 15 | null | 2 | null | null | Egorov, Ts A;Grishin, E V;Odintsova, T I;Pukhal'skiy, V A;Rogozhin, E A;Shiyan, A N;Slavokhotova, A A;Utkina, L L;Zhabon, E O | RUSS J GENET+ | Moscow, Russia;Vladimir Oblast, Russia |
Ang, J;Bagh, S;Ingalls, B P;McMillen, D R | 10.1016/j.jtbi.2010.07.034 | null | 24-28 OVAL RD, LONDON NW1 7DX, ENGLAND | 504w306c3c1z6p2e1j725p132k1q6q3d5q5z4v6j | Considerations for using integral feedback control to construct a perfectly adapting synthetic gene network | Univ Toronto | null | McMillen, DR (corresponding author), Univ Toronto, Dept Chem & Phys Sci, Mississauga, ON L5L 1C6, Canada. | null | Ang, Jordan;Bagh, Sangram;Ingalls, Brian P;McMillen, David R | Biology;Mathematical & Computational Biology | Natural Sciences and Engineering Research Council of Canada (NSERC); Ontario Research Fund (ORF); Canada Foundation for Innovation (CFI); Ontario Graduate Scholarship in Science and Technology (OGS-ST) | WOS | McMillen, D R | Univ Toronto, Mississauga ON, Canada;Univ Waterloo, Waterloo ON, Canada | 266 | a;adapting;considerations;construct;control;feedback;for;gene;integral;network;perfectly;synthetic;to;using | 1 | McMillen, David | ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD | Univ Toronto, Dept Chem & Phys Sci, Mississauga, ON L5L 1C6, Canada;Univ Toronto, Inst Opt Sci, Mississauga, ON L5L 1C6, Canada;Univ Waterloo, Dept Appl Math, Waterloo, ON N2L 3G1, Canada | Article | Univ Toronto | LONDON | null | null | Univ Toronto;Univ Waterloo | Canada Foundation for Innovation (CFI);Natural Sciences and Engineering Research Council of Canada (NSERC);Ontario Graduate Scholarship in Science and Technology (OGS-ST);Ontario Research Fund (ORF) | McMillen, DR (corresponding author), Univ Toronto, Dept Chem & Phys Sci, Mississauga, ON L5L 1C6, Canada. | 738 | Ang, Jordan;Bagh, Sangram;Ingalls, Brian P;McMillen, David R | 9 | 3 | 282,252,900,025 | Canada Foundation for Innovation (CFI);Natural Sciences and Engineering Research Council of Canada (NSERC);Ontario Graduate Scholarship in Science and Technology (OGS-ST);Ontario Research Fund (ORF) | Canada | JOURNAL OF THEORETICAL BIOLOGY | Canada | null | null | Univ Toronto, Dept Chem & Phys Sci, Mississauga, ON L5L 1C6, Canada | 0022-5193 | Ang, J;Bagh, S;Ingalls, B P;McMillen, D R | OCT 21 | david.mcmillen@utoronto.ca | considerations;integral feedback control;synthetic gene network | 4 | J | Life Sciences & Biomedicine - Other Topics;Mathematical & Computational Biology | adaptation;attractive prospect;available parts;bacterium Escherichia coli;BIOLOGY;c 2010 Elsevier Ltd;challenges;ClpXP;conditions;considerations;Control systems;DEGRADATION;DESIGN;device;ESCHERICHIA-COLI;expression;extensions;first-order protein removal effects;free-damped harmonic oscillator;gene regulation;generic two-promoter genetic regulatory network;genetic integral controller;genetic regulatory networks (density-dependent kinetics;input perturbations;integral feedback control;integral feedback control leads;MODEL;nature;necessary;network's transient response via analogy;numerical case study;perfect;perfect adaptation;proportional-integral controller;purpose;reach saturation);Regulatory feedback;REPRESSOR;rights reserved;robust control strategy;ROBUSTNESS;specific realization;straightforward;study;synthetic biology;synthetic gene network;systems;theorists;three-promoter network;treatment;two-promoter network | Ang, J | adaptation;BIOLOGY;CLPXP;Control systems;DEGRADATION;DESIGN;ESCHERICHIA-COLI;EXPRESSION;Gene regulation;MODEL;Regulatory feedback;REPRESSOR;ROBUSTNESS;Synthetic biology | 723 | [Ang, Jordan; Bagh, Sangram; McMillen, David R.] Univ Toronto, Dept Chem & Phys Sci, Mississauga, ON L5L 1C6, Canada. [Ang, Jordan; Bagh, Sangram; McMillen, David R.] Univ Toronto, Inst Opt Sci, Mississauga, ON L5L 1C6, Canada. [Ingalls, Brian P.] Univ Waterloo, Dept Appl Math, Waterloo, ON N2L 3G1, Canada. | This work was funded by the Natural Sciences and Engineering Research Council of Canada (NSERC), the Ontario Research Fund (ORF), the Canada Foundation for Innovation (CFI), and the Ontario Graduate Scholarship in Science and Technology (OGS-ST). | adaptation;attractive prospect;available parts;bacterium Escherichia coli;challenges;conditions;device;extensions;first-order protein removal effects;free-damped harmonic oscillator;generic two-promoter genetic regulatory network;genetic integral controller;genetic regulatory networks (density-dependent kinetics;input perturbations;integral feedback control leads;nature;necessary;network's transient response via analogy;numerical case study;perfect;perfect adaptation;proportional-integral controller;purpose;reach saturation);robust control strategy;specific realization;straightforward;study;synthetic gene network;systems;theorists;three-promoter network;treatment;two-promoter network | 10.1006/jtbi.2001.2422;10.1007/s002030050601;10.1016/0005-1098(76)90006-6;10.1016/0092-8674(80)90383-9;10.1016/S0006-3495(03)70021-6;10.1016/S0006-3495(71)86192-1;10.1016/S0167-6911(03)00136-1;10.1038/16483;10.1038/43199;10.1038/msb4100073;10.1038/msb4100168;10.1038/msb4100172;10.1038/nrg2697;10.1038/nrg2775;10.1038/nrm2698;10.1063/1.1345702;10.1073/pnas.0404733101;10.1073/pnas.1332628100;10.1073/pnas.97.9.4649;10.1093/nar/25.6.1203;10.1098/rsif.2008.0516.focus;10.1101/gad.12.9.1338;10.1103/PhysRevE.77.021919;10.1109/9.45168;10.1128/AEM.59.10.3485-3487.1993;10.1128/JB.164.3.1366-1369.1985;10.1146/annurev.bioeng.5.040202.121553;10.1161/01.RES.0000124921.81025.1F | Univ Toronto | Ang, J;Bagh, S;Ingalls, B P;McMillen, D R | Ang, J: Univ Toronto, Dept Chem & Phys Sci, Mississauga, ON L5L 1C6, Canada | null | null | 34 | null | Canada | Univ Toronto;Univ Waterloo | Ang, Jordan | null | ADAPTATION;BIOLOGY;CLPXP;DEGRADATION;DESIGN;ESCHERICHIA-COLI;EXPRESSION;MODEL;REPRESSOR;ROBUSTNESS | Ang, Jordan; Bagh, Sangram; Ingalls, Brian P.; McMillen, David R.; | null | Univ Toronto, Dept Chem & Phys Sci, Mississauga, ON L5L 1C6, Canada;Univ Toronto, Inst Opt Sci, Mississauga, ON L5L 1C6, Canada;Univ Waterloo, Dept Appl Math, Waterloo, ON N2L 3G1, Canada | Univ Toronto, Dept Chem & Phys Sci, Mississauga, ON L5L 1C6, Canada;Univ Toronto, Inst Opt Sci, Mississauga, ON L5L 1C6, Canada;Univ Waterloo, Dept Appl Math, Waterloo, ON N2L 3G1, Canada | 1095-8541 | Control systems;Gene regulation;Regulatory feedback;Synthetic biology | 4 | 1932;1971;1976;1980;1985;1986;1990;1993;1997;1998;1999;2000;2001;2002;2003;2004;2006;2007;2008;2009;2010;2013 | 66 | Univ Toronto, Dept Chem & Phys Sci, Mississauga, ON L5L 1C6, Canada | J. Theor. Biol. | McMillen, David R | ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD | ";(density-dependent;,;;;a;adaptation;also;an;analogy;and;attractive;available;bacterium;been;capable;case;challenges;coli;commonly;conditions;consequently;constructed;construction;control;controller;design;device;discuss;disrupt;easily;effects;engineers;Escherichia;exhibiting;extensions;feedback;finally;first-order;for;free-damped;from;gene;generic;genetic;harmonic;has;highlights;however;illustrate;implementation;implies;in;inherent;input;integral;is;it;kinetics;known;leads;linear;long;molecular;most;nature;necessary;network;network's;networks;not;numerical;of;optimizing;oscillator;otherwise;our;parts;perfect;perturbations;possibility;present;proportional-integral;propose;prospect;protein;purpose;reach;realization;regulatory;removal;response;robust;saturation);signals;specific;step;straightforward;strategy;study;such;synthetic;systems;that;the;theorists;this;three-promoter;to;transient;treatment;two-promoter;under;using;via;we;where;would | Univ Toronto | It has long been known to control theorists and engineers that integral feedback control leads to, and is necessary for, "perfect" adaptation to step input perturbations in most systems. Consequently, implementation of this robust control strategy in a synthetic gene network is an attractive prospect. However, the nature of genetic regulatory networks (density-dependent kinetics and molecular signals that easily reach saturation) implies that the design and construction of such a device is not straightforward. In this study, we propose a generic two-promoter genetic regulatory network for the purpose of exhibiting perfect adaptation; our treatment highlights the challenges inherent in the implementation of a genetic integral controller. We also present a numerical case study for a specific realization of this two-promoter network, "constructed" using commonly available parts from the bacterium Escherichia coli. We illustrate the possibility of optimizing this network's transient response via analogy to a linear, free-damped harmonic oscillator. Finally, we discuss extensions of this two-promoter network to a proportional-integral controller and to a three-promoter network capable of perfect adaptation under conditions where first-order protein removal effects would otherwise disrupt the adaptation. | null | ADAPTATION;BIOLOGY;CLPXP;DEGRADATION;DESIGN;ESCHERICHIA-COLI;EXPRESSION;MODEL;REPRESSOR;ROBUST | 0 | null | Control systems;Gene regulation;Regulatory feedback;Synthetic biology | 16 | ESCHERICHIA-COLI;adaptation;BIOLOGY;CLPXP;Control systems;DEGRADATION;DESIGN;EXPRESSION;Gene regulation;MODEL;Regulatory feedback;REPRESSOR;ROBUST;Synthetic biology | WOS:000282252900025 | Univ Toronto, Mississauga ON, Canada;Univ Waterloo, Waterloo ON, Canada | Canada | 2,010 | null | 0000-0003-2676-5450 | null | null | English | null | ANNU REV BIOMED ENG;APPL ENVIRON MICROB;ARCH MICROBIOL;AUTOMATICA;BIOPHYS J;CELL;CHAOS;CIRC RES;Feedback Control Theory;GENE DEV;GENETIC SWITCH;GENETIC SWITCH PHAGE;IEEE T AUTOMAT CONTR;J BACTERIOL;J R SOC INTERFACE;J THEOR BIOL;MOL SYST BIOL;NAT REV GENET;NAT REV MOL CELL BIO;Natural Computing;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PHYS REV E;Physical Review Letters;SYST CONTROL LETT;System Modeling in Cellular Biology | Ang, Jordan;Bagh, Sangram;Ingalls, Brian P;McMillen, David R | 2024-03-11
ER | Alon, U;Andrianantoandro, E;Bagh, S;Barkai, N;Cannon, W B;Doyle J. C.;El-Samad, H;Francis, B A;Gottesman, S;Grilly, C;Hasty J.;Hasty, J;Hersch, G L;Isaacs, F J;Isidori, A;Karn M.;Khalil, A S;Kærn, M;Lutz, R;Mello, B A;Mieschendahl, M;Mukherji, S;Pedersen, M;Ptashne, M;Ptashne, M A;Purnick, P E M;Rosati, B;Sontag, E D;Trueba, F J;Villaverde, A;Weiss R.;Wong, W W;Yagil, G;Yi, T M | 655MA | Mississauga ON, Canada | 76 | null | 2 | null | 20,688,080 | Ang, Jordan;Bagh, Sangram;Ingalls, Brian P;McMillen, David R | J THEOR BIOL | Mississauga ON, Canada;Waterloo ON, Canada |
Allert, M;Cox, J C;Hellinga, H W | 10.1016/j.jmb.2010.08.010 | null | 24-28 OVAL RD, LONDON NW1 7DX, ENGLAND | 5j5d6o2r6d5t196m4b3x62701h1h26472w2m6q | Multifactorial Determinants of Protein Expression in Prokaryotic Open Reading Frames | Duke Univ | null | Hellinga, HW (corresponding author), Duke Univ, Med Ctr, Dept Biochem, Box 3711, Durham, NC 27710 USA. | null | Allert, Malin;Cox, J Colin;Hellinga, Homme W | Biochemistry & Molecular Biology | NIH [5DPI OD000122] | WOS | Hellinga, H W | Duke Univ, Durham, NC USA | 402 | Determinants;expression;Frames;in;multifactorial;of;Open;Prokaryotic;protein;Reading | 1 | null | ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD | Duke Univ, Med Ctr, Dept Biochem, Box 3711, Durham, NC 27710 USA;Duke Univ, Med Ctr, Dept Biochem, Durham, NC 27710 USA | Article | Duke Univ | LONDON | null | null | Duke Univ | NIH | Hellinga, HW (corresponding author), Duke Univ, Med Ctr, Dept Biochem, Box 3711, Durham, NC 27710 USA. | 918 | Allert, Malin;Cox, J Colin;Hellinga, Homme W | 21 | 1 | 284,182,500,011 | NIH [5DPI OD000122] | USA | JOURNAL OF MOLECULAR BIOLOGY | USA | null | null | Duke Univ, Med Ctr, Dept Biochem, Durham, NC 27710 USA | 0022-2836 | Allert, M;Cox, J C;Hellinga, H W | OCT 8 | hwh@biochem.duke.edu | multifactorial Determinants;Prokaryotic Open Reading Frames;protein expression | 3 | J | Biochemistry & Molecular Biology | 16S RIBOSOMAL-RNA;285 synthetic genes;3' terminal AU content makes;816 bacterial genomes;bioinformatic analysis;c 2010 Elsevier Ltd;codon identity;CODON USAGE;computation;control translation efficiency;dependent;designing synthetic systems;detectable contributions;determined corresponding expression levels;distinct regional trends;DOWNSTREAM BOX;effect;Effects;efficiency;elongation;ENHANCEMENT;equation;Escherichia coli extracts;ESCHERICHIA-COLI;expression;factors;features;GENE-EXPRESSION;heterologous expression;heterologous expression systems;high AU content;high-frequency codons;influence expression levels;INITIATION;lesser extent;low secondary structure;mathematical function;mechanistic insight;MESSENGER-RNA;mRNA secondary structure;multifactorial Determinants;nucleotide composition;open reading frame (ORF) nucleotide sequences;ORF 5' region;ORF nucleotide sequences;ORF sequences;ORFs;parameterized;practical application;Prokaryotic Open Reading Frames;PROTEIN EXPRESSION;protein expression levels;quantitative description;relationship;ribosomal function;rights reserved;SEQUENCES;synthetic gene data set;synthetic genes;termination;three phases;TRANSLATION INITIATION;understanding natural systems;vitro | Allert, M | 16S RIBOSOMAL-RNA;CODON USAGE;DOWNSTREAM BOX;EFFICIENCY;ENHANCEMENT;ESCHERICHIA-COLI;GENE-EXPRESSION;MESSENGER-RNA;mRNA secondary structure;nucleotide composition;PROTEIN EXPRESSION;SEQUENCES;Synthetic genes;TRANSLATION INITIATION | 905 | [Allert, Malin; Cox, J. Colin; Hellinga, Homme W.] Duke Univ, Med Ctr, Dept Biochem, Durham, NC 27710 USA. | We thank J. Will Thompson and the Duke University Proteomics Core Facility for protein identification by MS and Philippe Marguet, Curtis Layton, and Chris Nicchitta for critical reading of the manuscript. This work was supported by the NIH Director's Pioneer Award (5DPI OD000122). | 285 synthetic genes;3' terminal AU content makes;816 bacterial genomes;bioinformatic analysis;codon identity;computation;control translation efficiency;dependent;designing synthetic systems;detectable contributions;determined corresponding expression levels;distinct regional trends;effect;effects;elongation;equation;Escherichia coli extracts;expression;factors;features;heterologous expression;heterologous expression systems;high AU content;high-frequency codons;influence expression levels;initiation;lesser extent;low secondary structure;mathematical function;mechanistic insight;mRNA secondary structure;nucleotide composition;open reading frame (ORF) nucleotide sequences;ORF 5' region;ORF nucleotide sequences;ORF sequences;ORFs;parameterized;practical application;protein expression;protein expression levels;quantitative description;relationship;ribosomal function;synthetic gene data set;termination;three phases;understanding natural systems;vitro | 10.1002/bit.20026;10.1002/bit.20139;10.1002/j.1460-2075.1996.tb00399.x;10.1006/jmbi.1996.0524;10.1007/s00253-004-1814-0;10.1007/s10529-004-7664-0;10.1016/j.bbrc.2004.04.064;10.1016/j.bbrc.2006.09.072;10.1016/j.cell.2004.11.042;10.1016/j.cell.2010.03.031;10.1016/j.copbio.2009.08.001;10.1016/j.gene.2005.06.037;10.1016/j.sbi.2007.11.005;10.1016/j.tibs.2008.10.002;10.1016/j.tibtech.2008.10.007;10.1016/j.tim.2008.05.001;10.1016/S0092-8674(02)00619-0;10.1017/S0033583505004026;10.1021/pr049912g;10.1023/A:1023563600459;10.1038/35103511;10.1038/msb4100073;10.1038/msb4100175;10.1038/nature06716;10.1038/nrm1335;10.1038/nrm2352;10.1039/b908315d;10.1046/j.1365-2958.1999.01465.x;10.1073/pnas.0909910107;10.1073/pnas.83.24.9373;10.1073/pnas.86.2.448;10.1073/pnas.86.20.7706;10.1074/jbc.274.15.10079;10.1093/bioinformatics/15.7.578;10.1093/nar/15.3.1281;10.1093/nar/gkh834;10.1093/nar/gkl500;10.1093/nar/gkm219;10.1093/nar/gkm831;10.1093/nar/gng143;10.1098/rsif.2008.0520.focus;10.1101/gr.1257503;10.1110/ps.062591607;10.1126/science.1105639;10.1126/science.1168978;10.1126/science.1170160;10.1128/JB.183.11.3499-3505.2001;10.1146/annurev.genet.42.110807.091442;10.1146/annurev.micro.59.030804.121336;10.1146/annurev.micro.61.080706.093440;10.1159/000077244;10.1186/1472-6750-9-36;10.1371/journal.pone.0007002 | Duke Univ | Allert, M;Cox, J C;Hellinga, H W | Allert, M: Duke Univ, Med Ctr, Dept Biochem, Durham, NC 27710 USA | null | 5DPI OD000122 | 53 | null | USA | Duke Univ | Allert, Malin | Green Accepted | 16S RIBOSOMAL-RNA;CODON USAGE;DOWNSTREAM BOX;EFFICIENCY;ENHANCEMENT;ESCHERICHIA-COLI;GENE-EXPRESSION;MESSENGER-RNA;SEQUENCES;TRANSLATION INITIATION | Allert, Malin; Cox, J. Colin; Hellinga, Homme W.; | null | Duke Univ, Med Ctr, Dept Biochem, Durham, NC 27710 USA | Duke Univ, Med Ctr, Dept Biochem, Durham, NC 27710 USA | 1089-8638 | codon usage;mRNA secondary structure;nucleotide composition;protein expression;Synthetic gene | 5 | 1986;1987;1989;1996;1999;2001;2002;2003;2004;2005;2006;2007;2008;2009;2010 | 73 | Duke Univ, Med Ctr, Dept Biochem, Box 3711, Durham, NC 27710 USA | J. Mol. Biol. | Hellinga, Homme W | ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD | (ORF);,;285;3';5';816;:;a;addition;analysis;and;application;AU;bacterial;between;bioinformatic;but;choice;codon;codons;coli;composition;computation;content;contributes;contributions;control;corresponding;data;dependent;description;design;designed;designing;detectable;determined;developed;distinct;effect;effects;efficiency;elongation;enables;equation;Escherichia;expression;extent;extracts;factors;features;for;found;frame;from;function;gene;genes;genomes;heterologous;high;high-frequency;identity;important;in;influence;initiation;insight;into;investigate;is;its;lesser;levels;low;makes;markedly;mathematical;mechanistic;model;modest;mRNA;natural;nucleotide;of;on;open;optimizing;ORF;ORFs;parameterized;phases;practical;presence;present;protein;provides;quantitative;reading;region;regional;relationship;revealed;ribosomal;secondary;sequences;set;show;strongly;structure;synthetic;systems;terminal;termination;that;the;their;these;this;three;to;translation;trends;understanding;using;vitro;we;which;within | Duke Univ | A quantitative description of the relationship between protein expression levels and open reading frame (ORF) nucleotide sequences is important for understanding natural systems, designing synthetic systems, and optimizing heterologous expression. Codon identity, mRNA secondary structure, and nucleotide composition within ORFs markedly influence expression levels. Bioinformatic analysis of ORF sequences in 816 bacterial genomes revealed that these features show distinct regional trends. To investigate their effects on protein expression, we designed 285 synthetic genes and determined corresponding expression levels in vitro using Escherichia coli extracts. We developed a mathematical function, parameterized using this synthetic gene data set, which enables computation of protein expression levels from ORF nucleotide sequences. In addition to its practical application in the design of heterologous expression systems, this equation provides mechanistic insight into the factors that control translation efficiency. We found that expression is strongly dependent on the presence of high AU content and low secondary structure in the ORF 5' region. Choice of high-frequency codons contributes to a lesser extent. The 3' terminal AU content makes modest, but detectable contributions. We present a model for the effect of these factors on the three phases of ribosomal function: initiation, elongation, and termination. | null | 16S RIBOSOMAL-RNA;CODON USAGE;DOWNSTREAM BOX;EFFICIENT;ENHANCEMENT;ESCHERICHIA-COLI;GENE-EXPRESSION;MESSENGER-RNA;SEQUENCE;TRANSLATION INITIATION | 0 | null | codon usage;mRNA secondary structure;nucleotide composition;protein expression;Synthetic genes | 14 | ESCHERICHIA-COLI;16S RIBOSOMAL-RNA;CODON USAGE;DOWNSTREAM BOX;EFFICIENT;ENHANCEMENT;GENE-EXPRESSION;MESSENGER-RNA;mRNA secondary structure;nucleotide composition;PROTEIN EXPRESSION;SEQUENCE;Synthetic gene;TRANSLATION INITIATION | WOS:000284182500011 | Duke Univ, Durham, NC USA | USA | 2,010 | null | null | null | null | English | null | ANNU REV GENET;ANNU REV MICROBIOL;APPL MICROBIOL BIOT;BIOCHEM BIOPH RES CO;BIOINFORMATICS;BIOTECHNOL BIOENG;BIOTECHNOL LETT;BMC BIOTECHNOL;CELL;CURR OPIN BIOTECH;CURR OPIN STRUC BIOL;EMBO J;GENE;GENOME RES;J BACTERIOL;J BIOL CHEM;J MOL BIOL;J MOL MICROB BIOTECH;J PROTEOME RES;J R SOC INTERFACE;MOL BIOSYST;MOL MICROBIOL;MOL SYST BIOL;NAT REV GENET;NAT REV MOL CELL BIO;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PLOS ONE;PROTEIN SCI;Q REV BIOPHYS;SCIENCE;TRENDS BIOCHEM SCI;TRENDS BIOTECHNOL;TRENDS MICROBIOL | Allert, Malin;Cox, J Colin;Hellinga, Homme W | 2024-03-11
ER | Abreu, R D;Andrianantoandro, E;Bashan, A;Calderone, T L;Carothers, J M;Carpousis, A J;Coleman, M A;Cox, J C;Czar, M J;Dos Reis, M;Eddy, S R;Etchegaray, J P;Freier, S M;Gao, X X;Hershberg, R;Ingolia, N T;Iost, I;Jaeger, J A;Jana, S;Jenner, L;Jewett, M C;Katz, L;Keum, J W;Komar, A A;Kozak, M;Kudla, G;Lopez, P J;Lorimer, D;Marintchev, A;Mattheakis, L;Moll, I;Osada, Y;Petry, S;Puigbò, P;Puigbó, P;Qing, G L;Ramakrishnan, V;Rocak, S;Rush, G;Sharp, P M;Sprengart, M L;Steitz, T A;Takyar, S;Tuller, T;Voges, D;Welch, M;Wen, J D;Winkler, W C;Wu, G;Zhang, X L | 679TA | Durham, NC USA | 87 | null | 1 | null | 20,727,358 | Allert, Malin;Cox, J Colin;Hellinga, Homme W | J MOL BIOL | Durham, NC USA |
Fussenegger, M;Weber, W | 10.1016/j.copbio.2010.07.006 | null | THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, OXON, ENGLAND | 1m412q23114b23154j365wa5v216f5z5kx115w | Synthetic gene networks in mammalian cells | Swiss Fed Inst Technol | null | Fussenegger, M (corresponding author), Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Mattenstr 26, CH-4058 Basel, Switzerland. | null | Fussenegger, Martin;Weber, Wilfried | Biochemical Research Methods;Biotechnology & Applied Microbiology | Excellence Initiative of the German Federal and State Governments [EXC 294]; Swiss National Science Foundation [31003A-126022]; EC | WOS | Fussenegger, M | Swiss Fed Inst Technol, Basel, Switzerland;Univ Basel, Basel, Switzerland;Univ Freiburg, Freiburg, Germany | 21 | Cells;gene;in;mammalian;networks;synthetic | 2 | Weber, Wilfried | ELSEVIER SCI LTD | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, CH-4058 Basel, Switzerland;Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Mattenstr 26, CH-4058 Basel, Switzerland;Univ Basel, Fac Sci, CH-4058 Basel, Switzerland;Univ Freiburg, Ctr Biol Signalling Studies BIOSS, D-79108 Freiburg, Germany;Univ Freiburg, Fac Biol, D-79104 Freiburg, Germany | Review | Swiss Fed Inst Technol | OXFORD | null | null | Swiss Fed Inst Technol;Univ Basel;Univ Freiburg | EC;Excellence Initiative of the German Federal and State Governments;Swiss National Science Foundation | Fussenegger, M (corresponding author), Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Mattenstr 26, CH-4058 Basel, Switzerland. | 696 | Fussenegger, Martin;Weber, Wilfried | 18 | 4 | 283,700,300,018 | EC;Excellence Initiative of the German Federal and State Governments [EXC 294];Swiss National Science Foundation [31003A-126022] | Germany;Switzerland | CURRENT OPINION IN BIOTECHNOLOGY | Switzerland | null | null | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, CH-4058 Basel, Switzerland | 0958-1669 | Fussenegger, M;Weber, W | OCT | fussenegger@bsse.ethz.ch | mammalian cells;synthetic gene networks | 2 | J | Biochemistry & Molecular Biology;Biotechnology & Applied Microbiology | art;BACTERIA;circuit;complex spatiotemporal dynamics;current limitations;decade;expression;feature tunable oscillations;Genetic circuits;hormone;light;light-triggered genetic switches;living cells;mammalian cells;mammalian synthetic biology;metabolite;Mice;OSCILLATOR;possible ways;predictive engineering discipline;proteins;recent advances;review;synthetic;synthetic biologists;synthetic gene circuits;synthetic gene networks;synthetic mammalian systems | Weber, W | CIRCUIT;EXPRESSION;LIGHT;LIVING CELLS;MICE;OSCILLATOR;Proteins | 690 | [Weber, Wilfried; Fussenegger, Martin] Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, CH-4058 Basel, Switzerland. [Weber, Wilfried] Univ Freiburg, Fac Biol, D-79104 Freiburg, Germany. [Weber, Wilfried] Univ Freiburg, Ctr Biol Signalling Studies BIOSS, D-79108 Freiburg, Germany. [Fussenegger, Martin] Univ Basel, Fac Sci, CH-4058 Basel, Switzerland. | Work in the group of WW is supported by the Excellence Initiative of the German Federal and State Governments (EXC 294). Work in the group of MF is supported in part by the Swiss National Science Foundation (grant no. 31003A-126022) and in part by the EC Framework 7 (Persist). | art;bacteria;complex spatiotemporal dynamics;current limitations;decade;feature tunable oscillations;genetic circuits;hormone;light-triggered genetic switches;mammalian cells;mammalian synthetic biology;metabolite;possible ways;predictive engineering discipline;recent advances;review;synthetic;synthetic biologists;synthetic gene circuits;synthetic mammalian systems | 10.1002/bit.20142;10.1002/jgm.903;10.1016/j.cell.2006.07.025;10.1016/j.chembiol.2009.02.005;10.1016/j.copbio.2007.07.013;10.1016/j.copbio.2009.07.009;10.1016/j.tibtech.2007.07.002;10.1038/35002125;10.1038/nature07616;10.1038/nature08241;10.1038/nature08446;10.1038/nbt.1569;10.1038/nbt.1617;10.1038/nbt1307;10.1038/nbt980;10.1038/nmeth.1401;10.1038/nrg2775;10.1039/b902070p;10.1073/pnas.0500345102;10.1073/pnas.0606398104;10.1073/pnas.0701382104;10.1073/pnas.0800663105;10.1073/pnas.0901501106;10.1093/nar/gkn443;10.1093/nar/gkq121;10.1101/gad.1696108;10.1128/JVI.80.4.1939-1948.2006 | Swiss Fed Inst Technol | Fussenegger, M;Weber, W | Weber, W: Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, CH-4058 Basel, Switzerland | Weber, Wilfried | 31003A-126022;EXC 294 | 27 | null | Switzerland | Swiss Fed Inst Technol;Univ Basel;Univ Freiburg | Weber, Wilfried | null | CIRCUIT;EXPRESSION;LIGHT;LIVING CELLS;MICE;OSCILLATOR;PROTEINS | Weber, Wilfried; Fussenegger, Martin; | null | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, CH-4058 Basel, Switzerland;Univ Basel, Fac Sci, CH-4058 Basel, Switzerland;Univ Freiburg, Ctr Biol Signalling Studies BIOSS, D-79108 Freiburg, Germany;Univ Freiburg, Fac Biol, D-79104 Freiburg, Germany | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, CH-4058 Basel, Switzerland;Univ Basel, Fac Sci, CH-4058 Basel, Switzerland;Univ Freiburg, Ctr Biol Signalling Studies BIOSS, D-79108 Freiburg, Germany;Univ Freiburg, Fac Biol, D-79104 Freiburg, Germany | 1879-0429 | null | 5 | 2000;2004;2005;2006;2007;2008;2009;2010 | 25 | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Mattenstr 26, CH-4058 Basel, Switzerland | Curr. Opin. Biotechnol. | Fussenegger, Martin | ELSEVIER SCI LTD | ,;a;able;advances;almost;also;an;and;art;as;bacteria;biologists;biology;but;by;cells;circuits;complex;conclude;construct;construction;current;decade;describes;design;discipline;discussing;dynamics;engineering;feature;from;gene;genetic;highlights;hormone;in;into;it;light-triggered;limitations;mammalian;metabolite;most;networks;not;of;only;oscillations;pioneered;possible;predictive;recent;review;spatiotemporal;switches;synthetic;systems;that;the;this;to;took;transform;tunable;until;was;ways;we;well;were;with | Swiss Fed Inst Technol | The design and construction of synthetic gene circuits with complex spatiotemporal dynamics was pioneered in bacteria, but it took almost a decade until synthetic biologists were able to construct genetic circuits with complex spatiotemporal dynamics in mammalian cells. This review highlights the most recent advances in mammalian synthetic biology, and it describes metabolite, hormone, and light-triggered genetic switches as well as the design and construction of synthetic networks that feature tunable oscillations. We conclude by discussing not only the current limitations but also possible ways to transform the construction of synthetic mammalian systems from an art into a predictive engineering discipline. | B-4732-2012 | CIRCUITS;EXPRESSION;LIGHT;LIVING CELLS;MICE;OSCILLATIONS;PROTEIN | 0 | null | null | 7 | CIRCUITS;EXPRESSION;LIGHT;LIVING CELLS;MICE;OSCILLATIONS;PROTEIN | WOS:000283700300018 | Swiss Fed Inst Technol, Basel, Switzerland;Univ Basel, Basel, Switzerland;Univ Freiburg, Freiburg, Germany | Germany;Switzerland | 2,010 | null | 0000-0003-4340-4446 | null | null | English | null | BIOTECHNOL BIOENG;CELL;CHEM BIOL;CURR OPIN BIOTECH;GENE DEV;J GENE MED;J VIROL;MOL BIOSYST;NAT BIOTECHNOL;NAT METHODS;NAT REV GENET;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;TRENDS BIOTECHNOL | Fussenegger, Martin;Weber, Wilfried | 2024-03-11
ER | Banaszynski, L A;Browne, S M;Elowitz, M B;Gitzinger, M;Greber, D;Kemmer, C;Khalil, A S;Kramer, B P;Levskaya, A;Nishimura, K;Nov, D;Rinaudo, K;Swinburne, I A;Tan, W J;Tigges, M;Weber, W;Wu, Y I;Yazawa, M | 673YO | Basel, Switzerland | 29 | null | 3 | null | 20,691,580 | Fussenegger, Martin;Weber, Wilfried | CURR OPIN BIOTECH | Basel, Switzerland;Freiburg, Germany |
Benenson, Y;Bleris, L;Leisner, M;Lohmueller, J;Xie, Z | 10.1038/NNANO.2010.135 | null | MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND | 1t2n226f28y1ry4n3d5y394c92c283s643bu | Rationally designed logic integration of regulatory signals in mammalian cells | Harvard Univ | null | Leisner, M (corresponding author), Harvard Univ, FAS Ctr Syst Biol, 52 Oxford St, Cambridge, MA 02138 USA. | null | Benenson, Yaakov;Bleris, Leonidas;Leisner, Madeleine;Lohmueller, Jason;Xie, Zhen | Materials Science, Multidisciplinary;Nanoscience & Nanotechnology | Deutsche Forschungs Gemeinschaft; Bauer Fellows program; NIGMS [GM068763] | WOS | Leisner, M | Harvard Univ, Boston, MA USA;Harvard Univ, Cambridge, MA USA | 5 | Cells;designed;in;integration;logic;mammalian;of;rationally;regulatory;signals | 1 | Lohmueller, Jason | NATURE PUBLISHING GROUP | Harvard Univ, FAS Ctr Syst Biol, 52 Oxford St, Cambridge, MA 02138 USA;Harvard Univ, FAS Ctr Syst Biol, Cambridge, MA 02138 USA;Harvard Univ, Sch Med, Dept Biol & Biomed Sci, Boston, MA 02115 USA | Article | Harvard Univ | LONDON | null | null | Harvard Univ | Bauer Fellows program;Deutsche Forschungs Gemeinschaft;NIGMS | Leisner, M (corresponding author), Harvard Univ, FAS Ctr Syst Biol, 52 Oxford St, Cambridge, MA 02138 USA. | 670 | Benenson, Yaakov;Bleris, Leonidas;Leisner, Madeleine;Lohmueller, Jason;Xie, Zhen | 48 | 2 | 281,603,400,013 | Bauer Fellows program;Deutsche Forschungs Gemeinschaft;NIGMS [GM068763] | USA | NATURE NANOTECHNOLOGY | USA | null | null | Harvard Univ, FAS Ctr Syst Biol, Cambridge, MA 02138 USA | 1748-3387 | Benenson, Y;Bleris, L;Leisner, M;Lohmueller, J;Xie, Z | SEP | kobi.benenson@bsse.ethz.ch | designed logic integration;mammalian cells;regulatory signals | 5 | J | Materials Science;Science & Technology - Other Topics | 'smart';alternative approach;arbitrary logic relation;BIOLOGY;certain combinations;complex circuits;CONSTRUCTION;designed logic integration;ESCHERICHIA-COLI;expression;Gate;general-purpose control;interest (the output) via;logic integration;mammalian cells;messenger RNA (mRNA) synthesis;modular interactions;molecular-level information processing(1,2);mRNA;natural;output(16);platform;protein levels;regulation;regulatory signals;RNA interference pathway;RNAi;small regulatory RNAs (called microRNAs);special proteins;SWITCH;synthetic gene networks;synthetic genes coding;SYSTEM;systems(5-15);theory;three transcription factor inputs;transcription factor input signals;transcription factors;transcription factors(3,4);turn;vivo;vivo nanosystems | Leisner, M | BIOLOGY;CONSTRUCTION;ESCHERICHIA-COLI;EXPRESSION;GATE;RNAi;SWITCH;synthetic gene networks;SYSTEM | 666 | [Leisner, Madeleine; Bleris, Leonidas; Lohmueller, Jason; Xie, Zhen; Benenson, Yaakov] Harvard Univ, FAS Ctr Syst Biol, Cambridge, MA 02138 USA. [Lohmueller, Jason] Harvard Univ, Sch Med, Dept Biol & Biomed Sci, Boston, MA 02115 USA. | The authors would like to thank anonymous reviewers for thoughtful comments. M. L. is a recipient of Deutsche Forschungs Gemeinschaft scholarship. The research was funded by the Bauer Fellows program and by the NIGMS grant GM068763 for National Centres of Systems Biology. M. L. acknowledges her father R. Leisner, who passed away as this manuscript was prepared for submission: 'One learns most from those one loves' (Goethe). | 'smart';alternative approach;arbitrary logic relation;certain combinations;complex circuits;general-purpose control;interest (the output) via;logic integration;mammalian cells;messenger RNA (mRNA) synthesis;modular interactions;molecular-level information processing(1,2);mRNA;natural;output(16);platform;protein levels;regulation;RNA interference pathway;small regulatory RNAs (called microRNAs);special proteins;synthetic genes coding;systems(5-15);theory;three transcription factor inputs;transcription factor input signals;transcription factors;transcription factors(3,4);turn;vivo;vivo nanosystems | 10.1002/bit.20142;10.1002/bit.22604;10.1016/j.cell.2007.05.045;10.1016/j.tibtech.2005.02.008;10.1021/mp900090z;10.1021/nl0619305;10.1038/35002131;10.1038/msb4100173;10.1038/msb4100187;10.1038/nature03461;10.1038/nbt.1536;10.1038/nbt.1591;10.1038/nbt1307;10.1038/nbt1413;10.1038/ncb1596;10.1038/ng881;10.1038/scientificamerican0506-44;10.1039/b713852k;10.1073/pnas.0506306102;10.1073/pnas.0900267106;10.1073/pnas.0930314100;10.1093/nar/gkq117;10.1098/rsif.2006.0206;10.1126/science.1067407;10.1126/science.1075090;10.1128/AEM.01684-08;10.1371/journal.pbio.0040045;10.2976/1.2896331 | Harvard Univ | Benenson, Y;Bleris, L;Leisner, M;Lohmueller, J;Xie, Z | Leisner, M: Harvard Univ, FAS Ctr Syst Biol, Cambridge, MA 02138 USA | Benenson, Yaakov;Bleris, Leonidas;Xie, Zhen | GM068763 | 30 | null | USA | Harvard Univ | Leisner, Madeleine | Green Accepted | BIOLOGY;CONSTRUCTION;ESCHERICHIA-COLI;EXPRESSION;GATE;RNAI;SWITCH;SYNTHETIC GENE NETWORKS;SYSTEM | Leisner, Madeleine; Bleris, Leonidas; Lohmueller, Jason; Xie, Zhen; Benenson, Yaakov; | null | Harvard Univ, FAS Ctr Syst Biol, Cambridge, MA 02138 USA;Harvard Univ, Sch Med, Dept Biol & Biomed Sci, Boston, MA 02115 USA | Harvard Univ, FAS Ctr Syst Biol, Cambridge, MA 02138 USA;Harvard Univ, Sch Med, Dept Biol & Biomed Sci, Boston, MA 02115 USA | null | null | 9 | 1999;2000;2002;2003;2004;2005;2006;2007;2008;2009;2010 | 84 | Harvard Univ, FAS Ctr Syst Biol, 52 Oxford St, Cambridge, MA 02138 USA | Nat. Nanotechnol. | Benenson, Yaakov | NATURE PUBLISHING GROUP | 'smart';(called;(mRNA);(the;,;a;achieving;alternative;an;and;any;approach;arbitrary;as;between;by;called;can;cells;certain;circuits;coding;combinations;complex;computing;construct;control;engineered;essential;establishing;factor;factors;factors(3,4);for;general-purpose;genes;has;here;implement;in;increasingly;information;input;inputs;inspired;integration;interactions;interest;interference;is;it;levels;logic;makes;mammalian;messenger;microRNAs);modular;molecular;molecular-level;mRNA;nanosystems;natural;of;optimize;output(16);output);pathway;platform;possible;processing(1,2);protein;proteins;regulate;regulation;regulatory;relation;RNA;RNAs;show;signals;simplicity;small;special;such;synthesis;synthetic;systems(5-15);test;that;the;theory;these;three;to;transcription;turn;up;via;vivo;we;which;with | Harvard Univ | Molecular-level information processing(1,2) is essential for 'smart' in vivo nanosystems. Natural molecular computing, such as the regulation of messenger RNA (mRNA) synthesis by special proteins called transcription factors(3,4), has inspired engineered systems(5-15) that can control the levels of mRNA with certain combinations of transcription factors. Here, we show an alternative approach to achieving general-purpose control of mRNA and protein levels by logic integration of transcription factor input signals in mammalian cells. The transcription factors regulate synthetic genes coding for small regulatory RNAs (called microRNAs), which, in turn, control the mRNA of interest (the output) via an RNA interference pathway. The simplicity of these modular interactions makes it possible, in theory, to implement any arbitrary logic relation between the transcription factors and the output(16). We construct, test and optimize increasingly complex circuits with up to three transcription factor inputs, establishing a platform for in vivo molecular computing. | A-6761-2009;B-1433-2009;GPW-5925-2022 | BIOLOGY;CONSTRUCTION;ESCHERICHIA-COLI;EXPRESSION;GATES;RNAI;SWITCH;SYNTHETIC GENE NETWORKS;SYSTEM | 5 | null | null | 5 | ESCHERICHIA-COLI;BIOLOGY;CONSTRUCTION;EXPRESSION;GATES;RNAi;SWITCH;synthetic gene networks;SYSTEM | WOS:000281603400013 | Harvard Univ, Boston, MA USA;Harvard Univ, Cambridge, MA USA | USA | 2,010 | null | 0000-0001-6089-9992 | null | null | English | null | APPL ENVIRON MICROB;BIOTECHNOL BIOENG;CELL;EVOL COMPUT;HFSP J;J R SOC INTERFACE;MOL BIOSYST;MOL PHARMACEUT;MOL SYST BIOL;NANO LETT;NAT BIOTECHNOL;NAT CELL BIOL;NAT GENET;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PLOS BIOL;SCI AM;SCIENCE;TRENDS BIOTECHNOL | Benenson, Yaakov;Bleris, Leonidas;Leisner, Madeleine;Lohmueller, Jason;Xie, Zhen | 2024-03-11
ER | An, W L;Anderson, J C;Basu, S;Bronson, J E;Broz, P;Buchler, N E;Canton, B;Cox, R S;Deans, T L;Ellis, T;Fukuda Yoko;Gardner, T S;Guet, C C;Gullotti, E;Jungmann, R;Kramer, B P;Lee, T I;Lu, Q;Lu, T K;Marguet, P;Mayo, A E;Rinaudo, K;Sayut, D J;Schwake, G;Shapiro, E;Shen-Orr, S S;Stegmeier, F;Valadi, H;Weiss, R;Xie, Z | 647FO | Cambridge, MA USA | 97 | null | 1 | null | 20,622,866 | Benenson, Yaakov;Bleris, Leonidas;Leisner, Madeleine;Lohmueller, Jason;Xie, Zhen | NAT NANOTECHNOL | Boston, MA USA;Cambridge, MA USA |
Dong, T;Huang, C S;Shi, J C;Zhang, X Z | 10.1088/1478-3975/7/3/036006 | 036006 | TEMPLE CIRCUS, TEMPLE WAY, BRISTOL BS1 6BE, ENGLAND | 664e104t3s70f4wo3qjm1171v3s103f2d4h | High-frequency and low-frequency effects on vibrational resonance in a synthetic gene network | Guangxi Teachers Educ Univ | null | Shi, JC (corresponding author), Guangxi Teachers Educ Univ, Coll Chem & Life Sci, Nanning 530001, Peoples R China. | null | Dong, Tao;Huang, Chusheng;Shi, Jiancheng;Zhang, Xiuzhi | Biochemistry & Molecular Biology;Biophysics | Research Foundation of Education Bureau of Guangxi Province, China [200707LX178]; Graduate education innovation projects of Guangxi Province, China [2009106030817M07] | WOS | Shi, J C | Guangxi Teachers Educ Univ, Nanning, Peoples R China | 7 | a;and;Effects;gene;high-frequency;in;low-frequency;network;on;resonance;synthetic;vibrational | 1 | null | IOP PUBLISHING LTD | Guangxi Teachers Educ Univ, Coll Chem & Life Sci, Nanning 530001, Peoples R China | Article | Guangxi Teachers Educ Univ | BRISTOL | null | null | Guangxi Teachers Educ Univ | Graduate education innovation projects of Guangxi Province, China;Research Foundation of Education Bureau of Guangxi Province, China | Shi, JC (corresponding author), Guangxi Teachers Educ Univ, Coll Chem & Life Sci, Nanning 530001, Peoples R China. | null | Dong, Tao;Huang, Chusheng;Shi, Jiancheng;Zhang, Xiuzhi | 16 | 1 | 282,097,000,008 | Graduate education innovation projects of Guangxi Province, China [2009106030817M07];Research Foundation of Education Bureau of Guangxi Province, China [200707LX178] | China | PHYSICAL BIOLOGY | China | null | null | Guangxi Teachers Educ Univ, Coll Chem & Life Sci, Nanning 530001, Peoples R China | 1478-3967 | Dong, T;Huang, C S;Shi, J C;Zhang, X Z | SEP | null | high-frequency;low-frequency effects;synthetic gene network;vibrational resonance | 4 | J | Biochemistry & Molecular Biology;Biophysics | bell-shaped VR;BIOLOGY;COHERENT RESONANCE;control parameter;CONTROLLING STOCHASTIC RESONANCE;corresponding frequency (Omega);definite constant;effective value;high-frequency;high-frequency signal;higher amplitude;low-frequency effects;low-frequency signal;lower frequency;noise;optimal amplitude (B-opt);OSCILLATIONS;random state-state transitions;ratio;resonance phenomena;response;results;role;signal;stochastic resonance (SR);studied;suppressive role;SWITCH;synthetic gene network;SYSTEM;systems;tuning;vibrational resonance;vibrational resonance (VR);VR;VR acts | Shi, J C | BIOLOGY;COHERENT RESONANCE;CONTROLLING STOCHASTIC RESONANCE;NOISE;OSCILLATIONS;SIGNAL;SYSTEMS | null | [Shi, Jiancheng; Huang, Chusheng; Dong, Tao; Zhang, Xiuzhi] Guangxi Teachers Educ Univ, Coll Chem & Life Sci, Nanning 530001, Peoples R China. | The present work was supported by the Research Foundation of Education Bureau of Guangxi Province, China (grant no 200707LX178) and the Graduate education innovation projects of Guangxi Province, China (grant no 2009106030817M07). | bell-shaped VR;control parameter;corresponding frequency (Omega);definite constant;effective value;high-frequency;high-frequency signal;higher amplitude;low-frequency effects;low-frequency signal;lower frequency;noise;optimal amplitude (B-opt);random state-state transitions;ratio;resonance phenomena;response;results;role;stochastic resonance (SR);studied;suppressive role;switch;synthetic gene network;system;tuning;vibrational resonance (VR);VR;VR acts | 10.1002/1439-7641(20020315)3:3<285::AID-CPHC285>3.0.CO;2-A;10.1016/0022-5193(73)90208-7;10.1016/j.bpc.2006.09.006;10.1016/S0041-624X(02)00086-0;10.1016/S0041-624X(96)00086-8;10.1016/S0375-9601(03)00681-9;10.1016/S0896-6273(00)81194-0;10.1017/S0952523800176151;10.1023/A:1019837923906;10.1038/252546a0;10.1038/35066056;10.1038/376236a0;10.1053/apmr.2002.26254;10.1088/0305-4470/33/45/103;10.1103/PhysRevA.71.011801;10.1103/PhysRevE.62.1846;10.1103/PhysRevE.62.317;10.1103/PhysRevE.63.031906;10.1103/PhysRevE.67.066119;10.1103/PhysRevE.68.026214;10.1103/PhysRevE.69.031109;10.1103/PhysRevE.69.046108;10.1103/PhysRevE.71.031105;10.1103/PhysRevE.72.012902;10.1103/PhysRevE.73.061102;10.1103/PhysRevLett.82.4574;10.1103/PhysRevLett.88.148101;10.1103/RevModPhys.70.223;10.1140/epjb/e2008-00083-3;10.1209/epl/i2005-10246-4;10.1360/042004-85;[10.1209/epl/i2004-10287-1, 10.1209/epl/i2004-10287-l] | Guangxi Teachers Educ Univ | Dong, T;Huang, C S;Shi, J C;Zhang, X Z | Shi, J C: Guangxi Teachers Educ Univ, Coll Chem & Life Sci, Nanning 530001, Peoples R China | null | 200707LX178;2009106030817M07 | 33 | null | China | Guangxi Teachers Educ Univ | Shi, Jiancheng | null | BIOLOGY;COHERENT RESONANCE;CONTROLLING STOCHASTIC RESONANCE;NOISE;OSCILLATIONS;SIGNAL;SYSTEMS | Shi, Jiancheng; Huang, Chusheng; Dong, Tao; Zhang, Xiuzhi; | null | Guangxi Teachers Educ Univ, Coll Chem & Life Sci, Nanning 530001, Peoples R China | Guangxi Teachers Educ Univ, Coll Chem & Life Sci, Nanning 530001, Peoples R China | 1478-3975 | null | 3 | 1973;1974;1995;1997;1998;1999;2000;2001;2002;2003;2004;2005;2006;2007;2008 | 18 | Guangxi Teachers Educ Univ, Coll Chem & Life Sci, Nanning 530001, Peoples R China | Phys. Biol. | Zhang, Xiuzhi | IOP PUBLISHING LTD | (B-opt);(Omega);(SR);(VR);,;a;acts;amplitude;and;are;as;bell-shaped;can;change;constant;control;corresponding;definite;effective;effects;exhibited;favor;for;frequency;furthermore;gene;happen;high-frequency;higher;if;in;including;into;introduced;is;low-frequency;lower;namely;network;noise;occurs;of;on;optimal;parameter;phenomena;plays;random;ratio;resonance;response;results;role;show;signal;state-state;stochastic;studied;such;suppressive;switch;synthetic;system;tends;that;the;to;transitions;tuning;value;various;vibrational;VR;when;with;without | Guangxi Teachers Educ Univ | The high-frequency and low-frequency effects on vibrational resonance (VR) in a synthetic gene network are studied. Results show that the role of the high-frequency signal in VR acts as that of noise in stochastic resonance (SR), namely a high-frequency signal can change the effective value of the control parameter such that the random state-state transitions of the switch can happen. A low-frequency signal with lower frequency and higher amplitude tends to favor the response of the system. When VR occurs, the ratio of the optimal amplitude (B-opt) to the corresponding frequency (Omega) of the high-frequency signal is a definite constant. Furthermore, if noise is introduced into the system, noise plays a suppressive role for VR, and various resonance phenomena including the bell-shaped VR and VR without tuning are exhibited in the system. | null | BIOLOGY;COHERENCE RESONANCE;CONTROLLING STOCHASTIC RESONANCE;NOISE;OSCILLATIONS;SIGNAL;SYSTEM | 1 | null | null | 7 | BIOLOGY;COHERENCE RESONANCE;CONTROLLING STOCHASTIC RESONANCE;NOISE;OSCILLATIONS;SIGNAL;SYSTEM | WOS:000282097000008 | Guangxi Teachers Educ Univ, Nanning, Peoples R China | China | 2,010 | null | null | null | null | English | null | ARCH PHYS MED REHAB;BIOPHYS CHEM;CHEMPHYSCHEM;EUR PHYS J B;EUROPHYS LETT;J ATMOS SOL-TERR PHY;J PHYS A-MATH GEN;J THEOR BIOL;NAT REV GENET;NATURE;NEURON;PHARMACEUT RES;PHYS LETT A;PHYS REV A;PHYS REV E;PHYS REV LETT;REV MOD PHYS;SCI CHINA SER B;ULTRASONICS;VISUAL NEUROSCI | Dong, Tao;Huang, Chusheng;Shi, Jiancheng;Zhang, Xiuzhi | 2024-03-11
ER | Baltanás, J P;Borromeo, M;Casado-Pascual, J;Chizhevsky, V N;Cho, C W;Collins, J J;Cubero, D;Gammaitoni, L;Glass, L;Gong, P L;Harikrishnan, K P;Hasty, J;Hänggi, P;Jiang, Y J;Karnes, J L;Landa, P S;Li, Q S;Löcher, M;Maksimov, A O;Savageau, M A;Schläfer, O;Smolen, P;Ullner, E;Vadim, E G;Victor, J D;Volkov, E I;Wang, Z W;Yi, M | 653NA | Nanning, Peoples R China | 18 | null | 1 | null | 20,811,085 | Dong, Tao;Huang, Chusheng;Shi, Jiancheng;Zhang, Xiuzhi | PHYS BIOL | Nanning, Peoples R China |
Dzitac, I;Lascu, A E;Negulescu, S C | 10.15837/ijccc.2010.2.2476 | null | PIATA TINERETULUI 8, ORADEA, JUD, BIHOR, 410526, ROMANIA | 1m6k4e6z5u3e544gz1l315a4b2f4z55r4t3c2g | Synthetic Genes for Artificial Ants. Diversity in Ant Colony Optimization Algorithms | Lucian Blaga Univ Sibiu | null | Negulescu, SC (corresponding author), Lucian Blaga Univ Sibiu, Hermann Oberth Fac Engn, 10 Victoriei Bd, Sibiu 550024, Romania. | null | Dzitac, Ioan;Lascu, Alina E;Negulescu, Sorin C | Automation & Control Systems;Computer Science, Information Systems | null | WOS | Negulescu, S C | Aurel Vlaicu Univ Arad, Arad, Romania;Lucian Blaga Univ Sibiu, Sibiu, Romania;R&D Agora Ltd, Oradea, Romania | 5 | Algorithms;Ant;Ants;Artificial;Colony;diversity;for;genes;in;optimization;synthetic | 1 | ahmed, sayed;da Luz, Lara Emanuele;Dzitac, Ioan;Gull, Amir;Klotz, Wolfgang;Rossi, Jose Osvaldo | CCC PUBL-AGORA UNIV | Aurel Vlaicu Univ Arad, Fac Exact Sci, Dept Math Informat, Arad, Romania;Lucian Blaga Univ Sibiu, Hermann Oberth Fac Engn, 10 Victoriei Bd, Sibiu 550024, Romania;Lucian Blaga Univ Sibiu, Hermann Oberth Fac Engn, Sibiu 550024, Romania;R&D Agora Ltd, Oradea Cercetare Dezvoltare Agora, Oradea 410526, Romania | Article | Lucian Blaga Univ Sibiu | BIHOR | null | null | Aurel Vlaicu Univ Arad;Lucian Blaga Univ Sibiu;R&D Agora Ltd | null | Negulescu, SC (corresponding author), Lucian Blaga Univ Sibiu, Hermann Oberth Fac Engn, 10 Victoriei Bd, Sibiu 550024, Romania. | 223 | Dzitac, Ioan;Lascu, Alina E;Negulescu, Sorin C | 2 | 3 | 275,741,400,008 | null | Romania | INTERNATIONAL JOURNAL OF COMPUTERS COMMUNICATIONS & CONTROL | Romania | null | null | Lucian Blaga Univ Sibiu, Hermann Oberth Fac Engn, Sibiu 550024, Romania | 1841-9836 | Dzitac, I;Lascu, A E;Negulescu, S C | JUN | alina.lascu@ulbsibiu.ro;ioan.dzitac@uav.ro;sorin.negulescu@ulbsibiu.ro | Ant Colony Optimization Algorithms;Artificial Ants;diversity;Synthetic Genes | 3 | J | Automation & Control Systems;Computer Science | (as local variables;(possible;ACO algorithms;adapted ant colony optimisation (ACO) algorithm;agents;agents);Ant Colony Optimization;Ant Colony Optimization Algorithms;approach;approach sections;art;Artificial Ants;artificial ants);B;beginning;C;clones (although;colony;conclusions;convergence speed;current stigmergy-based algorithms;different behaviours);diversity;ending;first (introductory) section;Genetic Algorithms;genetic algorithms (GA);genetic concepts;history;ideas;latest ACO algorithm variants;look;main subject;MAS;methods;MODEL;Multiagent Systems;multiagent systems (MAS);next section;one another);paper (synthetic genes;preliminary simulation results;problems;properties;proposed solution;rationale;real world ants;self-adapting;specific problem;state;Stigmergy;synthetic genes;systems;verified) solution | Negulescu, S C | AGENTS;Ant Colony Optimization;Genetic Algorithms;Multiagent Systems;Stigmergy;SYSTEMS | 216 | [Negulescu, Sorin C.; Lascu, Alina E.] Lucian Blaga Univ Sibiu, Hermann Oberth Fac Engn, Sibiu 550024, Romania. [Dzitac, Ioan] Aurel Vlaicu Univ Arad, Fac Exact Sci, Dept Math Informat, Arad, Romania. [Dzitac, Ioan] R&D Agora Ltd, Oradea Cercetare Dezvoltare Agora, Oradea 410526, Romania. | null | (as local variables;(possible;ACO algorithms;adapted ant colony optimisation (ACO) algorithm;agents;agents);approach;approach sections;art;artificial ants);B;beginning;C;clones (although;colony;conclusions;convergence speed;current stigmergy-based algorithms;different behaviours);ending;first (introductory) section;genetic algorithms (GA);genetic concepts;history;ideas;latest ACO algorithm variants;look;main subject;MAS;methods;model;multiagent systems (MAS);next section;one another);paper (synthetic genes;preliminary simulation results;problems;properties;proposed solution;rationale;real world ants;self-adapting;specific problem;state;stigmergy;synthetic genes;verified) solution | 10.1016/S0167-739X(00)00043-1;10.1109/3477.484436;10.15837/ijccc.2008.4.2404;10.15837/ijccc.2009.1.2410 | Lucian Blaga Univ Sibiu | Dzitac, I;Lascu, A E;Negulescu, S C | Negulescu, S C: Lucian Blaga Univ Sibiu, Hermann Oberth Fac Engn, Sibiu 550024, Romania | Dzitac, Ioan;Lascu, Alina E.;Rossi, Jose Osvaldo | null | 17 | null | Romania | Aurel Vlaicu Univ Arad;Lucian Blaga Univ Sibiu;R&D Agora Ltd | Negulescu, Sorin C | gold, Green Submitted | AGENTS;SYSTEMS | Negulescu, Sorin C.; Dzitac, Ioan; Lascu, Alina E.; | null | Aurel Vlaicu Univ Arad, Fac Exact Sci, Dept Math Informat, Arad, Romania;Lucian Blaga Univ Sibiu, Hermann Oberth Fac Engn, Sibiu 550024, Romania;R&D Agora Ltd, Oradea Cercetare Dezvoltare Agora, Oradea 410526, Romania | Aurel Vlaicu Univ Arad, Fac Exact Sci, Dept Math Informat, Arad, Romania;Lucian Blaga Univ Sibiu, Hermann Oberth Fac Engn, Sibiu 550024, Romania;R&D Agora Ltd, Oradea Cercetare Dezvoltare Agora, Oradea 410526, Romania | null | Ant Colony Optimization;Genetic algorithm;Multiagent Systems;Stigmergy | 2 | 1992;1996;1999;2000;2004;2005;2006;2007;2008;2009 | 7 | Lucian Blaga Univ Sibiu, Hermann Oberth Fac Engn, 10 Victoriei Bd, Sibiu 550024, Romania | Int. J. Comput. Commun. Control | Lascu, Alina E | CCC PUBL-AGORA UNIV | ";(;(ACO);(although;(as;(GA);(introductory);(MAS);(possible;(synthetic;,;-;:;;;a;ACO;adapted;agents;agents);aiming;algorithm;algorithms;alike;an;and;another);ant;ants;ants);approach;are;art;artificial;as;at;authors;B;be;beginning;behaviours);C;can;clones;closing;colony;concepts;conclusions;convergence;current;different;easily;ending;fact;first;following;for;from;fully;genes;genetic;history;ideas;implemented;improved;in;incorporates;inspired;is;latest;local;look;main;MAS;may;methods;model;multiagent;needs;next;not;of;one;optimisation;optimized;or;paper;preliminary;presented;presenting;problem;problems;properties;proposed;proposing;rationale;real;regarding;results;section;sections;self-adapting;simulation;solution;some;specific;speed;state;stigmergy;stigmergy-based;subject;synthetic;systems;that;the;these;they;this;to;together;used;using;validating;variables;variants;verified);with;within;world;yet | Lucian Blaga Univ Sibiu | Inspired from the fact that the real world ants from within a colony are not clones (although they may look alike, they are different from one another), in this paper, the authors are presenting an adapted ant colony optimisation (ACO) algorithm that incorporates methods and ideas from genetic algorithms (GA). Following the first (introductory) section of the paper is presented the history and the state of the art, beginning with the stigmergy and genetic concepts and ending with the latest ACO algorithm variants as multiagent systems (MAS). The rationale and the approach sections are aiming at presenting the problems with current stigmergy-based algorithms and at proposing a (possible - yet to be fully verified) solution to some of the problems ("synthetic genes" for artificial ants). A model used for validating the proposed solution is presented in the next section together with some preliminary simulation results. Some of the conclusions regarding the main subject of the paper (synthetic genes: agents within the MAS with different behaviours) that are closing the paper are: a) the convergence speed of the ACO algorithms can be improved using this approach; b) these "synthetic genes" can be easily implemented (as local variables or properties of the agents); c) the MAS is self-adapting to the specific problem that needs to be optimized. | A-6169-2010;A-8653-2010;B-8006-2010;F-7391-2012;N-8695-2019;T-2471-2019 | AGENTS;SYSTEM | 0 | null | Ant Colony Optimization;Genetic Algorithms;Multiagent Systems;Stigmergy | 8 | AGENTS;Ant Colony Optimization;GENETIC ALGORITHM;Multiagent Systems;Stigmergy;SYSTEM | WOS:000275741400008 | Aurel Vlaicu Univ Arad, Arad, Romania;Lucian Blaga Univ Sibiu, Sibiu, Romania;R&D Agora Ltd, Oradea, Romania | Romania | 2,010 | null | 0000-0001-5284-238X;0000-0001-6396-3208;0000-0001-7269-3473;0000-0002-1421-163X;0000-0002-5415-9936;0000-0003-4574-4997 | null | null | English | null | 4 INT ICSC S ENG INT;ANT COL OPT;COMPUT SCI J MOLD;DIG ANTS;FUTURE GENER COMP SY;IEEE T SYST MAN CY B;INT J COMPUT COMMUN;MATH COMPUT SCI ENG;METAHEURISTIC SWARM;OPTIMIZATION LEARNIN;REC ADV COMPUT ENG;STUD INFORM CONTROL;Studies in Informatics and Control;SWARM INTELLIGENCE N | Dzitac, Ioan;Lascu, Alina E;Negulescu, Sorin C | 2024-03-11
ER | [Anonymous];[No Title Captured];Barbat, B E;Bonabeau, E;Dorigo, M;Dzitac, I;Gambardella, L M;Gordon, D;Negulescu S. C.;Negulescu S.C.;Negulescu, S C;Secui, D C;Stützle, T | 571HA | Sibiu, Romania | 7 | null | 3 | null | null | Dzitac, Ioan;Lascu, Alina E;Negulescu, Sorin C | INT J COMPUT COMMUN | Arad, Romania;Oradea, Romania;Sibiu, Romania |
Adams, R M;Balázsi, G;Collins, J J;Murphy, K F;Wang, X | 10.1093/nar/gkq091 | null | GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND | 1s362l5n422414531p5z6m6k5h6w531z6e5n3lk | Tuning and controlling gene expression noise in synthetic gene networks | Univ Texas MD Anderson Canc Ctr | null | Balázsi, G (corresponding author), Univ Texas MD Anderson Canc Ctr, Dept Syst Biol, Unit 950, Houston, TX 77030 USA. | null | Adams, Rhys M;Balazsi, Gabor;Collins, James J;Murphy, Kevin F;Wang, Xiao | Biochemistry & Molecular Biology | National Institutes of Health [DP1 OD00344, 1DP2 OD006481-01]; National Science Foundation; Howard Hughes Medical Institute; University of Texas M.D. Anderson Cancer Center | WOS | Balázsi, G | Boston Univ, Boston, MA USA;Harvard Univ, Boston, MA USA;Univ Texas MD Anderson Canc Ctr, Houston, TX USA | 38 | and;controlling;expression;gene;in;networks;noise;synthetic;Tuning | 1 | Balazsi, Gabor;Wang, Xiao | OXFORD UNIV PRESS | Boston Univ, Dept Biol, Boston, MA 02215 USA;Boston Univ, Howard Hughes Med Inst, Dept Biomed Engn, Ctr Adv Biotechnol, Boston, MA 02215 USA;Boston Univ, Howard Hughes Med Inst, Dept Biomed Engn, Ctr BioDynam, Boston, MA 02215 USA;Harvard Univ, Wyss Inst Biol Inspired Engn, Boston, MA 02115 USA;Univ Texas MD Anderson Canc Ctr, Dept Syst Biol, Unit 950, Houston, TX 77030 USA | Article | Univ Texas MD Anderson Canc Ctr | OXFORD | null | null | Boston Univ;Harvard Univ;Univ Texas MD Anderson Canc Ctr | Howard Hughes Medical Institute;National Institutes of Health;National Science Foundation;University of Texas M.D. Anderson Cancer Center | Balázsi, G (corresponding author), Univ Texas MD Anderson Canc Ctr, Dept Syst Biol, Unit 950, Houston, TX 77030 USA. | 2726 | Adams, Rhys M;Balazsi, Gabor;Collins, James J;Murphy, Kevin F;Wang, Xiao | 35 | 5 | 277,238,900,021 | Howard Hughes Medical Institute;National Institutes of Health [DP1 OD00344, 1DP2 OD006481-01];National Science Foundation;University of Texas M.D. Anderson Cancer Center | USA | NUCLEIC ACIDS RESEARCH | USA | null | null | Univ Texas MD Anderson Canc Ctr, Dept Syst Biol, Unit 950, Houston, TX 77030 USA | 0305-1048 | Adams, R M;Balázsi, G;Collins, J J;Murphy, K F;Wang, X | MAY | gbalazsi@mdanderson.org;jcollins@bu.edu | controlling gene expression noise;synthetic gene networks;tuning | 5 | J | Biochemistry & Molecular Biology | applications;basal expression;cellular differentiation;cellular phenotypes;computational modeling;controlling gene expression noise;controlling noise;decoupling;dynamic range;ESCHERICHIA-COLI;FLUCTUATING ENVIRONMENTS;gene expression;gene expression control;gene expression noise;gene regulatory cascades;highlights;important aspects;instances;method;MOLECULAR NOISE;MUTATIONS;need;negligible effects;networks;noise;noise levels;noise propagation;observed effects;PATHWAY;population-wide heterogeneity;practical implications;promoters driving TetR expression;reduction;regulatory networks;synthetic eukaryotic gene expression systems;synthetic gene networks;SYSTEM;systematic means;TARGET GENE;TATA box mutations;TATA ELEMENT;toggle switch;transcriptional cascades;tuning;variability;variety;YEAST-CELLS | Murphy, K F | ESCHERICHIA-COLI;FLUCTUATING ENVIRONMENTS;MOLECULAR NOISE;PATHWAY;REGULATORY NETWORKS;SYSTEM;TATA ELEMENT;toggle switch;VARIABILITY;YEAST-CELLS | 2712 | [Adams, Rhys M.; Balazsi, Gabor] Univ Texas MD Anderson Canc Ctr, Dept Syst Biol, Unit 950, Houston, TX 77030 USA. [Murphy, Kevin F.; Wang, Xiao; Collins, James J.] Boston Univ, Howard Hughes Med Inst, Dept Biomed Engn, Ctr BioDynam, Boston, MA 02215 USA. [Murphy, Kevin F.; Wang, Xiao; Collins, James J.] Boston Univ, Howard Hughes Med Inst, Dept Biomed Engn, Ctr Adv Biotechnol, Boston, MA 02215 USA. [Murphy, Kevin F.] Boston Univ, Dept Biol, Boston, MA 02215 USA. [Collins, James J.] Harvard Univ, Wyss Inst Biol Inspired Engn, Boston, MA 02115 USA. | National Institutes of Health Director's Pioneer Award Program (DP1 OD00344 to J.J.C.); the National Institutes of Health Director's New Innovator Award Program (1DP2 OD006481-01 to G.B.); the National Science Foundation Frontiers in Integrative Biological Research Program (to J.J.C.); the Howard Hughes Medical Institute (to J.J.C.); an Institutional Research Grant from The University of Texas M.D. Anderson Cancer Center (to G.B.). Funding for open access charge: National Institutes of Health Director's New Innovator Award Program (1DP2 OD006481-01). | applications;basal expression;cellular differentiation;cellular phenotypes;computational modeling;controlling noise;decoupling;dynamic range;gene expression;gene expression control;gene expression noise;gene regulatory cascades;highlights;important aspects;instances;method;mutations;need;negligible effects;networks;noise;noise levels;noise propagation;observed effects;population-wide heterogeneity;practical implications;promoters driving TetR expression;reduction;synthetic eukaryotic gene expression systems;synthetic gene networks;systematic means;target gene;TATA box mutations;transcriptional cascades;variety | 10.1002/yea.320110408;10.1006/jmbi.1998.1651;10.1006/jmbi.1998.1775;10.1007/s00018-003-23147-z;10.1007/s00109-005-0009-1;10.1016/j.cell.2007.05.045;10.1016/j.cell.2008.09.050;10.1016/j.copbio.2008.10.014;10.1016/j.jtbi.2004.05.013;10.1016/j.molcel.2006.11.003;10.1016/j.plrev.2005.03.003;10.1016/S0006-3495(02)75635-X;10.1016/S0014-5793(03)00857-3;10.1016/S0092-8674(03)00346-5;10.1016/S0168-9525(98)01659-X;10.1021/bi961527k;10.1038/35002125;10.1038/35002131;10.1038/35014651;10.1038/msb.2009.58;10.1038/msb4100081;10.1038/msb4100135;10.1038/nature01258;10.1038/nature01546;10.1038/nature02404;10.1038/nature02491;10.1038/nature03461;10.1038/nature06965;10.1038/nature08187;10.1038/nbt.1536;10.1038/nbt986;10.1038/ng.110;10.1038/ng1616;10.1038/ng869;10.1038/nsmb.1514;10.1039/b801245h;10.1073/pnas.022628299;10.1073/pnas.022642299;10.1073/pnas.0402940101;10.1073/pnas.0408507102;10.1073/pnas.0608451104;10.1073/pnas.0706115104;10.1073/pnas.0809901106;10.1073/pnas.1332628100;10.1073/pnas.212386999;10.1073/pnas.85.15.5399;10.1073/pnas.85.8.2691;10.1073/pnas.94.3.814;10.1073/pnas.95.26.15641;10.1111/j.1365-2958.2007.05951.x;10.1111/j.1432-0436.2007.00219.x;10.1111/j.1432-1033.2004.04130.x;10.1126/science.1067407;10.1126/science.1098641;10.1126/science.1106914;10.1126/science.1109090;10.1126/science.1114383;10.1126/science.1137455;10.1126/science.1140247;10.1126/science.1140818;10.1126/science.1172005;10.1126/science.1174843;10.1128/AEM.02009-08;10.1142/S0219720005001144;10.1146/annurev.physchem.58.032806.104637;10.1186/1754-1611-3-1;10.1529/biophysj.105.060491;10.1529/biophysj.107.118687;10.1534/genetics.167.1.523 | Univ Texas MD Anderson Canc Ctr | Adams, R M;Balázsi, G;Collins, J J;Murphy, K F;Wang, X | Murphy, K F: Univ Texas MD Anderson Canc Ctr, Dept Syst Biol, Unit 950, Houston, TX 77030 USA | Wang, Xiao | 1DP2 OD006481-01;DP1 OD00344 | 73 | null | USA | Boston Univ;Harvard Univ;Univ Texas MD Anderson Canc Ctr | Murphy, Kevin F | Green Published, gold, Green Submitted | ESCHERICHIA-COLI;FLUCTUATING ENVIRONMENTS;MOLECULAR NOISE;PATHWAY;REGULATORY NETWORKS;SYSTEM;TATA ELEMENT;TOGGLE SWITCH;VARIABILITY;YEAST-CELLS | Murphy, Kevin F.; Adams, Rhys M.; Wang, Xiao; Balazsi, Gabor; Collins, James J.; | null | Boston Univ, Dept Biol, Boston, MA 02215 USA;Boston Univ, Howard Hughes Med Inst, Dept Biomed Engn, Ctr Adv Biotechnol, Boston, MA 02215 USA;Boston Univ, Howard Hughes Med Inst, Dept Biomed Engn, Ctr BioDynam, Boston, MA 02215 USA;Harvard Univ, Wyss Inst Biol Inspired Engn, Boston, MA 02115 USA;Univ Texas MD Anderson Canc Ctr, Dept Syst Biol, Unit 950, Houston, TX 77030 USA | Boston Univ, Dept Biol, Boston, MA 02215 USA;Boston Univ, Howard Hughes Med Inst, Dept Biomed Engn, Ctr Adv Biotechnol, Boston, MA 02215 USA;Boston Univ, Howard Hughes Med Inst, Dept Biomed Engn, Ctr BioDynam, Boston, MA 02215 USA;Harvard Univ, Wyss Inst Biol Inspired Engn, Boston, MA 02115 USA;Univ Texas MD Anderson Canc Ctr, Dept Syst Biol, Unit 950, Houston, TX 77030 USA | null | null | 8 | 1988;1995;1997;1998;1999;2000;2002;2003;2004;2005;2006;2007;2008;2009 | 108 | Univ Texas MD Anderson Canc Ctr, Dept Syst Biol, Unit 950, Houston, TX 77030 USA | Nucleic Acids Res. | Collins, James J | OXFORD UNIV PRESS | ,;a;accordingly;and;applications;apply;aspects;basal;be;behave;box;by;can;cascades;cases;cellular;computational;control;controlling;create;decoupling;develop;differentiation;driving;due;dynamic;e.g.;effectively;effects;eukaryotic;experimentally;explain;expression;for;from;gene;harnessed;has;here;heterogeneity;highlights;however;implementing;implications;important;in;instances;into;introduce;is;it;levels;many;mathematical;mean;means;method;modeling;mutations;need;negligible;networks;noise;observed;of;on;others;phenotypes;population-wide;practical;present;promoters;propagation;range;reduction;regulatory;show;so;some;specifically;such;suppressed;synthetic;systematic;systems;target;TATA;TetR;that;the;there;these;this;to;transcriptional;tune;unreliably;used;utilizing;variety;we;which;while;with;work | Univ Texas MD Anderson Canc Ctr | Synthetic gene networks can be used to control gene expression and cellular phenotypes in a variety of applications. In many instances, however, such networks can behave unreliably due to gene expression noise. Accordingly, there is a need to develop systematic means to tune gene expression noise, so that it can be suppressed in some cases and harnessed in others, e.g. in cellular differentiation to create population-wide heterogeneity. Here, we present a method for controlling noise in synthetic eukaryotic gene expression systems, utilizing reduction of noise levels by TATA box mutations and noise propagation in transcriptional cascades. Specifically, we introduce TATA box mutations into promoters driving TetR expression and show that these mutations can be used to effectively tune the noise of a target gene while decoupling it from the mean, with negligible effects on the dynamic range and basal expression. We apply mathematical and computational modeling to explain the experimentally observed effects of TATA box mutations. This work, which highlights some important aspects of noise propagation in gene regulatory cascades, has practical implications for implementing gene expression control in synthetic gene networks. | A-8414-2008 | ESCHERICHIA-COLI;FLUCTUATING ENVIRONMENTS;MOLECULAR NOISE;PATHWAY;REGULATORY NETWORKS;SYSTEM;TATA ELEMENT;TOGGLE SWITCH;VARIABILITY;YEAST-CELLS | 0 | null | null | 15 | ESCHERICHIA-COLI;FLUCTUATING ENVIRONMENTS;MOLECULAR NOISE;PATHWAY;REGULATORY NETWORKS;SYSTEM;TATA ELEMENT;toggle switch;VARIABILITY;YEAST-CELLS | WOS:000277238900021 | Boston Univ, Boston, MA USA;Harvard Univ, Boston, MA USA;Univ Texas MD Anderson Canc Ctr, Houston, TX USA | USA | 2,010 | null | 0000-0002-4056-0155;0000-0002-6865-5818 | null | null | English | null | ANNU REV PHYS CHEM;APPL ENVIRON MICROB;BIOCHEMISTRY-US;BIOPHYS J;CELL;CELL MOL LIFE SCI;CURR OPIN BIOTECH;CURRENT PROTOCOLS MO;DIFFERENTIATION;EUR J BIOCHEM;FEBS LETT;GENETICS;J Bioinform Comput Biol;J Biol Eng;J MOL BIOL;J MOL MED;J THEOR BIOL;MOL BIOSYST;MOL CELL;MOL MICROBIOL;MOL SYST BIOL;NAT BIOTECHNOL;NAT GENET;NAT STRUCT MOL BIOL;NATURE;NONPARAMETRIC STAT B;P NATL ACAD SCI USA;PHYS LIFE REV;SCIENCE;TRENDS GENET;YEAST | Adams, Rhys M;Balazsi, Gabor;Collins, James J;Murphy, Kevin F;Wang, Xiao | 2024-03-11
ER | Acar, M;Amberg Dc.;Arkin, A;Atkinson, M R;Backes, H;Basu, S;Bayer Travis, S;Becskei, A;Blake, W J;Chang, H H;Chen, W;Cook, D L;Deans, T L;Dublanche, Y;Dwyer, D J;El-Samad, H;Ellis, T;Elowitz, M B;Friedland, A E;Gardner, T S;Gietz, R D;Gillespie, D T;Gonze, D;Guet, C C;Guido, N J;Hoopes, B C;Hooshangi, S;Isaacs, F J;Kemkemer, R;Kobayashi, H;Korobkova, E;Kussell, E;Landry, C R;Lee, S K;Levin, M D;Lu, T;Maamar, H;Mcadams, H H;Mcmillen, D;Murphy, K F;Neildez-Nguyen, T M A;Nevozhay, D;Orrell, D;Orth, P;Ozbudak, E M;Paldi, A;Paulsson, J;Pedraza, J M;Raj, A;Ramsey Stephen;Rao, C V;Raser, J M;Rosenfeld, N;Schubert, P;Selleck, S B;Siegel S.;Sipo, I;Smith, M C A;Smolke, C D;Struhl K.;Süel, G M;Tabor, J J;Thattai, M;Waks, Z;Wang, H H;You, L C;Zenklusen, D;Zhang, Z H | 590PK | Houston, TX USA | 139 | null | 3 | null | 20,211,838 | Adams, Rhys M;Balazsi, Gabor;Collins, James J;Murphy, Kevin F;Wang, Xiao | NUCLEIC ACIDS RES | Boston, MA USA;Houston, TX USA |
Aubel, D;Fussenegger, M | 10.1002/bies.200900149 | null | 111 RIVER ST, HOBOKEN 07030-5774, NJ USA | b5m4v156sd5t6o3t6z3k531m0323b49322150 | Mammalian synthetic biology - from tools to therapies | Swiss Fed Inst Technol | null | Fussenegger, M (corresponding author), Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Mattenstr 26, CH-4058 Basel, Switzerland. | SI | Aubel, Dominique;Fussenegger, Martin | Biochemistry & Molecular Biology;Biology | Swiss National Science Foundation [3100A0-112549]; EC Framework 7 (Persist) | WOS | Fussenegger, M | Swiss Fed Inst Technol, Basel, Switzerland;Univ Lyon, Villeurbanne, France | 32 | -;biology;From;mammalian;synthetic;therapies;to;Tools | 2 | null | WILEY | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, CH-4058 Basel, Switzerland;Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Mattenstr 26, CH-4058 Basel, Switzerland;Univ Lyon, F-69622 Villeurbanne, France | Review | Swiss Fed Inst Technol | HOBOKEN | null | null | Swiss Fed Inst Technol;Univ Lyon | EC Framework 7 (Persist);Swiss National Science Foundation | Fussenegger, M (corresponding author), Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Mattenstr 26, CH-4058 Basel, Switzerland. | 345 | Aubel, Dominique;Fussenegger, Martin | 23 | 2 | 276,787,300,009 | EC Framework 7 (Persist);Swiss National Science Foundation [3100A0-112549] | France;Switzerland | BIOESSAYS | Switzerland | null | null | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, CH-4058 Basel, Switzerland | 0265-9247 | Aubel, D;Fussenegger, M | APR | fussenegger@bsse.ethz.ch | mammalian synthetic biology;therapies;tools | 2 | J | Biochemistry & Molecular Biology;Life Sciences & Biomedicine - Other Topics | 21(st) century;biochemical reaction networks;biologic gates;cancer therapy;catalogued items;cell-based therapies;Circadian clock;complete;comprehensive details;constructive systems biology discipline;cover prototype therapeutic circuits;design new biological devices;drug discovery;drug discovery circuits;DYNAMICS;electro-genetic devices;encyclopedic information;epigenetic toggle switch;ESCHERICHIA-COLI;first success stories;future gene-;gene memory;gene regulation;gene-function correlations;highlight state-of-the-art synthetic gene network design;hysteresis;IMPACT;IN-VIVO;intronic siRNA;inventory;latest generation;life;life science revolution;living organisms;mammalian synthetic biology;mammalian transgene control devices;new era;novel;OSCILLATOR;planet;postgenomic era;premise;PRODUCT GENE-EXPRESSION;promise;providing novel therapeutic strategies;regulation systems;regulatory networks;reported;RNA interference;synthetic biology;synthetic gene networks;synthetic hormone systems;systematic manner;systems;systems biology;therapies;tight control;time;time-delay circuit;toggle switch;tools;transcription factor;transcriptional cascade;TRANSGENE EXPRESSION;tuberculosis treatment;useful functionality;will | Aubel, D | biologic gates;cancer therapy;Circadian clock;drug discovery circuits;electro-genetic devices;epigenetic toggle switch;ESCHERICHIA-COLI;gene memory;Gene regulation;hysteresis;IN-VIVO;intronic siRNA;OSCILLATOR;PRODUCT GENE-EXPRESSION;REGULATION SYSTEMS;REGULATORY NETWORKS;RNA INTERFERENCE;synthetic gene networks;synthetic hormone systems;TIGHT CONTROL;time-delay circuit;toggle switch;transcription factor;transcriptional cascade;TRANSGENE EXPRESSION;tuberculosis treatment | 332 | [Aubel, Dominique; Fussenegger, Martin] Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, CH-4058 Basel, Switzerland. [Aubel, Dominique] Univ Lyon, F-69622 Villeurbanne, France. | We thank John and Claire Bendix for editorial and critical comments on this manuscript. Our laboratory work is supported in part by the Swiss National Science Foundation (grant No. 3100A0-112549) and in part by the EC Framework 7 (Persist). | 21(st) century;biochemical reaction networks;catalogued items;cell-based therapies;complete;comprehensive details;constructive systems biology discipline;cover prototype therapeutic circuits;design new biological devices;drug discovery;dynamics;encyclopedic information;first success stories;future gene-;gene-function correlations;highlight state-of-the-art synthetic gene network design;impact;inventory;latest generation;life;life science revolution;living organisms;mammalian synthetic biology;mammalian transgene control devices;new era;novel;planet;postgenomic era;premise;promise;providing novel therapeutic strategies;reported;synthetic biology;systematic manner;systems;systems biology;time;useful functionality;will | 10.1002/(SICI)1097-0290(19980105)57:1<1::AID-BIT1>3.0.CO;2-M;10.1002/bit.10731;10.1002/jgm.903;10.1006/mthe.2002.0531;10.1006/mthe.2002.0717;10.1016/j.arcmed.2005.06.009;10.1016/j.cell.2007.05.045;10.1016/j.chembiol.2009.02.005;10.1016/j.cmet.2009.04.008;10.1016/j.copbio.2007.09.002;10.1016/j.jmb.2005.10.076;10.1016/j.ymben.2005.02.005;10.1016/j.ymben.2006.07.005;10.1016/j.ymben.2008.12.001;10.1016/j.ymthe.2004.02.013;10.1016/S0022-2836(83)80166-1;10.1016/S0958-1669(02)00356-7;10.1021/bp000129c;10.1021/bp970108r;10.1023/B:DRUG.0000026251.00854.77;10.1038/35002125;10.1038/35002131;10.1038/79194;10.1038/81208;10.1038/msb.2008.24;10.1038/msb4100202;10.1038/nature02089;10.1038/nature02724;10.1038/nature03453;10.1038/nature03461;10.1038/nature04640;10.1038/nature07616;10.1038/nbt0598-468;10.1038/nbt1021;10.1038/nbt1083;10.1038/nbt1307;10.1038/nbt731;10.1038/nbt980;10.1038/NMETH1107;10.1038/nrm2698;10.1039/b901484e;10.1046/j.1365-2958.2003.03809.x;10.1073/pnas.0500345102;10.1073/pnas.0606398104;10.1073/pnas.0701382104;10.1073/pnas.0704624104;10.1073/pnas.0800442106;10.1073/pnas.0800663105;10.1073/pnas.0901501106;10.1073/pnas.89.12.5547;10.1089/hum.1998.9.13-1939;10.1093/nar/19.17.4647;10.1093/nar/23.17.3605;10.1093/nar/gkm466;10.1093/nar/gkm652;10.1093/nar/gkn443;10.1093/nar/gkp014;10.1093/nar/gng071;10.1096/fj.05-4446fje;10.1097/00001813-200503000-00001;10.1101/gad.1696108;10.1103/PhysRevLett.88.148101;10.1111/j.1742-4658.2005.05003.x;10.1126/science.1112304;10.1126/science.291.5503.490;10.1126/science.7792603;10.1186/1472-6750-6-43;10.1242/jeb.00467;10.1371/journal.pone.0002372;10.1517/14656566.2.11.1903;10.1523/JNEUROSCI.3842-04.2005;10.7164/antibiotics.54.44 | Swiss Fed Inst Technol | Aubel, D;Fussenegger, M | Aubel, D: Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, CH-4058 Basel, Switzerland | null | 3100A0-112549 | 79 | null | Switzerland | Swiss Fed Inst Technol;Univ Lyon | Aubel, Dominique | null | CIRCADIAN CLOCK;ESCHERICHIA-COLI;IN-VIVO;PRODUCT GENE-EXPRESSION;REGULATION SYSTEMS;REGULATORY NETWORKS;TIGHT CONTROL;TOGGLE SWITCH;TRANSCRIPTION FACTOR;TRANSGENE EXPRESSION | Aubel, Dominique; Fussenegger, Martin; | null | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, CH-4058 Basel, Switzerland;Univ Lyon, F-69622 Villeurbanne, France | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, CH-4058 Basel, Switzerland;Univ Lyon, F-69622 Villeurbanne, France | 1521-1878 | biologic gate;cancer therapy;drug discovery circuits;electro-genetic devices;epigenetic toggle switch;gene memory;Gene regulation;hysteresis;intronic siRNA;oscillations;RNA interference;Synthetic gene network;synthetic hormone systems;time-delay circuit;transcriptional cascade;tuberculosis treatment | 4 | 1961;1983;1991;1992;1995;1997;1998;2000;2001;2002;2003;2004;2005;2006;2007;2008;2009;2010 | 32 | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Mattenstr 26, CH-4058 Basel, Switzerland | Bioessays | Fussenegger, Martin | WILEY | ,;21(st);a;an;and;are;be;become;becoming;beginning;biochemical;biological;biology;bring;catalogued;cell-based;century;circuits;come;complete;comprehensive;constructive;control;correlations;cover;delivering;design;details;devices;discipline;discovery;drug;dynamics;encyclopedic;era;essential;first;focus;for;functionality;future;gene;gene-;gene-function;generation;has;have;help;here;highlight;holds;impact;in;increasingly;information;into;inventory;is;items;latest;life;likely;living;mammalian;manner;network;networks;new;novel;now;of;on;organisms;parts;planet;postgenomic;premise;promise;prototype;provided;providing;rational;reaction;reassemble;reported;revolution;science;state-of-the-art;stories;strategies;success;synthetic;systematic;systems;that;the;therapeutic;therapies;these;this;time;to;transgene;useful;we;will;with | Swiss Fed Inst Technol | Mammalian synthetic biology holds the promise of providing novel therapeutic strategies, and the first success stories are beginning to be reported. Here we focus on the latest generation of mammalian transgene control devices, highlight state-of-the-art synthetic gene network design, and cover prototype therapeutic circuits. These will have an impact on future gene- and cell-based therapies and help bring drug discovery into a new era. The inventory of biological parts that are essential for life on this planet is becoming increasingly complete. The postgenomic era has provided encyclopedic information on gene-function correlations and systems biology is now delivering comprehensive details on the dynamics of biochemical reaction networks in living organisms. The time has come to reassemble these catalogued items and design new biological devices and systems with novel and useful functionality in a rational and systematic manner. This is the premise of synthetic biology, a constructive systems biology discipline likely to become the life science revolution of the 21(st) century. | null | CIRCADIAN CLOCK;ESCHERICHIA-COLI;IN-VIVO;PRODUCT GENE-EXPRESSION;REGULATOR SYSTEM;REGULATORY NETWORKS;TIGHT CONTROL;TOGGLE SWITCH;TRANSCRIPTION FACTORS;TRANSGENE EXPRESSION | 1 | null | biologic gates;cancer therapy;drug discovery circuits;electro-genetic devices;epigenetic toggle switch;gene memory;Gene regulation;hysteresis;intronic siRNA;oscillator;RNA interference;synthetic gene networks;synthetic hormone systems;time-delay circuit;transcriptional cascade;tuberculosis treatment | 14 | ESCHERICHIA-COLI;biologic gate;cancer therapy;Circadian clock;drug discovery circuits;electro-genetic devices;epigenetic toggle switch;gene memory;Gene regulation;hysteresis;IN-VIVO;intronic siRNA;OSCILLATIONS;PRODUCT GENE-EXPRESSION;REGULATOR SYSTEM;REGULATORY NETWORKS;RNA INTERFERENCE;synthetic gene networks;synthetic hormone systems;TIGHT CONTROL;time-delay circuit;toggle switch;transcription factor;transcriptional cascade;TRANSGENE EXPRESSION;tuberculosis treatment | WOS:000276787300009 | Swiss Fed Inst Technol, Basel, Switzerland;Univ Lyon, Villeurbanne, France | France;Switzerland | 2,010 | null | null | null | null | English | null | ANTI-CANCER DRUG;ARCH MED RES;BIOTECHNOL BIOENG;BIOTECHNOL PROGR;BMC BIOTECHNOL;CELL;CELL METAB;CHEM BIOL;CURR OPIN BIOTECH;Expert Opin Pharmacother;FASEB J;FEBS J;GENE DEV;Handb Exp Pharmacol;HUM GENE THER;INT J CLIN PRACT;INVEST NEW DRUG;J ANTIBIOT;J EXP BIOL;J GENE MED;J MOL BIOL;J NEUROSCI;METAB ENG;MOL BIOSYST;MOL CELL BIOL;MOL MICROBIOL;MOL SYST BIOL;MOL THER;NAT BIOTECHNOL;NAT GENET;NAT METHODS;NAT REV MOL CELL BIO;NATURE;NUCL ACIDS IN PRESS;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PHYS REV LETT;PLOS ONE;SCIENCE | Aubel, Dominique;Fussenegger, Martin | 2024-03-11
ER | Agapakis, C M;Alanis, A J;Alper, H;Anderson, J C;Aubel, D;Bachman, G C;Balagadde, F K;Baron, U;Basu, S;Chong, H;Covert, M W;Dean, J T;Deans, T L;Deuschle, U;Elowitz, M B;Engohang-Ndong, J;Fussenegger, M;Gardner, T S;Gitzinger, M;Gonzalez-Nicolini, V;Gossen, M;Greber, D;Hartenbach, S;Hasty, J;Hillen, W;Jacob, J F;Jin, L Q;Kaasik, K;Kahan B, D;Kramer, B P;Lahav, G;Lu, T K;Malphettes, L;May, T;Morton, A J;Mullick, A;Nordstrom, J L;Palli, S R;Purnick, P E M;Rinaudo, K;Ro, D K;Roscilli, G;Royo, J L;Sarkar, N N;Serrano, L;Stokkan, K A;Swinburne, I A;Tascou, S;Tigges, M;Weber, W;Wu, Y H;Wyborski, D L;Xiong, W;Xu, Y;Yao, F | 584XK | Basel, Switzerland | 46 | null | 2 | null | 20,238,390 | Aubel, Dominique;Fussenegger, Martin | BIOESSAYS | Basel, Switzerland;Villeurbanne, France |
Bandiera, A | 10.1080/10826068.2010.488541 | PII 924023741 | 325 CHESTNUT ST, SUITE 800, PHILADELPHIA, PA 19106 USA | 1u272e3i29522w5a1p5l2vx35495iho46o | ASSEMBLY AND OPTIMIZATION OF EXPRESSION OF SYNTHETIC GENES DERIVED FROM THE HUMAN ELASTIN REPEATED MOTIF | Univ Trieste | null | Bandiera, A (corresponding author), Univ Trieste, Dept Life Sci, Via Giorgieri 1, I-34127 Trieste, Italy. | null | Bandiera, Antonella | Biochemical Research Methods;Biochemistry & Molecular Biology;Biotechnology & Applied Microbiology | MIUR | WOS | Bandiera, A | null | 40 | and;Assembly;DERIVED;ELASTIN;expression;From;genes;human;MOTIF;of;optimization;REPEATED;synthetic;the | 1 | null | TAYLOR & FRANCIS INC | Univ Trieste, Dept Life Sci, I-34127 Trieste, Italy;Univ Trieste, Dept Life Sci, Via Giorgieri 1, I-34127 Trieste, Italy | Article | Univ Trieste | PHILADELPHIA | null | null | Univ Trieste | MIUR | Bandiera, A (corresponding author), Univ Trieste, Dept Life Sci, Via Giorgieri 1, I-34127 Trieste, Italy. | 212 | null | 5 | 1 | 279,720,500,004 | MIUR | Italy | PREPARATIVE BIOCHEMISTRY & BIOTECHNOLOGY | Italy | null | null | Univ Trieste, Dept Life Sci, I-34127 Trieste, Italy | 1082-6068 | Bandiera, A | null | abandiera@units.it | Assembly;expression;HUMAN ELASTIN REPEATED MOTIF;optimization;SYNTHETIC GENES DERIVED | 1 | J | Biochemistry & Molecular Biology;Biotechnology & Applied Microbiology | accumulation;artificial polypeptides;assembly;attention;BACTERIA;biomedical;biotechnological applications;BLOCK-COPOLYMERS;conditions;crucial step;DESIGN;different conditions;elastin;elastin-derived polypeptides;electron micrographs;Escherichia coli strain;ESCHERICHIA-COLI;expression;extraction procedure led;hexapeptidic motif;huge potential;human elastin;HUMAN ELASTIN REPEATED MOTIF;induced cells;innovative biomaterials;interesting properties;large quantities;mammalian elastin;material;MIMETIC POLYPEPTIDE;monomeric unit;optimization;POLYPEPTIDE SEQUENCES;production;PROTEIN POLYMERS;proteins;PURIFICATION;PURPOSES;realization;reason;recombinant biotechnology;recombinant product;recombinant products;recovery;repeated domains;repetitive artificial polypeptides;responsive behavior;significant improvement;smart properties;starting;synthetic genes;SYNTHETIC GENES DERIVED;wide range;yield | Bandiera, A | artificial polypeptides;BLOCK-COPOLYMERS;DESIGN;elastin;ESCHERICHIA-COLI;EXPRESSION;MIMETIC POLYPEPTIDE;POLYPEPTIDE SEQUENCES;PROTEIN POLYMERS;PURIFICATION;PURPOSES;Synthetic genes | 198 | Univ Trieste, Dept Life Sci, I-34127 Trieste, Italy. | I am grateful to Dr. G. Manzini for helpful discussion and critical reading of the article, to Dr. P. Sist and Dr. R. Urbani for their encouragement and support, and to F. Micali for electron microscopy images and skillful assistance. This research was supported by MIUR-PRIN2007, "Bioinspired HELP (Human Elastin-like Polypeptides)-based nanostructure matrices for regenerative medicine." "Fondazione CRTrieste" is also acknowledged. | accumulation;artificial polypeptides;attention;bacteria;biomedical;biotechnological applications;conditions;crucial step;different conditions;elastin-derived polypeptides;electron micrographs;Escherichia coli strain;expression;extraction procedure led;hexapeptidic motif;huge potential;human elastin;induced cells;innovative biomaterials;interesting properties;large quantities;mammalian elastin;material;monomeric unit;optimization;production;protein polymers;proteins;realization;reason;recombinant biotechnology;recombinant product;recombinant products;recovery;repeated domains;repetitive artificial polypeptides;responsive behavior;significant improvement;smart properties;starting;synthetic genes;wide range;yield | 10.1002/bip.10431;10.1002/bip.10512;10.1002/jbm.10272;10.1006/prep.1996.0008;10.1007/978-0-387-26575-9_268;10.1007/BF01025240;10.1016/0005-2795(74)90057-9;10.1016/j.ab.2006.09.020;10.1016/j.actbio.2007.07.007;10.1016/j.biomaterials.2004.11.027;10.1016/j.matbio.2005.01.004;10.1016/S0167-4838(01)00262-X;10.1016/S0167-7799(99)01306-2;10.1016/S0169-409X(02)00059-5;10.1021/bm000284f;10.1021/bm015630n;10.1021/bp0503742;10.1021/es034210y;10.1021/ja047417f;10.1021/ma001973m;10.1021/ma980875m;10.1021/ma981660f;10.1023/B:JMSM.0000021124.58688.7a;10.1042/BA20050114;10.1083/jcb.99.3.870;10.1093/hmg/4.9.1677 | Univ Trieste | Bandiera, A | Bandiera, A: Univ Trieste, Dept Life Sci, I-34127 Trieste, Italy | null | null | 31 | null | Italy | Univ Trieste | Bandiera, Antonella | null | BLOCK-COPOLYMERS;DESIGN;ESCHERICHIA-COLI;MIMETIC POLYPEPTIDE;POLYPEPTIDE SEQUENCES;PROTEIN POLYMERS;PURIFICATION;PURPOSES | Bandiera, Antonella; | null | null | Univ Trieste, Dept Life Sci, I-34127 Trieste, Italy | null | artificial polypeptides;elastin;expression;Synthetic gene | 3 | 1974;1978;1984;1988;1990;1995;1996;1997;1999;2000;2001;2002;2003;2004;2005;2006;2007;2008 | 19 | Univ Trieste, Dept Life Sci, Via Giorgieri 1, I-34127 Trieste, Italy | Prep. Biochem. Biotechnol. | Bandiera, Antonella | TAYLOR & FRANCIS INC | ,;a;accumulation;and;applications;artificial;assayed;assembled;attention;attractive;bacteria;based;been;behavior;biomaterials;biomedical;biotechnological;biotechnology;by;cells;coli;conditions;crucial;different;domains;due;elastin;elastin-derived;electron;enhancing;Escherichia;even;expressing;expression;extraction;focused;for;from;genes;have;hexapeptidic;highly;huge;human;improvement;in;induced;innovative;interesting;is;large;led;make;mammalian;material;micrographs;modeled;monomeric;motif;naturally;occurring;of;often;on;optimization;optimize;optimized;our;polymers;polypeptides;possess;potential;procedure;produced;product;production;products;properties;protein;proteins;purified;quantities;range;realization;reason;recombinant;recovery;repeated;repetitive;responsive;retaining;show;showed;significant;smart;starting;step;strain;synthetic;that;the;their;them;thermally;these;this;to;typical;under;unit;we;were;wide;yield | Univ Trieste | Naturally occurring proteins often possess interesting properties that make them attractive for the realization of innovative biomaterials. Repetitive artificial polypeptides have been modeled on the repeated domains of mammalian elastin, retaining and even enhancing their thermally responsive behavior. These protein polymers have been produced by recombinant biotechnology and due to their smart properties show a huge potential for a wide range of biomedical and biotechnological applications. For this reason, production of large quantities of highly purified material is a crucial step. We focused our attention on elastin-derived polypeptides based on the hexapeptidic motif typical of human elastin. Synthetic genes were assembled starting from a monomeric unit, and the different conditions were assayed to optimize the yield of the artificial polypeptides. Optimization of Escherichia coli strain and of the extraction procedure led to significant improvement in expression and recovery of the recombinant products. Electron micrographs of expressing bacteria under optimized conditions showed the accumulation of the recombinant product in the induced cells. | null | BLOCK-COPOLYMERS;DESIGN;ESCHERICHIA-COLI;MIMETIC POLYPEPTIDE;POLYPEPTIDE SEQUENCES;PROTEIN POLYMERS;PURIFICATION;PURPOSES | 1 | null | artificial polypeptides;elastin;expression;Synthetic genes | 15 | ESCHERICHIA-COLI;artificial polypeptides;BLOCK-COPOLYMERS;DESIGN;elastin;EXPRESSION;MIMETIC POLYPEPTIDE;POLYPEPTIDE SEQUENCES;PROTEIN POLYMERS;PURIFICATION;PURPOSES;Synthetic gene | WOS:000279720500004 | Univ Trieste, Trieste, Italy | Italy | 2,010 | null | null | null | null | English | null | ACTA BIOMATER;ADV DRUG DELIVER REV;ANAL BIOCHEM;BBA-PROTEIN STRUCT M;BIOCHIM BIOPHYS ACTA;BIOMACROMOLECULES;BIOMATERIALS;BIOPOLYMERS;BIOTECHNOL APPL BIOC;BIOTECHNOL LETT;BIOTECHNOL PROGR;ENVIRON SCI TECHNOL;HUM MOL GENET;INT J PEPT PROT RES;J AM CHEM SOC;J BIOMED MATER RES;J CELL BIOL;J MATER SCI-MATER M;J PROTEIN CHEM;Journal de la Societe de Biologie;MACROMOLECULES;MATRIX BIOL;METHOD ENZYMOL;METHODS MOL BIOL;PROTEIN EXPRES PURIF;TRENDS BIOTECHNOL;UNDERSTANDING BIOLOGY USING PEPTIDES | null | 2024-03-11
ER | Alix Alain J. P.;Bandiera, A;Bellingham, C M;Chow, D C;Christensen, T;Daniell, H;Girotti, A;Guda, C;Hong, M;Kobatake, E;Kostal, J;Mcmillan, R A;Mcpherson, D T;Meyer, D E;Nagapudi, K;Nagarsekar, A;Okamoto, K;Olson, T M;Osborne, J L;Panitch, A;Pepe, A;Rapaka, R S;Reguera, J;Senior, R M;Studier, F W;Urry, D W;Wright, E R | 623EI | Trieste, Italy | 19 | null | 1 | null | 20,623,431 | Bandiera, Antonella | PREP BIOCHEM BIOTECH | Trieste, Italy |
Andrews, B;Baryshnikova, A;Boone, C;Costanzo, M;Dixon, S;Myers, C L;Vizeacoumar, F J | 10.1016/S0076-6879(10)70007-0 | null | 525 B STREET, SUITE 1900, SAN DIEGO, CA 92101-4495 USA | 5s1u18q5q6r6v4r51472z57726z526h106d5hk | SYNTHETIC GENETIC ARRAY (SGA) ANALYSIS IN <i>SACCHAROMYCES CEREVISIAE</i> <i>AND SCHIZOSACCHAROMYCES POMBE</i> | Univ Toronto | Methods in Enzymology | Baryshnikova, A (corresponding author), Univ Toronto, Banting & Best Dept Med Res, Toronto, ON, Canada. | null | Andrews, Brenda;Baryshnikova, Anastasia;Boone, Charles;Costanzo, Michael;Dixon, Scott;Myers, Chad L;Vizeacoumar, Franco J | Biochemical Research Methods;Biochemistry & Molecular Biology | null | WOS | Baryshnikova, A | Columbia Univ, New York, NY USA;Univ Minnesota Twin Cities, Minneapolis, MN USA;Univ Toronto, Toronto ON, Canada | 470 | (SGA);<i>AND;<i>Saccharomyces;Analysis;Array;cerevisiae</i>;genetic;in;POMBE</i>;SCHIZOSACCHAROMYCES;synthetic | 2 | Baryshnikova, Anastasia | ELSEVIER ACADEMIC PRESS INC | Columbia Univ, Dept Biol Sci, New York, NY 10027 USA;Univ Minnesota Twin Cities, Dept Comp Sci & Engn, Minneapolis, MN USA;Univ Toronto, Banting & Best Dept Med Res, Toronto, ON, Canada;Univ Toronto, Dept Mol Genet, Terrence Donnelly Ctr Cellular & Biomol Res, Toronto, ON, Canada | Review; Book Chapter | Univ Toronto | SAN DIEGO | null | null | Canada;Columbia Univ;Univ Minnesota Twin Cities;Univ Toronto | null | Baryshnikova, A (corresponding author), Univ Toronto, Banting & Best Dept Med Res, Toronto, ON, Canada. | 179 | Andrews, Brenda;Baryshnikova, Anastasia;Boone, Charles;Costanzo, Michael;Dixon, Scott;Myers, Chad L;Vizeacoumar, Franco J | 25 | 4 | 275,827,900,007 | null | Canada;USA | METHODS IN ENZYMOLOGY, VOL 470: GUIDE TO YEAST GENETICS:: FUNCTIONAL GENOMICS, PROTEOMICS, AND OTHER SYSTEMS ANALYSIS, 2ND EDITION | Canada | null | null | Univ Toronto, Banting & Best Dept Med Res, Toronto, ON, Canada | 0076-6879 | Andrews, B;Baryshnikova, A;Boone, C;Costanzo, M;Dixon, S;Myers, C L;Vizeacoumar, F J | null | null | <i>SACCHAROMYCES CEREVISIAE</i> <i>AND SCHIZOSACCHAROMYCES POMBE</i>;SYNTHETIC GENETIC ARRAY (SGA) ANALYSIS | 7 | S | Biochemistry & Molecular Biology | 5000 viable gene deletion mutants (representing;6000 genes;80%;<i>SACCHAROMYCES CEREVISIAE</i> <i>AND SCHIZOSACCHAROMYCES POMBE</i>;activation;activity;approach;array-based approach;bioactive compounds;buffer one;chemical-genetic interaction profiles;combination;comparative analysis;complex multiple mutant backgrounds;COMPLEXES;conservation;corresponding double mutant;deletion;different genetic screens;distinguishing negative (synthetic lethal);double mutants;efficient approach;essential genes;evolution;exploration;expression;fission yeast Schizosaccharomyces pombe;fitness;fitness defects;GENE;general;genes;genetic interaction;genetic interaction profiles group genes;genetic interactions;Genetic networks;genome;genome-wide sets;global analysis;high-content screening systems;hypomorphic alleles;INHIBITORS;meiotic progeny;method;millions;mutants;MUTATIONS;networks;number;ordered array;ORDERED ARRAYS;positive (within pathway;potential;products;profile;providing another model system;quantitative measurement;query mutation;related;relevant pathways;repository;rich phenotypic signature;same essential pathway;screens;SGA system;single;specific reporters;suppression) interactions;synthetic genetic array (SGA) analysis;synthetic genetic interactions;synthetic lethal genetic interactions;systematic construction;TARGETS;two mutations leads;two single mutants;typical SGA screen;unexpected phenotype;use;years;yeast;yeast arrays;yeast genes);yeast genetic analysis;yeast Saccharomyces cerevisiae | Baryshnikova, A | ACTIVATION;DELETION;EXPLORATION;EXPRESSION;GENOME;INHIBITORS;NETWORKS;ORDERED ARRAYS;REPOSITORY;YEAST | 145 | [Baryshnikova, Anastasia; Costanzo, Michael; Vizeacoumar, Franco J.; Andrews, Brenda; Boone, Charles] Univ Toronto, Banting & Best Dept Med Res, Toronto, ON, Canada. [Baryshnikova, Anastasia; Costanzo, Michael; Vizeacoumar, Franco J.; Andrews, Brenda; Boone, Charles] Univ Toronto, Dept Mol Genet, Terrence Donnelly Ctr Cellular & Biomol Res, Toronto, ON, Canada. [Dixon, Scott] Columbia Univ, Dept Biol Sci, New York, NY 10027 USA. [Myers, Chad L.] Univ Minnesota Twin Cities, Dept Comp Sci & Engn, Minneapolis, MN USA. | null | 5000 viable gene deletion mutants (representing;6000 genes;80%;activity;approach;array-based approach;bioactive compounds;buffer one;chemical-genetic interaction profiles;combination;comparative analysis;complex multiple mutant backgrounds;complexes;conservation;corresponding double mutant;different genetic screens;distinguishing negative (synthetic lethal);double mutants;efficient approach;essential genes;evolution;fission yeast Schizosaccharomyces pombe;fitness;fitness defects;gene;general;genes;genetic interaction;genetic interaction profiles group genes;genetic interactions;genetic networks;genome-wide sets;global analysis;high-content screening systems;hypomorphic alleles;meiotic progeny;method;millions;mutants;mutations;number;ordered array;positive (within pathway;potential;products;profile;providing another model system;quantitative measurement;query mutation;related;relevant pathways;rich phenotypic signature;same essential pathway;screens;SGA system;single;specific reporters;suppression) interactions;synthetic genetic array (SGA) analysis;synthetic genetic interactions;synthetic lethal genetic interactions;systematic construction;targets;two mutations leads;two single mutants;typical SGA screen;unexpected phenotype;use;years;yeast arrays;yeast genes);yeast genetic analysis;yeast Saccharomyces cerevisiae | 10.1002/(SICI)1097-0061(199910)15:14<1541::AID-YEA476>3.0.CO;2-K;10.1002/yea.1130;10.1016/j.cell.2004.05.024;10.1016/j.cell.2004.06.013;10.1016/j.cell.2005.08.031;10.1016/j.cell.2005.12.036;10.1016/j.cub.2004.03.003;10.1016/j.febslet.2009.03.068;10.1016/j.molcel.2004.09.035;10.1016/j.molcel.2005.12.011;10.1016/j.molcel.2008.02.021;10.1016/j.molcel.2009.06.023;10.1038/37108;10.1038/6791;10.1038/msb4100034;10.1038/nature00935;10.1038/nature05649;10.1038/nature724;10.1038/nbt.1534;10.1038/nbt1096;10.1038/nbt919;10.1038/nbt924;10.1038/nchembio.2007.15;10.1038/ng1489;10.1038/ng1640;10.1038/ng1948;10.1038/ng1994;10.1038/NMETH1032;10.1038/NMETH1098;10.1038/nrg2085;10.1038/sj.emboj.7600684;10.1038/sj.emboj.7601847;10.1073/pnas.0710533105;10.1073/pnas.0712255105;10.1073/pnas.0806261105;10.1073/pnas.200346997;10.1083/jcb.200909013;10.1093/nar/28.24.e108;10.1101/gad.1362105;10.1101/gad.952302;10.1101/gr.1239303;10.1101/gr.6037607;10.1126/science.1061603;10.1126/science.1065810;10.1126/science.1091317;10.1126/science.1140324;10.1126/science.1150021;10.1126/science.1167983;10.1126/science.285.5429.901;10.1126/science.291.5506.1001;10.1146/annurev.genet.39.073003.114751;10.1158/1078-0432.CCR-06-0168;10.1186/1471-2164-7-187;10.1186/gb-2006-7-1-r6;10.1186/gb-2006-7-7-r63;10.1371/journal.pbio.0020379;10.1371/journal.pbio.0030128;10.1371/journal.pbio.0050254;10.1371/journal.pcbi.1000065;[10.1038/nmeth.1181, 10.1038/NMETH.1181] | Univ Toronto | Andrews, B;Baryshnikova, A;Boone, C;Costanzo, M;Dixon, S;Myers, C L;Vizeacoumar, F J | Baryshnikova, A: Univ Toronto, Banting & Best Dept Med Res, Toronto, ON, Canada | Vizeacoumar, Franco;Ｂｏｏｎｅ, Ｃｈａｒｌｅｓ | null | 68 | 978-0-12-375172-0 | Canada | Columbia Univ;Univ Minnesota Twin Cities;Univ Toronto | Baryshnikova, Anastasia | null | ACTIVATION;DELETION;EXPLORATION;EXPRESSION;GENOME;INHIBITORS;NETWORKS;ORDERED ARRAYS;REPOSITORY;YEAST | Baryshnikova, Anastasia; Costanzo, Michael; Dixon, Scott; Vizeacoumar, Franco J.; Myers, Chad L.; Andrews, Brenda; Boone, Charles; | null | Columbia Univ, Dept Biol Sci, New York, NY 10027 USA;Univ Minnesota Twin Cities, Dept Comp Sci & Engn, Minneapolis, MN USA;Univ Toronto, Banting & Best Dept Med Res, Toronto, ON, Canada;Univ Toronto, Dept Mol Genet, Terrence Donnelly Ctr Cellular & Biomol Res, Toronto, ON, Canada | Columbia Univ, Dept Biol Sci, New York, NY 10027 USA;Univ Minnesota Twin Cities, Dept Comp Sci & Engn, Minneapolis, MN USA;Univ Toronto, Banting & Best Dept Med Res, Toronto, ON, Canada;Univ Toronto, Dept Mol Genet, Terrence Donnelly Ctr Cellular & Biomol Res, Toronto, ON, Canada | null | null | null | 1957;1968;1997;1999;2000;2001;2002;2003;2004;2005;2006;2007;2008;2009;2010 | 130 | Univ Toronto, Banting & Best Dept Med Res, Toronto, ON, Canada | Methods Enzymol. | Boone, Charles | ELSEVIER ACADEMIC PRESS INC | (representing;(SGA);(synthetic;(within;,;5000;6000;80%;a;activity;adapted;all;alleles;also;an;analysis;and;another;approach;are;array;array-based;arrays;automates;backgrounds;be;been;bioactive;both;Buffer;can;carrying;cerevisiae;chemical-genetic;clustering;combination;combined;comparative;comparison;complex;complexes;compounds;conditional;conservation;construction;containing;corresponding;crossed;defects;deletion;developed;different;distinguishing;double;each;easily;efficient;enables;essential;estimating;evolution;extended;extensively;finally;fission;fitness;for;functionally;gene;general;genes;genes);genetic;genome-wide;global;group;harboring;have;high-content;hypomorphic;identify;impinge;in;interaction;interactions;into;is;leads;lethal;lethal);link;measurement;meiotic;method;millions;model;more;multiple;mutant;mutants;mutation;mutations;negative;networks;number;occurs;of;offers;often;on;one;or;ordered;over;particular;pathway;pathways;phenotype;phenotypic;pombe;positive;potential;products;profile;profiles;progeny;providing;quantify;quantitative;query;related;relevant;reporters;represents;rich;Saccharomyces;same;Schizosaccharomyces;scored;screen;screening;screens;sets;SGA;signature;similar;single;specific;such;suppression);synthetic;system;systematic;systems;targets;termed;testing;that;the;their;this;through;to;two;typical;unexpected;use;used;viable;we;when;which;whose;with;years;yeast | Univ Toronto | A genetic interaction occurs when the combination of two mutations leads to an unexpected phenotype. Screens for synthetic genetic interactions have been used extensively to identify genes whose products are functionally related. In particular, synthetic lethal genetic interactions often identify genes that buffer one another or impinge on the same essential pathway. For the yeast Saccharomyces cerevisiae, we developed a method termed synthetic genetic array (SGA) analysis, which offers an efficient approach for the systematic construction of double mutants and enables a global analysis of synthetic genetic interactions. In a typical SGA screen, a query mutation is crossed to an ordered array of similar to 5000 viable gene deletion mutants (representing similar to 80% of all yeast genes) such that meiotic progeny harboring both mutations can be scored for fitness defects. This approach can be extended to all similar to 6000 genes through the use of yeast arrays containing mutants carrying conditional or hypomorphic alleles of essential genes. Estimating the fitness for the two single mutants and their corresponding double mutant enables a quantitative measurement of genetic interactions, distinguishing negative (synthetic lethal) and positive (within pathway and suppression) interactions. The profile of genetic interactions represents a rich phenotypic signature for each gene and clustering genetic interaction profiles group genes into functionally relevant pathways and complexes. This array-based approach automates yeast genetic analysis in general and can be easily adapted for a number of different genetic screens or combined with high-content screening systems to quantify the activity of specific reporters in genome-wide sets of single or more complex multiple mutant backgrounds. Comparison of genetic and chemical-genetic interaction profiles offers the potential to link bioactive compounds to their targets. Finally, we also developed an SGA system for the fission yeast Schizosaccharomyces pombe, providing another model system for comparative analysis of genetic networks and testing the conservation of genetic networks over millions of years of evolution. | GLS-7161-2022;IQX-0075-2023 | ACTIVATION;DELETION;EXPLORATION;EXPRESSION;GENOME;INHIBITOR;NETWORKS;ORDERED ARRAYS;REPOSITORY;YEAST | 0 | null | null | 35 | YEAST;ACTIVATION;DELETION;EXPLORATION;EXPRESSION;GENOME;INHIBITOR;NETWORKS;ORDERED ARRAYS;REPOSITORY | WOS:000275827900007 | Columbia Univ, New York, NY USA;Univ Minnesota Twin Cities, Minneapolis, MN USA;Univ Toronto, Toronto ON, Canada | Canada;USA | 2,010 | null | 0000-0002-0123-2052 | null | Fink, GR;Guthrie, C;Weissman, J | English | null | ANNU REV GENET;BMC GENOMICS;CELL;CLIN CANCER RES;CURR BIOL;CURR TOP MICROBIOL;EMBO J;FEBS LETT;GENE DEV;GENETICS;GENOME BIOL;GENOME RES;J CELL BIOL;METHODS MOL BIOL;MOL CELL;MOL SYST BIOL;NAT BIOTECHNOL;NAT CHEM BIOL;NAT GENET;NAT METHODS;NAT REV GENET;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PLOS BIOL;PLOS COMPUT BIOL;REPORTS EVOLUTION CO;SCIENCE;STRATEGY GENE;YEAST | Andrews, Brenda;Baryshnikova, Anastasia;Boone, Charles;Costanzo, Michael;Dixon, Scott;Myers, Chad L;Vizeacoumar, Franco J | 2024-03-11
ER | Aravind, L;Bader, J S;Bakal, C;Bandyopadhyay, S;Bateson, W R S;Ben-Aroya, S;Boone, C;Carpenter, A E;Chang, M;Cheng, T H;Collins, S R;Corcoran, L J;Costanzo, M;Davierwala, A P;Decourty, L;Dixon, S J;Eggert, U S;Elena, S F;Fay, D S;Fillingham, J;Gelperin, D M;Giaever, G;Goldstein, A L;Gururaja, T L;Hartman, J L;Hillenmeyer, M E;Ho, C H;Hu, Y H;Jones, G M;Jonikas, M C;Jorgensen, P;Kelley, R;Kim, S K;Koh;Levy, S;Loo, L H;Lucchesi, J C;Mani, R;Menne, T F;Mnaimneh, S;Myers, C L;Narayanaswamy, R;Pan, X W;Parsons, A B;Roguev, A;Schuldiner, M;Segrè, D;Shannon, P;Sheff, M A;Sopko, R;St Onge, R P;Tanaka, M;Tong Amy Hin Yan;Tong, A H Y;Vizeacoumar, F J;Waddington Ch.;White, S A;Winzeler, E A;Wood, V;Ye, P | BNX73 | Toronto ON, Canada | 175 | null | 3 | null | 20,946,810 | Andrews, Brenda;Baryshnikova, Anastasia;Boone, Charles;Costanzo, Michael;Dixon, Scott;Myers, Chad L;Vizeacoumar, Franco J | METHOD ENZYMOL | Minneapolis, MN USA;New York, NY USA;Toronto ON, Canada |
Patole, M S;Rao, M;Umasankar, P K;Vathipadiekal, V | 10.1016/j.peptides.2009.09.034 | null | STE 800, 230 PARK AVE, NEW YORK, NY 10169 USA | 1511e1x4js3l3t32x6rcy6e3l182w61s68 | Molecular cloning, over expression, and activity studies of a peptidic HIV-1 protease inhibitor: Designed synthetic gene to functional recombinant peptide | Natl Chem Lab | null | Rao, M (corresponding author), Natl Chem Lab, Div Biochem Sci, Pune 411008, Maharashtra, India. | null | Patole, Milind S;Rao, Mala;Umasankar, Perunthottathu K;Vathipadiekal, Vinod | Biochemistry & Molecular Biology;Endocrinology & Metabolism;Pharmacology & Pharmacy | Department of Biotechnology (Govt. of India); CSIR Emeritus Scientist Scheme (Govt. of India); UGC | WOS | Rao, M | Natl Chem Lab, Maharashtra, India;Natl Ctr Cell Sci, Maharashtra, India | 31 | ,;:;a;activity;and;cloning;designed;expression;functional;gene;HIV-1;inhibitor;molecular;of;over;peptide;peptidic;protease;recombinant;studies;synthetic;to | 1 | /0000-0002-8181-6890;Umasankar, Perunthottathu | ELSEVIER SCIENCE INC | Natl Chem Lab, Div Biochem Sci, Pune 411008, Maharashtra, India;Natl Ctr Cell Sci, Mol Biol Unit, Pune 411007, Maharashtra, India | Article | Natl Chem Lab | NEW YORK | null | null | Natl Chem Lab;Natl Ctr Cell Sci | CSIR Emeritus Scientist Scheme (Govt. of India);Department of Biotechnology (Govt. of India);UGC | Rao, M (corresponding author), Natl Chem Lab, Div Biochem Sci, Pune 411008, Maharashtra, India. | 21 | Patole, Milind S;Rao, Mala;Umasankar, Perunthottathu K;Vathipadiekal, Vinod | 13 | 2 | 274,375,500,003 | CSIR Emeritus Scientist Scheme (Govt. of India);Department of Biotechnology (Govt. of India);UGC | India | PEPTIDES | India | null | null | Natl Chem Lab, Div Biochem Sci, Pune 411008, Maharashtra, India | 0196-9781 | Patole, M S;Rao, M;Umasankar, P K;Vathipadiekal, V | JAN | mb.rao@ncl.res.in | activity studies;Designed synthetic gene;expression;functional recombinant peptide;peptidic HIV-1 protease inhibitor | 4 | J | Biochemistry & Molecular Biology;Endocrinology & Metabolism;Pharmacology & Pharmacy | 1186 Da;active;activity studies;amino acids present;arabinose;aspartic protease inhibitor (ATBI);ASPARTIC PROTEINASE;ATBI;ATBI molecule;Bacillus sp;C 2009 Elsevier Inc;CATHEPSIN-D INHIBITOR;complementary oligonucleotides;designed synthetic gene;E. coli BL21-A1 cells;eleven amino acids;Escherichia coli;expression;EXTREMOPHILIC BACILLUS SP;Factor Xa;functional recombinant peptide;fungal aspartic protease;Gateway cloning;GENE;glutathione-S-transferase (GST);GST tag;HIV-1 protease;homogeneity;in-frame;INHIBITOR;KINETIC-PARAMETERS;mass spectroscopy analysis;molecular weight;nature;NEUROTOXIN;PEPSIN;peptide sequence data;peptidic;peptidic HIV-1 protease inhibitor;pharmaceutically important peptide molecules;potent inhibitor;Proteases;protocol;PURIFICATION;purification Protocol;purified peptide;recombinant HIV-1 protease;recombinant peptide;reduced glutathione column;resultant product;resulting fusion protein;rights reserved;RP-HPLC;several proteases;study;synthetic gene;synthetic gene coding;theoretical molecular weight;vitro;XYLANASE | Vathipadiekal, V | ASPARTIC PROTEINASE;CATHEPSIN-D INHIBITOR;EXTREMOPHILIC BACILLUS SP;Gateway cloning;HIV-1 protease;INHIBITOR;KINETIC-PARAMETERS;NEUROTOXIN;PEPSIN;Proteases;PURIFICATION;Synthetic gene;XYLANASE | 16 | [Vathipadiekal, Vinod; Rao, Mala] Natl Chem Lab, Div Biochem Sci, Pune 411008, Maharashtra, India. [Umasankar, Perunthottathu K.; Patole, Milind S.] Natl Ctr Cell Sci, Mol Biol Unit, Pune 411007, Maharashtra, India. | The authors thank Dr. Callum Sloss, Harvard Medical School, Boston, MA for the critical reading of the manuscript. The authors acknowledge Dr. Mahesh. J. Kulkarni, NCL and Badrinarayanan Natarajan NCCS for their help in few experiments. Dr. Mala Rao acknowledges Department of Biotechnology (Govt. of India) and CSIR Emeritus Scientist Scheme (Govt. of India) for financial support. VV and PKU acknowledge the research fellowships from UGC and CSIR resp. from Govt. of India. | 1186 Da;active;amino acids present;arabinose;aspartic protease inhibitor (ATBI);ATBI;ATBI molecule;Bacillus sp;complementary oligonucleotides;E. coli BL21-A1 cells;eleven amino acids;Escherichia coli;expression;Factor Xa;fungal aspartic protease;gene;glutathione-S-transferase (GST);GST tag;HIV-1 protease;homogeneity;in-frame;mass spectroscopy analysis;molecular weight;nature;pepsin;peptide sequence data;peptidic;pharmaceutically important peptide molecules;potent inhibitor;protocol;purification Protocol;purified peptide;recombinant HIV-1 protease;recombinant peptide;reduced glutathione column;resultant product;resulting fusion protein;RP-HPLC;several proteases;study;synthetic gene;synthetic gene coding;theoretical molecular weight;vitro | 10.1016/0006-291X(90)91412-L;10.1016/0014-5793(89)81435-8;10.1016/0014-5793(91)80558-K;10.1016/0378-1119(88)90005-4;10.1016/0378-1119(93)90168-3;10.1016/0958-1669(95)80085-9;10.1016/j.bbrc.2005.06.029;10.1016/j.ibmb.2009.03.005;10.1016/j.molbiopara.2005.01.018;10.1016/S0041-0101(99)00123-3;10.1016/S0167-4838(02)00206-6;10.1016/S0168-1656(00)00213-3;10.1016/S1046-5928(03)00170-0;10.1021/bi010594y;10.1038/77950;10.1038/nbt0196-28;10.1046/j.1432-1327.1998.2530804.x;10.1046/j.1432-1327.1998.2540160.x;10.1074/jbc.274.2.563;10.1074/jbc.M005662200;10.1074/jbc.M008520200;10.1074/jbc.M111250200;10.1128/AAC.37.8.1614;10.1128/AAC.45.7.2008-2017.2001;10.1135/cccc19760489 | Natl Chem Lab | Patole, M S;Rao, M;Umasankar, P K;Vathipadiekal, V | Vathipadiekal, V: Natl Chem Lab, Div Biochem Sci, Pune 411008, Maharashtra, India | null | null | 33 | null | India | Natl Chem Lab;Natl Ctr Cell Sci | Vathipadiekal, Vinod | null | ASPARTIC PROTEINASE;CATHEPSIN-D INHIBITOR;EXTREMOPHILIC BACILLUS SP;KINETIC-PARAMETERS;NEUROTOXIN;PEPSIN;PURIFICATION;XYLANASE | Vathipadiekal, Vinod; Umasankar, Perunthottathu K.; Patole, Milind S.; Rao, Mala; | null | Natl Chem Lab, Div Biochem Sci, Pune 411008, Maharashtra, India;Natl Ctr Cell Sci, Mol Biol Unit, Pune 411007, Maharashtra, India | Natl Chem Lab, Div Biochem Sci, Pune 411008, Maharashtra, India;Natl Ctr Cell Sci, Mol Biol Unit, Pune 411007, Maharashtra, India | 1873-5169 | Gateway cloning;HIV-1 protease;Inhibitor;protease;Synthetic gene | 1 | 1974;1976;1988;1989;1990;1991;1993;1995;1996;1998;1999;2000;2001;2002;2003;2005;2009 | 4 | Natl Chem Lab, Div Biochem Sci, Pune 411008, Maharashtra, India | Peptides | Rao, Mala | ELSEVIER SCIENCE INC | (ATBI);(GST);,;1186;a;acids;active;against;amino;analysis;and;annealed;arabinose;aspartic;ATBI;Bacillus;be;BL21-A1;cells;cleaved;clone;cloned;cloning;coding;coli;column;complementary;consists;Da;data;described;E.;eleven;Escherichia;establish;expression;factor;for;found;from;fungal;further;fusion;gene;glutathione;glutathione-S-transferase;GST;had;HIV-1;homogeneity;important;in;in-frame;including;induced;inhibitor;is;mass;matches;may;molecular;molecule;molecules;nature;of;oligonucleotides;over;pepsin;peptide;peptidic;pharmaceutically;potent;present;product;protease;proteases;protein;protocol;purification;purified;recombinant;reduced;remove;report;resultant;resulting;revealed;RP-HPLC;sequence;several;sp;spectroscopy;study;subsequently;synthesize;synthetic;tag;that;the;theoretical;this;to;used;using;vitro;was;we;weight;were;which;with;Xa | Natl Chem Lab | The aspartic protease inhibitor (ATBI) purified from a Bacillus sp. is a potent inhibitor of several proteases including recombinant HIV-1 protease, pepsin, and fungal aspartic protease. In this study, we report the cloning, and over expression of a synthetic gene coding for ATBI in Escherichia coli and establish a purification Protocol. The ATBI molecule consists of eleven amino acids and is peptidic in nature. We used the peptide sequence data of ATBI to synthesize complementary oligonucleotides, which were annealed and subsequently cloned in-frame with the gene for glutathione-S-transferase (GST). The expression of the resulting fusion protein was induced in E. coli BL21-A1 cells using arabinose. The recombinant peptide was Purified using a reduced glutathione column, and cleaved with Factor Xa to remove the GST tag. The resultant product was further purified to homogeneity using RP-HPLC. Mass spectroscopy analysis revealed that the purified peptide had a molecular weight of 1186 Da which matches the theoretical molecular weight of the amino acids present in the synthetic gene. The recombinant peptide was found to be active in vitro against HIV-1 protease, pepsin, and fungal aspartic protease. The protocol described in this study may be used to clone pharmaceutically important peptide molecules. | null | ASPARTIC PROTEINASE;CATHEPSIN-D INHIBITOR;EXTREMOPHILIC BACILLUS SP;KINETIC-PARAMETERS;NEUROTOXIN;PEPSIN;PURIFICATION;XYLANASE | 0 | null | Gateway cloning;HIV-1 protease;Inhibitor;Proteases;Synthetic gene | 6 | ASPARTIC PROTEINASE;CATHEPSIN-D INHIBITOR;EXTREMOPHILIC BACILLUS SP;Gateway cloning;HIV-1 protease;INHIBITOR;kinetic parameters;NEUROTOXIN;PEPSIN;PROTEASE;PURIFICATION;Synthetic gene;XYLANASE | WOS:000274375500003 | Natl Chem Lab, Maharashtra, India;Natl Ctr Cell Sci, Maharashtra, India | India | 2,010 | null | 0000-0001-5548-1022;0000-0002-8181-6890 | null | null | English | null | Angers;ANTIMICROB AGENTS CH;ASPARTIC PROTEINASES;BBA-PROTEIN STRUCT M;BIO-TECHNOL;BIOCHEM BIOPH RES CO;BIOCHEMISTRY-US;COLLECT CZECH CHEM C;CURR OPIN BIOTECH;EUR J BIOCHEM;FEBS LETT;GENE;INSECT BIOCHEM MOLEC;J BIOL CHEM;J BIOTECHNOL;MOL BIOCHEM PARASIT;NAT STRUCT BIOL;PROTEASES INFECT AGE;PROTEIN EXPRES PURIF;TOXICON | Patole, Milind S;Rao, Mala;Umasankar, Perunthottathu K;Vathipadiekal, Vinod | 2024-03-11
ER | Abuerreish, G M;Brandwijk Rjmge;Breugelmans, B;Callaway, J E;Cater, S A;Christeller, J T;Dash, C;De Maere, V;Galleschi L.;Gavit, P;Georgiou George;Howell, M L;James, M N G;Kageyama, T;Keilova, H;Kelley, W S;Lenarcic, B;Li, M;Mares, M;Ng, K K S;Phylip, L H;Piers, K L;Richards, A D;Rudolph Rainer;Schu, P;Simonet, G;Smith, D B;Stewart K.W.;Wong, S L | 553OA | Maharashtra, India | 4 | null | 2 | null | 19,818,820 | Patole, Milind S;Rao, Mala;Umasankar, Perunthottathu K;Vathipadiekal, Vinod | PEPTIDES | Maharashtra, India |
Krainer, A R;Lin, K T | 10.1093/bioinformatics/btz438 | null | GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND | ty5m35541b531it2y9274t1p4a4v1sn5xj | PSI-Sigma: a comprehensive splicing-detection method for short-read and long-read RNA-seq analysis | Cold Spring Harbor Lab | null | Krainer, AR (corresponding author), Cold Spring Harbor Lab, POB 100, Cold Spring Harbor, NY 11724 USA. | null | Krainer, Adrian R;Lin, Kuan-Ting | Biochemical Research Methods;Biotechnology & Applied Microbiology;Computer Science, Interdisciplinary Applications;Mathematical & Computational Biology;Statistics & Probability | National Cancer Institute [CA13106]; National Cancer Institute Cancer Center Support Grant [5P30CA045508] | WOS | Krainer, A R | Cold Spring Harbor Lab, Cold Spring Harbor, NY USA | 35 | :;a;Analysis;and;comprehensive;for;long-read;method;PSI-Sigma;RNA-seq;short-read;splicing-detection | 1 | Lin, Kuan-Ting | OXFORD UNIV PRESS | Cold Spring Harbor Lab, POB 100, Cold Spring Harbor, NY 11724 USA | Article | Cold Spring Harbor Lab | OXFORD | null | null | Cold Spring Harbor Lab | National Cancer Institute;National Cancer Institute Cancer Center Support Grant | Krainer, AR (corresponding author), Cold Spring Harbor Lab, POB 100, Cold Spring Harbor, NY 11724 USA. | 5054 | Krainer, Adrian R;Lin, Kuan-Ting | 19 | 1 | 506,808,900,023 | National Cancer Institute [CA13106];National Cancer Institute Cancer Center Support Grant [5P30CA045508] | USA | BIOINFORMATICS | USA | null | null | Cold Spring Harbor Lab, POB 100, Cold Spring Harbor, NY 11724 USA | 1367-4803 | Krainer, A R;Lin, K T | DEC 1 | krainer@cshl.edu | comprehensive splicing-detection method;long-read RNA-seq analysis;PSI-Sigma;short-read | 2 | J | Biochemistry & Molecular Biology;Biotechnology & Applied Microbiology;Computer Science;Mathematical & Computational Biology;Mathematics | alternative pre-mRNA splicing (AS) changes;benchmark;case;comprehensive splicing-detection method;correlation);developed PSI-Sigma;employed actual (non-simulated) RNA-seq data;events;expression;false positive rate;human RNAs;intron-retention events;long-read RNA-seq analysis;MESSENGER-RNA;mixture;motivation;multiple alternative exons;nanopore long-read sequencers;new PSI index;Percent Spliced-In (PSI) values;performance (i.e;precision;previous PSI-detection tools;PSI-Sigma;PSI-Sigma outperformed;recall;results;RNA Sequins;short-read;silico RNA-seq data;specific;SUPPA2;synthetic genes (RNA Sequins);three leading tools (rMATS;tools;Whippet) | Lin, K T | EXPRESSION;MESSENGER-RNA | 5048 | [Lin, Kuan-Ting; Krainer, Adrian R.] Cold Spring Harbor Lab, POB 100, Cold Spring Harbor, NY 11724 USA. | This work was supported by National Cancer Institute [grant number CA13106]. We acknowledge assistance from the CSHL Shared Resources, funded in part by National Cancer Institute Cancer Center Support Grant [grant number 5P30CA045508]. | alternative pre-mRNA splicing (AS) changes;benchmark;case;correlation);developed PSI-Sigma;employed actual (non-simulated) RNA-seq data;events;false positive rate;human RNAs;intron-retention events;long-read RNA-seq analysis;mixture;motivation;multiple alternative exons;nanopore long-read sequencers;new PSI index;Percent Spliced-In (PSI) values;performance (i.e;precision;previous PSI-detection tools;PSI-Sigma outperformed;recall;results;RNA Sequins;silico RNA-seq data;specific;SUPPA2;synthetic genes (RNA Sequins);three leading tools (rMATS;tools;Whippet) | 10.1002/jcb.26636;10.1016/j.molcel.2018.08.018;10.1038/ncomms16027;10.1038/ncomms9768;10.1038/ng.2653;10.1038/NMETH.1528;10.1038/nrneurol.2017.148;10.1038/nsmb.1750;10.1073/pnas.1419161111;10.1073/pnas.1806018115;10.1093/bib/bbs017;10.1093/bioinformatics/bti310;10.1093/bioinformatics/bts635;10.1093/emboj/20.7.1785;10.1101/gr.227181.117;10.1128/MCB.00070-15;10.1186/s13059-018-1417-1;10.1210/jc.84.3.1149;10.7554/eLife.11752;[10.1038/nmeth.3958, 10.1038/NMETH.3958];[10.1038/nmeth.4577, 10.1038/NMETH.4577] | Cold Spring Harbor Lab | Krainer, A R;Lin, K T | Lin, K T: Cold Spring Harbor Lab, POB 100, Cold Spring Harbor, NY 11724 USA | null | 5P30CA045508;CA13106 | 21 | null | USA | Cold Spring Harbor Lab | Lin, Kuan-Ting | Green Published | EXPRESSION;MESSENGER-RNA | Lin, Kuan-Ting; Krainer, Adrian R.; | null | Cold Spring Harbor Lab, POB 100, Cold Spring Harbor, NY 11724 USA | Cold Spring Harbor Lab, POB 100, Cold Spring Harbor, NY 11724 USA | 1460-2059 | null | 23 | 1999;2001;2005;2010;2013;2014;2015;2016;2017;2018 | 24 | Cold Spring Harbor Lab, POB 100, Cold Spring Harbor, NY 11724 USA | Bioinformatics | Krainer, Adrian R | OXFORD UNIV PRESS | (AS);(i.e;(non-simulated);(PSI);(rMATS;(RNA;,;:;a;actual;also;alternative;analysis;and;are;as;benchmark;briefly;by;case;changes;commonly;comparison;correlation);data;developed;employed;especially;evaluated;events;exons;false;from;genes;human;in;index;intron-retention;its;leading;limited;long-read;mixture;motivation;multiple;nanopore;new;of;outperformed;Percent;performance;positive;pre-mRNA;precision;previous;PSI;PSI-detection;PSI-Sigma;rate;recall;report;results;RNA;RNA-seq;RNAs;sequencers;sequencing;Sequins;Sequins);silico;specific;spliced;Spliced-In;splicing;SUPPA2;synthetic;the;these;three;to;tools;used;uses;values;we;were;which;Whippet);with | Cold Spring Harbor Lab | Motivation: Percent Spliced-In (PSI) values are commonly used to report alternative pre-mRNA splicing (AS) changes. Previous PSI-detection tools were limited to specific AS events and were evaluated by in silico RNA-seq data. We developed PSI-Sigma, which uses a new PSI index, and we employed actual (non-simulated) RNA-seq data from spliced synthetic genes (RNA Sequins) to benchmark its performance (i.e. precision, recall, false positive rate and correlation) in comparison with three leading tools (rMATS, SUPPA2 and Whippet). Results: PSI-Sigma outperformed these tools, especially in the case of AS events with multiple alternative exons and intron-retention events. We also briefly evaluated its performance in long-read RNA-seq analysis, by sequencing a mixture of human RNAs and RNA Sequins with nanopore long-read sequencers. | null | EXPRESSION;MESSENGER-RNA | 4 | null | null | 7 | EXPRESSION;MESSENGER-RNA | WOS:000506808900023 | Cold Spring Harbor Lab, Cold Spring Harbor, NY USA | USA | 2,019 | null | 0000-0003-1294-1142 | null | null | English | null | BIOINFORMATICS;BRIEF BIOINFORM;ELIFE;EMBO J;GENOME BIOL;GENOME RES;J CELL BIOCHEM;J CLIN ENDOCR METAB;MOL CELL;MOL CELL BIOL;NAT COMMUN;NAT GENET;NAT METHODS;NAT REV NEUROL;NAT STRUCT MOL BIOL;P NATL ACAD SCI USA | Krainer, Adrian R;Lin, Kuan-Ting | 2024-03-11
ER | Bergeron, D;Bhate, A;Byrne, A;Dobin, A;Garalde, D R;Hardwick, S A;Katz, Y;Lin, K T;Lonsdale, J;Manukyan, A;Prezant, T R;Rinaldi, C;Shen, S H;Sterne-Weiler, T;Sun, S Y;Sureau, A;Thorvaldsdóttir, H;Trincado, J L;Vaquero-Garcia, J;Wang, Q Q;Wu, T D | KB9LO | Cold Spring Harbor, NY USA | 25 | null | 1 | null | 31,135,034 | Krainer, Adrian R;Lin, Kuan-Ting | BIOINFORMATICS | Cold Spring Harbor, NY USA |
Ahyudanari, R R;Fadhlillah, M;Kusuma, S A F;Parwati, I;Rostinawati, T;Rukayadi, Y;Subroto, T;Yusuf, M | 10.1016/j.heliyon.2019.e02741 | e02741 | THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, OXON, ENGLAND | 5x1d5t1q25z1y1v6w332c3o542w3k376h35263m | Optimization of culture conditions for <i>Mpt64</i> synthetic gene expression in <i>Escherichia coli</i> BL21 (DE3) using surface response methodology | Univ Padjadjaran | null | Subroto, T (corresponding author), Univ Padjadjaran, Fac Math & Nat Sci, Dept Chem, Sumedang, Indonesia.;Subroto, T (corresponding author), Univ Padjadjaran, Res Ctr Mol Biotechnol & Bioinformat, Bandung, Indonesia. | null | Ahyudanari, Risa R;Fadhlillah, Muhammad;Kusuma, Sri Agung Fitri;Parwati, Ida;Rostinawati, Tina;Rukayadi, Yaya;Subroto, Toto;Yusuf, Muhammad | Multidisciplinary Sciences | DIKTI (Directorate General of Higher Education of Indonesia); Universitas Padjadjaran through ALG (Academic Leadership Grant) | WOS | Subroto, T | PT Genpro Multiguna Sejahtera, Sumedang, Indonesia;Univ Padjadjaran, Bandung, Indonesia;Univ Padjadjaran, Sumedang, Indonesia;Univ Padjadjaran, West Java, Indonesia;Univ Putra Malaysia, Serdang, Malaysia | 5 | (DE3);<i>Escherichia;<i>Mpt64</i>;BL21;coli</i>;conditions;culture;expression;for;gene;in;methodology;of;optimization;response;surface;synthetic;using | 2 | Fadhlillah, Muhammad;Kusuma, Sri Agung Fitri;Parwati, Ida;Rostinawati, Tina;Subroto, Toto;Yusuf, Muhammad | ELSEVIER SCI LTD | PT Genpro Multiguna Sejahtera, Sumedang, Indonesia;Univ Padjadjaran, Fac Math & Nat Sci, Dept Chem, Sumedang, Indonesia;Univ Padjadjaran, Fac Math & Nat Sci, Dept Chem, Sumedang, Indonesia.; Subroto, T (corresponding author), Univ Padjadjaran, Res Ctr Mol Biotechnol & Bioinformat, Bandung, Indonesia;Univ Padjadjaran, Fac Med, Dept Clin Pathol, Bandung, Indonesia;Univ Padjadjaran, Fac Pharm, Dept Biol Pharm, Sumedang, West Java, Indonesia;Univ Padjadjaran, Res Ctr Mol Biotechnol & Bioinformat, Bandung, Indonesia;Univ Putra Malaysia, Fac Food Sci & Technol, Dept Food Sci, Serdang, Malaysia | Article | Univ Padjadjaran | OXFORD | null | null | PT Genpro Multiguna Sejahtera;Univ Padjadjaran;Univ Putra Malaysia | DIKTI (Directorate General of Higher Education of Indonesia);Universitas Padjadjaran through ALG (Academic Leadership Grant) | Subroto, T (corresponding author), Univ Padjadjaran, Fac Math & Nat Sci, Dept Chem, Sumedang, Indonesia.; Subroto, T (corresponding author), Univ Padjadjaran, Res Ctr Mol Biotechnol & Bioinformat, Bandung, Indonesia. | null | Ahyudanari, Risa R;Fadhlillah, Muhammad;Kusuma, Sri Agung Fitri;Parwati, Ida;Rostinawati, Tina;Rukayadi, Yaya;Subroto, Toto;Yusuf, Muhammad | 9 | 6 | 500,530,100,032 | DIKTI (Directorate General of Higher Education of Indonesia);Universitas Padjadjaran through ALG (Academic Leadership Grant) | Indonesia;Malaysia | HELIYON | Indonesia;Indonesia.; | null | null | Univ Padjadjaran, Fac Math & Nat Sci, Dept Chem, Sumedang, Indonesia | null | Ahyudanari, R R;Fadhlillah, M;Kusuma, S A F;Parwati, I;Rostinawati, T;Rukayadi, Y;Subroto, T;Yusuf, M | NOV | t.subroto@unpad.ac.id | <i>Escherichia coli</i> BL21 (DE3);<i>Mpt64</i> synthetic gene expression;culture conditions;optimization;surface response methodology | 8 | J | Science & Technology - Other Topics | 0.0311 mg/mL;0.0392 mg/mL;15 treatments;4 mM rhamnose;5 h;<i>Escherichia coli</i> BL21 (DE3);<i>Mpt64</i> synthetic gene expression;accordance;ASSAY;average concentration;Box-Behnken design;CELL-DENSITY CULTIVATION;conclusion;confirmation;culture conditions;cytoplasm;Diagnosis;different cultivation conditions (medium concentration;E. coli BL21 (DE3);E. coli cell;Environmental science;Escherichia coli BL21 (DE3);expression methods;factorial Box-Bhenken;flask scale fermentation;IDENTIFICATION;ImageJ program;inducer concentration);induction;induction time;infection;medium;Microbiology;Minicab 17 statistical software;MPT64;MPT64 gene expression;MPT64 protein;MPT64 synthetic gene expression;Mycobacterium tuberculosis complex (MTBC);MYCOBACTERIUM-TUBERCULOSIS COMPLEX;optimization;optimum conditions;optimum culture conditions;predetermined design;predicted concentration;PROTEIN-PRODUCTION;randomized combination;recombinant MPT64;relationship;response surface methodology;response surface methodology (RSM);Rhamnose;RSM;secretion;selected optimization parameters;sodium chloride 20 mg/mL);sodium dodecyl sulfate polyacrilamide electrophoresis (SDS-PAGE);specific protein;study;surface response methodology;three center point repetitions;two-fold medium concentration (tryptone 20 mg/mL;yeast extract 10 mg/mL | Kusuma, S A F | ASSAY;Box-Behnken design;CELL-DENSITY CULTIVATION;CONFIRMATION;DIAGNOSIS;Environmental science;IDENTIFICATION;INDUCTION;INFECTION;Medium;Microbiology;MPT64;MYCOBACTERIUM-TUBERCULOSIS COMPLEX;PROTEIN-PRODUCTION;Response surface methodology;Rhamnose;SECRETION | null | [Kusuma, Sri Agung Fitri; Yusuf, Muhammad; Fadhlillah, Muhammad; Ahyudanari, Risa R.; Subroto, Toto] Univ Padjadjaran, Fac Math & Nat Sci, Dept Chem, Sumedang, Indonesia. [Kusuma, Sri Agung Fitri; Rostinawati, Tina] Univ Padjadjaran, Fac Pharm, Dept Biol Pharm, Sumedang, West Java, Indonesia. [Parwati, Ida] Univ Padjadjaran, Fac Med, Dept Clin Pathol, Bandung, Indonesia. [Rukayadi, Yaya] Univ Putra Malaysia, Fac Food Sci & Technol, Dept Food Sci, Serdang, Malaysia. [Yusuf, Muhammad; Fadhlillah, Muhammad; Subroto, Toto] Univ Padjadjaran, Res Ctr Mol Biotechnol & Bioinformat, Bandung, Indonesia. [Fadhlillah, Muhammad] PT Genpro Multiguna Sejahtera, Sumedang, Indonesia. | This work was supported by DIKTI (Directorate General of Higher Education of Indonesia) and Universitas Padjadjaran through ALG (Academic Leadership Grant). | 0.0311 mg/mL;0.0392 mg/mL;15 treatments;4 mM rhamnose;5 h;accordance;average concentration;conclusion;culture conditions;cytoplasm;different cultivation conditions (medium concentration;E. coli BL21 (DE3);E. coli cell;Escherichia coli BL21 (DE3);expression methods;factorial Box-Bhenken;flask scale fermentation;ImageJ program;inducer concentration);induction time;Minicab 17 statistical software;MPT64;MPT64 gene expression;MPT64 protein;MPT64 synthetic gene expression;Mycobacterium tuberculosis complex (MTBC);optimum conditions;optimum culture conditions;predetermined design;predicted concentration;randomized combination;recombinant MPT64;relationship;response surface methodology (RSM);RSM;selected optimization parameters;sodium chloride 20 mg/mL);sodium dodecyl sulfate polyacrilamide electrophoresis (SDS-PAGE);specific protein;study;three center point repetitions;two-fold medium concentration (tryptone 20 mg/mL;yeast extract 10 mg/mL | 10.1002/bit.10034;10.1007/BF00128620;10.1007/BF01569997;10.1007/s002530050009;10.1007/s002530051411;10.1016/0168-1656(94)00143-Z;10.1016/j.aca.2007.07.011;10.1016/j.bej.2008.09.013;10.1016/j.bioeng.2006.10.001;10.1016/j.biotechadv.2004.11.003;10.1016/j.jtbi.2006.08.017;10.1016/j.molcatb.2010.12.012;10.1016/j.pep.2014.05.012;10.1016/S1004-9541(08)60334-1;10.1128/CMR.9.2.177;10.1128/JCM.03043-15;10.1128/JCM.37.11.3693-3697.1999;10.1128/JCM.37.6.2007-2009.1999;10.1128/JCM.40.3.908-912.2002;10.1186/s12985-018-1000-0;10.1590/S0074-02762011000600022;10.5812/jjm.8(4)2015.16236 | Univ Padjadjaran | Ahyudanari, R R;Fadhlillah, M;Kusuma, S A F;Parwati, I;Rostinawati, T;Rukayadi, Y;Subroto, T;Yusuf, M | Kusuma, S A F: Univ Padjadjaran, Fac Math & Nat Sci, Dept Chem, Sumedang, Indonesia | Kusuma, Sri Agung Fitri;Rostinawati, Tina;Subroto, Toto;Yusuf, Muhammad | null | 31 | null | Indonesia | PT Genpro Multiguna Sejahtera;Univ Padjadjaran;Univ Putra Malaysia | Kusuma, Sri Agung Fitri | Green Accepted, gold, Green Published | ASSAY;CELL-DENSITY CULTIVATION;CONFIRMATION;DIAGNOSIS;IDENTIFICATION;INFECTION;MYCOBACTERIUM-TUBERCULOSIS COMPLEX;PROTEIN-PRODUCTION;SECRETION | Kusuma, Sri Agung Fitri; Parwati, Ida; Rostinawati, Tina; Yusuf, Muhammad; Fadhlillah, Muhammad; Ahyudanari, Risa R.; Rukayadi, Yaya; Subroto, Toto; | null | PT Genpro Multiguna Sejahtera, Sumedang, Indonesia;Univ Padjadjaran, Fac Math & Nat Sci, Dept Chem, Sumedang, Indonesia;Univ Padjadjaran, Fac Med, Dept Clin Pathol, Bandung, Indonesia;Univ Padjadjaran, Fac Pharm, Dept Biol Pharm, Sumedang, West Java, Indonesia;Univ Padjadjaran, Res Ctr Mol Biotechnol & Bioinformat, Bandung, Indonesia;Univ Putra Malaysia, Fac Food Sci & Technol, Dept Food Sci, Serdang, Malaysia | PT Genpro Multiguna Sejahtera, Sumedang, Indonesia;Univ Padjadjaran, Fac Math & Nat Sci, Dept Chem, Sumedang, Indonesia;Univ Padjadjaran, Fac Med, Dept Clin Pathol, Bandung, Indonesia;Univ Padjadjaran, Fac Pharm, Dept Biol Pharm, Sumedang, West Java, Indonesia;Univ Padjadjaran, Res Ctr Mol Biotechnol & Bioinformat, Bandung, Indonesia;Univ Putra Malaysia, Fac Food Sci & Technol, Dept Food Sci, Serdang, Malaysia | 2405-8440 | Box-Behnken design;Environmental science;Induction;Medium;Microbiology;MPT64;Response surface methodology;Rhamnose | 11 | 1967;1994;1995;1996;1999;2000;2001;2002;2005;2007;2008;2009;2010;2011;2014;2015;2016;2018;2019 | 12 | Univ Padjadjaran, Fac Math & Nat Sci, Dept Chem, Sumedang, Indonesia;Univ Padjadjaran, Res Ctr Mol Biotechnol & Bioinformat, Bandung, Indonesia | Heliyon | Subroto, Toto | ELSEVIER SCI LTD | (DE3);(medium;(MTBC);(RSM);(SDS-PAGE);(tryptone;,;0.0311;0.0392;10;15;17;20;4;5;a;accordance;and;at;average;between;BL21;Box-Bhenken;by;carried;cell;center;characterized;chloride;coli;combination;complex;concentration;concentration);conclusion;conditions;cultivation;culture;cytoplasm;design;designed;different;dodecyl;E.;electrophoresis;Escherichia;expression;extract;factorial;fermentation;flask;for;from;furthermore;gene;h;higher;ImageJ;in;inducer;induction;influenced;is;isolated;level;medium;methodology;methods;mg/mL;mg/mL);Minicab;mM;MPT64;Mycobacterium;objective;obtain;obtained;of;optimization;optimize;optimum;out;parameters;point;polyacrilamide;predetermined;predicted;program;protein;quantified;randomized;recombinant;relationship;repetitions;response;rhamnose;RSM;scale;secreted;selected;sodium;software;specific;statistical;strongly;study;sulfate;surface;synthetic;than;that;the;then;this;three;time;to;treatments;tuberculosis;two-fold;under;undertaken;using;was;were;with;yeast | Univ Padjadjaran | MPT64 is a specific protein that is secreted by Mycobacterium tuberculosis complex (MTBC). The objective of this study was to obtain optimum culture conditions for MPT64 synthetic gene expression in Escherichia coli BL21 (DE3) by response surface methodology (RSM). The RSM was undertaken to optimize the culture conditions under different cultivation conditions (medium concentration, induction time and inducer concentration), designed by the factorial Box-Bhenken using Minicab 17 statistical software. From the randomized combination, 15 treatments and three center point repetitions were obtained. Furthermore, expression methods were carried out in the flask scale fermentation in accordance with the predetermined design. Then, the MPT64 protein in the cytoplasm of E. coli cell was isolated and characterized using sodium dodecyl sulfate polyacrilamide electrophoresis (SDS-PAGE) then quantified using the ImageJ program. The optimum conditions were two-fold medium concentration (tryptone 20 mg/mL, yeast extract 10 mg/mL, and sodium chloride 20 mg/mL), 5 h of induction time and 4 mM rhamnose. The average concentration of recombinant MPT64 at optimum conditions was 0.0392 mg/mL, higher than the predicted concentration of 0.0311 mg/mL. In conclusion, the relationship between the selected optimization parameters strongly influenced the level of MPT64 gene expression in E. coli BL21 (DE3). | AAU-9119-2020;HMO-5652-2023;KAM-6456-2024;R-8791-2019 | ASSAY;CELL-DENSITY CULTIVATION;CONFIRMATION;DIAGNOSIS;IDENTIFICATION;INFECTION;MYCOBACTERIUM-TUBERCULOSIS COMPLEX;PROTEIN-PRODUCTION;SECRETION | 2 | null | Box-Behnken design;Environmental science;Induction;Medium;Microbiology;MPT64;Response surface methodology;Rhamnose | 9 | ASSAY;Box-Behnken design;CELL-DENSITY CULTIVATION;CONFIRMATION;DIAGNOSIS;Environmental science;IDENTIFICATION;INDUCTION;INFECTION;Medium;Microbiology;MPT64;MYCOBACTERIUM-TUBERCULOSIS COMPLEX;PROTEIN-PRODUCTION;Response surface methodology;Rhamnose;SECRETION | WOS:000500530100032 | PT Genpro Multiguna Sejahtera, Sumedang, Indonesia;Univ Padjadjaran, Bandung, Indonesia;Univ Padjadjaran, Sumedang, Indonesia;Univ Padjadjaran, West Java, Indonesia;Univ Putra Malaysia, Serdang, Malaysia | Indonesia;Malaysia | 2,019 | null | 0000-0001-5277-0427;0000-0001-8342-0112;0000-0002-1629-407X;0000-0002-7139-8250;0000-0002-9700-589X;0000-0003-1627-1553 | null | null | English | null | ANAL CHIM ACTA;APPL MICROBIOL BIOT;BIOCHEM ENG J;BIOMOL ENG;BIOTECHNOL ADV;BIOTECHNOL BIOENG;BIOTECHNOL LETT;CAN MED ASSOC J;CHINESE J CHEM ENG;CLIN MICROBIOL REV;ENVIRONMENTAL MICROBIOLOGY;GEN CALIBRATION MICR;INT J RES PHARM SCI;INT J TUBERC LUNG D;IOSR J PHARM;Iranian Journal of Biotechnology;J BIOTECHNOL;J CLIN MICROBIOL;J IND MICROBIOL;J MOL CATAL B-ENZYM;J THEOR BIOL;JUNDISHAPUR J MICROB;MEM I OSWALDO CRUZ;PROTEIN EXPRES PURIF;SCI REP;TXB PEDIAT INFECT DI;VIROL J | Ahyudanari, Risa R;Fadhlillah, Muhammad;Kusuma, Sri Agung Fitri;Parwati, Ida;Rostinawati, Tina;Rukayadi, Yaya;Subroto, Toto;Yusuf, Muhammad | 2024-03-11
ER | Abe, C;Ashley, M J;Cruz, A T;Delisa, M P;Donovan, R S;Dunn, J J;Falkinham, J O;Ferreira, S L C;Hasegawa, N;Hillemann, D;Indriyani A.;Jain, J;Korz, D J;Lim, H K;Maier, R M;Maldonado, L M T P;Mergulhao, F J M;Morowvat, M H;Namkoong H.;Pournejati, R;Salihu, A;Setiawan D.;Shojaosadati Seyed Abbas;Stevenson K.;Toihir, A H O S;Tsutsumi, H;Turner, C;Yates, G T;Zhang, C;Zhang, H Y;Zhang, J | JS8CO | Bandung, Indonesia;Sumedang, Indonesia. | 12 | null | 3 | null | 31,844,694 | Ahyudanari, Risa R;Fadhlillah, Muhammad;Kusuma, Sri Agung Fitri;Parwati, Ida;Rostinawati, Tina;Rukayadi, Yaya;Subroto, Toto;Yusuf, Muhammad | HELIYON | Bandung, Indonesia;Serdang, Malaysia;Sumedang, Indonesia;West Java, Indonesia |
Hwang, J;Jang, S;Jung, G Y;Kim, M | 10.1007/s10295-019-02191-5 | null | TIERGARTENSTRASSE 17, D-69121 HEIDELBERG, GERMANY | 3k3m4t3s5s1cq94f44496c2oz5l3d1t6p4b1 | Tools and systems for evolutionary engineering of biomolecules and microorganisms | Pohang Univ Sci & Technol | null | Jung, GY (corresponding author), Pohang Univ Sci & Technol, Dept Chem Engn, 77 Cheongam Ro, Pohang 37673, Gyeongbuk, South Korea.;Jung, GY (corresponding author), Pohang Univ Sci & Technol, Sch Interdisciplinary Biosci & Bioengn, 77 Cheongam Ro, Pohang 37673, Gyeongbuk, South Korea. | SI | Hwang, Jaeseong;Jang, Sungho;Jung, Gyoo Yeol;Kim, Minsun | Biotechnology & Applied Microbiology | C1 Gas Refinery Program - Ministry of Science and ICT of the Republic of Korea through the National Research Foundation of Korea [NRF-2018M3D3A1A01055754]; Global Research Laboratory Program - Ministry of Science and ICT of the Republic of Korea through the National Research Foundation of Korea [NRF-2016K1A1A2912829]; Korea Institute of Energy Technology Evaluation and Planning (KETEP); Ministry of Trade, Industry & Energy (MOTIE) of the Republic of Korea [20174030201600] | WOS | Jung, G Y | Pohang Univ Sci & Technol, Gyeongbuk, South Korea | 46 | and;biomolecules;engineering;evolutionary;for;microorganisms;of;systems;Tools | 1 | Jang, Sungho;Jung, Gyoo Yeol;Kim, Minsun | SPRINGER HEIDELBERG | Pohang Univ Sci & Technol, Dept Chem Engn, 77 Cheongam Ro, Pohang 37673, Gyeongbuk, South Korea;Pohang Univ Sci & Technol, Dept Chem Engn, 77 Cheongam Ro, Pohang 37673, Gyeongbuk, South Korea.; Jung, GY (corresponding author), Pohang Univ Sci & Technol, Sch Interdisciplinary Biosci & Bioengn, 77 Cheongam Ro, Pohang 37673, Gyeongbuk, South Korea;Pohang Univ Sci & Technol, Sch Interdisciplinary Biosci & Bioengn, 77 Cheongam Ro, Pohang 37673, Gyeongbuk, South Korea | Review | Pohang Univ Sci & Technol | HEIDELBERG | null | null | Pohang Univ Sci & Technol | C1 Gas Refinery Program - Ministry of Science and ICT of the Republic of Korea through the National Research Foundation of Korea;Global Research Laboratory Program - Ministry of Science and ICT of the Republic of Korea through the National Research Foundation of Korea;Korea Institute of Energy Technology Evaluation and Planning (KETEP);Ministry of Trade, Industry & Energy (MOTIE) of the Republic of Korea | Jung, GY (corresponding author), Pohang Univ Sci & Technol, Dept Chem Engn, 77 Cheongam Ro, Pohang 37673, Gyeongbuk, South Korea.; Jung, GY (corresponding author), Pohang Univ Sci & Technol, Sch Interdisciplinary Biosci & Bioengn, 77 Cheongam Ro, Pohang 37673, Gyeongbuk, South Korea. | 1326 | Hwang, Jaeseong;Jang, Sungho;Jung, Gyoo Yeol;Kim, Minsun | 64 | 2 | 490,009,800,008 | C1 Gas Refinery Program - Ministry of Science and ICT of the Republic of Korea through the National Research Foundation of Korea [NRF-2018M3D3A1A01055754];Global Research Laboratory Program - Ministry of Science and ICT of the Republic of Korea through the National Research Foundation of Korea [NRF-2016K1A1A2912829];Korea Institute of Energy Technology Evaluation and Planning (KETEP);Ministry of Trade, Industry & Energy (MOTIE) of the Republic of Korea [20174030201600] | South Korea | JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY | South Korea;South Korea.; | null | null | Pohang Univ Sci & Technol, Dept Chem Engn, 77 Cheongam Ro, Pohang 37673, Gyeongbuk, South Korea | 1367-5435 | Hwang, J;Jang, S;Jung, G Y;Kim, M | OCT | gyjung@postech.ac.kr | biomolecules;evolutionary engineering;microorganisms;systems;tools | 4 | J | Biotechnology & Applied Microbiology | ADAPTIVE LABORATORY EVOLUTION;artificial equivalent;bioengineering challenges;biomolecules;combining;CONTINUOUS DIRECTED EVOLUTION;Continuous evolution;DESIGN;directed evolution;DNA;double-strand breaks;efficient manner;ESCHERICHIA-COLI;evolutionary approaches;Evolutionary engineering;fluidic systems;high-throughput screening;metabolite production;microorganisms;modern tools;multiplexed continuous cultivation;mutagenesis;natural evolution;new era;optimization;overall;phenotypes;PROTEIN;recent advances;research applications;RIBOSWITCH;screening;SELECTION;synthetic biology;synthetic genetic circuits;systems;tools;traditional adaptive laboratory evolution | Jang, S | ADAPTIVE LABORATORY EVOLUTION;CONTINUOUS DIRECTED EVOLUTION;Continuous evolution;DESIGN;DNA;DOUBLE-STRAND BREAKS;ESCHERICHIA-COLI;Evolutionary engineering;high-throughput screening;mutagenesis;OPTIMIZATION;PROTEIN;RIBOSWITCH;SELECTION | 1313 | [Jang, Sungho; Jung, Gyoo Yeol] Pohang Univ Sci & Technol, Dept Chem Engn, 77 Cheongam Ro, Pohang 37673, Gyeongbuk, South Korea. [Kim, Minsun; Hwang, Jaeseong; Jung, Gyoo Yeol] Pohang Univ Sci & Technol, Sch Interdisciplinary Biosci & Bioengn, 77 Cheongam Ro, Pohang 37673, Gyeongbuk, South Korea. | This work was supported by the C1 Gas Refinery Program [Grant Number NRF-2018M3D3A1A01055754] and the Global Research Laboratory Program [Grant Number NRF-2016K1A1A2912829] funded by the Ministry of Science and ICT of the Republic of Korea through the National Research Foundation of Korea and by the Korea Institute of Energy Technology Evaluation and Planning (KETEP) and the Ministry of Trade, Industry & Energy (MOTIE) of the Republic of Korea [Grant Number 20174030201600]. | artificial equivalent;bioengineering challenges;combining;continuous directed evolution;directed evolution;efficient manner;evolutionary approaches;evolutionary engineering;fluidic systems;high-throughput screening;metabolite production;microorganisms;modern tools;multiplexed continuous cultivation;mutagenesis;natural evolution;new era;overall;phenotypes;recent advances;research applications;screening;synthetic biology;synthetic genetic circuits;systems;traditional adaptive laboratory evolution | 10.1002/aic.13995;10.1002/anie.201708408;10.1002/cbic.200700546;10.1002/cbic.201402501;10.1007/BF02761755;10.1007/s00253-017-8593-x;10.1007/s12257-017-0082-7;10.1007/s12257-018-0064-4;10.1007/s12257-018-0390-6;10.1016/0006-291X(70)90562-0;10.1016/bs.mie.2014.10.039;10.1016/j.algal.2016.06.023;10.1016/j.biotechadv.2017.07.005;10.1016/j.cbpa.2014.09.040;10.1016/j.cell.2018.10.021;10.1016/j.copbio.2009.08.005;10.1016/j.copbio.2011.03.007;10.1016/j.copbio.2012.01.005;10.1016/j.copbio.2016.03.005;10.1016/j.copbio.2017.10.005;10.1016/j.copbio.2017.12.020;10.1016/j.copbio.2018.01.011;10.1016/j.copbio.2018.08.011;10.1016/j.dnarep.2003.10.002;10.1016/j.sbi.2016.11.001;10.1016/j.sbi.2016.11.021;10.1016/j.synbio.2017.07.001;10.1016/j.tibtech.2007.01.003;10.1016/j.ymben.2011.09.004;10.1016/j.ymben.2012.04.004;10.1016/j.ymben.2015.01.004;10.1016/j.ymben.2016.11.008;10.1016/j.ymben.2018.03.009;10.1016/j.ymben.2018.04.015;10.1016/j.ymben.2018.07.001;10.1016/S0959-440X(97)80110-8;10.1021/acssynbio.5b00069;10.1021/acssynbio.7b00128;10.1021/acssynbio.8b00242;10.1021/acssynbio.8b00273;10.1021/cb900278x;10.1021/ja076298b;10.1021/jacs.8b04001;10.1021/sb300091d;10.1038/75398;10.1038/nature09929;10.1038/nature17938;10.1038/nature26155;10.1038/nbt.2149;10.1038/nbt.3718;10.1038/nbt.4151;10.1038/nbt0396-309;10.1038/nbt0398-258;10.1038/nchembio.2299;10.1038/ncomms13051;10.1038/ncomms2404;10.1038/ncomms3595;10.1038/ncomms9425;10.1038/nrg3927;10.1038/nrm2805;10.1038/s41467-017-00511-w;10.1038/s41467-017-01055-9;10.1038/s41467-018-03675-1;10.1038/s41586-018-0384-8;10.1038/s41589-018-0121-5;10.1038/srep19452;10.1039/b907749a;10.1039/c6lc00118a;10.1039/c6lc00367b;10.1042/BST20160076;10.1073/pnas.0911209107;10.1073/pnas.1333928100;10.1073/pnas.1406401111;10.1073/pnas.1409523111;10.1073/pnas.2036296100;10.1073/pnas.90.6.2117;10.1073/pnas.95.17.9997;10.1073/pnas.95.2.515;10.1080/15476286.2015.1062970;10.1093/nar/15.3.1031;10.1093/nar/25.6.1307;10.1093/nar/gkq789;10.1093/nar/gkt150;10.1100/tsw.2002.61;10.1111/j.1365-2958.1994.tb02178.x;10.1111/j.1742-4658.2007.06022.x;10.1126/science.1256272;10.1126/science.aad9822;10.1126/science.aah6219;10.1128/AEM.02246-14;10.1128/AEM.67.8.3645-3649.2001;10.1128/JVI.01624-06;10.1128/MCB.14.12.8096;10.1146/annurev-biochem-062608-095938;10.1186/1475-2859-11-117;10.1186/1475-2859-12-64;10.1186/1754-6834-6-70;10.1186/s12934-015-0311-8;10.1371/journal.pcbi.1004998;10.3791/57357;[10.1038/NCHEMBIO.1439, 10.1038/nchembio.1439];[10.1038/nchembio.2046, 10.1038/NCHEMBIO.2046];[10.1038/nchembio.2474, 10.1038/NCHEMBIO.2474];[10.1038/NMETH.3515, 10.1038/nmeth.3515];[10.1038/NMETH.3696, 10.1038/nmeth.3696] | Pohang Univ Sci & Technol | Hwang, J;Jang, S;Jung, G Y;Kim, M | Jang, S: Pohang Univ Sci & Technol, Dept Chem Engn, 77 Cheongam Ro, Pohang 37673, Gyeongbuk, South Korea | null | 20174030201600;NRF-2016K1A1A2912829;NRF-2018M3D3A1A01055754 | 105 | null | South Korea | Pohang Univ Sci & Technol | Jang, Sungho | Bronze | ADAPTIVE LABORATORY EVOLUTION;CONTINUOUS DIRECTED EVOLUTION;DESIGN;DNA;DOUBLE-STRAND BREAKS;ESCHERICHIA-COLI;MUTAGENESIS;OPTIMIZATION;PROTEIN;RIBOSWITCH | Jang, Sungho; Kim, Minsun; Hwang, Jaeseong; Jung, Gyoo Yeol; | null | Pohang Univ Sci & Technol, Dept Chem Engn, 77 Cheongam Ro, Pohang 37673, Gyeongbuk, South Korea;Pohang Univ Sci & Technol, Sch Interdisciplinary Biosci & Bioengn, 77 Cheongam Ro, Pohang 37673, Gyeongbuk, South Korea | Pohang Univ Sci & Technol, Dept Chem Engn, 77 Cheongam Ro, Pohang 37673, Gyeongbuk, South Korea;Pohang Univ Sci & Technol, Sch Interdisciplinary Biosci & Bioengn, 77 Cheongam Ro, Pohang 37673, Gyeongbuk, South Korea | 1476-5535 | Continuous evolution;Evolutionary engineering;high-throughput screening;mutagenesis;Selection | 9-10 | 1970;1987;1993;1994;1996;1997;1998;2000;2001;2002;2003;2004;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016;2017;2018;2019 | 10 | Pohang Univ Sci & Technol, Dept Chem Engn, 77 Cheongam Ro, Pohang 37673, Gyeongbuk, South Korea;Pohang Univ Sci & Technol, Sch Interdisciplinary Biosci & Bioengn, 77 Cheongam Ro, Pohang 37673, Gyeongbuk, South Korea | J. Ind. Microbiol. Biotechnol. | Jung, Gyoo Yeol | SPRINGER HEIDELBERG | ,;a;achieved;adaptive;addition;advances;all;an;and;applications;approaches;artificial;be;been;bioengineering;biology;by;can;challenges;circuits;combining;continuous;control;created;cultivation;directed;efficient;enable;engineering;equivalent;era;establish;evolution;evolutionary;fluidic;for;genetic;has;have;high-throughput;in;laboratory;manner;metabolite;microorganisms;modern;moreover;multiplexed;mutagenesis;natural;new;of;opened;overall;particularly;phenotypes;production;providing;recent;research;screening;solutions;steps;synthetic;systems;the;to;tools;traditional;used;various | Pohang Univ Sci & Technol | Evolutionary approaches have been providing solutions to various bioengineering challenges in an efficient manner. In addition to traditional adaptive laboratory evolution and directed evolution, recent advances in synthetic biology and fluidic systems have opened a new era of evolutionary engineering. Synthetic genetic circuits have been created to control mutagenesis and enable screening of various phenotypes, particularly metabolite production. Fluidic systems can be used for high-throughput screening and multiplexed continuous cultivation of microorganisms. Moreover, continuous directed evolution has been achieved by combining all the steps of evolutionary engineering. Overall, modern tools and systems for evolutionary engineering can be used to establish the artificial equivalent to natural evolution for various research applications. | null | ADAPTIVE LABORATORY EVOLUTION;CONTINUOUS DIRECTED EVOLUTION;DESIGN;DNA;DOUBLE-STRAND BREAKS;ESCHERICHIA-COLI;MUTAGENESIS;OPTIMIZATION;PROTEIN;RIBOSWITCHES | 2 | null | Continuous evolution;Evolutionary engineering;high-throughput screening;mutagenesis;Selection | 14 | ESCHERICHIA-COLI;ADAPTIVE LABORATORY EVOLUTION;CONTINUOUS DIRECTED EVOLUTION;Continuous evolution;DESIGN;DNA;DOUBLE-STRAND BREAKS;Evolutionary engineering;high-throughput screening;mutagenesis;OPTIMIZATION;PROTEIN;RIBOSWITCH;SELECTION | WOS:000490009800008 | Pohang Univ Sci & Technol, Gyeongbuk, South Korea | South Korea | 2,019 | null | 0000-0002-9742-3207;0000-0003-1080-2827;0000-0003-4368-3043 | null | null | English | null | ACS CHEM BIOL;ACS SYNTH BIOL;AICHE J;ALGAL RES;ANGEW CHEM INT EDIT;ANNU REV BIOCHEM;APPL ENVIRON MICROB;APPL MICROBIOL BIOT;BIOCHEM SOC T;Biochemical and Biophysical Research Communications;BIOTECHNOL ADV;BIOTECHNOL BIOFUELS;BIOTECHNOL BIOPROC E;CELL;CHEM SOC REV;CHEMBIOCHEM;CURR OPIN BIOTECH;CURR OPIN CHEM BIOL;CURR OPIN STRUC BIOL;DNA REPAIR;FEBS J;J AM CHEM SOC;J VIROL;JOVE-J VIS EXP;LAB CHIP;METAB ENG;METHOD ENZYMOL;MICROB CELL FACT;MOL BIOTECHNOL;MOL CELL BIOL;MOL MICROBIOL;NAT BIOTECHNOL;NAT CHEM BIOL;NAT COMMUN;NAT METHODS;NAT REV GENET;NAT REV MOL CELL BIO;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PLOS COMPUT BIOL;RNA BIOL;SCI REP-UK;SCIENCE;ScientificWorldJournal;SYN SYST BIOTECHNO;TRENDS BIOTECHNOL | Hwang, Jaeseong;Jang, Sungho;Jung, Gyoo Yeol;Kim, Minsun | 2024-03-11
ER | Arnold, F H;Badran, A H;Betteridge, A L;Bjork, S M;Boiteux, S;Bryson, D I;Bull, J J;Camps, M;Carter, J L L;Chang, A L;Chou, H H;Cobb, R E;Crook, N;D'Oelsnitz, S;Dar, D;Dietrich, J A;Dixon, N;Dougherty, M J;Dragosits, M;Esvelt, K M;Farmer, W R;Farzadfard, F;Finney-Manchester, S P;Frommer, W B;Garst, A D;Glassner, B J;Greener, A;Halperin, S O;Hu, J H;Huang, G G;Hubbard, B P;Jakociunas, T;Jang, S;Jester, B W;Johnson, T J;Ju, M S;Kaminski, T S;Kan, S B J;Kellenberger, C A;Kingsbury D, T;Korman, T P;Lacroix, R A;Lee, S W;Li, S J;Lim, H G;Lin, J L;Liu, J W;Liu, Y N;Maas, W K;Michener, J K;Moore, C L;Mundhada, H;Nguyen, N H;Nomura, Y;O'Brien, E J;Packer, M S;Pham, H L;Portnoy, V A;Pu, J Y;Raman, S;Ravikumar, A;Ravn, U;Rogers, J K;Romero, P A;Ronda, C;Rong, M Q;Rouet, P;Scalcinati, G;Selifonova, O;Seo, J H;Seok, J Y;Simon, A J;Stemmer Willem P, C;Storici, F;Tapsin, S;Taylor, N D;Tizei, P A G;Tokunaga, M;Topp, S;Tyo, K E;Vaughan, T J;Wagner, J M;Wang, T N;Wei, X;Wong, B G;Wrenbeck, E E;Xiao, Y;Xu, P;Yang, J;Yang, W;Zhang, F Z;Zhao, H M;Zheng, X | JD5FV | Gyeongbuk, South Korea;Gyeongbuk, South Korea. | 14 | null | 1 | null | 31,134,415 | Hwang, Jaeseong;Jang, Sungho;Jung, Gyoo Yeol;Kim, Minsun | J IND MICROBIOL BIOT | Gyeongbuk, South Korea |
Fussenegger, M;Stücheli, P;Tolle, F | 10.1016/j.copbio.2019.02.003 | null | THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, OXON, ENGLAND | q71314r494n4d1k4m3y704b6m3d2hk2g606b5 | Genetic circuitry for personalized human cell therapy | Swiss Fed Inst Technol | null | Fussenegger, M (corresponding author), Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Mattenstr 26, CH-4058 Basel, Switzerland.;Fussenegger, M (corresponding author), Univ Basel, Fac Sci, Mattenstr 26, CH-4058 Basel, Switzerland. | null | Fussenegger, Martin;Stuecheli, Pascal;Tolle, Fabian | Biochemical Research Methods;Biotechnology & Applied Microbiology | European Research Council (ERC); National Centre of Competence in Research (NCCR) for Molecular Systems Engineering | WOS | Fussenegger, M | Swiss Fed Inst Technol, Basel, Switzerland;Univ Basel, Basel, Switzerland | 59 | cell;circuitry;for;genetic;human;personalized;therapy | 1 | Tolle, Fabian | ELSEVIER SCI LTD | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Mattenstr 26, CH-4058 Basel, Switzerland;Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Mattenstr 26, CH-4058 Basel, Switzerland.; Fussenegger, M (corresponding author), Univ Basel, Fac Sci, Mattenstr 26, CH-4058 Basel, Switzerland;Univ Basel, Fac Sci, Mattenstr 26, CH-4058 Basel, Switzerland | Review | Swiss Fed Inst Technol;Univ Basel | OXFORD | null | null | Swiss Fed Inst Technol;Univ Basel | European Research Council (ERC);National Centre of Competence in Research (NCCR) for Molecular Systems Engineering | Fussenegger, M (corresponding author), Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Mattenstr 26, CH-4058 Basel, Switzerland.; Fussenegger, M (corresponding author), Univ Basel, Fac Sci, Mattenstr 26, CH-4058 Basel, Switzerland. | 38 | Fussenegger, Martin;Stuecheli, Pascal;Tolle, Fabian | 30 | 2 | 494,891,200,006 | European Research Council (ERC);National Centre of Competence in Research (NCCR) for Molecular Systems Engineering | Switzerland | CURRENT OPINION IN BIOTECHNOLOGY | Switzerland | null | null | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Mattenstr 26, CH-4058 Basel, Switzerland | 0958-1669 | Fussenegger, M;Stücheli, P;Tolle, F | OCT | fussenegger@bsse.ethz.ch | genetic circuitry;personalized human cell therapy | 3 | J | Biochemistry & Molecular Biology;Biotechnology & Applied Microbiology | advanced gene circuitry;applications;basis;biological components;cells;complex gene circuits;conditions;DESIGNER CELLS;Gene circuits;genetic circuitry;genetic engineering;integrating diverse input signals;limitations;living cells;personalized human cell therapy;personalized human medicine;pre-programmed combinations;precise spatiotemporal control;principles;selected recent examples;sensing;specified response;synthetic biology;synthetic biology uses engineering principles;synthetic gene switches;SYSTEM;systems;target gene expression;therapeutic modalities;therapeutic protein production;traditional medical treatments;variety | Tolle, F | DESIGNER CELLS;PRINCIPLES;Synthetic biology;SYSTEM | 31 | [Tolle, Fabian; Stuecheli, Pascal; Fussenegger, Martin] Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Mattenstr 26, CH-4058 Basel, Switzerland. [Fussenegger, Martin] Univ Basel, Fac Sci, Mattenstr 26, CH-4058 Basel, Switzerland. | Work in the laboratory of M.F. is financially supported in part through a European Research Council (ERC) advanced grant and in part by the National Centre of Competence in Research (NCCR) for Molecular Systems Engineering. The authors would like to thank Leo Scheller for critical reading of the manuscript and helpful discussions. | advanced gene circuitry;applications;basis;biological components;cells;complex gene circuits;conditions;designer cells;gene circuits;genetic engineering;integrating diverse input signals;limitations;living cells;personalized human medicine;pre-programmed combinations;precise spatiotemporal control;selected recent examples;sensing;specified response;synthetic biology uses engineering principles;synthetic gene switches;systems;target gene expression;therapeutic modalities;therapeutic protein production;traditional medical treatments;variety | 10.1002/advs.201800952;10.1002/anie.201609229;10.1002/bit.25828;10.1016/j.cbpa.2017.06.003;10.1016/j.cell.2016.09.011;10.1016/j.cell.2018.03.038;10.1016/j.cell.2018.05.015;10.1016/j.cell.2018.05.039;10.1016/j.cobme.2017.09.010;10.1016/j.copbio.2016.06.003;10.1016/j.copbio.2017.03.011;10.1016/j.copbio.2017.06.010;10.1016/j.copbio.2017.06.011;10.1016/j.copbio.2018.08.008;10.1016/j.jbiotec.2017.07.018;10.1021/acs.nanolett.7b02270;10.1021/acssynbio.8b00271;10.1038/d41586-018-05164-3;10.1038/nature23271;10.1038/nbt.3805;10.1038/nchembio.2290;10.1038/nchembio.2554;10.1038/ncomms11247;10.1038/ncomms11529;10.1038/ncomms15028;10.1038/ng.3915;10.1038/nmeth.4635;10.1038/nrm.2015.2;10.1038/s41467-018-03733-8;10.1038/s41467-018-04223-7;10.1038/s41467-018-04744-1;10.1038/s41551-016-0005;10.1038/s41589-018-0046-z;10.1038/s41589-018-0091-7;10.1038/s41589-018-0146-9;10.1038/s41592-018-0048-5;10.1073/pnas.1611142114;10.1089/rej.2013.1527;10.1101/cshperspect.a023770;10.1126/science.1217622;10.1126/science.aab4077;10.1126/science.aac7341;10.1126/science.aad1067;10.1126/science.aaf4006;10.1126/science.aaf6850;10.1126/science.aan4672;10.1126/science.aas9315;10.1126/science.aat0271;10.1126/scitranslmed.aal2298;10.1126/scitranslmed.aap8562;10.1186/s13073-017-0450-0;[10.1038/nchembio.2498, 10.1038/NCHEMBIO.2498];[10.1038/NMETH.2926, 10.1038/nmeth.2926];[10.1038/NMETH.4505, 10.1038/nmeth.4505] | Swiss Fed Inst Technol | Fussenegger, M;Stücheli, P;Tolle, F | Tolle, F: Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Mattenstr 26, CH-4058 Basel, Switzerland | null | null | 56 | null | Switzerland | Swiss Fed Inst Technol;Univ Basel | Tolle, Fabian | null | DESIGNER CELLS;PRINCIPLES;SYNTHETIC BIOLOGY;SYSTEM | Tolle, Fabian; Stuecheli, Pascal; Fussenegger, Martin; | null | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Mattenstr 26, CH-4058 Basel, Switzerland;Univ Basel, Fac Sci, Mattenstr 26, CH-4058 Basel, Switzerland | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Mattenstr 26, CH-4058 Basel, Switzerland;Univ Basel, Fac Sci, Mattenstr 26, CH-4058 Basel, Switzerland | 1879-0429 | null | null | 2012;2014;2015;2016;2017;2018;2019 | 12 | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Mattenstr 26, CH-4058 Basel, Switzerland;Univ Basel, Fac Sci, Mattenstr 26, CH-4058 Basel, Switzerland | Curr. Opin. Biotechnol. | Fussenegger, Martin | ELSEVIER SCI LTD | ,;a;advanced;and;applications;are;as;assemble;automatically;basis;be;biological;biology;can;capable;cells;circuitry;circuits;combinations;complex;components;conditions;construct;control;design;designer;diverse;enabling;engineered;engineering;equipped;examples;expression;for;gene;genetic;have;herein;highlight;human;in;input;integrating;interconnected;limitations;living;medical;medicine;modalities;of;on;personalized;pre-programmed;precise;precisely;principles;production;promising;protein;react;recent;response;selected;sensing;signals;spatiotemporal;specified;such;switches;synthetic;systems;target;targeted;the;them;therapeutic;to;toward;traditional;treatments;triggering;uses;variety;we;where;with | Swiss Fed Inst Technol;Univ Basel | Synthetic biology uses engineering principles to design and assemble biological components and systems for a variety of applications. On the basis of genetic engineering, synthetic gene switches can be interconnected to construct complex gene circuits, capable of sensing and integrating diverse input signals for precise spatiotemporal control of target gene expression in living cells, Designer cells can be equipped with advanced gene circuitry enabling them to react precisely to pre-programmed combinations of conditions, automatically triggering a specified response, such as therapeutic protein production. Such cells are promising therapeutic modalities for applications where traditional medical treatments have limitations. Herein, we highlight selected recent examples of designer cells with engineered gene circuits targeted toward applications in personalized human medicine. | null | DESIGNER CELLS;PRINCIPLES;SYNTHETIC BIOLOGY;SYSTEM | 0 | null | null | 8 | DESIGNER CELLS;PRINCIPLES;Synthetic biology;SYSTEM | WOS:000494891200006 | Swiss Fed Inst Technol, Basel, Switzerland;Univ Basel, Basel, Switzerland | Switzerland | 2,019 | null | 0000-0002-4221-0167 | null | null | English | null | ACS SYNTH BIOL;ADV SCI;ANGEW CHEM INT EDIT;BIOTECHNOL BIOENG;CELL;CSH PERSPECT BIOL;CURR OPIN BIOMED ENG;CURR OPIN BIOTECH;CURR OPIN CHEM BIOL;GENOME MED;J BIOTECHNOL;NANO LETT;NAT BIOMED ENG;NAT BIOTECHNOL;NAT CHEM BIOL;NAT COMMUN;NAT GENET;NAT METHODS;NAT REV MOL CELL BIO;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;REJUV RES;SCI TRANSL MED;SCIENCE | Fussenegger, Martin;Stuecheli, Pascal;Tolle, Fabian | 2024-03-11
ER | Ausländer, D;Ausländer, S;Baumgart, L;Benner, S A;Boeke, J D;Bojar, D;Brenner, M;Brophy, J A N;Camacho, D M;Ceroni, F;Cho, J H;Didovyk, A;Dominguez, A A;Dunbar, C E;Eguchi, A;Foo, J L;Green, A A;Haellman, V;Higashikuni, Y;Ho, P;Hwang, I Y;Kaczmarek, J C;Kim, S;Kitada, T;Kojima, R;Kolar, K;Kong, W T;Liu, C C;Liu, Y;Mansouri, M;Mimee, M;Nielsen, A A K;Pinheiro, V B;Roybal, K T;Saxena, P;Scheller, L;Schukur, L;Sedlmayer, F;Shao, J W;Stambler, I;Tastanova, A;Teixeira, A P;Toda, S;Wagner, T E;Weinberg, B H;Wu, C Y;Xie, M;Ye, H F;Yeo, N C | JK5NX | Basel, Switzerland;Basel, Switzerland. | 12 | null | 2 | null | 30,852,360 | Fussenegger, Martin;Stuecheli, Pascal;Tolle, Fabian | CURR OPIN BIOTECH | Basel, Switzerland |
Paris, J R;Usher, J | 10.1038/s41598-019-48303-0 | 11827 | MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND | 6d4u3o3l5s3i5y636m295r4f484c461a5w6u405h | Functional genomic characterization of metallothioneins in brown trout (<i>Salmo trutta</i> L.). using synthetic genetic analysis | Univ Exeter | null | Usher, J (corresponding author), Univ Exeter, Coll Life & Environm Sci, Sch Biosci, Exeter, Devon, England. | null | Paris, Josephine R;Usher, Jane | Multidisciplinary Sciences | MRC [MR/N006364/1] Funding Source: UKRI; Medical Research Council [MR/N006364/1] Funding Source: Medline | WOS | Usher, J | Univ Exeter, Devon, England;Univ Sussex, E Sussex, England | 9 | (<i>Salmo;Analysis;brown;characterization;functional;genetic;Genomic;in;L;metallothioneins;of;synthetic;trout;trutta</i>;using | 1 | Paris, Josephine Rosanna | NATURE PUBLISHING GROUP | Univ Exeter, Coll Life & Environm Sci, Sch Biosci, Exeter, Devon, England;Univ Sussex, Sch Life Sci, Brighton, E Sussex, England | Article | Univ Exeter | LONDON | null | null | Univ Exeter;UNIV SUSSEX | Medical Research Council;MRC | Usher, J (corresponding author), Univ Exeter, Coll Life & Environm Sci, Sch Biosci, Exeter, Devon, England. | null | Paris, Josephine R;Usher, Jane | 8 | 2 | 480,678,100,026 | Medical Research Council [MR/N006364/1] Funding Source: Medline;MRC [MR/N006364/1] Funding Source: UKRI | UK | SCIENTIFIC REPORTS | UK | null | null | Univ Exeter, Coll Life & Environm Sci, Sch Biosci, Exeter, Devon, England | 2045-2322 | Paris, J R;Usher, J | AUG 14 | j.usher@exeter.ac.uk | brown trout (<i>Salmo trutta</i> L;functional genomic characterization;metallothioneins;synthetic genetic analysis | 2 | J | Science & Technology - Other Topics | (i);(ii);(iii);adaptation;approaches;body;brown trout (<i>Salmo trutta</i> L;brown trout (Salmo trutta L;cadmium;control river;COPPER;cysteine-rich metal-ion binding proteins;driving metal tolerance;earth's ecosystems;ecology;England;evolution;experimental system;functional genomic characterization;functional genomics;functional genomics approach leveraged;genetic interaction maps;genetic interactions;group;interactions;isoforms;key physiological mechanism;MetA;metal pollution;METAL TOLERANCE;metal toxicity;metal-tolerant trout;metallothionein (MetA;metallothionein isoforms;METALLOTHIONEINS;metals;MetB isoforms;MetB);model yeast;model yeast Saccharomyces cerevisiae;non-model species;POLLUTION;population;POPULATIONS;pre-exposure;regulating protection;rivers;role;S. Cerevisiae;Saccharomyces cerevisiae;SACCHAROMYCES-CEREVISIAE;SALMO-TRUTTA;significant impact;southwest;species;synthetic genetic analysis;synthetic genetic array (SGA) analyses;tolerance;TOXICITY;TRANSCRIPTION;trout;two isoforms;wide variety | Paris, J R | adaptation;CADMIUM;COPPER;METAL TOLERANCE;POLLUTION;POPULATION;SACCHAROMYCES-CEREVISIAE;SALMO-TRUTTA;TOXICITY;TRANSCRIPTION | null | [Paris, Josephine R.; Usher, Jane] Univ Exeter, Coll Life & Environm Sci, Sch Biosci, Exeter, Devon, England. [Paris, Josephine R.] Univ Sussex, Sch Life Sci, Brighton, E Sussex, England. | null | (i);(ii);(iii);approaches;body;brown trout (Salmo trutta L;control river;cysteine-rich metal-ion binding proteins;driving metal tolerance;earth's ecosystems;ecology;England;evolution;experimental system;functional genomics;functional genomics approach leveraged;genetic interaction maps;genetic interactions;group;interactions;isoforms;key physiological mechanism;MetA;metal pollution;metal toxicity;metal-tolerant trout;metallothionein (MetA;metallothionein isoforms;metallothioneins;metals;MetB isoforms;MetB);model yeast;model yeast Saccharomyces cerevisiae;non-model species;populations;pre-exposure;regulating protection;rivers;role;S. Cerevisiae;Saccharomyces cerevisiae;significant impact;southwest;species;synthetic genetic array (SGA) analyses;tolerance;trout;two isoforms;wide variety | 10.1002/jobm.200510609;10.1002/yea.1502;10.1007/s00244-007-9063-8;10.1016/0166-445X(92)90026-J;10.1016/0169-5347(87)90135-2;10.1016/0269-7491(87)90057-1;10.1016/0742-8413(93)90251-F;10.1016/j.aquatox.2014.05.019;10.1016/j.bbagen.2014.01.032;10.1016/j.bbrc.2004.03.003;10.1016/j.cellbi.2004.11.001;10.1016/j.envpol.2011.08.005;10.1016/j.fgb.2010.12.005;10.1016/j.scient.2011.05.015;10.1016/S0065-2504(08)60202-0;10.1016/S0166-445X(02)00131-5;10.1021/es401380p;10.1038/nature03443;10.1074/jbc.M313746200;10.1089/dna.1987.6.519;10.1091/mbc.E08-04-0438;10.1111/1567-1364.12220;10.1111/eva.12266;10.1111/j.1567-1364.2009.00486.x;10.1111/j.1574-6976.2010.00217.x;10.1126/science.1065810;10.1126/science.1180823;10.1128/AEM.62.11.3960-3966.1996;10.1128/MCB.11.1.476;10.1139/f82-215;10.1186/1471-2164-10-524;10.1897/06-376R.1;10.1897/06-380R.1 | Univ Exeter | Paris, J R;Usher, J | Paris, J R: Univ Exeter, Coll Life & Environm Sci, Sch Biosci, Exeter, Devon, England | Paris, Josephine Rosanna;Usher, Jane | MR/N006364/1 | 39 | null | UK | Univ Exeter;UNIV SUSSEX | Paris, Josephine R | Green Published, gold | ADAPTATION;CADMIUM;COPPER;METAL TOLERANCE;POLLUTION;POPULATION;SACCHAROMYCES-CEREVISIAE;SALMO-TRUTTA;TOXICITY;TRANSCRIPTION | Paris, Josephine R.; Usher, Jane; | null | Univ Exeter, Coll Life & Environm Sci, Sch Biosci, Exeter, Devon, England;Univ Sussex, Sch Life Sci, Brighton, E Sussex, England | Univ Exeter, Coll Life & Environm Sci, Sch Biosci, Exeter, Devon, England;Univ Sussex, Sch Life Sci, Brighton, E Sussex, England | null | null | null | 1956;1971;1982;1987;1991;1992;1993;1996;2001;2003;2004;2005;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015 | 2 | Univ Exeter, Coll Life & Environm Sci, Sch Biosci, Exeter, Devon, England | Sci Rep | Usher, Jane | NATURE PUBLISHING GROUP | (i);(ii);(iii);(MetA;(Salmo;(SGA);,;;;a;across;affected;against;analyses;and;approach;approaches;are;array;be;between;binding;body;both;brown;but;by;cerevisiae;control;could;cysteine-rich;demonstrate;determine;detrimentally;differences;driving;earth's;ecology;ecosystems;England;evolution;evolved;examined;experimental;explore;from;functional;genetic;genomics;group;harnessing;has;how;identify;impact;in;influences;interaction;interactions;is;isoforms;isolated;key;known;L;leveraged;made;many;maps;mechanism;MetA;metal;metal-ion;metal-tolerant;metallothionein;metallothioneins;metals;MetB;MetB);model;non-model;occupying;of;on;physiological;polluted;pollution;populations;pre-exposure;protection;proteins;regulating;reside;river;rivers;role;S.;Saccharomyces;significant;southwest;species;such;synthetic;system;that;the;them;these;this;to;tolerance;toxicity;trout;trutta;two;understanding;used;using;variety;we;wide;within;work;yeast | Univ Exeter | Metal pollution has made a significant impact on the earth's ecosystems and tolerance to metals in a wide variety of species has evolved. Metallothioneins, a group of cysteine-rich metal-ion binding proteins, are known to be a key physiological mechanism in regulating protection against metal toxicity. Many rivers across the southwest of England are detrimentally affected by metal pollution, but brown trout (Salmo trutta L.) populations are known to reside within them. In this body of work, two isoforms of metallothionein (MetA and MetB) isolated from trout occupying a polluted and a control river are examined. Using synthetic genetic array (SGA) analyses in the model yeast, Saccharomyces cerevisiae, functional genomics is used to explore the role of metallothionein isoforms in driving metal tolerance. By harnessing this experimental system, S. cerevisiae is used to (i) determine the genetic interaction maps of MetA and MetB isoforms; (ii) identify differences between the genetic interactions in both isoforms and (iii) demonstrate that pre-exposure to metals in metal-tolerant trout influences these interactions. By using a functional genomics approach leveraged from the model yeast Saccharomyces cerevisiae, we demonstrate how such approaches could be used in understanding the ecology and evolution of a non-model species. | ABB-4880-2021;J-1981-2014 | ADAPTATION;CADMIUM;COPPER;METAL TOLERANCE;POLLUTION;POPULATION;SACCHAROMYCES-CEREVISIAE;SALMO-TRUTTA;TOXICITY;TRANSCRIPTION | 0 | null | null | 8 | SACCHAROMYCES-CEREVISIAE;adaptation;CADMIUM;COPPER;METAL TOLERANCE;POLLUTION;POPULATION;SALMO-TRUTTA;TOXICITY;TRANSCRIPTION | WOS:000480678100026 | Univ Exeter, Devon, England;UNIV SUSSEX, E SUSSEX, ENGLAND | UK | 2,019 | null | 0000-0001-6868-3416 | null | null | English | null | Advances in Ecological Research;APPL ENVIRON MICROB;AQUAT TOXICOL;ARCH ENVIRON CON TOX;BBA-GEN SUBJECTS;BIOCHEM BIOPH RES CO;BMC GENOMICS;CAN J FISH AQUAT SCI;CELL BIOL INT;COMP BIOCHEM PHYS C;CORNISH MINING IND B;DNA-J MOLEC CELL BIO;ENVIRON POLLUT;ENVIRON SCI TECHNOL;ENVIRON TOXICOL CHEM;EVOL APPL;FEMS MICROBIOL REV;FEMS YEAST RES;FOOD TECHNOL BIOTECH;FUNGAL GENET BIOL;J BASIC MICROB;J BIOL CHEM;METALLIFEROUS MINING;MOL BIOL CELL;MOL CELL BIOL;NATURE;SCI IRAN;SCIENCE;TRENDS ECOL EVOL;YEAST | Paris, Josephine R;Usher, Jane | 2024-03-11
ER | Alberti, S;Anahid, S;Antonovics J.;Arita, A;Avery, S V;Bonham, K;Brinkman, S F;Bryant, H E;Buckley J. A.;Butler, G;Casagrande, V;Costanzo, M;Dines H. G.;Durrant, C J;Environment Agency Abandoned Mines And The Water Environment;Environment Agency Assessment Of Metal Mining-Contaminated River Sediments In England And Wales;Farmer, H;Hansen, B H;Harper, D D;Hosiner, D;Jiang, L H;Klerks, P L;Liu, Z J;Lushchak, V I;Macnair, M R;Minghetti, M;Pane, E F;Paris, J R;Pimentel, C;Posthuma, L;Roch, M;Roesijadi, G;Serrano, R;Stehlik-Tomas, V;Thorne, T W;Tong, A H Y;Vadkertiová, R;Webster, T M U;Wysocki, R | IQ3UW | Devon, England | 2 | null | 2 | null | 31,413,359 | Paris, Josephine R;Usher, Jane | SCI REP-UK | Devon, England;E SUSSEX, ENGLAND |
Baker, D;Boyken, S E;Dods, G;Dueber, J E;El-Samad, H;Gómez-Schiavon, M;Langan, R A;Ng, A H;Nguyen, T H;Samson, J A;Waldburger, L M | 10.1038/s41586-019-1425-7 | null | MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND | 3x2f2v44i175w5j6hh4e492a551w6r2w1y452h | Modular and tunable biological feedback control using a de novo protein switch | Univ Calif San Francisco | null | El-Samad, H (corresponding author), Chan Zuckerberg Biohub, San Francisco, CA 94158 USA.;El-Samad, H (corresponding author), Univ Calif San Francisco, Cell Design Initiat, San Francisco, CA 94143 USA.;El-Samad, H (corresponding author), Univ Calif San Francisco, Dept Biochem & Biophys, San Francisco, CA 94143 USA. | null | Baker, David;Boyken, Scott E;Dods, Galen;Dueber, John E;El-Samad, Hana;Gomez-Schiavon, Mariana;Langan, Robert A;Ng, Andrew H;Nguyen, Taylor H;Samson, Jennifer A;Waldburger, Lucas M | Multidisciplinary Sciences | Defense Advanced Research Projects Agency [HR0011-16-2-0045]; Department of Defense (DoD) through the National Defense Science & Engineering Graduate Fellowship (NDSEG) Program; Scientific Interface from Burroughs Wellcome Fund | WOS | El-Samad, H | Chan Zuckerberg Biohub, San Francisco, CA USA;Univ Calif Berkeley, Berkeley, CA USA;Univ Calif San Francisco, San Francisco, CA USA;Univ Washington, Seattle, WA USA | 572 | a;and;biological;control;de;feedback;Modular;novo;protein;Switch;tunable;using | 1 | Boyken, Scott;Dods, Galen;Gómez-Schiavon, Mariana;Nguyen, Taylor | NATURE PUBLISHING GROUP | Chan Zuckerberg Biohub, San Francisco, CA 94158 USA;Univ Calif Berkeley, Dept Bioengn, Berkeley, CA 94720 USA;Univ Calif Berkeley, UCSF Grad Program Bioengn, Berkeley, CA USA;Univ Calif San Francisco, Cell Design Initiat, San Francisco, CA 94143 USA;Univ Calif San Francisco, Dept Biochem & Biophys, San Francisco, CA 94143 USA;Univ Calif San Francisco, Dept Biochem & Biophys, San Francisco, CA 94143 USA.; El-Samad, H (corresponding author), Univ Calif San Francisco, Cell Design Initiat, San Francisco, CA 94143 USA.; El-Samad, H (corresponding author), Chan Zuckerberg Biohub, San Francisco, CA 94158 USA;Univ Washington, Dept Biochem, Seattle, WA 98195 USA;Univ Washington, Grad Program Biol Phys Struct & Design, Seattle, WA 98195 USA;Univ Washington, Howard Hughes Med Inst, Seattle, WA 98195 USA;Univ Washington, Inst Prot Design, Seattle, WA 98195 USA | Article | Chan Zuckerberg Biohub;Univ Calif San Francisco | LONDON | null | null | Chan Zuckerberg Biohub;Univ Calif Berkeley;Univ Calif San Francisco;Univ Washington | Defense Advanced Research Projects Agency;Department of Defense (DoD) through the National Defense Science & Engineering Graduate Fellowship (NDSEG) Program;Scientific Interface from Burroughs Wellcome Fund | El-Samad, H (corresponding author), Univ Calif San Francisco, Dept Biochem & Biophys, San Francisco, CA 94143 USA.; El-Samad, H (corresponding author), Univ Calif San Francisco, Cell Design Initiat, San Francisco, CA 94143 USA.; El-Samad, H (corresponding author), Chan Zuckerberg Biohub, San Francisco, CA 94158 USA. | + | Baker, David;Boyken, Scott E;Dods, Galen;Dueber, John E;El-Samad, Hana;Gomez-Schiavon, Mariana;Langan, Robert A;Ng, Andrew H;Nguyen, Taylor H;Samson, Jennifer A;Waldburger, Lucas M | 113 | 9 | 479,172,800,051 | Defense Advanced Research Projects Agency [HR0011-16-2-0045];Department of Defense (DoD) through the National Defense Science & Engineering Graduate Fellowship (NDSEG) Program;Scientific Interface from Burroughs Wellcome Fund | USA | NATURE | USA;USA.; | null | null | Univ Calif San Francisco, Dept Biochem & Biophys, San Francisco, CA 94143 USA | 0028-0836 | Baker, D;Boyken, S E;Dods, G;Dueber, J E;El-Samad, H;Gómez-Schiavon, M;Langan, R A;Ng, A H;Nguyen, T H;Samson, J A;Waldburger, L M | AUG 8 | hana.el-samad@ucsf.edu | de novo protein switch;tunable biological feedback control | 11 | J | Science & Technology - Other Topics | 'latching orthogonal cage-key proteins' (LOCKR) technology(8)-is;ability;biotechnological;building blocks;cells;CIRCUITS;complex endogenous pathways;de novo design;de novo protein switch;de novo-designed proteins(1-3) hold great promise;DEGRADATION;degronLOCKR;degronLOCKR proteins;DESIGN;designed nature;designer protein-degronLOCKR;ease;feedback behaviour;feedback capabilities;feedback control;feedback control circuit;full potential;GENE-EXPRESSION;implement complex synthetic functionalities;important milestone;induction;interest;KINASE;living cells;mating pathway;MOLECULES;natural proteins(4-7);one;operational range;pathways;plug-and-play nature;Positive feedback;PROTEIN;proteins;rational modifications;simple;small peptide;strategy;SWITCH;synthetic biology(10,11,12);synthetic circuit;synthetic circuits;synthetic gene circuit(9);synthetic gene circuits;synthetic negative;therapeutic applications;tunable biological feedback control;untapped potential;use;VARIANTS;vivo;yeast;yeast mating pathway | Ng, A H | CIRCUITS;DEGRADATION;DESIGN;GENE-EXPRESSION;KINASE;YEAST | 265 | [Ng, Andrew H.; Nguyen, Taylor H.; Gomez-Schiavon, Mariana; Dods, Galen; El-Samad, Hana] Univ Calif San Francisco, Dept Biochem & Biophys, San Francisco, CA 94143 USA. [Ng, Andrew H.; Samson, Jennifer A.; Waldburger, Lucas M.; Dueber, John E.] Univ Calif Berkeley, Dept Bioengn, Berkeley, CA 94720 USA. [Ng, Andrew H.] Univ Calif Berkeley, UCSF Grad Program Bioengn, Berkeley, CA USA. [Ng, Andrew H.; El-Samad, Hana] Univ Calif San Francisco, Cell Design Initiat, San Francisco, CA 94143 USA. [Langan, Robert A.; Boyken, Scott E.; Baker, David] Univ Washington, Dept Biochem, Seattle, WA 98195 USA. [Langan, Robert A.; Boyken, Scott E.; Baker, David] Univ Washington, Inst Prot Design, Seattle, WA 98195 USA. [Langan, Robert A.] Univ Washington, Grad Program Biol Phys Struct & Design, Seattle, WA 98195 USA. [Baker, David] Univ Washington, Howard Hughes Med Inst, Seattle, WA 98195 USA. [El-Samad, Hana] Chan Zuckerberg Biohub, San Francisco, CA 94158 USA. | We thank W. Lim, O. Weiner, and M. Lajoie for helpful discussions and P. Harrigan for assistance with hardware. This work was supported by the Defense Advanced Research Projects Agency, Contract No. HR0011-16-2-0045 to H.E.-S. The content and information does not necessarily reflect the position or the policy of the government, and no official endorsement should be inferred. H.E.-S. is a Chan-Zuckerberg investigator. A.H.N. was supported by the Department of Defense (DoD) through the National Defense Science & Engineering Graduate Fellowship (NDSEG) Program. R.A.L. was supported by Bruce and Jeannie Nordstrom, thanks to the Patty and Jimmy Barrier Gift for the Institute for Protein Design Directors Fund. S.E.B. is supported by a Career Award at the Scientific Interface from Burroughs Wellcome Fund. | 'latching orthogonal cage-key proteins' (LOCKR) technology(8)-is;ability;biotechnological;building blocks;cells;complex endogenous pathways;de novo design;de novo-designed proteins(1-3) hold great promise;degronLOCKR;degronLOCKR proteins;designed nature;designer protein-degronLOCKR;ease;feedback behaviour;feedback capabilities;feedback control;feedback control circuit;full potential;implement complex synthetic functionalities;important milestone;induction;interest;living cells;mating pathway;molecules;natural proteins(4-7);one;operational range;pathways;plug-and-play nature;positive feedback;protein;proteins;rational modifications;simple;small peptide;strategy;switch;synthetic biology(10,11,12);synthetic circuit;synthetic circuits;synthetic gene circuit(9);synthetic gene circuits;synthetic negative;therapeutic applications;untapped potential;use;variants;vivo;yeast mating pathway | 10.1016/j.cell.2009.06.013;10.1016/j.cell.2017.01.016;10.1016/j.cell.2018.09.044;10.1016/j.chembiol.2013.03.005;10.1016/j.peptides.2004.10.001;10.1021/acssynbio.6b00251;10.1021/sb500366v;10.1038/nature11259;10.1038/nature19946;10.1038/nbt.2149;10.1038/ncb2097;10.1038/s41586-018-0802-y;10.1038/s41586-019-1321-1;10.1038/s41586-019-1432-8;10.1074/jbc.M211802200;10.1098/rsif.2016.0380;10.1126/science.1151153;10.1126/science.aad8865;10.1126/science.aap8987;10.1126/science.aat0271;10.1126/science.aat5062;10.1126/science.aau8287;10.1128/MCB.00361-10;[10.1016/j.cels.2016.01.004, 10.1016/j.cels.2016.02.010] | Univ Calif San Francisco | Baker, D;Boyken, S E;Dods, G;Dueber, J E;El-Samad, H;Gómez-Schiavon, M;Langan, R A;Ng, A H;Nguyen, T H;Samson, J A;Waldburger, L M | Ng, A H: Univ Calif San Francisco, Dept Biochem & Biophys, San Francisco, CA 94143 USA | Gómez-Schiavon, Mariana | HR0011-16-2-0045 | 25 | null | USA | Chan Zuckerberg Biohub;Univ Calif Berkeley;Univ Calif San Francisco;Univ Washington | Ng, Andrew H | null | CIRCUITS;DEGRADATION;DESIGN;GENE-EXPRESSION;KINASE;YEAST | Ng, Andrew H.; Nguyen, Taylor H.; Gomez-Schiavon, Mariana; Dods, Galen; Langan, Robert A.; Boyken, Scott E.; Samson, Jennifer A.; Waldburger, Lucas M.; Dueber, John E.; Baker, David; El-Samad, Hana; | null | Chan Zuckerberg Biohub, San Francisco, CA 94158 USA;Univ Calif Berkeley, Dept Bioengn, Berkeley, CA 94720 USA;Univ Calif Berkeley, UCSF Grad Program Bioengn, Berkeley, CA USA;Univ Calif San Francisco, Cell Design Initiat, San Francisco, CA 94143 USA;Univ Calif San Francisco, Dept Biochem & Biophys, San Francisco, CA 94143 USA;Univ Washington, Dept Biochem, Seattle, WA 98195 USA;Univ Washington, Grad Program Biol Phys Struct & Design, Seattle, WA 98195 USA;Univ Washington, Howard Hughes Med Inst, Seattle, WA 98195 USA;Univ Washington, Inst Prot Design, Seattle, WA 98195 USA | Chan Zuckerberg Biohub, San Francisco, CA 94158 USA;Univ Calif Berkeley, Dept Bioengn, Berkeley, CA 94720 USA;Univ Calif Berkeley, UCSF Grad Program Bioengn, Berkeley, CA USA;Univ Calif San Francisco, Cell Design Initiat, San Francisco, CA 94143 USA;Univ Calif San Francisco, Dept Biochem & Biophys, San Francisco, CA 94143 USA;Univ Washington, Dept Biochem, Seattle, WA 98195 USA;Univ Washington, Grad Program Biol Phys Struct & Design, Seattle, WA 98195 USA;Univ Washington, Howard Hughes Med Inst, Seattle, WA 98195 USA;Univ Washington, Inst Prot Design, Seattle, WA 98195 USA | 1476-4687 | null | 7768 | 1975;2003;2005;2008;2009;2010;2012;2013;2015;2016;2017;2018;2019 | 73 | Chan Zuckerberg Biohub, San Francisco, CA 94158 USA;Univ Calif San Francisco, Cell Design Initiat, San Francisco, CA 94143 USA;Univ Calif San Francisco, Dept Biochem & Biophys, San Francisco, CA 94143 USA | Nature | El-Samad, Hana | NATURE PUBLISHING GROUP | 'latching;(LOCKR);,;a;ability;achieving;an;and;applications;as;based;be;behaviour;biology(10,11,12);biotechnological;blocks;both;broadly;building;by;cage-key;can;capabilities;cells;circuit;circuit(9);circuits;complement;complex;control;de;degrades;degronLOCKR;demonstrates;design;designed;designer;ease;enables;encoded;endogenous;engineer;engineered;evaluate;feedback;first;for;full;functionalities;fusing;gene;generate;generating;genetically;great;here;hold;illustrating;implement;important;in;induction;interest;into;is;large;leverage;living;mating;mediated;milestone;modifications;molecules;more;natural;nature;negative;next;novo;novo-designed;of;on;one;operational;Orthogonal;pathway;pathways;peptide;plug-and-play;positive;potential;promise;protein;protein-degronLOCKR;proteins;proteins';proteins(1-3);proteins(4-7);quantify;range;rational;represents;rewire;signalling;simple;small;strategy;such;switch;synthetic;technology(8)-is;that;the;therapeutic;this;to;tools;tune;untapped;upon;use;used;variants;vivo;we;which;with;work;yeast | Chan Zuckerberg Biohub;Univ Calif San Francisco | De novo-designed proteins(1-3) hold great promise as building blocks for synthetic circuits, and can complement the use of engineered variants of natural proteins(4-7). One such designer protein-degronLOCKR, which is based on 'latching orthogonal cage-key proteins' (LOCKR) technology(8)-is a switch that degrades a protein of interest in vivo upon induction by a genetically encoded small peptide. Here we leverage the plug-and-play nature of degronLOCKR to implement feedback control of endogenous signalling pathways and synthetic gene circuits. We first generate synthetic negative and positive feedback in the yeast mating pathway by fusing degronLOCKR to endogenous signalling molecules, illustrating the ease with which this strategy can be used to rewire complex endogenous pathways. We next evaluate feedback control mediated by degronLOCKR on a synthetic gene circuit(9), to quantify the feedback capabilities and operational range of the feedback control circuit. The designed nature of degronLOCKR proteins enables simple and rational modifications to tune feedback behaviour in both the synthetic circuit and the mating pathway. The ability to engineer feedback control into living cells represents an important milestone in achieving the full potential of synthetic biology(10,11,12). More broadly, this work demonstrates the large and untapped potential of de novo design of proteins for generating tools that implement complex synthetic functionalities in cells for biotechnological and therapeutic applications. | AAC-7322-2019 | CIRCUITS;DEGRADATION;DESIGN;GENE-EXPRESSION;KINASE;YEAST | 4 | null | null | 17 | YEAST;CIRCUITS;DEGRADATION;DESIGN;GENE-EXPRESSION;KINASE | WOS:000479172800051 | Chan Zuckerberg Biohub, San Francisco, CA USA;Univ Calif Berkeley, Berkeley, CA USA;Univ Calif San Francisco, San Francisco, CA USA;Univ Washington, Seattle, WA USA | USA | 2,019 | null | 0000-0001-5512-835X;0000-0002-0955-7257;0000-0002-1288-8882;0000-0002-5378-0632 | null | null | English | null | ACS SYNTH BIOL;CELL;CELL SYST;CHEM BIOL;J BIOL CHEM;J R SOC INTERFACE;MOL CELL BIOL;NAT BIOTECHNOL;NAT CELL BIOL;NATURE;PEPTIDES;SCIENCE | Baker, David;Boyken, Scott E;Dods, Galen;Dueber, John E;El-Samad, Hana;Gomez-Schiavon, Mariana;Langan, Robert A;Ng, Andrew H;Nguyen, Taylor H;Samson, Jennifer A;Waldburger, Lucas M | 2024-03-11
ER | Andrews, L B;Aoki, S K;Aranda-Díaz, A;Bardwell, L;Bashor, C J;Boyken, S E;Briat, C;Chen, R E;Chen, Z B;Del Vecchio, D;Gao, X J;Harrigan, P;Hoyt, M A;Huang, P S;Langan, R A;Lee, M E;Lim, W A;Ma, W Z;Mccullagh, E;Moore G. E.;Renicke, C;Toda, S;Wei, P;Zhang, F Z | IO1WO | San Francisco, CA USA;San Francisco, CA USA. | 101 | null | 4 | null | 31,341,280 | Baker, David;Boyken, Scott E;Dods, Galen;Dueber, John E;El-Samad, Hana;Gomez-Schiavon, Mariana;Langan, Robert A;Ng, Andrew H;Nguyen, Taylor H;Samson, Jennifer A;Waldburger, Lucas M | NATURE | Berkeley, CA USA;San Francisco, CA USA;Seattle, WA USA |
Watanabe, N;Yang, Z Y;Zeng, L T | 10.1080/10408398.2018.1506907 | null | 530 WALNUT STREET, STE 850, PHILADELPHIA, PA 19106 USA | 6k4ym5fu3z5h3f542m24n3m6h6a5aq94j8 | Understanding the biosyntheses and stress response mechanisms of aroma compounds in tea (<i>Camellia sinensis</i>) to safely and effectively improve tea aroma | Chinese Acad Sci | null | Yang, ZY (corresponding author), Chinese Acad Sci, Guangdong Prov Key Lab Appl Bot, South China Bot Garden, Xingke Rd 723, Guangzhou 510650, Guangdong, Peoples R China.;Yang, ZY (corresponding author), Chinese Acad Sci, Key Lab South China Agr Plant Mol Anal & Genet Im, South China Bot Garden, Xingke Rd 723, Guangzhou 510650, Guangdong, Peoples R China. | null | Watanabe, Naoharu;Yang, Ziyin;Zeng, Lanting | Food Science & Technology;Nutrition & Dietetics | National Natural Science Foundation of China [31670690, 31601787, 31500244]; National Key Research and Development Program of China; Guangdong Natural Science Foundation [2016A030313652, 2016A030306039, 2014A030310131]; Guangdong Innovation Team of Modern Agricultural Industry Technology System [2017LM1143]; Guangdong Special Support Plan for Training High-Level Talents [2016TQ03N617] | WOS | Yang, Z Y | Chinese Acad Sci, Guangdong, Peoples R China;Shizuoka Univ, Shizuoka, Japan;Univ Chinese Acad Sci, Beijing, Peoples R China | 59 | (<i>Camellia;and;aroma;biosyntheses;compounds;effectively;improve;in;mechanisms;of;response;safely;sinensis</i>);stress;tea;the;to;understanding | 2 | null | TAYLOR & FRANCIS INC | Chinese Acad Sci, Guangdong Prov Key Lab Appl Bot, South China Bot Garden, Xingke Rd 723, Guangzhou 510650, Guangdong, Peoples R China;Chinese Acad Sci, Key Lab South China Agr Plant Mol Anal & Genet Im, South China Bot Garden, Xingke Rd 723, Guangzhou 510650, Guangdong, Peoples R China;Chinese Acad Sci, Key Lab South China Agr Plant Mol Anal & Genet Im, South China Bot Garden, Xingke Rd 723, Guangzhou 510650, Guangdong, Peoples R China.; Yang, ZY (corresponding author), Chinese Acad Sci, Guangdong Prov Key Lab Appl Bot, South China Bot Garden, Xingke Rd 723, Guangzhou 510650, Guangdong, Peoples R China;Shizuoka Univ, Grad Sch Sci & Technol, Naka Ku, Hamamatsu, Shizuoka, Japan;Univ Chinese Acad Sci, Coll Adv Agr Sci, Beijing, Peoples R China | Review | Chinese Acad Sci | PHILADELPHIA | null | null | Chinese Acad Sci;Shizuoka Univ;Univ Chinese Acad Sci | Guangdong Innovation Team of Modern Agricultural Industry Technology System;Guangdong Natural Science Foundation;Guangdong Special Support Plan for Training High-Level Talents;National Key Research and Development Program of China;National Natural Science Foundation of China | Yang, ZY (corresponding author), Chinese Acad Sci, Key Lab South China Agr Plant Mol Anal & Genet Im, South China Bot Garden, Xingke Rd 723, Guangzhou 510650, Guangdong, Peoples R China.; Yang, ZY (corresponding author), Chinese Acad Sci, Guangdong Prov Key Lab Appl Bot, South China Bot Garden, Xingke Rd 723, Guangzhou 510650, Guangdong, Peoples R China. | 2334 | Watanabe, Naoharu;Yang, Ziyin;Zeng, Lanting | 581 | 4 | 477,963,300,011 | Guangdong Innovation Team of Modern Agricultural Industry Technology System [2017LM1143];Guangdong Natural Science Foundation [2016A030313652, 2016A030306039, 2014A030310131];Guangdong Special Support Plan for Training High-Level Talents [2016TQ03N617];National Key Research and Development Program of China;National Natural Science Foundation of China [31670690, 31601787, 31500244] | China;Japan | CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION | China | null | null | Chinese Acad Sci, Key Lab South China Agr Plant Mol Anal & Genet Im, South China Bot Garden, Xingke Rd 723, Guangzhou 510650, Guangdong, Peoples R China | 1040-8398 | Watanabe, N;Yang, Z Y;Zeng, L T | AUG 6 | zyyang@scbg.ac.cn | aroma compounds;biosyntheses;stress response mechanisms;tea (<i>Camellia sinensis</i>);tea aroma | 3 | J | Food Science & Technology;Nutrition & Dietetics | 1-PHENYLETHANOL;abiotic stress (such;abundant accumulation;Aroma;aroma compounds;aroma formation;aroma synthetic genes;BETA-PRIMEVEROSIDASE;BIOCHEMICAL FORMATION;biosyntheses;biosynthesis;biotic stress (such;BLACK TEA;Camellia sinensis;characteristic aroma;characteristic aroma compounds;characterized;crops;defense responses;environmental response;environmental stresses;evolutionary process;expression;GENE-EXPRESSION;important factor affecting tea character;important quality components;improving tea quality;increasing research interest;key;key enzyme;LEAVES;light;LINALOOL;metabolite formation;metabolites help;natural quality components;o. Kuntze);oolong tea;phenylpropanoids/benzenoids;physiological feature;PLANT VOLATILES;plants;popular beverage;postharvest (tea manufacturing) processing;preharvest (tea growth process);quality;recent investigations;result;several characteristic aroma compounds;several key aroma synthetic genes;specific relationships;Stress;stress response;stress response mechanisms;stresses;Tea;tea (<i>Camellia sinensis</i>);tea aroma;tea green leafhopper attack);tea leaves;tea plant (Camellia sinensis (L;teas;temperature;tender shoots;terpenes;volatile fatty acid derivatives;volatiles;WATER;wounding) | Zeng, L T | 1-PHENYLETHANOL;Aroma;BETA-PRIMEVEROSIDASE;BIOCHEMICAL FORMATION;BIOSYNTHESIS;BLACK TEA;Camellia sinensis;GENE-EXPRESSION;KEY ENZYME;LEAVES;LINALOOL;OOLONG TEA;PLANT VOLATILES;Stress;Tea;volatiles | 2321 | [Zeng, Lanting; Yang, Ziyin] Chinese Acad Sci, Key Lab South China Agr Plant Mol Anal & Genet Im, South China Bot Garden, Xingke Rd 723, Guangzhou 510650, Guangdong, Peoples R China. [Zeng, Lanting; Yang, Ziyin] Chinese Acad Sci, Guangdong Prov Key Lab Appl Bot, South China Bot Garden, Xingke Rd 723, Guangzhou 510650, Guangdong, Peoples R China. [Zeng, Lanting; Yang, Ziyin] Univ Chinese Acad Sci, Coll Adv Agr Sci, Beijing, Peoples R China. [Watanabe, Naoharu] Shizuoka Univ, Grad Sch Sci & Technol, Naka Ku, Hamamatsu, Shizuoka, Japan. | A part of the research aspects done by the authors are supported by the financial supports from the National Natural Science Foundation of China (31670690, 31601787, and 31500244), the National Key Research and Development Program of China, the Guangdong Natural Science Foundation (2016A030313652, 2016A030306039, and 2014A030310131), the Guangdong Innovation Team of Modern Agricultural Industry Technology System (2017LM1143), and the Guangdong Special Support Plan for Training High-Level Talents (2016TQ03N617). | abiotic stress (such;abundant accumulation;aroma;aroma formation;aroma synthetic genes;biosyntheses;biotic stress (such;characteristic aroma;characteristic aroma compounds;characterized;crops;defense responses;environmental response;environmental stresses;evolutionary process;expression;important factor affecting tea character;important quality components;improving tea quality;increasing research interest;key;leaves;light;metabolite formation;metabolites help;natural quality components;o. Kuntze);phenylpropanoids/benzenoids;physiological feature;plants;popular beverage;postharvest (tea manufacturing) processing;preharvest (tea growth process);quality;recent investigations;result;several characteristic aroma compounds;several key aroma synthetic genes;specific relationships;stress response;stresses;tea;tea green leafhopper attack);tea leaves;tea plant (Camellia sinensis (L;teas;temperature;tender shoots;terpenes;volatile fatty acid derivatives;water;wounding) | 10.1007/978-0-387-85498-4_7;10.1007/BF00046410;10.1007/s10886-007-9344-8;10.1007/s11703-007-0015-x;10.1007/S11703-007-0015-X];10.1007/s13197-017-2558-z;10.1016/j.aca.2006.01.001;10.1016/j.envexpbot.2018.02.005;10.1016/j.foodchem.2012.07.066;10.1016/j.foodchem.2013.10.069;10.1016/j.foodchem.2017.03.122;10.1016/j.foodchem.2017.05.124;10.1016/j.foodchem.2017.05.137;10.1016/j.foodchem.2018.03.095;10.1016/j.foodchem.2018.07.056;10.1016/j.foodres.2013.02.011;10.1016/j.foodres.2017.03.049;10.1016/j.phytochem.2008.08.023;10.1016/j.tplants.2005.11.002;10.1016/j.tplants.2007.06.001;10.1016/j.tplants.2011.01.006;10.1016/S1369-5266(02)00251-0;10.1021/acs.jafc.5b02741;10.1021/acs.jafc.5b05072;10.1021/acs.jafc.5b05748;10.1021/acs.jafc.6b01742;10.1021/acs.jafc.7b04575;10.1021/acs.jafc.8b00515;10.1021/jf001077+;10.1021/jf010235+;10.1021/jf010681x;10.1021/jf052495n;10.1021/jf203396a;10.1021/jf5022658;10.1021/jf60230a037;10.1038/s41477-017-0063-z;10.1038/srep16858;10.1039/c7ra03219f;10.1073/pnas.0602328103;10.1073/pnas.0705947104;10.1073/pnas.92.6.2036;10.1074/mcp.M114.038190;10.1080/00021369.1980.10864444;10.1080/10942910902716976;10.1093/aob/mci165;10.1093/jn/133.10.3285S;10.1093/pcp/pcy091;10.1104/pp.102.011023;10.1104/pp.104.051144;10.1104/pp.111.185710;10.1104/pp.15.00403;10.1111/nph.12145;10.1111/nph.14929;10.1111/pce.13080;10.1111/tpj.13822;10.1126/science.1191634;10.1126/science.276.5314.945;10.1146/annurev.pp.33.060182.002405;10.1186/s13007-018-0285-8;10.1271/bbb.60708;10.1271/bbb.65.2719;10.1890/10-1945.1;10.3390/molecules21020124;10.4236/AJAC.2014.59070, 10.4236/ajac.2014.59070];[10.1104/pp.010280, 10.1104/pp.127.2.685] | Chinese Acad Sci | Watanabe, N;Yang, Z Y;Zeng, L T | Zeng, L T: Chinese Acad Sci, Key Lab South China Agr Plant Mol Anal & Genet Im, South China Bot Garden, Xingke Rd 723, Guangzhou 510650, Guangdong, Peoples R China | Watanabe, Naoharu;Zeng, lanting | 2014A030310131;2016A030306039;2016A030313652;2016TQ03N617;2017LM1143;31500244;31601787;31670690 | 72 | null | China | Chinese Acad Sci;Shizuoka Univ;Univ Chinese Acad Sci | Zeng, Lanting | null | 1-PHENYLETHANOL;BETA-PRIMEVEROSIDASE;BIOCHEMICAL FORMATION;BLACK TEA;GENE-EXPRESSION;KEY ENZYME;LEAVES;LINALOOL;OOLONG TEA;PLANT VOLATILES | Zeng, Lanting; Watanabe, Naoharu; Yang, Ziyin; | null | Chinese Acad Sci, Guangdong Prov Key Lab Appl Bot, South China Bot Garden, Xingke Rd 723, Guangzhou 510650, Guangdong, Peoples R China;Chinese Acad Sci, Key Lab South China Agr Plant Mol Anal & Genet Im, South China Bot Garden, Xingke Rd 723, Guangzhou 510650, Guangdong, Peoples R China;Shizuoka Univ, Grad Sch Sci & Technol, Naka Ku, Hamamatsu, Shizuoka, Japan;Univ Chinese Acad Sci, Coll Adv Agr Sci, Beijing, Peoples R China | Chinese Acad Sci, Guangdong Prov Key Lab Appl Bot, South China Bot Garden, Xingke Rd 723, Guangzhou 510650, Guangdong, Peoples R China;Chinese Acad Sci, Key Lab South China Agr Plant Mol Anal & Genet Im, South China Bot Garden, Xingke Rd 723, Guangzhou 510650, Guangdong, Peoples R China;Shizuoka Univ, Grad Sch Sci & Technol, Naka Ku, Hamamatsu, Shizuoka, Japan;Univ Chinese Acad Sci, Coll Adv Agr Sci, Beijing, Peoples R China | 1549-7852 | Aroma;biosynthesis;Camellia sinensis;Stress;Tea;volatiles | 14 | 1980;1982;1987;1995;1997;2001;2002;2003;2005;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016;2017;2018;2019 | 151 | Chinese Acad Sci, Guangdong Prov Key Lab Appl Bot, South China Bot Garden, Xingke Rd 723, Guangzhou 510650, Guangdong, Peoples R China;Chinese Acad Sci, Key Lab South China Agr Plant Mol Anal & Genet Im, South China Bot Garden, Xingke Rd 723, Guangzhou 510650, Guangdong, Peoples R China | Crit. Rev. Food Sci. Nutr. | Yang, Ziyin | TAYLOR & FRANCIS INC | (Camellia;(L;(such;(tea;,;a;abiotic;abundant;accumulation;acid;affecting;after;against;also;an;and;are;aroma;as;attack);attracted;been;between;beverage;biochemical;biosyntheses;biotic;but;by;can;character;characteristic;characterized;cloned;components;compounds;could;crops;defend;defense;derivatives;derived;developed;during;effectively;enhance;environmental;evolutionary;expression;factor;fatty;feature;formation;from;functionally;genes;green;growth;has;have;help;herein;important;improve;improving;in;increasing;interest;into;investigations;is;isolated;key;Kuntze);leafhopper;leaves;light;manufacturing);metabolite;metabolites;most;natural;o.;of;or;phenylpropanoids/benzenoids;physiological;plant;plants;popular;postharvest;preharvest;prevalent;process;process);processed;processing;quality;recent;relationships;research;response;responses;result;resulting;safely;second;sequenced;several;shoots;sinensis;specific;stress;stresses;summarize;synthetic;tea;teas;temperature;tender;terpenes;the;these;to;understanding;utilizing;various;volatile;water;we;which;worldwide;wounding) | Chinese Acad Sci | Metabolite formation is a biochemical and physiological feature of plants developed as an environmental response during the evolutionary process. These metabolites help defend plants against environmental stresses, but are also important quality components in crops. Utilizing the stress response to improve natural quality components in plants has attracted increasing research interest. Tea, which is processed by the tender shoots or leaves of tea plant (Camellia sinensis (L.) O. Kuntze), is the second most popular beverage worldwide after water. Aroma is an important factor affecting tea character and quality. The defense responses of tea leaves against various stresses during preharvest (tea growth process) and postharvest (tea manufacturing) processing can result in aroma formation. Herein, we summarize recent investigations into the biosyntheses of several characteristic aroma compounds prevalent in teas and derived from volatile fatty acid derivatives, terpenes, and phenylpropanoids/benzenoids. Several key aroma synthetic genes from tea leaves have been isolated, cloned, sequenced, and functionally characterized. Biotic stress (such as tea green leafhopper attack) and abiotic stress (such as light, temperature, and wounding) could enhance the expression of aroma synthetic genes, resulting in the abundant accumulation of characteristic aroma compounds in tea leaves. Understanding the specific relationships between characteristic aroma compounds and stresses is key to improving tea quality safely and effectively. | AAG-7919-2019;JAA-9491-2023 | 1-PHENYLETHANOL;BETA-PRIMEVEROSIDASE;BIOCHEMICAL FORMATION;BLACK TEA;GENE-EXPRESSION;KEY ENZYME;LEAVES;LINALOOL;OOLONG TEA;PLANT VOLATILES | 67 | null | Aroma;biosynthesis;Camellia sinensis;Stress;Tea;volatiles | 14 | 1-PHENYLETHANOL;Aroma;BETA-PRIMEVEROSIDASE;BIOCHEMICAL FORMATION;BIOSYNTHESIS;BLACK TEA;Camellia sinensis;GENE-EXPRESSION;KEY ENZYME;LEAVES;LINALOOL;OOLONG TEA;PLANT VOLATILES;Stress;Tea;volatiles | WOS:000477963300011 | Chinese Acad Sci, Guangdong, Peoples R China;Shizuoka Univ, Shizuoka, Japan;Univ Chinese Acad Sci, Beijing, Peoples R China | China;Japan | 2,019 | null | null | null | null | English | null | Acta Agronomica Sinica;Adv Biochem Eng Biotechnol;ADV CHALLENGES FLAVO;AGR BIOL CHEM TOKYO;AGROFOREST SYST;AM J ANAL CHEM;ANAL CHIM ACTA;ANN BOT-LONDON;ANNU REV PLANT PHYS;BIOSCI BIOTECH BIOCH;CURR OPIN PLANT BIOL;ECOLOGY;ENVIRON EXP BOT;FOOD CHEM;FOOD RES INT;FRONT AGRI CHINA;Frontiers of Agriculture in China;Function;INT J FOOD PROP;J AGR FOOD CHEM;J CHEM ECOL;J FOOD SCI TECH MYS;J NUTR;MOL CELL PROTEOMICS;MOLECULES;NAT PLANTS;NEW PHYTOL;P NATL ACAD SCI USA;PHYTOCHEMISTRY;PLANT CELL ENVIRON;PLANT CELL PHYSIOL;PLANT J;PLANT METHODS;PLANT PHYSIOL;RSC ADV;SCI REP-UK;SCIENCE;Tea Biochemistry;THESIS;TRENDS PLANT SCI | Watanabe, Naoharu;Yang, Ziyin;Zeng, Lanting | 2024-03-11
ER | [Anonymous];Ai, Z Y;Alagarsamy, K;Alborn, H T;Allmann, S;Arrivault, S;Baldermann S.;Beer, J;Bonaventure, G;Cao F.R.;Cao Panrong;Cho, J Y;Cui, J L;Deng, W W;Dong, F;Dudareva, N;Etoh, H;Farré, E M;Franklin, K A;Fu, X M;Gui, J D;Han, B Y;Heskes, A M;Ishiwari, H;Jang, J;Katsuno, T;Kessler, A;Kinoshita, T;Liu X.;Liu, G F;Luan, F;Ma, S J;Maffei, M E;Mattiacci, L;Mei, X;Mittler, R;Mizutani, M;O'Connor, S;Ohgami, S;Peng Zhang;Pichersky, E;Rietveld, A;Schmelz, E A;Schuh, C;Schullehner, K;Smith, H;Tocci, N;Tohge, T;Underwood, B A;Wan X.C.;Wang, D M;Wang, X Q;Williams, P J;Winterhalter, P;Xu, Q S;Yang Z. Y.;Yang, Z Y;Zeng, L T;Zhao, X;Zhou, Y;Zhu, J Y | IM4KL | Guangdong, Peoples R China;Guangdong, Peoples R China. | 181 | null | 3 | null | 30,277,806 | Watanabe, Naoharu;Yang, Ziyin;Zeng, Lanting | CRIT REV FOOD SCI | Beijing, Peoples R China;Guangdong, Peoples R China;Shizuoka, Japan |
Bai, P;Fussenegger, M;Hamri, G C E;Liu, Y;Saxena, P;Xie, M Q;Xue, S;Ye, H F | 10.1038/s41591-019-0501-8 | null | 75 VARICK ST, 9TH FLR, NEW YORK, NY 10013-1917 USA | 4g195n2k526o732mf3u4e3d1s1qg3l5y613d40 | A fully human transgene switch to regulate therapeutic protein production by cooling sensation | Swiss Fed Inst Technol | null | Fussenegger, M (corresponding author), Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland.;Fussenegger, M (corresponding author), Univ Basel, Fac Sci, Basel, Switzerland. | null | Bai, Peng;Fussenegger, Martin;Hamri, Ghislaine Charpin-El;Liu, Ying;Saxena, Pratik;Xie, Mingqi;Xue, Shuai;Ye, Haifeng | Biochemistry & Molecular Biology;Cell Biology;Medicine, Research & Experimental | Chinese Scholarship Council; National Centre of Competence in Research Molecular Systems Engineering; European Research Council [785800]; National Natural Science Foundation of China [31861143016]; Science and Technology Commission of Shanghai Municipality [18JC1411000]; Thousand Youth Talents Plan of China | WOS | Fussenegger, M | East China Normal Univ, Shanghai, Peoples R China;Inst Univ Technol Lyon, Villeurbanne, France;Swiss Fed Inst Technol, Basel, Switzerland;Univ Basel, Basel, Switzerland | 25 | a;by;cooling;fully;human;production;protein;regulate;sensation;Switch;therapeutic;to;transgene | 3 | Fussenegger, Martin;Xie, Mingqi;Ye, Haifeng | NATURE PUBLISHING GROUP | East China Normal Univ, Sch Life Sci, Shanghai, Peoples R China;East China Normal Univ, Shanghai Key Lab Regulatory Biol, Inst Biomed Sci, Shanghai, Peoples R China;Inst Univ Technol Lyon 1, Dept Genie Biol, Villeurbanne, France;Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland;Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland.; Fussenegger, M (corresponding author), Univ Basel, Fac Sci, Basel, Switzerland;Univ Basel, Fac Sci, Basel, Switzerland | Article | Swiss Fed Inst Technol;Univ Basel | NEW YORK | null | null | East China Normal Univ;Inst Univ Technol Lyon 1;Swiss Fed Inst Technol;Univ Basel | Chinese Scholarship Council;European Research Council;National Centre of Competence in Research Molecular Systems Engineering;National Natural Science Foundation of China;Science and Technology Commission of Shanghai Municipality;Thousand Youth Talents Plan of China | Fussenegger, M (corresponding author), Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland.; Fussenegger, M (corresponding author), Univ Basel, Fac Sci, Basel, Switzerland. | + | Bai, Peng;Fussenegger, Martin;Hamri, Ghislaine Charpin-El;Liu, Ying;Saxena, Pratik;Xie, Mingqi;Xue, Shuai;Ye, Haifeng | 73 | 5 | 480,414,600,025 | Chinese Scholarship Council;European Research Council [785800];National Centre of Competence in Research Molecular Systems Engineering;National Natural Science Foundation of China [31861143016];Science and Technology Commission of Shanghai Municipality [18JC1411000];Thousand Youth Talents Plan of China | China;France;Switzerland | NATURE MEDICINE | Switzerland | null | null | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland | 1078-8956 | Bai, P;Fussenegger, M;Hamri, G C E;Liu, Y;Saxena, P;Xie, M Q;Xue, S;Ye, H F | AUG | fussenegger@bsse.ethz.ch | cooling sensation;human transgene switch;therapeutic protein production | 8 | J | Biochemistry & Molecular Biology;Cell Biology;Research & Experimental Medicine | ability;activated T cells;activin type IIB;alloxan-treated mice (a model;BETA-CELLS;bind nuclear factor;CACHEXIA;CANCER;cell types;cells;CHANNELS;clinical applications;COLD;control transgene expression;cool environment;cool environment (15-18 degrees C);cooling compound;cooling sensation;dexamethasone-treated mice (a model;effective gene-and cell-based therapies;ELEMENTS;exposure;expression;gene circuit;Gene switch;homeostasis;hTRPM8-induced signaling;human primary cells;human transgene switch;human transient receptor potential (TRP) melastatin 8 (hTRPM8);human TRPM8 signaling;human-derived orthogonal transgene switch;hyperglycemia;insulin;MENTHOL;Mice;microencapsulated cell implants;muscle wasting);natural;present study;receptor;receptor ligand trap protein (mActRIIB(ECD)-hFc;response;reverse muscle atrophy;signaling pathway;simple synthetic gene switches;Synthetic gene circuit;synthetic promoter;therapeutic protein production;transdermal delivery;TRANSGENE EXPRESSION;TRP channel family member(1);TRPM8;two therapeutic proteins;type 1 diabetes);wide range | Bai, P | BETA-CELLS;CACHEXIA;CANCER;CHANNELS;COLD;EXPRESSION;HOMEOSTASIS;MENTHOL;RECEPTOR;TRPM8 | 1266 | [Bai, Peng; Liu, Ying; Saxena, Pratik; Xie, Mingqi; Fussenegger, Martin] Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland. [Xue, Shuai; Ye, Haifeng] East China Normal Univ, Shanghai Key Lab Regulatory Biol, Inst Biomed Sci, Shanghai, Peoples R China. [Xue, Shuai; Ye, Haifeng] East China Normal Univ, Sch Life Sci, Shanghai, Peoples R China. [Hamri, Ghislaine Charpin-El] Inst Univ Technol Lyon 1, Dept Genie Biol, Villeurbanne, France. [Fussenegger, Martin] Univ Basel, Fac Sci, Basel, Switzerland. | We thank F. Viana for providing prTRPM8, F. Kuhn for providing phTRPM8 and X. Dong for providing pmTRPM8. We also thank M. Daoud-El Baba, J. Jiang and J. Yin for supporting the in vivo work; V. Jaggin, M. Di Tacchio and Y. Zhang for assistance with flow cytometry; T. Lummen for help with time-lapse microscopy and A. Ponti for support with statistical analysis. This work was supported by a personal fellowship from the Chinese Scholarship Council to P. B., by the National Centre of Competence in Research Molecular Systems Engineering and in part by the European Research Council advanced grant (ElectroGene, no. 785800) (both to M. F.). This work was also financially supported by grants from the National Natural Science Foundation of China (no. 31861143016), the Science and Technology Commission of Shanghai Municipality (no. 18JC1411000) and the Thousand Youth Talents Plan of China to H.Y. | ability;activated T cells;activin type IIB;alloxan-treated mice (a model;bind nuclear factor;cell types;cells;clinical applications;control transgene expression;cool environment;cool environment (15-18 degrees C);cooling compound;dexamethasone-treated mice (a model;effective gene-and cell-based therapies;elements;exposure;expression;gene circuit;gene switch;hTRPM8-induced signaling;human primary cells;human transient receptor potential (TRP) melastatin 8 (hTRPM8);human TRPM8 signaling;human-derived orthogonal transgene switch;hyperglycemia;insulin;menthol;mice;microencapsulated cell implants;muscle wasting);natural;present study;receptor ligand trap protein (mActRIIB(ECD)-hFc;response;reverse muscle atrophy;signaling pathway;simple synthetic gene switches;synthetic gene circuit;synthetic promoter;transdermal delivery;transgene expression;TRP channel family member(1);two therapeutic proteins;type 1 diabetes);wide range | 10.1002/anie.201609229;10.1002/emmm.201202287;10.1002/j.1460-2075.1994.tb06300.x;10.1007/BF00327154;10.1007/s00125-013-2906-0;10.1007/s00125-016-4059-4;10.1016/0378-1119(88)90219-3;10.1016/j.cell.2009.06.026;10.1016/j.cell.2010.07.011;10.1016/j.jaad.2007.04.008;10.1016/j.jconrel.2008.07.036;10.1016/j.jhep.2016.03.020;10.1016/j.molcel.2014.06.007;10.1016/j.tibtech.2003.11.004;10.1016/j.tips.2015.05.003;10.1016/j.ymben.2013.02.004;10.1016/j.ymeth.2012.01.005;10.1016/S0092-8674(02)00699-2;10.1016/S0092-8674(03)00158-2;10.1016/S0378-1119(01)00824-1;10.1016/S1470-2045(16)00167-4;10.1038/39807;10.1038/mt.2011.256;10.1038/nature05910;10.1038/nature719;10.1038/nbt.2960;10.1038/nbt.3645;10.1038/nbt0602-592;10.1038/ng.343;10.1038/nm.4030;10.1038/nprot.2008.73;10.1038/nri2818;10.1038/nrm1155;10.1038/s41551-018-0192-3;10.1074/jbc.M114.610873;10.1083/jcb.106.3.761;10.1093/nar/gky805;10.1111/j.1399-3089.1995.tb00076.x;10.1111/j.1399-3089.2006.00349.x;10.1124/pr.113.008268;10.1126/science.1203535;10.1126/science.aaf4006;10.1126/scitranslmed.3005568;10.1126/scitranslmed.aac4964;10.1126/scitranslmed.aal2298;10.1128/MCB.01307-13;10.1158/2326-6066.CIR-13-0006;10.1371/journal.pone.0059120;10.1523/JNEUROSCI.3189-10.2010;10.1681/ASN.2006010083 | Swiss Fed Inst Technol | Bai, P;Fussenegger, M;Hamri, G C E;Liu, Y;Saxena, P;Xie, M Q;Xue, S;Ye, H F | Bai, P: Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland | null | 18JC1411000;31861143016;785800 | 52 | null | Switzerland | East China Normal Univ;Inst Univ Technol Lyon 1;Swiss Fed Inst Technol;Univ Basel | Bai, Peng | Green Accepted | BETA-CELLS;CACHEXIA;CANCER;CHANNELS;COLD;EXPRESSION;HOMEOSTASIS;MENTHOL;RECEPTOR;TRPM8 | Bai, Peng; Liu, Ying; Xue, Shuai; Hamri, Ghislaine Charpin-El; Saxena, Pratik; Ye, Haifeng; Xie, Mingqi; Fussenegger, Martin; | null | East China Normal Univ, Sch Life Sci, Shanghai, Peoples R China;East China Normal Univ, Shanghai Key Lab Regulatory Biol, Inst Biomed Sci, Shanghai, Peoples R China;Inst Univ Technol Lyon 1, Dept Genie Biol, Villeurbanne, France;Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland;Univ Basel, Fac Sci, Basel, Switzerland | East China Normal Univ, Sch Life Sci, Shanghai, Peoples R China;East China Normal Univ, Shanghai Key Lab Regulatory Biol, Inst Biomed Sci, Shanghai, Peoples R China;Inst Univ Technol Lyon 1, Dept Genie Biol, Villeurbanne, France;Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland;Univ Basel, Fac Sci, Basel, Switzerland | 1546-170X | null | 8 | 1988;1994;1995;1997;2002;2003;2004;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016;2017;2018 | 34 | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland;Univ Basel, Fac Sci, Basel, Switzerland | Nat. Med. | Fussenegger, Martin | NATURE PUBLISHING GROUP | (15-18;(a;(hTRPM8);(mActRIIB(ECD)-hFc;(TRP);,;1;8;a;ability;activated;activin;adjusted;alleviate;alloxan-treated;amenable;an;and;applications;as;atrophy;be;bind;by;C);can;cell;cell-based;cells;channel;circuit;clinical;compound;containing;control;controlled;COOL;cooling;could;coupled;critical;degrees;delivery;designed;dexamethasone-treated;diabetes);effective;either;elements;engineered;environment;exposure;expression;factor;family;for;fully;functional;functionally;gene;gene-and;harboring;harnessed;hTRPM8-induced;human;human-derived;hyperglycemia;IIB;implanted;implants;in;innocuous;insulin;is;it;ligand;linking;melastatin;member(1);menthol;mice;microencapsulated;model;modified;muscle;natural;nuclear;of;or;Orthogonal;pathway;potential;present;primary;promoter;protein;proteins;range;receptor;respectively;response;reverse;safely;should;shown;signaling;simple;stimulated;study;switch;switches;synthetic;T;that;the;therapeutic;therapies;this;to;transdermal;transgene;transient;trap;TRP;TRPM8;two;type;types;various;was;wasting);well;wide;with | Swiss Fed Inst Technol;Univ Basel | The ability to safely control transgene expression with simple synthetic gene switches is critical for effective gene-and cell-based therapies. In the present study, the signaling pathway controlled by human transient receptor potential (TRP) melastatin 8 (hTRPM8), a TRP channel family member(1), is harnessed to control transgene expression. Human TRPM8 signaling is stimulated by menthol, an innocuous, natural, cooling compound, or by exposure to a cool environment (15-18 degrees C). By functionally linking hTRPM8-induced signaling to a synthetic promoter containing elements that bind nuclear factor of activated T cells, a synthetic gene circuit was designed that can be adjusted by exposure to either a cool environment or menthol. It was shown that this gene switch is functional in various cell types and human primary cells, as well as in mice implanted with engineered cells. In response to transdermal delivery of menthol, microencapsulated cell implants harboring this gene circuit, coupled to expression of either of two therapeutic proteins, insulin or a modified, activin type IIB, receptor ligand trap protein (mActRIIB(ECD)-hFc), could alleviate hyperglycemia in alloxan-treated mice (a model of type 1 diabetes) or reverse muscle atrophy in dexamethasone-treated mice (a model of muscle wasting), respectively. This fully human-derived orthogonal transgene switch should be amenable to a wide range of clinical applications. | null | BETA-CELLS;CACHEXIA;CANCER;CHANNELS;COLD;EXPRESSION;HOMEOSTASIS;MENTHOL;RECEPTOR;TRPM8 | 9 | null | null | 23 | BETA-CELLS;CACHEXIA;CANCER;CHANNELS;COLD;EXPRESSION;HOMEOSTASIS;MENTHOL;RECEPTOR;TRPM8 | WOS:000480414600025 | East China Normal Univ, Shanghai, Peoples R China;Inst Univ Technol Lyon, Villeurbanne, France;Swiss Fed Inst Technol, Basel, Switzerland;Univ Basel, Basel, Switzerland | China;France;Switzerland | 2,019 | null | 0000-0001-5657-532X;0000-0002-5482-8116;0009-0006-9312-9306 | null | null | English | null | ANGEW CHEM INT EDIT;CANCER IMMUNOL RES;CELL;CURR GENE THER;DIABETOLOGIA;EMBO J;EMBO MOL MED;European Patent;GENE;J AM ACAD DERMATOL;J AM SOC NEPHROL;J BIOL CHEM;J CELL BIOL;J CONTROL RELEASE;J HEPATOL;J NEUROSCI;LANCET ONCOL;METAB ENG;METHODS;MOL CELL;MOL CELL BIOL;MOL THER;NAT BIOMED ENG;NAT BIOTECHNOL;NAT GENET;NAT MED;NAT PROTOC;NAT REV IMMUNOL;NAT REV MOL CELL BIO;NATURE;NUCLEIC ACIDS RES;PHARMACOL REV;PLOS ONE;SCI TRANSL MED;SCIENCE;TRANSPLANT INT;TRENDS BIOTECHNOL;TRENDS PHARMACOL SCI;XENOTRANSPLANTATION | Bai, Peng;Fussenegger, Martin;Hamri, Ghislaine Charpin-El;Liu, Ying;Saxena, Pratik;Xie, Mingqi;Xue, Shuai;Ye, Haifeng | 2024-03-11
ER | Anguela, X M;Asuthkar, S;Ausländer, D;Ausländer, S;Bai, P;Bautista, D M;Berger, J;Berridge, M J;Boukamp, P;Caterina, M J;Crabtree, G R;Fischbach, M A;Fluri, D A;Fritschy, W M;Heng, B C;Hq Han X., Z;Jacobs-Tulleneers-Thevissen, D;Johnson, J D;Kaufmann, K B;Kobayashi, T;Lach-Trifilieff, E;Lanitis, E;Le Guiner, C;Lecker, S H;Liu, Y;Maus, M V;Mckemy, D D;Mátés, L;Müller, M R;Nilius, B;Orive, G;Patel, T;Rooney, J W;Schlatter, S;Schmittgen, T D;Schukur, L;Shao, J W;Simonsen, J L;Story, G M;Vaithilingam, V;Vegas, A J;Wang, H;Wieland, M;Williams, G R;Xie, M;Ye, H F;Zakharian, E;Zakrzewski, J L;Zekorn Tobias D. C.;Zhou, X L | IQ0BI | Basel, Switzerland;Basel, Switzerland. | 36 | null | 4 | null | 31,285,633 | Bai, Peng;Fussenegger, Martin;Hamri, Ghislaine Charpin-El;Liu, Ying;Saxena, Pratik;Xie, Mingqi;Xue, Shuai;Ye, Haifeng | NAT MED | Basel, Switzerland;Shanghai, Peoples R China;Villeurbanne, France |
de Greef, T F A;Dubuc, E;Huck, W T S;Pieters, P A;van der Linden, A J;van Hest, J C M | 10.1016/j.copbio.2018.10.006 | null | THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, OXON, ENGLAND | 3v6u3u4x4z3r271d3i66594g324gj416t2c574y | Cell-free microcompartmentalised transcription-translation for the prototyping of synthetic communication networks | Eindhoven Univ Technol | null | de Greef, TFA (corresponding author), Eindhoven Univ Technol, Dept Biomed Engn, Lab Chem Biol, NL-5600 MB Eindhoven, Netherlands.;de Greef, TFA (corresponding author), Eindhoven Univ Technol, Inst Complex Mol Syst, Dept Biomed Engn, NL-5600 MB Eindhoven, Netherlands.;de Greef, TFA (corresponding author), Radboud Univ Nijmegen, Inst Mol & Mat, Heyendaalseweg 135, NL-6525 AJ Nijmegen, Netherlands. | null | de Greef, Tom F A;Dubuc, Emilien;Huck, Wilhelm T S;Pieters, Pascal A;van der Linden, Ardjan J;van Hest, Jan C M | Biochemical Research Methods;Biotechnology & Applied Microbiology | European Research Council, ERG [677313 BioCircuit]; NWO-VIDI grant from the Netherlands Organization for Scientific Research (NWO) [723.016.003]; Ministry of Education, Culture and Science [024.001.035, 024.003.013] | WOS | de Greef, T F A | Eindhoven Univ Technol, Eindhoven, Netherlands;Radboud Univ Nijmegen, Nijmegen, Netherlands | 58 | Cell-Free;communication;for;microcompartmentalised;networks;of;prototyping;synthetic;the;transcription-translation | 1 | Pieters, Pascal;van der Linden, Ardjan;van Hest, Jan | ELSEVIER SCI LTD | Eindhoven Univ Technol, Dept Biomed Engn, Computat Biol Grp, NL-5600 MB Eindhoven, Netherlands;Eindhoven Univ Technol, Dept Biomed Engn, Lab Chem Biol, NL-5600 MB Eindhoven, Netherlands;Eindhoven Univ Technol, Dept Biomed Engn, Lab Chem Biol, NL-5600 MB Eindhoven, Netherlands.; de Greef, TFA (corresponding author), Eindhoven Univ Technol, Inst Complex Mol Syst, Dept Biomed Engn, NL-5600 MB Eindhoven, Netherlands.; de Greef, TFA (corresponding author), Radboud Univ Nijmegen, Inst Mol & Mat, Heyendaalseweg 135, NL-6525 AJ Nijmegen, Netherlands;Eindhoven Univ Technol, Dept Biomed Engn, POB 513, NL-5600 MB Eindhoven, Netherlands;Eindhoven Univ Technol, Dept Chem Engn & Chem, POB 513, NL-5600 MB Eindhoven, Netherlands;Eindhoven Univ Technol, Inst Complex Mol Syst, Dept Biomed Engn, NL-5600 MB Eindhoven, Netherlands;Radboud Univ Nijmegen, Inst Mol & Mat, Dept Phys Organ Chem, NL-6525 HP Nijmegen, Netherlands;Radboud Univ Nijmegen, Inst Mol & Mat, Heyendaalseweg 135, NL-6525 AJ Nijmegen, Netherlands | Review | Eindhoven Univ Technol;Radboud Univ Nijmegen | OXFORD | null | null | Eindhoven Univ Technol;Radboud Univ Nijmegen | European Research Council, ERG;Ministry of Education, Culture and Science;NWO-VIDI grant from the Netherlands Organization for Scientific Research (NWO) | de Greef, TFA (corresponding author), Eindhoven Univ Technol, Dept Biomed Engn, Lab Chem Biol, NL-5600 MB Eindhoven, Netherlands.; de Greef, TFA (corresponding author), Eindhoven Univ Technol, Inst Complex Mol Syst, Dept Biomed Engn, NL-5600 MB Eindhoven, Netherlands.; de Greef, TFA (corresponding author), Radboud Univ Nijmegen, Inst Mol & Mat, Heyendaalseweg 135, NL-6525 AJ Nijmegen, Netherlands. | 80 | de Greef, Tom F A;Dubuc, Emilien;Huck, Wilhelm T S;Pieters, Pascal A;van der Linden, Ardjan J;van Hest, Jan C M | 38 | 7 | 484,879,000,011 | European Research Council, ERG [677313 BioCircuit];Ministry of Education, Culture and Science [024.001.035, 024.003.013];NWO-VIDI grant from the Netherlands Organization for Scientific Research (NWO) [723.016.003] | Netherlands | CURRENT OPINION IN BIOTECHNOLOGY | Netherlands | null | null | Eindhoven Univ Technol, Dept Biomed Engn, Lab Chem Biol, NL-5600 MB Eindhoven, Netherlands | 0958-1669 | de Greef, T F A;Dubuc, E;Huck, W T S;Pieters, P A;van der Linden, A J;van Hest, J C M | AUG | t.f.a.d.greef@tue.nl | cell-free microcompartmentalised transcription-translation;prototyping;synthetic communication networks | 6 | J | Biochemistry & Molecular Biology;Biotechnology & Applied Microbiology | cell individuality;cell size;cell-free microcompartmentalised transcription-translation;cell-free transcription-translation (TXTL) reactions;cell-free transcription-translation reactions;CHEMICAL COMMUNICATION;CHIP;communication pathways;community;COMPARTMENTS;critical cell features;development;DNA;engineering distributed functions;FREE GENE-EXPRESSION;FREE PROTEIN-SYNTHESIS;gene expression;Genetic circuits;integration;living cells;microcompartments;molecular communication;molecular communication channels;non-living microcompartments;PHASE-SEPARATION;POPULATIONS;prototyping;QUORUM;reaction;recent efforts;review;several studies;special focus;step;synthetic biology;synthetic communication networks;synthetic genetic circuits;systems;use | Dubuc, E | CHEMICAL COMMUNICATION;CHIP;COMPARTMENTS;DNA;FREE GENE-EXPRESSION;FREE PROTEIN-SYNTHESIS;PHASE-SEPARATION;QUORUM;STEP;SYSTEMS | 72 | [Dubuc, Emilien; Pieters, Pascal A.; van der Linden, Ardjan J.; de Greef, Tom F. A.] Eindhoven Univ Technol, Dept Biomed Engn, Lab Chem Biol, NL-5600 MB Eindhoven, Netherlands. [Dubuc, Emilien; Pieters, Pascal A.; van der Linden, Ardjan J.; de Greef, Tom F. A.] Eindhoven Univ Technol, Inst Complex Mol Syst, Dept Biomed Engn, NL-5600 MB Eindhoven, Netherlands. [Dubuc, Emilien; Pieters, Pascal A.; van der Linden, Ardjan J.; de Greef, Tom F. A.] Eindhoven Univ Technol, Dept Biomed Engn, Computat Biol Grp, NL-5600 MB Eindhoven, Netherlands. [van Hest, Jan C. M.] Eindhoven Univ Technol, Dept Biomed Engn, POB 513, NL-5600 MB Eindhoven, Netherlands. [van Hest, Jan C. M.] Eindhoven Univ Technol, Dept Chem Engn & Chem, POB 513, NL-5600 MB Eindhoven, Netherlands. [Huck, Wilhelm T. S.] Radboud Univ Nijmegen, Inst Mol & Mat, Dept Phys Organ Chem, NL-6525 HP Nijmegen, Netherlands. [de Greef, Tom F. A.] Radboud Univ Nijmegen, Inst Mol & Mat, Heyendaalseweg 135, NL-6525 AJ Nijmegen, Netherlands. | This work was supported by the European Research Council, ERG (project n. 677313 BioCircuit) an NWO-VIDI grant from the Netherlands Organization for Scientific Research (NWO, 723.016.003), funding from the Ministry of Education, Culture and Science (Gravity programs, 024.001.035 & 024.003.013) | cell individuality;cell size;cell-free transcription-translation (TXTL) reactions;cell-free transcription-translation reactions;communication pathways;community;critical cell features;development;engineering distributed functions;gene expression;genetic circuits;integration;living cells;microcompartments;molecular communication;molecular communication channels;non-living microcompartments;populations;prototyping;reaction;recent efforts;review;several studies;special focus;synthetic biology;synthetic genetic circuits;use | 10.1002/adhm.201701163;10.1002/anie.201800281;10.1002/bit.26333;10.1002/cbic.201500560;10.1002/smll.200600489;10.1016/j.bej.2017.11.013;10.1016/j.cbpa.2016.06.013;10.1016/j.cell.2012.01.035;10.1016/j.cell.2014.10.004;10.1016/j.cell.2016.04.059;10.1016/j.cels.2017.06.001;10.1016/j.cub.2017.08.069;10.1016/j.mib.2016.07.009;10.1016/j.molcel.2017.12.007;10.1016/j.nbt.2017.06.014;10.1016/j.tcb.2018.02.004;10.1016/j.ymben.2016.09.008;10.1016/j.ymben.2017.11.005;10.1016/j.ymeth.2017.12.003;10.1021/acscentsci.6b00330;10.1021/acssynbio.5b00286;10.1021/acssynbio.5b00296;10.1021/acssynbio.6b00017;10.1021/acssynbio.7b00219;10.1021/acssynbio.7b00306;10.1021/acssynbio.7b00376;10.1021/acssynbio.7b00387;10.1021/acssynbio.7b00440;10.1021/acssynbio.8b00139;10.1021/acssynbio.8b00252;10.1021/acssynbio.8b00271;10.1021/la404146g;10.1021/sb200016s;10.1038/nature07389;10.1038/nature08753;10.1038/nature18930;10.1038/nmeth.4635;10.1038/NPHYS3469;10.1038/nrg2775;10.1038/nrm.2017.7;10.1038/nrmicro.2017.149;10.1038/s41467-018-03926-1;10.1038/s41467-018-03970-x;10.1038/s41467-018-05046-2;10.1038/s41598-018-21739-6;10.1038/s41598-018-25532-3;10.1038/srep39349;10.1039/c3lc51427g;10.1039/c5cc04220h;10.1039/c5ib00301f;10.1039/c7cc03455e;10.1039/c7lc00552k;10.1039/c8sc00383a;10.1073/pnas.0408236101;10.1073/pnas.1205693109;10.1073/pnas.1222321110;10.1073/pnas.1311166110;10.1073/pnas.1710620114;10.1073/pnas.1715806115;10.1083/jcb.201707004;10.1126/sciadv.1600056;10.1126/science.1255550;10.1126/science.aal5240;10.1177/1535370217711441;10.1371/journal.pbio.0030064;10.15252/msb.20145735;10.3389/fmicb.2018.01146;10.3389/fnhum.2010.00219;10.7554/eLife.09771;10.7554/eLife.33549;[10.1038/NCHEM.2644, 10.1038/nchem.2644];[10.1038/NMAT2419, 10.1038/nmat2419] | Eindhoven Univ Technol | de Greef, T F A;Dubuc, E;Huck, W T S;Pieters, P A;van der Linden, A J;van Hest, J C M | Dubuc, E: Eindhoven Univ Technol, Dept Biomed Engn, Lab Chem Biol, NL-5600 MB Eindhoven, Netherlands | de Greef, Tom F. A.;Huck, Wilhelm T.S.;van Hest, Jan | 024.001.035;024.003.013;677313 BioCircuit;723.016.003 | 75 | null | Netherlands | Eindhoven Univ Technol;Radboud Univ Nijmegen | Dubuc, Emilien | Green Published, hybrid | CHEMICAL COMMUNICATION;CHIP;COMPARTMENTS;DNA;FREE GENE-EXPRESSION;FREE PROTEIN-SYNTHESIS;PHASE-SEPARATION;QUORUM;STEP;SYSTEMS | Dubuc, Emilien; Pieters, Pascal A.; van der Linden, Ardjan J.; van Hest, Jan C. M.; Huck, Wilhelm T. S.; de Greef, Tom F. A.; | null | Eindhoven Univ Technol, Dept Biomed Engn, Computat Biol Grp, NL-5600 MB Eindhoven, Netherlands;Eindhoven Univ Technol, Dept Biomed Engn, Lab Chem Biol, NL-5600 MB Eindhoven, Netherlands;Eindhoven Univ Technol, Dept Biomed Engn, POB 513, NL-5600 MB Eindhoven, Netherlands;Eindhoven Univ Technol, Dept Chem Engn & Chem, POB 513, NL-5600 MB Eindhoven, Netherlands;Eindhoven Univ Technol, Inst Complex Mol Syst, Dept Biomed Engn, NL-5600 MB Eindhoven, Netherlands;Radboud Univ Nijmegen, Inst Mol & Mat, Dept Phys Organ Chem, NL-6525 HP Nijmegen, Netherlands;Radboud Univ Nijmegen, Inst Mol & Mat, Heyendaalseweg 135, NL-6525 AJ Nijmegen, Netherlands | Eindhoven Univ Technol, Dept Biomed Engn, Computat Biol Grp, NL-5600 MB Eindhoven, Netherlands;Eindhoven Univ Technol, Dept Biomed Engn, Lab Chem Biol, NL-5600 MB Eindhoven, Netherlands;Eindhoven Univ Technol, Dept Biomed Engn, POB 513, NL-5600 MB Eindhoven, Netherlands;Eindhoven Univ Technol, Dept Chem Engn & Chem, POB 513, NL-5600 MB Eindhoven, Netherlands;Eindhoven Univ Technol, Inst Complex Mol Syst, Dept Biomed Engn, NL-5600 MB Eindhoven, Netherlands;Radboud Univ Nijmegen, Inst Mol & Mat, Dept Phys Organ Chem, NL-6525 HP Nijmegen, Netherlands;Radboud Univ Nijmegen, Inst Mol & Mat, Heyendaalseweg 135, NL-6525 AJ Nijmegen, Netherlands | 1879-0429 | null | null | 2004;2005;2007;2008;2009;2010;2012;2013;2014;2015;2016;2017;2018 | 41 | Eindhoven Univ Technol, Dept Biomed Engn, Lab Chem Biol, NL-5600 MB Eindhoven, Netherlands;Eindhoven Univ Technol, Inst Complex Mol Syst, Dept Biomed Engn, NL-5600 MB Eindhoven, Netherlands;Radboud Univ Nijmegen, Inst Mol & Mat, Heyendaalseweg 135, NL-6525 AJ Nijmegen, Netherlands | Curr. Opin. Biotechnol. | de Greef, Tom F A | ELSEVIER SCI LTD | (TXTL);,;a;and;as;been;between;biology;by;cell;cell-free;cells;channels;circuits;communication;community;critical;development;discuss;distributed;efforts;enable;encapsulated;encoded;engineered;engineering;expression;features;focus;for;functions;gene;genetic;genetically;have;highlight;highly;in;individuality;integration;into;living;microcompartments;mimicking;molecular;non-living;of;on;Orthogonal;pathways;populations;possibility;prototyping;reaction;reactions;recent;requires;review;several;shown;size;special;studies;successfully;such;supporting;synthetic;the;their;this;transcription-translation;use;uses;we;where;which;with;within | Eindhoven Univ Technol;Radboud Univ Nijmegen | Recent efforts in synthetic biology have shown the possibility of engineering distributed functions in populations of living cells, which requires the development of highly orthogonal, genetically encoded communication pathways. Cell-free transcription-translation (TXTL) reactions encapsulated in microcompartments enable prototyping of molecular communication channels and their integration into engineered genetic circuits by mimicking critical cell features, such as gene expression, cell size, and cell individuality within a community. In this review, we discuss the uses of cell-free transcription-translation reactions for the development of synthetic genetic circuits, with a special focus on the use of microcompartments supporting this reaction. We highlight several studies where molecular communication between non-living microcompartments and living cells have been successfully engineered. | B-1471-2012;D-5625-2012;I-8124-2014 | CHEMICAL COMMUNICATION;CHIP;COMPARTMENTS;DNA;FREE GENE-EXPRESSION;FREE PROTEIN-SYNTHESIS;PHASE-SEPARATION;QUORUM;STEP;SYSTEM | 1 | null | null | 9 | CHEMICAL COMMUNICATION;CHIP;COMPARTMENTS;DNA;FREE GENE-EXPRESSION;FREE PROTEIN-SYNTHESIS;PHASE-SEPARATION;QUORUM;STEP;SYSTEM | WOS:000484879000011 | Eindhoven Univ Technol, Eindhoven, Netherlands;Radboud Univ Nijmegen, Nijmegen, Netherlands | Netherlands | 2,019 | null | 0000-0001-7973-2404;0000-0002-9582-8462;0000-0003-2032-0100 | null | null | English | null | ACS CENTRAL SCI;ACS SYNTH BIOL;ADV HEALTHC MATER;ANGEW CHEM INT EDIT;BIOCHEM ENG J;BIOTECHNOL BIOENG;CELL;CELL SYST;CHEM COMMUN;CHEM SCI;CHEMBIOCHEM;CURR BIOL;CURR OPIN CHEM BIOL;CURR OPIN MICROBIOL;ELIFE;EXP BIOL MED;FRONT HUM NEUROSCI;FRONT MICROBIOL;INTEGR BIOL-UK;J CELL BIOL;J ROY SOC;LAB CHIP;LANGMUIR;METAB ENG;METHODS;MOL CELL;MOL SYST BIOL;NAT CHEM;NAT COMMUN;NAT MATER;NAT METHODS;NAT PHYS;NAT REV GENET;NAT REV MICROBIOL;NAT REV MOL CELL BIO;NATURE;NEW BIOTECHNOL;P NATL ACAD SCI USA;PLOS BIOL;SCI ADV;SCI REP-UK;SCIENCE;SMALL;TRENDS CELL BIOL | de Greef, Tom F A;Dubuc, Emilien;Huck, Wilhelm T S;Pieters, Pascal A;van der Linden, Ardjan J;van Hest, Jan C M | 2024-03-11
ER | [王树凤 Wang Shufeng];Adamala, K P;Alberti, S;Banani, S F;Boeynaems, S;Booth, M J;Borkowski, O;Brown, J M;Bullman, S;Buxboim, A;Ceroni, F;Clemente, J C;Collins, J;Danino, T;Delvecchio D.;Des Soye, B J;Din, M O;Egbert, R G;Failmezger, J;Findlay, H E;Garamella, J;Guan, Y;Halleran, A D;Hansen, M M K;Helekar, S A;Hori, Y;Hu, C Y;Isalan, M;Jia, H Y;Jung, W;Karim, A S;Karzbrun, E;Kelwick, R;Khalil, A S;Kim, S;Krinsky, N;Kylilis, N;Lentini, R;Li, J;Maddalena Lea L De;Majumder, S;Marshall, R;Moore, S J;Niederholtmeyer, H;Nielsen, A A;Noireaux, V;Norred, S E;Pardatscher, G;Pardee, K;Park, N;Sakamoto, R;Salehi-Reyhani, A;Schwarz-Schilling, M;Scott, S R;Senoussi, A;Shi, X Y;Shin, J;Sokolova, E;Stricker, J;Tang, T Y D;Tayar, A M;Thiele, J;Torre, P;Van Nies, P;Wen, K Y;Wu, C;Yeung, E;Zhou, X Y | IW3KN | Eindhoven, Netherlands.;Nijmegen, Netherlands | 44 | null | 2 | null | 30,594,098 | de Greef, Tom F A;Dubuc, Emilien;Huck, Wilhelm T S;Pieters, Pascal A;van der Linden, Ardjan J;van Hest, Jan C M | CURR OPIN BIOTECH | Eindhoven, Netherlands;Nijmegen, Netherlands |
Bhalla, P;Mishra, S S;Mohapatra, S;Thatoi, H | 10.1007/s00425-019-03218-y | null | 233 SPRING ST, NEW YORK, NY 10013 USA | q3t3i5lhx32d3w6l3c72514h4n6c6h12h4e | Engineering grass biomass for sustainable and enhanced bioethanol production | Biju Patnaik Univ Technol | null | Mohapatra, S (corresponding author), Biju Patnaik Univ Technol, Coll Engn & Technol, Dept Biotechnol, Bhubaneswar 751003, India. | null | Bhalla, Prerna;Mishra, Suruchee Samparana;Mohapatra, Sonali;Thatoi, Hrudayanath | Plant Sciences | null | WOS | Mohapatra, S | Biju Patnaik Univ Technol, Bhubaneswar, India;Indian Inst Technol Madras, Tamil Nadu, India;North Orissa Univ, Odisha, India | 250 | and;bioethanol;biomass;engineering;enhanced;for;grass;production;sustainable | 1 | mohapatra, sonali;Thatoi, Hrudayanath | SPRINGER | Biju Patnaik Univ Technol, Coll Engn & Technol, Dept Biotechnol, Bhubaneswar 751003, India;Indian Inst Technol Madras, Bhupat & Jyoti Mehta Sch Biosci Bldg, Chennai, Tamil Nadu, India;North Orissa Univ, Dept Biotechnol, Baripada 757003, Odisha, India | Review | Biju Patnaik Univ Technol | NEW YORK | null | null | Biju Patnaik Univ Technol;Indian Inst Technol Madras;North Orissa Univ | null | Mohapatra, S (corresponding author), Biju Patnaik Univ Technol, Coll Engn & Technol, Dept Biotechnol, Bhubaneswar 751003, India. | 412 | Bhalla, Prerna;Mishra, Suruchee Samparana;Mohapatra, Sonali;Thatoi, Hrudayanath | 49 | 3 | 474,429,800,001 | null | India | PLANTA | India | null | null | Biju Patnaik Univ Technol, Coll Engn & Technol, Dept Biotechnol, Bhubaneswar 751003, India | 0032-0935 | Bhalla, P;Mishra, S S;Mohapatra, S;Thatoi, H | AUG | sonalimohapatra85@gmail.com | engineering grass biomass;enhanced bioethanol production;sustainable | 4 | J | Plant Sciences | 1st mutant generation;ahead;application;attractive methods;barricade;basis;BINDING;bioethanol;bioethanol production;biofuel feedstock;biorefinery-based bioethanol concepts;biorefinery-based bioethanol concepts.Graphic abstract;biorefinery-based bioethanol production;Breeding techniques;carbohydrate content;carbohydrate-carbohydrate linkages;carbohydrates;cell wall components;commercialization;costly;CRISPR systems;Designer lignin;designer lignins;designing synthetic;desired traits/heritable mutations;development;developments;DOWN-REGULATION;engineering grass biomass;enhanced bioethanol production;enzymatic hydrolysis;expression pattern;feedstock;FERMENTATION;fertile land;final point;flexibility;food system;foreseeable genome location;fundamentals;future energy requirements;GENE;generation dependent;Genetic circuits;genetic makeup;genetics;grass;Grass biomass;grass biomass.AbstractGrasses;grass cell wall;grass feedstocks;health;i.e;improvement;improvements;IMPROVES SACCHARIFICATION;increase;induction;innovative approaches;interspaced short palindromic repeats (CRISPR) systems;lignin recalcitrance;lignin-carbohydrate;lignin-polysaccharide linkages;lignocellulosic biomass;main conclusionBioethanol;maximum utilisation;mixed-linkage glucans;modern breeding techniques;nature epitomise attractive lignocellulosic feedstocks;noninterference;outcomes;plant growth;PLANT-CELL WALL;planta;planta genetic engineering aspects;planta modifications;planta saccharification efficiency;polysaccharides;possibilities;post-harvest techniques;potential lignocellulosic biomass;present review;pretreatment;processes;progress;promising step;qualitable lignins;qualitative traits;rational approach;reduced lignin;REDUCED-RECALCITRANCE;remodelling;requirement;review;RICE;robust variety;role;SACCHARIFICATION EFFICIENCY;shortening;simple breeding techniques;sophisticated genome editing technologies;sophisticated techniques;suitable feedstock;sustainable;SWITCHGRASS;synthetic genetic circuits;synthetic genetic circuits (SGC);TALL FESCUE;terms;time;time period;transgenic crops will;transgenic grasses;transgenic processes;understanding;valuable feedstock;XYLAN;year around production | Mohapatra, S | Breeding techniques;Designer lignin;DOWN-REGULATION;GENE;Genetic circuits;Grass biomass;IMPROVES SACCHARIFICATION;PLANT-CELL WALL;REDUCED-RECALCITRANCE;RICE;SACCHARIFICATION EFFICIENCY;SWITCHGRASS;TALL FESCUE;XYLAN | 395 | [Mohapatra, Sonali; Mishra, Suruchee Samparana] Biju Patnaik Univ Technol, Coll Engn & Technol, Dept Biotechnol, Bhubaneswar 751003, India. [Bhalla, Prerna] Indian Inst Technol Madras, Bhupat & Jyoti Mehta Sch Biosci Bldg, Chennai, Tamil Nadu, India. [Thatoi, Hrudayanath] North Orissa Univ, Dept Biotechnol, Baripada 757003, Odisha, India. | null | 1st mutant generation;ahead;application;attractive methods;barricade;basis;binding;bioethanol;bioethanol production;biofuel feedstock;biorefinery-based bioethanol concepts;biorefinery-based bioethanol concepts.Graphic abstract;biorefinery-based bioethanol production;carbohydrate content;carbohydrate-carbohydrate linkages;carbohydrates;cell wall components;commercialization;costly;CRISPR systems;designer lignins;designing synthetic;desired traits/heritable mutations;development;developments;enhanced bioethanol production;enzymatic hydrolysis;expression pattern;feedstock;fermentation;fertile land;final point;flexibility;food system;foreseeable genome location;fundamentals;future energy requirements;generation dependent;genetic makeup;genetics;grass;grass biomass;grass biomass.AbstractGrasses;grass cell wall;grass feedstocks;health;i.e;improvement;improvements;increase;induction;innovative approaches;interspaced short palindromic repeats (CRISPR) systems;lignin recalcitrance;lignin-carbohydrate;lignin-polysaccharide linkages;lignocellulosic biomass;main conclusionBioethanol;maximum utilisation;mixed-linkage glucans;modern breeding techniques;nature epitomise attractive lignocellulosic feedstocks;noninterference;outcomes;plant growth;planta;planta genetic engineering aspects;planta modifications;planta saccharification efficiency;polysaccharides;possibilities;post-harvest techniques;potential lignocellulosic biomass;present review;pretreatment;processes;progress;promising step;qualitable lignins;qualitative traits;rational approach;reduced lignin;remodelling;requirement;review;robust variety;role;shortening;simple breeding techniques;sophisticated genome editing technologies;sophisticated techniques;suitable feedstock;synthetic genetic circuits;synthetic genetic circuits (SGC);terms;time;time period;transgenic crops will;transgenic grasses;transgenic processes;understanding;valuable feedstock;year around production | 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10.1038/nmeth.3659];[10.1186/1754-6834-5-8, 10.1186/1754-6834-5-60] | Biju Patnaik Univ Technol | Bhalla, P;Mishra, S S;Mohapatra, S;Thatoi, H | Mohapatra, S: Biju Patnaik Univ Technol, Coll Engn & Technol, Dept Biotechnol, Bhubaneswar 751003, India | null | null | 118 | null | India | Biju Patnaik Univ Technol;Indian Inst Technol Madras;North Orissa Univ | Mohapatra, Sonali | null | DOWN-REGULATION;GENE;IMPROVES SACCHARIFICATION;PLANT-CELL WALL;REDUCED-RECALCITRANCE;RICE;SACCHARIFICATION EFFICIENCY;SWITCHGRASS;TALL FESCUE;XYLAN | Mohapatra, Sonali; Mishra, Suruchee Samparana; Bhalla, Prerna; Thatoi, Hrudayanath; | null | Biju Patnaik Univ Technol, Coll Engn & Technol, Dept Biotechnol, Bhubaneswar 751003, India;Indian Inst Technol Madras, Bhupat & Jyoti Mehta Sch Biosci Bldg, Chennai, Tamil Nadu, India;North Orissa Univ, Dept Biotechnol, Baripada 757003, Odisha, India | Biju Patnaik Univ Technol, Coll Engn & Technol, Dept Biotechnol, Bhubaneswar 751003, India;Indian Inst Technol Madras, Bhupat & Jyoti Mehta Sch Biosci Bldg, Chennai, Tamil Nadu, India;North Orissa Univ, Dept Biotechnol, Baripada 757003, Odisha, India | 1432-2048 | Breeding techniques;Designer lignin;Genetic circuits;Grass biomass | 2 | 1983;1997;1998;2000;2001;2002;2005;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016;2017;2018;2019 | 23 | Biju Patnaik Univ Technol, Coll Engn & Technol, Dept Biotechnol, Bhubaneswar 751003, India | Planta | Thatoi, Hrudayanath | SPRINGER | (CRISPR);(SGC);,;1st;a;about;abstract;abundant;advantageous;ahead;aimed;all;along;also;although;always;and;anticipated;application;approach;approaches;are;around;as;aspects;attractive;barricade;basis;be;better;binding;bioethanol;biofuel;biomass;biomass.AbstractGrasses;biorefinery-based;both;breeding;by;can;carbohydrate;carbohydrate-carbohydrate;carbohydrates;cell;circuits;clustered;commercialization;complexity;components;compromising;concepts;concepts.Graphic;conclusionBioethanol;consuming;content;costly;CRISPR;crops;dependent;designer;designing;desired;developing;development;developments;discuss;due;editing;efficiency;emphasise;energy;engineering;enhanced;enhancing;enzymatic;epitomise;exhibit;expression;feedstock;feedstocks;fermentation;fertile;field;final;flexibility;focus;food;for;foreseeable;forging;forms;from;fundamentals;further;future;generation;genetic;genetics;genome;glucans;grass;grasses;growth;health;highlight;however;hydrolysis;i.e;improvement;improvements;in;increase;induction;innovative;inspired;interspaced;involved;is;it;its;land;less;lignin;lignin-carbohydrate;lignin-polysaccharide;lignins;lignocellulosic;limited;linkages;location;made;main;makeup;maximum;methods;mixed-linkage;modern;modifications;more;mutant;mutations;nature;nevertheless;noninterference;not;obtaining;of;offered;on;or;our;outcomes;palindromic;pattern;period;plant;planta;point;polysaccharides;possibilities;post-harvest;potential;predictable;present;pretreatment;processes;production;progress;promising;promote;provide;qualitable;qualitative;rational;recalcitrance;reduced;regularly;remain;remodelling;rendered;repeats;required;requirement;requirements;review;rewiring;robust;role;saccharification;short;shortening;simple;sophisticated;step;such;suitable;synthetic;system;systems;targeted;techniques;technologies;terms;that;the;these;this;thus;time;to;towards;traits;traits/heritable;transgenic;understanding;utilisation;utilised;valuable;variety;wall;we;which;widespread;will;with;without;year | Biju Patnaik Univ Technol | Main conclusionBioethanol from lignocellulosic biomass is a promising step for the future energy requirements. Grass is a potential lignocellulosic biomass which can be utilised for biorefinery-based bioethanol production. Grass biomass is a suitable feedstock for bioethanol production due to its all the year around production, requirement of less fertile land and noninterference with food system. However, the processes involved, i.e. pretreatment, enzymatic hydrolysis and fermentation for bioethanol production from grass biomass, are both time consuming and costly. Developing the grass biomass in planta for enhanced bioethanol production is a promising step for maximum utilisation of this valuable feedstock and, thus, is the focus of the present review. Modern breeding techniques and transgenic processes are attractive methods which can be utilised for development of the feedstock. However, the outcomes are not always predictable and the time period required for obtaining a robust variety is generation dependent. Sophisticated genome editing technologies such as synthetic genetic circuits (SGC) or clustered regularly interspaced short palindromic repeats (CRISPR) systems are advantageous for induction of desired traits/heritable mutations in a foreseeable genome location in the 1st mutant generation. Although, its application in grass biomass for bioethanol is limited, these sophisticated techniques are anticipated to exhibit more flexibility in engineering the expression pattern for qualitative and qualitative traits. Nevertheless, the fundamentals rendered by the genetics of the transgenic crops will remain the basis of such developments for obtaining biorefinery-based bioethanol concepts from grass biomass.AbstractGrasses which are abundant and widespread in nature epitomise attractive lignocellulosic feedstocks for bioethanol production. The complexity offered by the grass cell wall in terms of lignin recalcitrance and its binding to polysaccharides forms a barricade for its commercialization as a biofuel feedstock. Inspired by the possibilities for rewiring the genetic makeup of grass biomass for reduced lignin and lignin-polysaccharide linkages along with increase in carbohydrates, innovative approaches for in planta modifications are forging ahead. In this review, we highlight the progress made in the field of transgenic grasses for bioethanol production and focus our understanding on improvements of simple breeding techniques and post-harvest techniques for development in shortening of lignin-carbohydrate and carbohydrate-carbohydrate linkages. Further, we discuss about the designer lignins which are aimed for qualitable lignins and also emphasise on remodelling of polysaccharides and mixed-linkage glucans for enhancing carbohydrate content and in planta saccharification efficiency. As a final point, we discuss the role of synthetic genetic circuits and CRISPR systems in targeted improvement of cell wall components without compromising the plant growth and health. It is anticipated that this review can provide a rational approach towards a better understanding of application of in planta genetic engineering aspects for designing synthetic genetic circuits which can promote grass feedstocks for biorefinery-based bioethanol concepts.Graphic abstract | null | DOWN-REGULATION;GENE;IMPROVES SACCHARIFICATION;PLANT-CELL WALL;REDUCED-RECALCITRANCE;RICE;SACCHARIFICATION EFFICIENCY;SWITCHGRASS;TALL FESCUE;XYLAN | 1 | null | Breeding techniques;Designer lignin;Genetic circuits;Grass biomass | 18 | Breeding techniques;Designer lignin;DOWN-REGULATION;GENE;Genetic circuits;Grass biomass;IMPROVES SACCHARIFICATION;plant cell wall;REDUCED-RECALCITRANCE;RICE;SACCHARIFICATION EFFICIENCY;SWITCHGRASS;TALL FESCUE;XYLAN | WOS:000474429800001 | Biju Patnaik Univ Technol, Bhubaneswar, India;Indian Inst Technol Madras, Tamil Nadu, India;North Orissa Univ, Odisha, India | India | 2,019 | null | 0000-0002-3368-1266;0000-0002-5747-3365 | null | null | English | null | AGRON J;ANNU REV PLANT BIOL;APPL BIOCHEM BIOTECH;APPL ENVIRON MICROB;BIOENERG RES;BIOFUELS BIOENERGY;BIORESOURCE TECHNOL;BIORESOURCES;BIOTECHNOL ADV;BIOTECHNOL BIOENG;BIOTECHNOL BIOFUELS;BMC PLANT BIOL;CARBOHYD POLYM;CELL SYST;CHEM REV;COMMUN SOIL SCI PLAN;CRIT REV BIOTECHNOL;CROP SCI;CURR OPIN BIOTECH;CURR OPIN PLANT BIOL;ENERG FUEL;FRONT PLANT SCI;GCB BIOENERGY;INT J PLANT GENOMICS;J BIOL CHEM;J EXP BOT;J IND MICROBIOL BIOT;J PHYS CHEM LETT;J WOOD CHEM TECHNOL;JOVE-J VIS EXP;MACROMOL RAPID COMM;MOL PLANT;NAT BIOTECHNOL;NAT METHODS;NEW PHYTOL;NPJ SYST BIOL APPL;P NATL ACAD SCI USA;PHYTOCHEM REV;PHYTOCHEMISTRY;PLANT BIOTECHNOL J;PLANT CELL;PLANT CELL ENVIRON;PLANT J;PLANT PHYSIOL;PLANT SCI;PLANT SIGNAL BEHAV;PLANTA;PLOS ONE;RENEW SUST ENERG REV;REPORTS;S BREED DIV WITZ;SCI REP-UK;THESIS;TOOLS RESOUR;TRENDS PLANT SCI | Bhalla, Prerna;Mishra, Suruchee Samparana;Mohapatra, Sonali;Thatoi, Hrudayanath | 2024-03-11
ER | Abraham, A;Abramson, M;Adler, P R;Anders, N;Andres, S N;Aznar, A;Banerjee, G;Bartley, L E;Bashline, L;Baxter, H L;Bhatia, R;Biely, P;Bosch, M;Brown, D M;Buanafina, M M D;Burton, R A;Caddick, M X;Carpita, N C;Chandel, A K;Chen, S Y;Chen, X W;Chiniquy, D;Clifton-Brown, J;Da Costa, R M F;Daniell, H;De Buanafina, M M O;De Lange, O;De Souza, A P;Devries, R P;Doblin, M S;Dumitrache, A;Ebringerová, A;Energy Information Administration (Eia);Eucarpia;Eudes, A;Fan, X R;Farrar, K;Feltus, F A;Francocci, F;Gedye, K R;Grabber, J H;Harris, P J;Hatfield, R D;Huang, C X;Ibn Yaich, A;Kering, M K;Khakhar, A;Klose, H;Latarullo, M B G;Lee, C R;Lee, S;Lee, Y;Li, W Y;Lionetti, V;Liu, W S;Lo, T M;Lombardo, L;Lovegrove, A;Macadam, J W;Mchughen, A;Mnich, E;Mohapatra, S;Mohnen, D;Mosier, N;Moxley, G;Na, C I;Nelissen, H;Numan-Al-Mobin, A M;Park, J J;Parthasarathi, R;Pawar, P M A;Pelloux, J;Peterson, K M;Quarton, T;Rai, K M;Ralph, J;Rennie, E A;Roslan, H A;Schaumberg, K A;Scheben, A;Scheller, H V;Schreiber, M;Schultink, A;Shadle, G;Shahandeh, H;Shen, H;Smith, H;Smith, R;Sumiyoshi, M;Sykes, R V;Taketa, S;Talbert, L E;Tan, H T;Van Der Weijde, T;Vanholme, R;Vega-Sánchez, M E;Venter, M;Voorend, W;Wagner, A;Waramit, N;Warnasooriya, S N;Willis, J D;Wong, D W S;Wuddineh, W A;Xiao, C;Xu, B;Yang, Q;Yao, L;Yoon, J;Yuan, Y X;Zhao, C Q;Zhao, X;Zong, Y | IH3YW | Bhubaneswar, India | 23 | null | 3 | null | 31,236,698 | Bhalla, Prerna;Mishra, Suruchee Samparana;Mohapatra, Sonali;Thatoi, Hrudayanath | PLANTA | Bhubaneswar, India;Odisha, India;Tamil Nadu, India |
Raftery, A E;Yeung, K Y;Young, W C | 10.1177/1471082X18776577 | null | 1 OLIVERS YARD, 55 CITY ROAD, LONDON EC1Y 1SP, ENGLAND | 4b2f4b2d465x654v166z4x393x2k133u3x1q4p | Identifying dynamical time series model parameters from equilibrium samples, with application to gene regulatory networks | Fred Hutchinson Canc Res Ctr | null | Raftery, AE (corresponding author), Univ Washington, Dept Stat, POB 354322, Seattle, WA 98195 USA. | null | Raftery, Adrian E;Yeung, Ka Yee;Young, William Chad | Statistics & Probability | NIH [U54-HL127624, R01-HD054511, R01-HD070936]; Center for Advanced Study in the Behavioral Sciences at Stanford University | WOS | Raftery, A E | Fred Hutchinson Canc Res Ctr, Seattle, WA USA;Univ Washington, Seattle, WA USA;Univ Washington, Tacoma, WA USA | 19 | ,;application;dynamical;equilibrium;From;gene;identifying;model;networks;Parameters;regulatory;samples;series;time;to;with | 1 | null | SAGE PUBLICATIONS LTD | Fred Hutchinson Canc Res Ctr, Vaccine & Infect Dis Div, 1124 Columbia St, Seattle, WA 98104 USA;Univ Washington, Dept Stat, POB 354322, Seattle, WA 98195 USA;Univ Washington, Inst Technol, Tacoma, WA USA | Article | Univ Washington | LONDON | null | null | Fred Hutchinson Canc Res Ctr;Univ Washington | Center for Advanced Study in the Behavioral Sciences at Stanford University;NIH | Raftery, AE (corresponding author), Univ Washington, Dept Stat, POB 354322, Seattle, WA 98195 USA. | 465 | Raftery, Adrian E;Yeung, Ka Yee;Young, William Chad | 4 | 3 | 476,721,000,005 | Center for Advanced Study in the Behavioral Sciences at Stanford University;NIH [U54-HL127624, R01-HD054511, R01-HD070936] | USA | STATISTICAL MODELLING | USA | null | null | Fred Hutchinson Canc Res Ctr, Vaccine & Infect Dis Div, 1124 Columbia St, Seattle, WA 98104 USA | 1471-082X | Raftery, A E;Yeung, K Y;Young, W C | AUG | raftery@uw.edu | application;equilibrium samples;gene regulatory networks;identifying dynamical time series model parameters | 3 | J | Mathematics | application;attempt;available data;data;equilibrium distribution;equilibrium samples;essential task;expression;gene networks;gene regulatory network reconstruction;gene regulatory networks;GeneNetWeaver;genes;genomics;IDENTIFIABILITY;identifying dynamical time series model parameters;individual genes;INFERENCE;knockout;method;network inference;network reconstruction;new framework;over-expression experiments;relational dynamics;SAMPLES;steady-state gene expression data;steady-state observations;synthetic gene expression data;theoretical aspects;time series;understanding;VAR equilibrium;vector autoregressive (VAR) time-series | Young, W C | gene networks;IDENTIFIABILITY;INFERENCE;network reconstruction;time series;VAR equilibrium | 444 | [Young, William Chad] Fred Hutchinson Canc Res Ctr, Vaccine & Infect Dis Div, 1124 Columbia St, Seattle, WA 98104 USA. [Yeung, Ka Yee] Univ Washington, Inst Technol, Tacoma, WA USA. [Raftery, Adrian E.] Univ Washington, Dept Stat, POB 354322, Seattle, WA 98195 USA. | This research was supported by NIH grants U54-HL127624, R01-HD054511 and R01-HD070936. Raftery's research was also partly supported by the Center for Advanced Study in the Behavioral Sciences at Stanford University. | attempt;available data;data;equilibrium distribution;essential task;expression;gene regulatory network reconstruction;GeneNetWeaver;genes;genomics;individual genes;knockout;method;network inference;new framework;over-expression experiments;relational dynamics;samples;steady-state gene expression data;steady-state observations;synthetic gene expression data;theoretical aspects;understanding;vector autoregressive (VAR) time-series | 10.1006/jmva.1999.1837;10.1007/978-3-540-27752-1;10.1007/BF02293905;10.1007/s10959-010-0329-0;10.1016/j.mbs.2013.10.003;10.1038/ng1532;10.1038/srep20533;10.1073/pnas.091062498;10.1073/pnas.1116442108;10.1089/cmb.2008.09TT;10.1093/bioinformatics/btr373;10.1093/comjnl/13.3.317;10.1093/imamat/6.1.76;10.1109/ISCAS.1992.229956;10.1109/TCBB.2015.2450740;10.1111/sjos.12227;10.1155/2007/79879;10.1186/1471-2105-7-S1-S7;10.1186/1752-0509-8-47;10.1214/10-AOS859;10.1371/journal.pbio.0050008;10.1371/journal.pone.0082393;10.18637/jss.v033.i01;10.2307/2004873;10.3934/mbe.2016041 | Fred Hutchinson Canc Res Ctr | Raftery, A E;Yeung, K Y;Young, W C | Young, W C: Fred Hutchinson Canc Res Ctr, Vaccine & Infect Dis Div, 1124 Columbia St, Seattle, WA 98104 USA | Raftery, Adrian M | R01-HD054511;R01-HD070936;U54-HL127624 | 28 | null | USA | Fred Hutchinson Canc Res Ctr;Univ Washington | Young, William Chad | hybrid, Green Accepted | IDENTIFIABILITY;INFERENCE | Young, William Chad; Yeung, Ka Yee; Raftery, Adrian E.; | null | Fred Hutchinson Canc Res Ctr, Vaccine & Infect Dis Div, 1124 Columbia St, Seattle, WA 98104 USA;Univ Washington, Dept Stat, POB 354322, Seattle, WA 98195 USA;Univ Washington, Inst Technol, Tacoma, WA USA | Fred Hutchinson Canc Res Ctr, Vaccine & Infect Dis Div, 1124 Columbia St, Seattle, WA 98104 USA;Univ Washington, Dept Stat, POB 354322, Seattle, WA 98195 USA;Univ Washington, Inst Technol, Tacoma, WA USA | 1477-0342 | gene networks;network reconstruction;time series;VAR equilibrium | 4 | 1970;1980;1992;1996;2000;2001;2005;2006;2007;2009;2010;2011;2012;2013;2014;2016 | 1 | Univ Washington, Dept Stat, POB 354322, Seattle, WA 98195 USA | Stat. Model. | Raftery, Adrian E | SAGE PUBLICATIONS LTD | (VAR);,;a;about;an;and;applied;apply;are;as;aspects;attempt;autoregressive;available;be;between;can;control;data;develop;distribution;dynamically;dynamics;each;equilibrium;essential;experiments;explore;expression;for;framework;from;further;gene;GeneNetWeaver;generated;genes;genomics;how;however;in;individual;inference;informative;interact;is;knockout;method;model;most;network;new;not;observations;of;or;order;other;our;over-expression;readily;reconstruction;regulatory;relational;samples;steady-state;synthetic;task;the;theoretical;these;time-series;to;understanding;using;vector;we;which;with | Univ Washington | Gene regulatory network reconstruction is an essential task of genomics in order to further our understanding of how genes interact dynamically with each other. The most readily available data, however, are from steady-state observations. These data are not as informative about the relational dynamics between genes as knockout or over-expression experiments, which attempt to control the expression of individual genes. We develop a new framework for network inference using samples from the equilibrium distribution of a vector autoregressive (VAR) time-series model which can be applied to steady-state gene expression data. We explore the theoretical aspects of our method and apply the method to synthetic gene expression data generated using GeneNetWeaver. | P-2042-2015 | IDENTIFY;INFERENCE | 0 | null | gene networks;network reconstruction;time series;VAR equilibrium | 22 | gene networks;IDENTIFIABILITY;INFERENCE;network reconstruction;TIME-SERIES;VAR equilibrium | WOS:000476721000005 | Fred Hutchinson Canc Res Ctr, Seattle, WA USA;Univ Washington, Seattle, WA USA;Univ Washington, Tacoma, WA USA | USA | 2,019 | null | null | null | null | English | null | 1992 IEEE INTERNATIONAL SYMPOSIUM ON CIRCUITS AND SYSTEMS;ANN STAT;BIOINFORMATICS;BMC BIOINFORMATICS;BMC SYST BIOL;COMPUT J;COURSE LARGE SAMPLE;EURASIP J BIOINFORM;FINANCIAL ECONOMETRI;IEEE ACM T COMPUT BI;J COMPUT BIOL;J MULTIVARIATE ANAL;J STAT SOFTW;J THEOR PROBAB;MATH BIOSCI;MATH BIOSCI ENG;MATH COMPUT;NAT GENET;NEW INTRO MULTIPLE T;P NATL ACAD SCI USA;PLOS BIOL;PLOS ONE;PSYCHOMETRIKA;SCAND J STAT;SCI REP-UK | Raftery, Adrian E;Yeung, Ka Yee;Young, William Chad | 2024-03-11
ER | Anderson, T W;Basso, K;Bentler, P M;Brito, C;Broyden Cg.;Drton, M;Faith, J J;Ferguson Thomas Shelburne;Fletcher, R;Friedman, J;Goldfarb, D;Li, W B V;Lutkepohl Helmut;Marbach, D;Margolin, A A;Meyer, P E;Michailidis, G;Omranian, N;Schaffter, T;Sheppard K.;Shojaie, A;Singh, N;Tong, L;Tusher, V G;Yeung, K Y;Young, W C | IK6TI | Seattle, WA USA | 1 | null | 2 | null | 33,824,624 | Raftery, Adrian E;Yeung, Ka Yee;Young, William Chad | STAT MODEL | Seattle, WA USA;Tacoma, WA USA |
Durai, L;Karunagaran, D;Vijayalakshmi, R | 10.1016/j.ejphar.2019.04.037 | null | PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS | t471wg1l2z1lt432b6c2k6z1o2a5m73v1n4b | A novel reporter system for cyclic AMP mediated gene expression in mammalian cells based on synthetic transgene expression system | Indian Inst Technol Madras | null | Karunagaran, D (corresponding author), Indian Inst Technol Madras, Bhupat & Jyoti Mehta Sch Biosci, Dept Biotechnol, Chennai 600036, Tamil Nadu, India. | null | Durai, Latha;Karunagaran, Devarajan;Vijayalakshmi, Ramshankar | Pharmacology & Pharmacy | DST, Government of India [SR-LS-1028-2014] | WOS | Karunagaran, D | Canc Inst, Tamil Nadu, India;Indian Inst Technol Madras, Tamil Nadu, India | 855 | a;AMP;based;Cells;CYCLIC;expression;for;gene;in;mammalian;mediated;novel;on;Reporter;synthetic;system;transgene | 1 | null | ELSEVIER SCIENCE BV | Canc Inst, Dept Prevent Oncol Res, Chennai, Tamil Nadu, India;Indian Inst Technol Madras, Bhupat & Jyoti Mehta Sch Biosci, Dept Biotechnol, Chennai 600036, Tamil Nadu, India | Article | Indian Inst Technol Madras | AMSTERDAM | null | null | Canc Inst;Indian Inst Technol Madras | DST, Government of India | Karunagaran, D (corresponding author), Indian Inst Technol Madras, Bhupat & Jyoti Mehta Sch Biosci, Dept Biotechnol, Chennai 600036, Tamil Nadu, India. | 64 | Durai, Latha;Karunagaran, Devarajan;Vijayalakshmi, Ramshankar | 6 | 2 | 468,869,300,007 | DST, Government of India [SR-LS-1028-2014] | India | EUROPEAN JOURNAL OF PHARMACOLOGY | India | null | null | Indian Inst Technol Madras, Bhupat & Jyoti Mehta Sch Biosci, Dept Biotechnol, Chennai 600036, Tamil Nadu, India | 0014-2999 | Durai, L;Karunagaran, D;Vijayalakshmi, R | JUL 15 | karuna@iitm.ac.in | cyclic AMP;gene expression;mammalian cells;novel reporter system;synthetic transgene expression system | 3 | J | Pharmacology & Pharmacy | (PKA)-cyclic AMP response element binding protein (CREB);aberrant cAMP signaling;artificial mammalian transactivator;BINDING;biological functions;BIOLOGY;cAMP;cAMP reporter system works;cAMP signaling;cAMP-based signaling;CANCER;CATABOLITE ACTIVATOR PROTEIN;chimeric promoter (O-CRP- PhCMVmin- Luciferase);concentration dependent manner;CREB mutations;CRP;CRP specific operator site present;cyclic AMP;cyclic AMP (cAMP);cyclic AMP response element (CRE) signaling;Escherichia call;eukaryotes;function;gene expression;H-8 (N-[2-(methylamino) ethyl]-5-isoquinoline-sulfonamide;Herpes simplex virus;important second messenger;increasing significance;KINASE;luciferase activity;Mammalian cAMP transactivator;mammalian cells;mammalian expression vector (pLA1);modulation;novel reporter system;PKA;PKA inhibitor H-89 (derived;prokaryotes;Protein kinase;protein-based biosensor;REGULATORY SUBUNIT;reporting;results;signaling pathways;significant role;synthetic biology;synthetic gene;Synthetic gene circuit;synthetic transcription factor;synthetic transgene approach;synthetic transgene expression system;TARGETS;tools;transactivator;transcriptional regulatory element cAMP receptor protein (CRP);tumorigenic cells;VP16 transactivation domain | Durai, L | BINDING;BIOLOGY;cAMP;CANCER;CATABOLITE ACTIVATOR PROTEIN;CRP;KINASE;Mammalian cAMP transactivator;REGULATORY SUBUNIT;SIGNALING PATHWAYS;Synthetic biology;Synthetic gene circuit;TARGETS;TOOLS | 56 | [Durai, Latha; Karunagaran, Devarajan] Indian Inst Technol Madras, Bhupat & Jyoti Mehta Sch Biosci, Dept Biotechnol, Chennai 600036, Tamil Nadu, India. [Durai, Latha; Vijayalakshmi, Ramshankar] Canc Inst, Dept Prevent Oncol Res, Chennai, Tamil Nadu, India. | We are thankful to DST, Government of India, for the financial support (Grant No: SR-LS-1028-2014), and Indian Institute of Technology Madras (IITM), India for all other facilities. | (PKA)-cyclic AMP response element binding protein (CREB);aberrant cAMP signaling;artificial mammalian transactivator;biological functions;cAMP;cAMP reporter system works;cAMP signaling;cAMP-based signaling;chimeric promoter (O-CRP- PhCMVmin- Luciferase);concentration dependent manner;CREB mutations;CRP specific operator site present;cyclic AMP (cAMP);cyclic AMP response element (CRE) signaling;Escherichia call;eukaryotes;function;gene expression;H-8 (N-[2-(methylamino) ethyl]-5-isoquinoline-sulfonamide;Herpes simplex virus;important second messenger;increasing significance;luciferase activity;mammalian cells;mammalian expression vector (pLA1);modulation;PKA;PKA inhibitor H-89 (derived;prokaryotes;Protein kinase;protein-based biosensor;reporting;results;significant role;synthetic gene;synthetic transcription factor;synthetic transgene approach;transactivator;transcriptional regulatory element cAMP receptor protein (CRP);tumorigenic cells;VP16 transactivation domain | 10.1006/jmbi.1999.3161;10.1007/s00125-015-3825-z;10.1016/0092-8674(87)90234-0;10.1016/j.cell.2007.05.045;10.1016/j.copbio.2005.10.008;10.1016/j.coph.2011.09.014;10.1016/j.febslet.2012.02.032;10.1016/j.ijrobp.2007.12.010;10.1016/j.mib.2014.01.003;10.1016/j.pbiomolbio.2016.01.001;10.1016/j.sbi.2004.01.012;10.1016/j.yexcr.2007.11.023;10.1016/S0014-5793(03)00563-5;10.1016/S0962-8924(02)02294-8;10.1038/aps.2011.173;10.1038/bjc.1994.139;10.1038/nature09937;10.1038/nrm2904;10.1038/nrm3738;10.1038/nrm911;10.1038/s41598-017-12162-4;10.1038/srep09980;10.1073/pnas.79.24.7679;10.1073/pnas.88.3.698;10.1089/104303403322542266;10.1098/rsif.2014.1000;10.1111/j.1476-5381.2010.00779.x;10.1111/j.1574-695X.2008.00500.x;10.1111/j.1742-4658.2005.04763.x;10.1126/science.7792603;10.1152/physrev.00001.2005;10.1186/s12918-015-0252-1;10.1371/journal.pone.0007189;10.2741/Skalhegg;10.3390/cancers6010436 | Indian Inst Technol Madras | Durai, L;Karunagaran, D;Vijayalakshmi, R | Durai, L: Indian Inst Technol Madras, Bhupat & Jyoti Mehta Sch Biosci, Dept Biotechnol, Chennai 600036, Tamil Nadu, India | null | SR-LS-1028-2014 | 40 | null | India | Canc Inst;Indian Inst Technol Madras | Durai, Latha | null | BINDING;BIOLOGY;CAMP;CANCER;CATABOLITE ACTIVATOR PROTEIN;KINASE;REGULATORY SUBUNIT;SIGNALING PATHWAYS;TARGETS;TOOLS | Durai, Latha; Vijayalakshmi, Ramshankar; Karunagaran, Devarajan; | null | Canc Inst, Dept Prevent Oncol Res, Chennai, Tamil Nadu, India;Indian Inst Technol Madras, Bhupat & Jyoti Mehta Sch Biosci, Dept Biotechnol, Chennai 600036, Tamil Nadu, India | Canc Inst, Dept Prevent Oncol Res, Chennai, Tamil Nadu, India;Indian Inst Technol Madras, Bhupat & Jyoti Mehta Sch Biosci, Dept Biotechnol, Chennai 600036, Tamil Nadu, India | 1879-0712 | cAMP;CRP;Mammalian cAMP transactivator;Synthetic biology;Synthetic gene circuit | null | 1982;1987;1991;1994;1995;1999;2000;2001;2002;2003;2004;2005;2007;2008;2009;2010;2011;2012;2014;2015;2016;2017;2018 | 0 | Indian Inst Technol Madras, Bhupat & Jyoti Mehta Sch Biosci, Dept Biotechnol, Chennai 600036, Tamil Nadu, India | Eur. J. Pharmacol. | Karunagaran, Devarajan | ELSEVIER SCIENCE BV | (cAMP);(CRE);(CREB);(CRP);(derived;(N-[2-(methylamino);(O-CRP-;(PKA)-cyclic;(pLA1);,;-;a;aberrant;activates;activity;AMP;an;and;approach;artificial;based;binding;biological;biosensor;both;by;call;cAMP;cAMP-based;cells;chimeric;concentration;construct;CREB;CRP;cyclic;dependent;develop;developed;directly;domain;due;element;engineered;Escherichia;ethyl]-5-isoquinoline-sulfonamide;eukaryotes;even;ever;expression;factor;from;function;functions;furthermore;fusing;gene;H-8;H-89;herpes;important;in;increasing;inhibitor;irrespective;is;it;kinase;luciferase;Luciferase);mammalian;manner;mediated;mediates;mediating;messenger;modulation;mutations;of;on;operator;our;PhCMVmin-;PKA;plays;possess;presence;present;prokaryotes;promoter;protein;protein-based;receptor;regulatory;report;reporter;reporting;reports;response;results;reveal;role;second;seen;signaling;SIGNIFICANCE;significant;simplex;since;site;specific;studying;synthetic;system;that;the;this;to;transactivation;transactivator;transcription;transcriptional;transgene;tumorigenic;various;vector;virus;VP16;was;which;works | Indian Inst Technol Madras | Cyclic AMP (cAMP) is an important second messenger that mediates various biological functions in both prokaryotes and eukaryotes. Due to the ever increasing significance in studying the function and modulation of cAMP-based signaling, it is important to develop a protein-based biosensor that reports the cAMP mediated gene expression. Based on a synthetic transgene approach, an artificial mammalian transactivator was developed by fusing a transcriptional regulatory element cAMP receptor protein (CRP) of Escherichia call to the VP16 transactivation domain of Herpes simplex virus in a mammalian expression vector (pLA1) that activates CRP specific operator site present in a chimeric promoter (O-CRP- PhCMVmin- Luciferase) in a concentration dependent manner in mammalian cells. Our results reveal that the engineered transactivator report the gene expression mediated by cAMP directly in mammalian cells and this cAMP reporter system works irrespective of Protein kinase A (PKA)-cyclic AMP response element binding protein (CREB) - cyclic AMP response element (CRE) signaling since the luciferase activity mediated by synthetic gene construct is seen even in the presence of PKA inhibitor H-89 (derived from H-8 (N-[2-(methylamino) ethyl]-5-isoquinoline-sulfonamide). Furthermore this synthetic transcription factor plays a significant role in reporting and mediating cAMP signaling in tumorigenic cells which possess an aberrant cAMP signaling due to PKA and CREB mutations. | null | BINDING;BIOLOGY;CAMP;CANCER;CATABOLITE ACTIVATOR PROTEIN;KINASE;REGULATORY SUBUNIT;SIGNALING PATHWAYS;TARGETS;TOOL | 0 | null | cAMP;CRP;Mammalian cAMP transactivator;Synthetic biology;Synthetic gene circuit | 9 | BINDING;BIOLOGY;cAMP;CANCER;CATABOLITE ACTIVATOR PROTEIN;CRP;KINASE;Mammalian cAMP transactivator;REGULATORY SUBUNIT;SIGNALING PATHWAYS;Synthetic biology;synthetic gene circuits;TARGETS;TOOL | WOS:000468869300007 | Canc Inst, Tamil Nadu, India;Indian Inst Technol Madras, Tamil Nadu, India | India | 2,019 | null | null | null | null | English | null | ACTA PHARMACOL SIN;AM J TRANSL RES;BMC SYST BIOL;BRIT J CANCER;BRIT J PHARMACOL;CANCERS;CELL;CELL SIGNAL;CURR OPIN BIOTECH;CURR OPIN MICROBIOL;CURR OPIN PHARMACOL;CURR OPIN STRUC BIOL;DIABETOLOGIA;EXP CELL RES;FEBS J;FEBS LETT;FEMS IMMUNOL MED MIC;FRONT BIOSCI-LANDMRK;HUM GENE THER;INT J RADIAT ONCOL;J CELL SCI;J MOL BIOL;J R SOC INTERFACE;MAR PROTEIN KINASE C;NAT REV MOL CELL BIO;NATURE;P NATL ACAD SCI USA;P NATL ACAD SCI-BIOL;PHYSIOL REV;PLOS ONE;PROG BIOPHYS MOL BIO;SCI REP-UK;SCIENCE;TRENDS CELL BIOL;Zhonghua Zhongliu Zazhi | Durai, Latha;Karunagaran, Devarajan;Vijayalakshmi, Ramshankar | 2024-03-11
ER | Antonio Caretta;Bai, G C;Beavo, J A;Bradbury, A W;Burbelo, P D;Busby, S;Chen, Y C;Deans, T L;Dumaz, N;Fajardo, A M;Fimia, G M;Gossen, M;Green, J;Hill, S J;Hu, M C T;Hörner, M;Jens A. N. L.;Khor, L Y;Kis, Z;Kolar, K;Kopperud, R;Lawson, C L;Lienert, F;Lim, W A;Ornitz, D M;Reimann, F;Schindler, R F R;Seino, S;Shi Su-Sheng;Siso-Nadal, F;Skålhegg, B S;Stork, P J S;Tanwar, M;Thomsen, W;Wang, W D;Weber, I T;Windbichler, N;Zaccolo, M;Zhang, R;Zhao, H F | HZ5CW | Tamil Nadu, India | 1 | null | 2 | null | 31,034,821 | Durai, Latha;Karunagaran, Devarajan;Vijayalakshmi, Ramshankar | EUR J PHARMACOL | Tamil Nadu, India |
Krishnan, J;Menon, G | 10.1021/acssynbio.8b00522 | null | 1155 16TH ST, NW, WASHINGTON, DC 20036 USA | 103u4os67641e3u465k5s185y4r445g5r33z6s | Design Principles for Compartmentalization and Spatial Organization of Synthetic Genetic Circuits | Imperial Coll London | null | Krishnan, J (corresponding author), Imperial Coll London, Ctr Proc Syst Engn, Dept Chem Engn, London SW7 2AZ, England.;Krishnan, J (corresponding author), Imperial Coll London, Inst Syst & Synthet Biol, London SW7 2AZ, England. | null | Krishnan, J;Menon, Govind | Biochemical Research Methods | null | WOS | Krishnan, J | Imperial Coll London, London, England | 8 | and;circuits;Compartmentalization;design;for;genetic;of;Organization;principles;spatial;synthetic | 1 | Menon, Govind | AMER CHEMICAL SOC | Imperial Coll London, Ctr Proc Syst Engn, Dept Chem Engn, London SW7 2AZ, England;Imperial Coll London, Ctr Proc Syst Engn, Dept Chem Engn, London SW7 2AZ, England.; Krishnan, J (corresponding author), Imperial Coll London, Inst Syst & Synthet Biol, London SW7 2AZ, England;Imperial Coll London, Inst Syst & Synthet Biol, London SW7 2AZ, England | Article | Imperial Coll London | WASHINGTON | null | null | Imperial Coll London | null | Krishnan, J (corresponding author), Imperial Coll London, Ctr Proc Syst Engn, Dept Chem Engn, London SW7 2AZ, England.; Krishnan, J (corresponding author), Imperial Coll London, Inst Syst & Synthet Biol, London SW7 2AZ, England. | 1619 | Krishnan, J;Menon, Govind | 19 | 2 | 476,957,300,016 | null | UK | ACS SYNTHETIC BIOLOGY | UK | null | null | Imperial Coll London, Ctr Proc Syst Engn, Dept Chem Engn, London SW7 2AZ, England | 2161-5063 | Krishnan, J;Menon, G | JUL | j.krishnan@imperial.ac.uk | Compartmentalization;design Principles;Spatial Organization;synthetic genetic circuits | 2 | J | Biochemistry & Molecular Biology | (0;(ii) hidden constraints;(iii) appealing new features;adaptation;BACTERIA;basic;broad range;cell-free systems;Cellular systems;CHEMICAL COMMUNICATION;CIRCUITS;COMMUNICATION;COMPARTMENTALIZATION;compartmentalized circuits;COMPARTMENTS;CONSEQUENCES;demonstrated important experimental capabilities;Design principles;distributed circuit;droplets;elusive;evolution;exemplar applications;expression;general considerations;genetic circuit;Genetic circuits;hallmark;ingredient;insights;interplay;multiple ways;nature;number;operational state (well-mixed;otherwise);settings;spatial design;Spatial Organization;synthetic;synthetic biology;synthetic genetic circuits;systems analysis;systems framework;template-based circuits;trade-offs;understanding design principles;unexpected features | Menon, G | adaptation;BACTERIA;cell-free systems;CHEMICAL COMMUNICATION;COMMUNICATION;COMPARTMENTALIZATION;DROPLETS;EXPRESSION;spatial design;systems analysis | 1601 | [Menon, Govind; Krishnan, J.] Imperial Coll London, Ctr Proc Syst Engn, Dept Chem Engn, London SW7 2AZ, England. [Krishnan, J.] Imperial Coll London, Inst Syst & Synthet Biol, London SW7 2AZ, England. | null | (0;(ii) hidden constraints;(iii) appealing new features;basic;broad range;cellular systems;circuits;compartmentalization;compartmentalized circuits;compartments;consequences;demonstrated important experimental capabilities;design principles;distributed circuit;elusive;evolution;exemplar applications;general considerations;genetic circuit;genetic circuits;hallmark;ingredient;insights;interplay;multiple ways;nature;number;operational state (well-mixed;otherwise);settings;spatial organization;synthetic;synthetic biology;systems framework;template-based circuits;trade-offs;understanding design principles;unexpected features | 10.1002/anie.201308141;10.1002/anie.201800281;10.1016/j.bpj.2015.05.012;10.1016/j.cels.2018.03.013;10.1016/j.ymeth.2014.01.015;10.1021/acscentsci.6b00254;10.1021/acscentsci.6b00330;10.1021/acsnano.5b07689;10.1021/acssynbio.7b00306;10.1021/ja411132w;10.1021/la404146g;10.1021/sb400206c;10.1038/msb.2011.49;10.1038/nature07389;10.1038/nchem.2544;10.1038/ncomms6305;10.1038/NPHYS3469;10.1038/s41467-018-03491-7;10.1038/srep45167;10.1039/c4cp05933f;10.1039/c5cc04220h;10.1039/c5ib00301f;10.1073/pnas.0408236101;10.1073/pnas.1212069109;10.1098/rsif.2018.0157;10.1103/PhysRevLett.108.018102;10.1126/science.1255550;10.1371/journal.pcbi.1003486;10.1371/journal.pone.0005399;10.4161/cib.4.1.13550;10.4161/trns.19734;10.7554/eLife.09771;[10.1038/NCHEM.2617, 10.1038/nchem.2617];[10.1038/NCHEM.2644, 10.1038/nchem.2644];[10.1038/nnano.2016.299, 10.1038/NNANO.2016.299];[10.1038/nnano.2017.127, 10.1038/NNANO.2017.127] | Imperial Coll London | Krishnan, J;Menon, G | Menon, G: Imperial Coll London, Ctr Proc Syst Engn, Dept Chem Engn, London SW7 2AZ, England | null | null | 36 | null | UK | Imperial Coll London | Menon, Govind | null | BACTERIA;CHEMICAL COMMUNICATION;DROPLETS;EXPRESSION | Menon, Govind; Krishnan, J.; | null | Imperial Coll London, Ctr Proc Syst Engn, Dept Chem Engn, London SW7 2AZ, England;Imperial Coll London, Inst Syst & Synthet Biol, London SW7 2AZ, England | Imperial Coll London, Ctr Proc Syst Engn, Dept Chem Engn, London SW7 2AZ, England;Imperial Coll London, Inst Syst & Synthet Biol, London SW7 2AZ, England | null | adaptation;cell-free systems;communication;compartmentalization;spatial design;systems analysis | 7 | 2004;2008;2009;2011;2012;2014;2015;2016;2017;2018 | 7 | Imperial Coll London, Ctr Proc Syst Engn, Dept Chem Engn, London SW7 2AZ, England;Imperial Coll London, Inst Syst & Synthet Biol, London SW7 2AZ, England | ACS Synth. Biol. | Krishnan, J | AMER CHEMICAL SOC | (0;(ii);(iii);(well-mixed;,;a;actively;also;an;and;appealing;applications;are;associated;basic;be;been;being;between;biology;broad;build;capabilities;cellular;circuit;circuits;circumvented;compartmentalization;compartmentalized;compartmentalizing;compartments;consequences;considerations;consolidate;constraints;demonstrated;design;develop;distributed;distributing;doing;elucidate;elusive;emerge;engineered;evolution;examine;exemplar;experimental;exploited;extend;features;framework;from;general;genetic;hallmark;has;have;hidden;how;important;in;include;including;ingredient;insights;interplay;is;it;may;most;multiple;nature;new;number;obtained;of;on;operational;or;organization;otherwise);our;principles;range;realizing;relevant;reveal;settings;so;spatial;state;synthetic;systems;template-based;the;their;these;they;this;to;trade-offs;underpinning;understanding;unexpected;ways;we;which;while;with | Imperial Coll London | Compartmentalization is a hallmark of cellular systems and an ingredient actively exploited in evolution. It is also being engineered and exploited in synthetic biology, in multiple ways. While these have demonstrated important experimental capabilities, understanding design principles underpinning compartmentalization of genetic circuits has been elusive. We develop a systems framework to elucidate the interplay between the nature of the genetic circuit, the spatial organization of compartments, and their operational state (well-mixed or otherwise). In so doing, we reveal a number of unexpected features associated with compartmentalizing synthetic and template-based circuits. These include (0 the consequences of distributing circuits including trade-offs and how they may be circumvented, (ii) hidden constraints in realizing a distributed circuit, and (iii) appealing new features of compartmentalized circuits. We build on this to examine exemplar applications, which consolidate and extend the design principles we have obtained. Our insights, which emerge from the most basic and general considerations of compartmentalizing genetic circuits, are relevant in a broad range of settings. | null | BACTERIA;CHEMICAL COMMUNICATION;DROPLETS;EXPRESSION | 0 | null | adaptation;cell-free systems;communication;compartmentalization;spatial design;systems analysis | 37 | adaptation;systems analysis;BACTERIA;cell-free systems;CHEMICAL COMMUNICATION;COMMUNICATION;COMPARTMENTALIZATION;DROPLETS;EXPRESSION;spatial design | WOS:000476957300016 | Imperial Coll London, London, England | UK | 2,019 | null | 0000-0002-1028-5463 | null | null | English | null | ACS CENTRAL SCI;ACS NANO;ACS SYNTH BIOL;ANGEW CHEM INT EDIT;BIOPHYS J;CELL SYST;CHEM COMMUN;ELIFE;INTEGR BIOL-UK;J AM CHEM SOC;J R SOC INTERFACE;LANGMUIR;METHODS;MOL SYST BIOL;NAT CHEM;NAT COMMUN;NAT NANOTECHNOL;NAT PHYS;NATURE;P NATL ACAD SCI USA;PHYS CHEM CHEM PHYS;PHYS REV LETT;PLOS COMPUT BIOL;PLOS ONE;SCI REP-UK;SCIENCE;TRANSCR-AUSTIN | Krishnan, J;Menon, Govind | 2024-03-11
ER | Abdelmohsen, L K E A;Adamala, K P;Alam-Nazki, A;Baccouche, A;Bayoumi, M;Bleris, L;Chatterjee, G;Elani, Y;Genot, A J;Gines, G;Gyorgy, A;Haglund Kaisa;Hindley, J W;Karzbrun, E;Lentini, R;Niederholtmeyer, H;Nijemeisland, M;Noireaux, V;Padirac, A;Page, K M;Pardatscher, G;Peters, R J R W;Qiao, Y;Rondelez, Y;Schwarz-Schilling, M;Stricker, J;Takahashi, M K;Tang, T Y D;Tayar, A M;Tomazou, M;Torre, P;Weitz, M;Widder, S | IL0AB | London, England;London, England. | 7 | null | 1 | null | 31,257,861 | Krishnan, J;Menon, Govind | ACS SYNTH BIOL | London, England |
Choi, Y R;Collins, K H;Guilak, F;Katz, D B;Klimak, M;Nims, R J;Pferdehirt, L;Pham, C T N;Ross, A K;Tabbaa, S | 10.1002/jor.24304 | null | 111 RIVER ST, HOBOKEN 07030-5774, NJ USA | 2h103u5q6n1p335dt1z581q4pu474u3r6f38u | Designer Stem Cells: Genome Engineering and the Next Generation of Cell-Based Therapies | Univ Washington | null | Guilak, F (corresponding author), Shriners Hosp Children, St Louis, MO 63110 USA.;Guilak, F (corresponding author), Washington Univ, Dept Biomed Engn, St Louis, MO 63110 USA.;Guilak, F (corresponding author), Washington Univ, Dept Orthopaed Surg, St Louis, MO 63110 USA. | SI | Choi, Yun-Rak;Collins, Kelsey H;Guilak, Farshid;Katz, Dakota B;Klimak, Molly;Nims, Robert J;Pferdehirt, Lara;Pham, Christine T N;Ross, Alison K;Tabbaa, Suzanne | Orthopedics | NIH [AR50245, AR48852, AG15768, AR48182, AG46927, OD10707, AR057235, AR073752, DK108742, EB018266, AR074240]; Arthritis Foundation; Nancy Taylor Foundation for Chronic Diseases, an NSF Graduate Research Fellowship; Washington University Center of Regenerative Medicine | WOS | Guilak, F | Shriners Hosp Children, St Louis, MO USA;SymplexBio Consulting LLC, Flagstaff, AZ USA;Washington Univ, St Louis, MO USA;Yonsei Univ, Seoul, South Korea | 37 | :;and;Cell-Based;Cells;Designer;engineering;Generation;genome;next;of;stem;the;therapies | 2 | Klimak, Molly;Pferdehirt, Lara | WILEY | Shriners Hosp Children, St Louis, MO 63110 USA;SymplexBio Consulting LLC, Flagstaff, AZ USA;Washington Univ, Dept Biomed Engn, St Louis, MO 63110 USA;Washington Univ, Dept Med, Div Rheumatol, St Louis, MO USA;Washington Univ, Dept Orthopaed Surg, St Louis, MO 63110 USA;Washington Univ, Dept Orthopaed Surg, St Louis, MO 63110 USA.; Guilak, F (corresponding author), Shriners Hosp Children, St Louis, MO 63110 USA.; Guilak, F (corresponding author), Washington Univ, Dept Biomed Engn, St Louis, MO 63110 USA;Yonsei Univ, Coll Med, Dept Orthopaed Surg, Seoul, South Korea | Review | Shriners Hosp Children;Univ Washington | HOBOKEN | null | null | Shriners Hosp Children;SymplexBio Consulting LLC;Washington Univ;Yonsei Univ | Arthritis Foundation;Nancy Taylor Foundation for Chronic Diseases, an NSF Graduate Research Fellowship;NIH;Washington University Center of Regenerative Medicine | Guilak, F (corresponding author), Washington Univ, Dept Orthopaed Surg, St Louis, MO 63110 USA.; Guilak, F (corresponding author), Shriners Hosp Children, St Louis, MO 63110 USA.; Guilak, F (corresponding author), Washington Univ, Dept Biomed Engn, St Louis, MO 63110 USA. | 1293 | Choi, Yun-Rak;Collins, Kelsey H;Guilak, Farshid;Katz, Dakota B;Klimak, Molly;Nims, Robert J;Pferdehirt, Lara;Pham, Christine T N;Ross, Alison K;Tabbaa, Suzanne | 17 | 6 | 470,781,400,010 | Arthritis Foundation;Nancy Taylor Foundation for Chronic Diseases, an NSF Graduate Research Fellowship;NIH [AR50245, AR48852, AG15768, AR48182, AG46927, OD10707, AR057235, AR073752, DK108742, EB018266, AR074240];Washington University Center of Regenerative Medicine | South Korea;USA | JOURNAL OF ORTHOPAEDIC RESEARCH | USA;USA.; | null | null | Washington Univ, Dept Orthopaed Surg, St Louis, MO 63110 USA | 0736-0266 | Choi, Y R;Collins, K H;Guilak, F;Katz, D B;Klimak, M;Nims, R J;Pferdehirt, L;Pham, C T N;Ross, A K;Tabbaa, S | JUN | guilak@wustl.edu | Cell-Based Therapies;designer Stem Cells;Genome Engineering;Next Generation | 10 | J | Orthopedics | 1287-1293;2019;ADIPOSE-TISSUE;AUTOLOGOUS CHONDROCYTE IMPLANTATION;autoregulated drug delivery;BONE-MARROW;CARTILAGE;cell survival;cell-based therapies;cell-surface molecules;cells;cellular engineering approaches;certain types;challenges;clinical practice;combining recent advances;CRISPR-Cas9;DELIVERY;DESIGNER;designer Stem Cells;development;differentiation;engraftment;enhanced tissue repair;factors;GENE;gene editing;Genome Engineering;immunomodulatory signaling;inc;inflammation;interdonor variability;intradonor;iPSC;J Orthop Res 37;limited therapeutic biological activity;MESENCHYMAL STEM;MSC;multipotency;musculoskeletal conditions;new classes;new therapeutic approaches;next generation;patient indications;potential;PURIFICATION;receptors;recipient microenvironment;regard;regenerative medicine;SPINAL-CORD;stem cell therapies;stem cell-based therapies;stem cells;stem cells exhibit immunomodulatory;success;synthetic biology;synthetic gene;tissue engineering;tissue repair;translation;tremendous promise;TRIAL;trophic effects;variability;Wiley Periodicals | Guilak, F | ADIPOSE-TISSUE;AUTOLOGOUS CHONDROCYTE IMPLANTATION;BONE-MARROW;CARTILAGE;CRISPR-Cas9;DELIVERY;DIFFERENTIATION;GENE;iPSC;MESENCHYMAL STEM;MSC;regenerative medicine;SPINAL-CORD;Synthetic biology;TRIAL | 1287 | [Guilak, Farshid; Pferdehirt, Lara; Ross, Alison K.; Choi, Yun-Rak; Collins, Kelsey H.; Nims, Robert J.; Katz, Dakota B.; Klimak, Molly] Washington Univ, Dept Orthopaed Surg, St Louis, MO 63110 USA. [Guilak, Farshid; Pferdehirt, Lara; Ross, Alison K.; Choi, Yun-Rak; Collins, Kelsey H.; Nims, Robert J.; Katz, Dakota B.; Klimak, Molly] Shriners Hosp Children, St Louis, MO 63110 USA. [Guilak, Farshid; Pferdehirt, Lara; Ross, Alison K.; Katz, Dakota B.; Klimak, Molly] Washington Univ, Dept Biomed Engn, St Louis, MO 63110 USA. [Choi, Yun-Rak] Yonsei Univ, Coll Med, Dept Orthopaed Surg, Seoul, South Korea. [Tabbaa, Suzanne] SymplexBio Consulting LLC, Flagstaff, AZ USA. [Pham, Christine T. N.] Washington Univ, Dept Med, Div Rheumatol, St Louis, MO USA. | This study was supported in part by NIH grants AR50245, AR48852, AG15768, AR48182, AG46927, OD10707, AR057235, AR073752, DK108742, EB018266, AR074240, the Arthritis Foundation, the Nancy Taylor Foundation for Chronic Diseases, an NSF Graduate Research Fellowship (A.K.R.), and the Philip and Sima Needleman Fellowship for Regenerative Medicine from the Washington University Center of Regenerative Medicine to L.P. and A.K.R. | 1287-1293;2019;autoregulated drug delivery;cell survival;cell-surface molecules;cells;cellular engineering approaches;certain types;challenges;clinical practice;combining recent advances;designer;development;engraftment;enhanced tissue repair;factors;gene editing;immunomodulatory signaling;Inc;inflammation;interdonor variability;intradonor;J Orthop Res 37;limited therapeutic biological activity;multipotency;musculoskeletal conditions;new classes;new therapeutic approaches;patient indications;potential;purification;receptors;recipient microenvironment;regard;stem cell therapies;stem cell-based therapies;stem cells;stem cells exhibit immunomodulatory;success;synthetic biology;synthetic gene;tissue engineering;tissue repair;translation;tremendous promise;trophic effects;variability;Wiley Periodicals | 10.1002/art.11365;10.1002/art.21779;10.1002/art.23598;10.1002/art.24352;10.1002/art.38780;10.1002/art.39982;10.1002/jcp.27833;10.1002/jor.1100090504;10.1002/sctm.17-0051;10.1002/sctm.17-0282;10.1002/stem.2657;10.1002/stem.2931;10.1002/stem.708;10.1002/term.502;10.1007/BF02367396;10.1007/s00167-018-4955-x;10.1007/s10561-015-9525-6;10.1016/j.biomaterials.2012.08.045;10.1016/j.biomaterials.2014.03.073;10.1016/j.colsurfb.2017.07.051;10.1016/j.copbio.2009.08.009;10.1016/j.jcyt.2017.06.008;10.1016/j.joca.2005.05.005;10.1016/j.molmed.2017.08.002;10.1016/j.orthres.2003.12.002;10.1016/j.scr.2012.12.003;10.1016/j.stem.2008.07.003;10.1016/j.stem.2011.06.008;10.1016/j.stem.2016.06.007;10.1016/j.stem.2016.12.006;10.1016/j.stem.2017.02.005;10.1016/j.stemcr.2017.03.013;10.1016/j.stemcr.2017.03.022;10.1016/j.tem.2019.01.001;10.1016/j.tibtech.2013.04.004;10.1038/d41586-018-06756-9;10.1038/ijo.2012.171;10.1038/mt.2016.10;10.1038/nm1703;10.1038/nprot.2013.143;10.1038/s41536-018-0041-8;10.1038/s41584-018-0125-2;10.1038/sj.mt.6300250;10.1056/NEJMc1600188;10.1056/NEJMoa1609583;10.1056/NEJMp1613723;10.1073/pnas.1601639113;10.1097/00007890-196803000-00009;10.1126/science.1258096;10.1126/science.284.5411.143;10.1136/bjsports-2016-096793;10.1136/bjsports-2016-096794;10.1159/000124281;10.1177/0363546513508744;10.1177/0363546515591257;10.1517/14712598.2011.546338;10.15585/mmwr.mm6750a5;10.2106/JBJS.G.00003;10.2174/1574888X12666170608124303;10.22203/eCM.v033a14;10.3171/2014.5.SPINE13992;10.3727/096368912X653264;[10.1038/nmeth.2600, 10.1038/NMETH.2600];[10.1089/ten.TEA.2016.0441, 10.1089/ten.tea.2016.0441];[10.1089/ten.tea.2019.0027, 10.1089/ten.TEA.2019.0027] | Washington Univ | Choi, Y R;Collins, K H;Guilak, F;Katz, D B;Klimak, M;Nims, R J;Pferdehirt, L;Pham, C T N;Ross, A K;Tabbaa, S | Guilak, F: Washington Univ, Dept Orthopaed Surg, St Louis, MO 63110 USA | Choi, Yun-Rak | AG15768;AG46927;AR057235;AR073752;AR074240;AR48182;AR48852;AR50245;DK108742;EB018266;OD10707 | 72 | null | USA | Shriners Hosp Children;SymplexBio Consulting LLC;Washington Univ;Yonsei Univ | Guilak, Farshid | Green Accepted, Bronze | ADIPOSE-TISSUE;AUTOLOGOUS CHONDROCYTE IMPLANTATION;BONE-MARROW;CARTILAGE;DELIVERY;DIFFERENTIATION;GENE;MESENCHYMAL STEM;SPINAL-CORD;TRIAL | Guilak, Farshid; Pferdehirt, Lara; Ross, Alison K.; Choi, Yun-Rak; Collins, Kelsey H.; Nims, Robert J.; Katz, Dakota B.; Klimak, Molly; Tabbaa, Suzanne; Pham, Christine T. N.; | null | Shriners Hosp Children, St Louis, MO 63110 USA;SymplexBio Consulting LLC, Flagstaff, AZ USA;Washington Univ, Dept Biomed Engn, St Louis, MO 63110 USA;Washington Univ, Dept Med, Div Rheumatol, St Louis, MO USA;Washington Univ, Dept Orthopaed Surg, St Louis, MO 63110 USA;Yonsei Univ, Coll Med, Dept Orthopaed Surg, Seoul, South Korea | Shriners Hosp Children, St Louis, MO 63110 USA;SymplexBio Consulting LLC, Flagstaff, AZ USA;Washington Univ, Dept Biomed Engn, St Louis, MO 63110 USA;Washington Univ, Dept Med, Div Rheumatol, St Louis, MO USA;Washington Univ, Dept Orthopaed Surg, St Louis, MO 63110 USA;Yonsei Univ, Coll Med, Dept Orthopaed Surg, Seoul, South Korea | 1554-527X | CRISPR/Cas9;iPSC;MSC;regenerative medicine;Synthetic biology | 6 | 1968;1988;1991;1999;2000;2003;2004;2005;2006;2007;2008;2009;2011;2012;2013;2014;2015;2016;2017;2018;2019 | 18 | Shriners Hosp Children, St Louis, MO 63110 USA;Washington Univ, Dept Biomed Engn, St Louis, MO 63110 USA;Washington Univ, Dept Orthopaed Surg, St Louis, MO 63110 USA | J. Orthop. Res. | Pham, Christine T N | WILEY | ";,;1287-1293;2019;37;:;activity;addition;advances;and;approaches;as;autoregulated;benefit;biological;biology;by;can;cell;cell-based;cell-surface;cells;cellular;certain;challenges;circuits;classes;clinical;combining;conditions;create;delivery;designer;development;difficult;drug;due;editing;effects;engineering;engraftment;enhance;enhanced;exhibit;exists;factors;for;from;gene;has;have;homing;however;immunomodulatory;in;Inc;indications;inflammation;interdonor;intradonor;J;limited;may;microenvironment;mitigate;molecules;multipotency;musculoskeletal;new;of;or;Orthop;patient;Periodicals;potential;practice;prescribed;promise;proven;provide;published;purification;recent;receptors;recipient;regard;repair;Res;signaling;stem;success;such;survival;synthetic;that;the;their;therapeutic;therapies;this;tissue;to;translation;tremendous;trophic;types;variability;well;Wiley | Shriners Hosp Children;Washington Univ | Stem cells provide tremendous promise for the development of new therapeutic approaches for musculoskeletal conditions. In addition to their multipotency, certain types of stem cells exhibit immunomodulatory effects that can mitigate inflammation and enhance tissue repair. However, the translation of stem cell therapies to clinical practice has proven difficult due to challenges in intradonor and interdonor variability, engraftment, variability in recipient microenvironment and patient indications, and limited therapeutic biological activity. In this regard, the success of stem cell-based therapies may benefit from cellular engineering approaches to enhance factors such as purification, homing and cell survival, trophic effects, or immunomodulatory signaling. By combining recent advances in gene editing, synthetic biology, and tissue engineering, the potential exists to create new classes of "designer" cells that have prescribed cell-surface molecules and receptors as well as synthetic gene circuits that provide for autoregulated drug delivery or enhanced tissue repair. Published by Wiley Periodicals, Inc. J Orthop Res 37:1287-1293, 2019. | AAG-9914-2019 | ADIPOSE-TISSUE;AUTOLOGOUS CHONDROCYTE IMPLANTATION;BONE-MARROW;CARTILAGE;DELIVERY;DIFFERENTIATION;GENE;MESENCHYMAL STEM;SPINAL-CORD;TRIAL | 0 | null | CRISPR-Cas9;iPSC;MSC;regenerative medicine;Synthetic biology | 7 | ADIPOSE-TISSUE;AUTOLOGOUS CHONDROCYTE IMPLANTATION;BONE-MARROW;CARTILAGE;CRISPR-Cas9;DELIVERY;DIFFERENTIATION;GENE;iPSC;MESENCHYMAL STEM;MSC;regenerative medicine;SPINAL-CORD;Synthetic biology;TRIAL | WOS:000470781400010 | Shriners Hosp Children, St Louis, MO USA;SymplexBio Consulting LLC, Flagstaff, AZ USA;Washington Univ, St Louis, MO USA;Yonsei Univ, Seoul, South Korea | South Korea;USA | 2,019 | null | 0000-0002-1968-3636;0000-0003-4673-9540 | null | null | English | null | AM J SPORT MED;ANN BIOMED ENG;ARTHRITIS RHEUM-US;ARTHRITIS RHEUMATOL;BIOMATERIALS;BRIT J SPORT MED;CELL STEM CELL;CELL TISSUE BANK;CELL TRANSPLANT;CIBA F SYMP;CLIN ORTHOP RELAT R;COLLOID SURFACE B;CURR OPIN BIOTECH;CURR STEM CELL RES T;CYTOTHERAPY;EUR CELLS MATER;EXPERT OPIN BIOL TH;INT J OBESITY;J BONE JOINT SURG AM;J CELL PHYSIOL;J NEUROSURG-SPINE;J ORTHOP RES;J ORTHOPAED RES;J TISSUE ENG REGEN M;KNEE SURG SPORT TR A;MMWR-MORBID MORTAL W;MOL THER;NAT MED;NAT METHODS;NAT PROTOC;NAT REV MOL CELL BIO;NAT REV RHEUMATOL;NATURE;NEW ENGL J MED;NPJ REGEN MED;OSTEOARTHR CARTILAGE;P NATL ACAD SCI USA;SCIENCE;STEM CELL REP;STEM CELL RES;STEM CELL TRANSL MED;STEM CELLS;T ORTHOP RES SOC;TISSUE ENG PT A;TRANSFUS MED HEMOTH;TRANSPLANTATION;TRENDS BIOTECHNOL;TRENDS ENDOCRIN MET;TRENDS MOL MED;VET THER | Choi, Yun-Rak;Collins, Kelsey H;Guilak, Farshid;Katz, Dakota B;Klimak, Molly;Nims, Robert J;Pferdehirt, Lara;Pham, Christine T N;Ross, Alison K;Tabbaa, Suzanne | 2024-03-11
ER | Adkar, S S;Aghebati-Maleki, L;Anderson, J A;Bauer, G;Berkowitz, A L;Black, L L;Brunger, J M;Cano, E;Caplan, A I;Choi, Y R;Costa-Almeida, R;Crisan, M;Cucchiarini, M;De Windt, T S;Dennis, J E;Diekman, B O;Dlouhy, B J;Doudna, J A;Ebert, J R;Estes, B T;Farhang, N;Friedenstein, A J;Fung, M;Gaj, T;Gimble, J M;Glass, K A;Guimaraes-Camboa, N;Hellingman, C A;Hurley, E T;Huynh, N P;Iijima, H;Im, G I;Knutsen, G;Kuriyan, A E;Lau, T T;Li, Y;Lin, P;Lin, T;Maeder, M L;Marks, P W;Mckee, C;Mosca, J D;Moutos, F T;Murphy, J M;Nancarrow-Lei, R;Nerem, R M;Ousema, P H;Owen, M;Paladino, F V;Pas Himfl;Perez-Pinera, P;Perkins, K M;Pferdehirt, L;Pittenger, M F;Rachakonda, P S;Ran, F A;Roddy, G W;Sackstein, R;Sipp, D;Turner, L;Wagner, J;Wehling, N;Wells, C A;Willard, V P;Wu, C L;Xie, M | IC2HR | St Louis, MO USA;St Louis, MO USA. | 23 | null | 4 | null | 30,977,548 | Choi, Yun-Rak;Collins, Kelsey H;Guilak, Farshid;Katz, Dakota B;Klimak, Molly;Nims, Robert J;Pferdehirt, Lara;Pham, Christine T N;Ross, Alison K;Tabbaa, Suzanne | J ORTHOP RES | Flagstaff, AZ USA;Seoul, South Korea;ST LOUIS, MO USA |
Bashor, C J;Beyzavi, A;Choubey, S;Collins, J J;Khalil, A S;Kondev, J;Patel, N | 10.1126/science.aau8287 | null | 1200 NEW YORK AVE, NW, WASHINGTON, DC 20005 USA | 6p571h6ym4x4lc324b345d1u6e3m4r2t1z3w | Complex signal processing in synthetic gene circuits using cooperative regulatory assemblies | Rice Univ | null | Khalil, AS (corresponding author), Boston Univ, Biol Design Ctr, Boston, MA 02215 USA.;Khalil, AS (corresponding author), Boston Univ, Dept Biomed Engn, Boston, MA 02215 USA.;Khalil, AS (corresponding author), Harvard Univ, Wyss Inst Biol Inspired Engn, Boston, MA 02115 USA. | null | Bashor, Caleb J;Beyzavi, Ali;Choubey, Sandeep;Collins, James J;Khalil, Ahmad S;Kondev, Jane;Patel, Nikit | Multidisciplinary Sciences | NSF Expeditions in Computing grant [CCF-1522074]; DARPA [W911NF-11-2-0056, D16AP00142]; NSF CAREER award [MCB-1350949]; NIH [1DP2AI131083-01] | WOS | Khalil, A S | Boston Univ, Boston, MA USA;Brandeis Univ, Waltham, MA USA;Broad Inst MIT & Harvard, Cambridge, MA USA;Harvard Univ, Boston, MA USA;MIT, Cambridge, MA USA;Rice Univ, Houston, TX USA | 364 | assemblies;circuits;complex;cooperative;gene;in;processing;regulatory;signal;synthetic;using | 1 | Bashor, Caleb;Choubey, Sandeep;Collins, James;Kondev, Jane;Patel, Nikit | AMER ASSOC ADVANCEMENT SCIENCE | Boston Univ, Biol Design Ctr, Boston, MA 02215 USA;Boston Univ, Dept Biomed Engn, Boston, MA 02215 USA;Boston Univ, Dept Biomed Engn, Boston, MA 02215 USA.; Khalil, AS (corresponding author), Boston Univ, Biol Design Ctr, Boston, MA 02215 USA.; Khalil, AS (corresponding author), Harvard Univ, Wyss Inst Biol Inspired Engn, Boston, MA 02115 USA;Boston Univ, Dept Mech Engn, Boston, MA 02215 USA;Brandeis Univ, Dept Phys, Waltham, MA 02453 USA;Broad Inst MIT & Harvard, Cambridge, MA 02142 USA;Harvard Univ, Wyss Inst Biol Inspired Engn, Boston, MA 02115 USA;MIT, Inst Med Engn & Sci, Dept Biol Engn, 77 Massachusetts Ave, Cambridge, MA 02139 USA;MIT, Synthet Biol Ctr, 77 Massachusetts Ave, Cambridge, MA 02139 USA;Rice Univ, Dept Bioengn, Houston, TX 77030 USA | Article | Boston Univ;Harvard Univ | WASHINGTON | null | null | Boston Univ;Brandeis Univ;Broad Inst MIT & Harvard;Harvard Univ;MIT;Rice Univ | DARPA;NIH;NSF CAREER award;NSF Expeditions in Computing grant | Khalil, AS (corresponding author), Boston Univ, Dept Biomed Engn, Boston, MA 02215 USA.; Khalil, AS (corresponding author), Boston Univ, Biol Design Ctr, Boston, MA 02215 USA.; Khalil, AS (corresponding author), Harvard Univ, Wyss Inst Biol Inspired Engn, Boston, MA 02115 USA. | + | Bashor, Caleb J;Beyzavi, Ali;Choubey, Sandeep;Collins, James J;Khalil, Ahmad S;Kondev, Jane;Patel, Nikit | 106 | 9 | 467,631,800,044 | DARPA [W911NF-11-2-0056, D16AP00142];NIH [1DP2AI131083-01];NSF CAREER award [MCB-1350949];NSF Expeditions in Computing grant [CCF-1522074] | USA | SCIENCE | USA;USA.; | null | null | Rice Univ, Dept Bioengn, Houston, TX 77030 USA | 0036-8075 | Bashor, C J;Beyzavi, A;Choubey, S;Collins, J J;Khalil, A S;Kondev, J;Patel, N | MAY 10 | khalil@bu.edu | complex signal processing;cooperative regulatory assemblies;synthetic gene circuits | 7 | J | Science & Technology - Other Topics | affinity;assemblies;assembly subunits;BINDING;BIOLOGY;cell populations;cellular decision-making;circuit dynamics;COMBINATORIAL;complex signal processing;COMPLEXES;cooperative assemblies;cooperative regulatory assemblies;cooperative self-assembly;design principle;dynamic;enabling frequency-dependent decoding;engineerable behaviors;eukaryotic genes;expression;INFORMATION;model-guided approach;multi-input circuits;multivalent transcription factor complexes;network connections;nonlinear regulatory operations;nonlinear regulatory responses;nonlinearity;number;numbers;predictive tuning;principles;program nonlinear gene circuit behavior;programmable cooperative assembly;signal processing;single-;specificity;strength;study;synthetic circuits;synthetic gene circuits;synthetic networks;testing;transcriptional regulation;versatile way;yeast | Bashor, C J | AFFINITY;BINDING;BIOLOGY;COMBINATORIAL;EXPRESSION;INFORMATION;NUMBERS;PRINCIPLES;SPECIFICITY;Transcriptional regulation | 593 | [Bashor, Caleb J.] Rice Univ, Dept Bioengn, Houston, TX 77030 USA. [Patel, Nikit; Khalil, Ahmad S.] Boston Univ, Dept Biomed Engn, Boston, MA 02215 USA. [Patel, Nikit; Khalil, Ahmad S.] Boston Univ, Biol Design Ctr, Boston, MA 02215 USA. [Choubey, Sandeep; Kondev, Jane] Brandeis Univ, Dept Phys, Waltham, MA 02453 USA. [Beyzavi, Ali] Boston Univ, Dept Mech Engn, Boston, MA 02215 USA. [Collins, James J.] MIT, Inst Med Engn & Sci, Dept Biol Engn, 77 Massachusetts Ave, Cambridge, MA 02139 USA. [Collins, James J.] MIT, Synthet Biol Ctr, 77 Massachusetts Ave, Cambridge, MA 02139 USA. [Collins, James J.] Broad Inst MIT & Harvard, Cambridge, MA 02142 USA. [Collins, James J.; Khalil, Ahmad S.] Harvard Univ, Wyss Inst Biol Inspired Engn, Boston, MA 02115 USA. | This work was supported by NSF Expeditions in Computing grant CCF-1522074 (A.S.K.) and DARPA grant W911NF-11-2-0056 (J.J.C. and A.S.K.). A.S.K. also acknowledges funding from the NIH director's New Innovator award (1DP2AI131083-01), an NSF CAREER award (MCB-1350949), and a DARPA Young Faculty award (D16AP00142). | assemblies;assembly subunits;cell populations;cellular decision-making;circuit dynamics;complexes;cooperative assemblies;cooperative self-assembly;design principle;dynamic;enabling frequency-dependent decoding;engineerable behaviors;eukaryotic genes;model-guided approach;multi-input circuits;multivalent transcription factor complexes;network connections;nonlinear regulatory operations;nonlinear regulatory responses;nonlinearity;number;predictive tuning;program nonlinear gene circuit behavior;programmable cooperative assembly;signal processing;single-;strength;study;synthetic circuits;synthetic networks;testing;versatile way;yeast | 10.1002/cyto.a.20812;10.1016/0014-5793(95)00062-E;10.1016/0092-8674(84)90243-5;10.1016/0896-6273(91)90256-Y;10.1016/B978-0-12-381268-1.00014-8;10.1016/j.bpj.2009.11.021;10.1016/j.cell.2011.01.004;10.1016/j.cell.2012.05.045;10.1016/j.cell.2012.08.018;10.1016/j.cell.2013.02.005;10.1016/j.cell.2014.04.047;10.1016/j.cell.2016.06.012;10.1016/j.cell.2017.02.007;10.1016/j.cell.2017.08.015;10.1016/j.cub.2010.06.070;10.1016/j.gde.2005.02.006;10.1016/j.gde.2005.02.007;10.1016/j.jmb.2004.08.064;10.1016/j.tibs.2014.10.002;10.1016/S0092-8674(00)80893-4;10.1016/S0955-0674(02)00314-9;10.1017/CBO9781107415324.004;10.1017/S1464793102006036;10.1021/ac980656z;10.1021/bi010142l;10.1038/335683a0;10.1038/msb.2009.30;10.1038/msb.2010.83;10.1038/msb.2013.56;10.1038/msb4100032;10.1038/nature07211;10.1038/nature07521;10.1038/nchembio.102;10.1038/nchembio0808-435;10.1038/nrg3207;10.1038/nrm2698;10.1038/nrn.2016.18;10.1042/BJ20061644;10.1073/pnas.0809901106;10.1073/pnas.0913805107;10.1073/pnas.0930314100;10.1073/pnas.2133841100;10.1093/nar/gks1313;10.1098/rsob.130031;10.1126/science.1152398;10.1126/science.1239999;10.1126/science.2063199;10.1126/science.283.5400.381;10.1126/science.288.5463.113;10.1126/science.aab0892;10.1146/annurev.biophys.050708.133652;10.15252/msb.20178024;[10.1038/nchembio.915, 10.1038/NCHEMBIO.915];[10.1038/NMETH.2926, 10.1038/nmeth.2926] | Rice Univ | Bashor, C J;Beyzavi, A;Choubey, S;Collins, J J;Khalil, A S;Kondev, J;Patel, N | Bashor, C J: Rice Univ, Dept Bioengn, Houston, TX 77030 USA | null | 1DP2AI131083-01;CCF-1522074;D16AP00142;MCB-1350949;W911NF-11-2-0056 | 55 | null | USA | Boston Univ;Brandeis Univ;Broad Inst MIT & Harvard;Harvard Univ;MIT;Rice Univ | Bashor, Caleb J | Green Accepted, Bronze, Green Published | AFFINITY;BINDING;BIOLOGY;COMBINATORIAL;EXPRESSION;INFORMATION;NUMBERS;PRINCIPLES;SPECIFICITY;TRANSCRIPTIONAL REGULATION | Bashor, Caleb J.; Patel, Nikit; Choubey, Sandeep; Beyzavi, Ali; Kondev, Jane; Collins, James J.; Khalil, Ahmad S.; | null | Boston Univ, Biol Design Ctr, Boston, MA 02215 USA;Boston Univ, Dept Biomed Engn, Boston, MA 02215 USA;Boston Univ, Dept Mech Engn, Boston, MA 02215 USA;Brandeis Univ, Dept Phys, Waltham, MA 02453 USA;Broad Inst MIT & Harvard, Cambridge, MA 02142 USA;Harvard Univ, Wyss Inst Biol Inspired Engn, Boston, MA 02115 USA;MIT, Inst Med Engn & Sci, Dept Biol Engn, 77 Massachusetts Ave, Cambridge, MA 02139 USA;MIT, Synthet Biol Ctr, 77 Massachusetts Ave, Cambridge, MA 02139 USA;Rice Univ, Dept Bioengn, Houston, TX 77030 USA | Boston Univ, Biol Design Ctr, Boston, MA 02215 USA;Boston Univ, Dept Biomed Engn, Boston, MA 02215 USA;Boston Univ, Dept Mech Engn, Boston, MA 02215 USA;Brandeis Univ, Dept Phys, Waltham, MA 02453 USA;Broad Inst MIT & Harvard, Cambridge, MA 02142 USA;Harvard Univ, Wyss Inst Biol Inspired Engn, Boston, MA 02115 USA;MIT, Inst Med Engn & Sci, Dept Biol Engn, 77 Massachusetts Ave, Cambridge, MA 02139 USA;MIT, Synthet Biol Ctr, 77 Massachusetts Ave, Cambridge, MA 02139 USA;Rice Univ, Dept Bioengn, Houston, TX 77030 USA | 1095-9203 | null | 6440 | 1910;1984;1988;1991;1995;1998;1999;2000;2001;2003;2004;2005;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016;2017;2018 | 84 | Boston Univ, Biol Design Ctr, Boston, MA 02215 USA;Boston Univ, Dept Biomed Engn, Boston, MA 02215 USA;Harvard Univ, Wyss Inst Biol Inspired Engn, Boston, MA 02115 USA | Science | Khalil, Ahmad S | AMER ASSOC ADVANCEMENT SCIENCE | ,;a;adjusted;and;apply;approach;are;assemblies;assembly;available;be;behavior;behaviors;between;by;can;capability;cell;cellular;circuit;circuits;complexes;connections;control;cooperative;decision-making;decoding;demonstrate;design;dynamic;dynamics;enables;enabling;engineer;engineerable;engineered;eukaryotic;expanding;factor;filtering;for;frequency-dependent;gene;genes;harness;in;involved;linear;markedly;model-guided;multi-input;multivalent;network;networks;nonlinear;nonlinearity;number;of;operations;perform;populations;predictive;principle;processing;program;programmable;provides;regulated;regulatory;responses;self-assembly;show;signal;single-;specifying;strength;study;subunits;synthetic;testing;that;the;these;this;through;to;transcription;tune;tuning;using;versatile;way;we;whether;yeast | Boston Univ;Harvard Univ | Eukaryotic genes are regulated by multivalent transcription factor complexes. Through cooperative self-assembly, these complexes perform nonlinear regulatory operations involved in cellular decision-making and signal processing. In this study, we apply this design principle to synthetic networks, testing whether engineered cooperative assemblies can program nonlinear gene circuit behavior in yeast. Using a model-guided approach, we show that specifying the strength and number of assembly subunits enables predictive tuning between linear and nonlinear regulatory responses for single- and multi-input circuits. We demonstrate that assemblies can be adjusted to control circuit dynamics. We harness this capability to engineer circuits that perform dynamic filtering, enabling frequency-dependent decoding in cell populations. Programmable cooperative assembly provides a versatile way to tune the nonlinearity of network connections, markedly expanding the engineerable behaviors available to synthetic circuits. | null | AFFINITY;BINDING;BIOLOGY;COMBINATORIAL;EXPRESSION;INFORMATION;NUMBERS;PRINCIPLES;TRANSCRIPTIONAL REGULATION;SPECIFICITY | 4 | null | null | 78 | AFFINITY;BINDING;BIOLOGY;COMBINATORIAL;EXPRESSION;INFORMATION;NUMBERS;PRINCIPLES;Transcriptional regulation;SPECIFICITY | WOS:000467631800044 | Boston Univ, Boston, MA USA;Brandeis Univ, Waltham, MA USA;Broad Inst MIT & Harvard, Cambridge, MA USA;Harvard Univ, Boston, MA USA;MIT, Cambridge, MA USA;Rice Univ, Houston, TX USA | USA | 2,019 | null | 0000-0001-7522-7144;0000-0002-5033-8072;0000-0002-5560-8246;0000-0002-7387-6148;0000-0003-1354-2098 | null | null | English | null | ANAL CHEM;ANNU REV BIOPHYS;BIOCHEM J;BIOCHEMISTRY-US;BIOL REV;BIOL REV CAMBRIDGE P;BIOPHYS J;CELL;CURR BIOL;CURR OPIN CELL BIOL;CURR OPIN GENET DEV;CYTOM PART A;FEBS LETT;J MOL BIOL;METHOD ENZYMOL;MOL SYST BIOL;NAT CHEM BIOL;NAT METHODS;NAT REV GENET;NAT REV MOL CELL BIO;NAT REV NEUROSCI;NATURE;NEURON;NUCLEIC ACIDS RES;OPEN BIOL;P NATL ACAD SCI USA;piv;SCIENCE;TRENDS BIOCHEM SCI | Bashor, Caleb J;Beyzavi, Ali;Choubey, Sandeep;Collins, James J;Khalil, Ahmad S;Kondev, Jane;Patel, Nikit | 2024-03-11
ER | 2002;2003;Antebi, Y E;Aymoz, D;Baker, C R;Bashor, C J;Bennett, M R;Bhalla, U S;Bialek, W;Bintu, L;Brophy, J A N;Buchler, N E;Carey, M;Cookson, S;Duffy, D C;Estrada, J;Ferrell, J E;Garcia, H G;Gertz, J;Guarente, L;Hansen, A S;Harris, B Z;Hill A.V.;Hnisz, D;Jantz, D;Kang, J S;Keung, A J;Khalil, A S;Levine, J H;Levine, M;Mangan, S;Mao, C H;Mcisaac, R S;Mirny, L A;Mitchell, A;Nevozhay, D;Novershtern, N;Ptashne, M;Purnick, P E M;Purvis, J E;Spitz, F;Struhl, K;Tuch, B B;Unger, M A;Vega, N M;Veitia, R A;Wang, Q L;Wang, Z X;Whitty, A;Wiedemann, U;Williamson, J R;Zhang, Q;Zhu, J W | HX8BW | Boston, MA USA;Boston, MA USA. | 107 | null | 6 | null | 31,000,590 | Bashor, Caleb J;Beyzavi, Ali;Choubey, Sandeep;Collins, James J;Khalil, Ahmad S;Kondev, Jane;Patel, Nikit | SCIENCE | Boston, MA USA;Cambridge, MA USA;Houston, TX USA;Waltham, MA USA |
Chaplain, M A J;Macnamara, C K;Mitchell, E I | 10.1016/j.jtbi.2019.02.003 | null | 24-28 OVAL RD, LONDON NW1 7DX, ENGLAND | 2r3f1xs2jb6m455h542q591r611a3m621u206k | Spatial-Stochastic modelling of synthetic gene regulatory networks | Univ St Andrews | null | Chaplain, MAJ (corresponding author), Univ St Andrews, Math Inst, Sch Math & Stat, St Andrews KY16 9SS, Fife, Scotland. | null | Chaplain, Mark A J;Macnamara, Cicely K;Mitchell, Elaine, I | Biology;Mathematical & Computational Biology | EPSRC [EP/N014642/1]; EPSRC [EP/N014642/1] Funding Source: UKRI | WOS | Chaplain, M A J | Univ Dundee, Dundee DD1 4HN, Scotland;Univ St Andrews, Fife, Scotland | 468 | gene;modelling;networks;of;regulatory;spatial-Stochastic;synthetic | 1 | Chaplain, Mark;Macnamara, Cicely Krystyna | ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD | Univ Dundee, Div Math, Dundee DD1 4HN, Scotland;Univ St Andrews, Math Inst, Sch Math & Stat, St Andrews KY16 9SS, Fife, Scotland | Article | Univ St Andrews | LONDON | null | null | Univ Dundee;Univ St Andrews | EPSRC | Chaplain, MAJ (corresponding author), Univ St Andrews, Math Inst, Sch Math & Stat, St Andrews KY16 9SS, Fife, Scotland. | 44 | Chaplain, Mark A J;Macnamara, Cicely K;Mitchell, Elaine, I | 13 | 2 | 462,102,600,003 | EPSRC [EP/N014642/1];EPSRC [EP/N014642/1] Funding Source: UKRI | UK | JOURNAL OF THEORETICAL BIOLOGY | UK | null | null | Univ St Andrews, Math Inst, Sch Math & Stat, St Andrews KY16 9SS, Fife, Scotland | 0022-5193 | Chaplain, M A J;Macnamara, C K;Mitchell, E I | MAY 7 | ckm@st-andrews.ac.uk;emitchell@maths.dundee.ac.uk;majc@st-andrews.ac.uk | spatial-Stochastic modelling;synthetic gene regulatory networks | 3 | J | Life Sciences & Biomedicine - Other Topics;Mathematical & Computational Biology | activator-repressor systems;ACTIVE-TRANSPORT;actual numbers;apoptosis (e.g;area;C 2019 Elsevier Ltd;cell division;cells;cells);control;cytoplasm;data;DIFFUSION;down-regulating production;DYNAMICS;experimental data;feedback mechanisms;gene regulatory networks (GRNs);gene sites;GRNs;HES1;important molecules;important role;key cellular processes;leads;low;molecular interaction networks;molecular levels;MOLECULES;mRNA;necessary;NEGATIVE FEEDBACK;NETWORK;NF kappa B pathways);nucleus;OSCILLATORY EXPRESSION;P53;p53-Mdm2;part;previous work;problem;process;PROTEIN;protein levels;proteins;proteins binding;quantitative way;reduced;REPRESSILATORS;rights reserved;simulation;spatial aspect;spatial-stochastic modelling;stochastic approach;stochastic spatio-temporal models;synthetic gene regulatory networks;synthetic GRNs;systems;take;time;TIME DELAYS;transcription (the mechanism;transcription factors;transcription rate;translation (the mechanism;up-regulating;wider family | Macnamara, C K | Activator-repressor systems;ACTIVE-TRANSPORT;DIFFUSION;DYNAMICS;HES1;NEGATIVE FEEDBACK;OSCILLATORY EXPRESSION;P53;PROTEIN;REPRESSILATORS;SIMULATION;spatial-stochastic modelling;Synthetic gene regulatory networks;TIME DELAYS | 27 | [Macnamara, Cicely K.; Chaplain, Mark A. J.] Univ St Andrews, Math Inst, Sch Math & Stat, St Andrews KY16 9SS, Fife, Scotland. [Mitchell, Elaine, I] Univ Dundee, Div Math, Dundee DD1 4HN, Scotland. | MAJC and CKM gratefully acknowledge support of EPSRC Grant No. EP/N014642/1 (EPSRC Centre for Multiscale Soft Tissue Mechanics - With Application to Heart & Cancer). | activator-repressor systems;actual numbers;apoptosis (e.g;area;cell division;cells;cells);control;cytoplasm;data;down-regulating production;experimental data;feedback mechanisms;gene regulatory networks (GRNs);gene sites;GRNs;important molecules;important role;key cellular processes;leads;low;molecular interaction networks;molecular levels;molecules;mRNA;necessary;negative feedback;network;NF kappa B pathways);nucleus;p53-Mdm2;part;previous work;problem;process;protein levels;proteins;proteins binding;quantitative way;reduced;repressilators;spatial aspect;stochastic approach;stochastic spatio-temporal models;synthetic GRNs;systems;take;time;transcription (the mechanism;transcription factors;transcription rate;translation (the mechanism;up-regulating;wider family | 10.1007/BF00275860;10.1007/BF00276489;10.1007/s11538-012-9725-1;10.1007/s11538-017-0292-3;10.1016/0022-5193(68)90189-6;10.1016/0022-5193(72)90157-9;10.1016/0025-5564(88)90081-8;10.1016/0065-2571(65)90067-1;10.1016/j.bbapap.2013.09.019;10.1016/j.csbj.2014.05.007;10.1016/j.jtbi.2008.07.013;10.1016/j.jtbi.2010.08.017;10.1016/j.jtbi.2010.12.016;10.1016/j.jtbi.2012.08.035;10.1016/j.jtbi.2014.07.022;10.1016/j.jtbi.2016.07.021;10.1016/j.mbs.2012.01.001;10.1016/S0006-3495(02)75249-1;10.1016/S0014-5793(03)00279-5;10.1016/S0960-9822(03)00494-9;10.1016/S0960-9822(03)00534-7;10.1021/jp993732q;10.1021/sb400152n;10.1038/278261a0;10.1038/35002125;10.1038/35014651;10.1038/358015a0;10.1038/msb.2008.24;10.1038/ng1293;10.1063/1.1681157;10.1088/1478-3975/11/4/045001;10.1098/rsif.2010.0183;10.1098/rsif.2012.0988;10.1103/PhysRevE.85.046210;10.1126/science.1074560;10.1126/science.1099962;10.1126/science.1164860;10.1126/science.267326;10.1137/080721388;10.1140/epjb/e2002-00271-1;10.1142/S021820251550030X;10.1152/ajpcell.1999.277.4.C777;10.1175/1520-0477(1998)079<0061:APGTWA>2.0.CO;2;10.1186/1752-0509-6-76;10.1186/1756-0500-5-163;10.1186/gb-2012-13-2-240;10.1242/dev.000786;10.1523/JNEUROSCI.21-17-06644.2001 | Univ St Andrews | Chaplain, M A J;Macnamara, C K;Mitchell, E I | Macnamara, C K: Univ St Andrews, Math Inst, Sch Math & Stat, St Andrews KY16 9SS, Fife, Scotland | Chaplain, Mark | EP/N014642/1 | 51 | null | UK | Univ Dundee;Univ St Andrews | Macnamara, Cicely K | Green Accepted | ACTIVE-TRANSPORT;DIFFUSION;DYNAMICS;HES1;NEGATIVE FEEDBACK;OSCILLATORY EXPRESSION;P53;PROTEIN;SIMULATION;TIME DELAYS | Macnamara, Cicely K.; Mitchell, Elaine, I; Chaplain, Mark A. J.; | null | Univ Dundee, Div Math, Dundee DD1 4HN, Scotland;Univ St Andrews, Math Inst, Sch Math & Stat, St Andrews KY16 9SS, Fife, Scotland | Univ Dundee, Div Math, Dundee DD1 4HN, Scotland;Univ St Andrews, Math Inst, Sch Math & Stat, St Andrews KY16 9SS, Fife, Scotland | 1095-8541 | Activator-repressor systems;repressilator;Spatial stochastic model;synthetic gene regulatory network | null | 1965;1968;1972;1974;1977;1979;1984;1985;1988;1992;1998;1999;2000;2001;2002;2003;2004;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016;2018 | 3 | Univ St Andrews, Math Inst, Sch Math & Stat, St Andrews KY16 9SS, Fife, Scotland | J. Theor. Biol. | Chaplain, Mark A J | ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD | (e.g;(GRNs);(the;,;a;account;accurately;activator-repressor;actual;adopt;also;an;analysed;analysing;and;apoptosis;approach;are;area;as;aspect;B;be;between;binding;by;cases;cell;cells;cells);cellular;connect;control;cytoplasm;data;division;down-regulating;e.g.;either;exert;experimental;extend;factors;family;feedback;for;formulating;gene;GRNs;hence;important;in;interaction;into;involved;is;it;kappa;key;known;leads;levels;low;many;mechanism;mechanisms;model;models;modulating;molecular;molecules;mRNA;necessary;negative;network;networks;NF;noisy;nucleus;numbers;observed;of;or;order;oscillating;over;p53-Mdm2;paper;part;pathways);play;previous;problem;process;processes;produced;production;protein;proteins;quantitative;quite;rate;reduced;regulatory;Repressilators;role;sites;spatial;spatially;spatio-temporal;stochastic;such;synthetic;systems;take;the;there;therefore;this;through;time;to;transcription;translation;typically;up-regulating;way;we;well;when;which;wider;with;within;work | Univ St Andrews | Transcription factors are important molecules which control the levels of mRNA and proteins within cells by modulating the process of transcription (the mechanism by which mRNA is produced within cells) and hence translation (the mechanism by which proteins are produced within cells). Transcription factors are part of a wider family of molecular interaction networks known as gene regulatory networks (GRNs) which play an important role in key cellular processes such as cell division and apoptosis (e.g. the p53-Mdm2, NF kappa B pathways). Transcription factors exert control over molecular levels through feedback mechanisms, with proteins binding to gene sites in the nucleus and either up-regulating or down-regulating production of mRNA. In many GRNs, there is a negative feedback in the network and the transcription rate is reduced. Typically, this leads to the mRNA and protein levels oscillating over time and also spatially between the nucleus and cytoplasm. When experimental data for such systems is analysed, it is observed to be noisy and in many cases the actual numbers of molecules involved are quite low. In order to model such systems accurately and connect with the data in a quantitative way, it is therefore necessary to adopt a stochastic approach as well as take into account the spatial aspect of the problem. in this paper, we extend previous work in the area by formulating and analysing stochastic spatio-temporal models of synthetic GRNs e.g. repressilators and activator-repressor systems. | A-5355-2010 | ACTIVE-TRANSPORT;DIFFUSION;DYNAMICS;HES1;NEGATIVE FEEDBACK;OSCILLATORY EXPRESSION;P53;PROTEIN;SIMULATION;TIME DELAYS | 0 | null | Activator-repressor systems;repressilators;spatial-stochastic modelling;Synthetic gene regulatory networks | 18 | Activator-repressor systems;ACTIVE-TRANSPORT;DIFFUSION;DYNAMICS;HES1;NEGATIVE FEEDBACK;OSCILLATORY EXPRESSION;P53;PROTEIN;repressilator;SIMULATION;Spatial stochastic model;synthetic gene regulatory network;TIME DELAYS | WOS:000462102600003 | Univ Dundee, Dundee DD1 4HN, Scotland;Univ St Andrews, Fife, Scotland | UK | 2,019 | null | 0000-0001-5727-2160;0000-0003-4961-6052 | null | null | English | null | 2008022 UPPS U DEP I;ACS SYNTH BIOL;ADVANCE ENZYME REGULAT;AM J PHYSIOL-CELL PH;B AM METEOROL SOC;B MATH BIOL;BBA-PROTEINS PROTEOM;BIOPHYS J;BMC Res Notes;BMC SYST BIOL;COMPUT STRUCT BIOTEC;CURR BIOL;DEVELOPMENT;EUR PHYS J B;FEBS LETT;GENOME BIOL;J CHEM PHYS;J MATH BIOL;J NEUROSCI;J PHYS CHEM A;J R SOC INTERFACE;J THEOR BIOL;MATH BIOSCI;MATH MOD METH APPL S;MOL SYST BIOL;NAT GENET;NATURE;PHILOS T A;PHYS BIOL;PHYS REV E;SCIENCE;SIAM J SCI COMPUT | Chaplain, Mark A J;Macnamara, Cicely K;Mitchell, Elaine, I | 2024-03-11
ER | [Anonymous];Ashall, L;Balagadde, F K;Becskei, A;Bernard S.;Busenberg, S;Cangiani, A;Chaplain, M;Chen, Y Y;Cullhed J.;Dimitrio, L;Drawert, B;Elias, J;Elowitz, M B;Engblom, S;Gibson, M A;Glass, L;Goodwin Brian C.;Griffith, J S;Harang Richard;Hirata, H;Jensen, M H;Kageyama, R;Lahav, G;Lane, D P;Lewis, J;Mackey, M C;Macnamara, C K;Mahaffy, J M;Momiji, H;Monk, N A M;Naqib, F;Nelson, D E;O'Brien, E L;Purcell, O;Shymko, R M;Smolen, P;Sturrock, M;Szymanska, Z;Tiana, G;Torrence, C;Yordanov, B | HQ0RL | Fife, Scotland | 3 | null | 2 | null | 30,753,839 | Chaplain, Mark A J;Macnamara, Cicely K;Mitchell, Elaine, I | J THEOR BIOL | Dundee DD1 4HN, Scotland;Fife, Scotland |
Ferreira, B H;Gonçales, R A;Martins-Santana, L;Nora, L C;Rodrigues, F;Silva-Rocha, R | 10.1590/1678-4685-GMB-2018-0221 | null | RUA CAP ADELMIO NORBET DA SILVA, 736, ALTO DA BOA VISTA, 14025-670 RIBEIRAO PRET, BRAZIL | 5a1c3f2b666p3f3a415b3o4b2m4f5324t175e5w | Synthetic and minimalist vectors for <i>Agrobacterium tumefaciens</i>-mediated transformation of fungi | Univ Sao Paulo | null | Silva-Rocha, R (corresponding author), Univ Sao Paulo, Fac Med Ribeiao Preto, DepT Biol Celular & Mol Biol & Bioagentes Patogen, Av Banderiantes 3900, BR-14049900 Ribeirao Preto, SP, Brazil. | null | Ferreira, Beatriz Henriques;Goncales, Relber Aguiar;Martins-Santana, Leonardo;Nora, Luisa Czamanski;Rodrigues, Fernando;Silva-Rocha, Rafael | Biochemistry & Molecular Biology;Genetics & Heredity | FAPESP [2016/03763-3, 2016/01946-3, 2014/22561-7, 2012/22921-8]; Northern Portugal Regional Operational Programme (NORTE 2020), under the Portugal 2020 Partnership Agreement, through the European Regional Development Fund (FEDER) [NORTE-01-0145-FEDER-000013]; Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP) [16/01946-3, 14/22561-7] Funding Source: FAPESP | WOS | Silva-Rocha, R | Univ Minho, Braga, Portugal;Univ Sao Paulo, Ribeirao Preto SP, Brazil | 42 | <i>Agrobacterium;and;for;fungi;minimalist;of;synthetic;transformation;tumefaciens</i>-mediated;Vectors | 2 | Ferreira, Beatriz;Gonçales, Relber;Rodrigues, Fernando;Santana, Leonardo;Silva-Rocha, Rafael | SOC BRASIL GENETICA | Univ Minho, Sch Hlth Sci, Life & Hlth Sci Res Inst ICVS, Braga, Portugal;Univ Sao Paulo, Fac Med Ribeiao Preto, DepT Biol Celular & Mol Biol & Bioagentes Patogen, Av Banderiantes 3900, BR-14049900 Ribeirao Preto, SP, Brazil;Univ Sao Paulo, Fac Med Ribeiao Preto, Dept Biol Celular & Mol Biol & Bioagentes Patogen, Syst & Synthet Biol Lab, Ribeirao Preto, SP, Brazil;Univ Sao Paulo, Fac Med Ribeirao Preto, Dept Biol Celular & Mol Biol & Bioagentes Patogen, Immunochem & Glycobiol Lab, Ribeirao Preto, SP, Brazil | Article | Univ Sao Paulo | RIBEIRAO PRET | null | null | Brazil;Univ Minho;Univ Sao Paulo | FAPESP;Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP);Northern Portugal Regional Operational Programme (NORTE 2020), under the Portugal 2020 Partnership Agreement, through the European Regional Development Fund (FEDER) | Silva-Rocha, R (corresponding author), Univ Sao Paulo, Fac Med Ribeiao Preto, DepT Biol Celular & Mol Biol & Bioagentes Patogen, Av Banderiantes 3900, BR-14049900 Ribeirao Preto, SP, Brazil. | 398 | Ferreira, Beatriz Henriques;Goncales, Relber Aguiar;Martins-Santana, Leonardo;Nora, Luisa Czamanski;Rodrigues, Fernando;Silva-Rocha, Rafael | 7 | 3 | 483,927,900,010 | FAPESP [2016/03763-3, 2016/01946-3, 2014/22561-7, 2012/22921-8];Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP) [16/01946-3, 14/22561-7] Funding Source: FAPESP;Northern Portugal Regional Operational Programme (NORTE 2020), under the Portugal 2020 Partnership Agreement, through the European Regional Development Fund (FEDER) [NORTE-01-0145-FEDER-000013] | Brazil;Portugal | GENETICS AND MOLECULAR BIOLOGY | Brazil | null | null | Univ Sao Paulo, Fac Med Ribeiao Preto, Dept Biol Celular & Mol Biol & Bioagentes Patogen, Syst & Synthet Biol Lab, Ribeirao Preto, SP, Brazil | 1415-4757 | Ferreira, B H;Gonçales, R A;Martins-Santana, L;Nora, L C;Rodrigues, F;Silva-Rocha, R | APR-JUN | silvarochar@gmail.com | <i>Agrobacterium tumefaciens</i>-mediated transformation;fungi;minimalist vectors;synthetic | 6 | J | Biochemistry & Molecular Biology;Genetics & Heredity | <i>Agrobacterium tumefaciens</i>-mediated transformation;Agrobacterium tumefaciens;Agrobacterium tumefaciens recognition;alternate promoters;ATMT;collection;EGFP;expression;few primers;filamentous fungi;FILAMENTOUS FUNGUS;fluorescent proteins;four different versions;fungal transformation;fungi;Hygromicin B;left;mCherry;minimal broad-host range RK2 replication origin;minimalist;minimalist binary vectors;minimalist vectors;multiple;one;pathogenic fungus Paracoccidioides lutzii;pLUO plasmid binary vectors;PROTEIN;reliable molecular tool;reporter module;resistance;right borders;several fungi species;site;steps;synthetic;synthetic biology;synthetic gene;transcription terminator site;TRANSFORMATION;VECTORS;yeast | Nora, L C | Agrobacterium tumefaciens;EXPRESSION;FILAMENTOUS FUNGUS;fungi;PROTEIN;Synthetic biology;TRANSFORMATION;VECTORS | 395 | [Nora, Luisa Czamanski; Martins-Santana, Leonardo; Silva-Rocha, Rafael] Univ Sao Paulo, Fac Med Ribeiao Preto, Dept Biol Celular & Mol Biol & Bioagentes Patogen, Syst & Synthet Biol Lab, Ribeirao Preto, SP, Brazil. [Goncales, Relber Aguiar] Univ Sao Paulo, Fac Med Ribeirao Preto, Dept Biol Celular & Mol Biol & Bioagentes Patogen, Immunochem & Glycobiol Lab, Ribeirao Preto, SP, Brazil. [Ferreira, Beatriz Henriques; Rodrigues, Fernando] Univ Minho, Sch Hlth Sci, Life & Hlth Sci Res Inst ICVS, Braga, Portugal. | LCN, LMS, RAG and RSR were supported by FAPESP (Project numbers: 2016/03763-3, 2016/01946-3, 2014/22561-7 and 2012/22921-8). FR and BF were supported by the Northern Portugal Regional Operational Programme (NORTE 2020), under the Portugal 2020 Partnership Agreement, through the European Regional Development Fund (FEDER) (NORTE-01-0145-FEDER-000013). The authors are thankful to Maria Cristina Roque Barreira for insightful discussions and support. | Agrobacterium tumefaciens recognition;alternate promoters;ATMT;collection;EGFP;few primers;filamentous fungi;fluorescent proteins;four different versions;fungal transformation;Hygromicin B;left;mCherry;minimal broad-host range RK2 replication origin;minimalist;minimalist binary vectors;multiple;one;pathogenic fungus Paracoccidioides lutzii;pLUO plasmid binary vectors;reliable molecular tool;reporter module;resistance;right borders;several fungi species;site;steps;synthetic;synthetic gene;transcription terminator site;transformation;yeast | 10.1007/978-1-61779-539-8_12;10.1016/0378-1119(85)90120-9;10.1016/0378-1119(92)90454-W;10.1016/j.biotechadv.2011.09.012;10.1016/j.fgb.2007.04.004;10.1016/j.plasmid.2013.09.004;10.1016/S0734-9750(00)00041-0;10.1021/acssynbio.6b00354;10.1038/nprot.2008.154;10.1046/j.1365-2958.1998.00664.x;10.1093/nar/gks1119;10.1146/annurev-micro-092611-150044;10.1371/journal.pone.0052000;10.2174/1389202917666151116212255;10.3109/13693786.2013.794311 | Univ Sao Paulo | Ferreira, B H;Gonçales, R A;Martins-Santana, L;Nora, L C;Rodrigues, F;Silva-Rocha, R | Nora, L C: Univ Sao Paulo, Fac Med Ribeiao Preto, Dept Biol Celular & Mol Biol & Bioagentes Patogen, Syst & Synthet Biol Lab, Ribeirao Preto, SP, Brazil | Gonçales, Relber;Rodrigues, Fernando;Santana, Leonardo;Silva-Rocha, Rafael | 14/22561-7;16/01946-3;2012/22921-8;2014/22561-7;2016/01946-3;2016/03763-3;NORTE-01-0145-FEDER-000013 | 16 | null | Brazil | Univ Minho;Univ Sao Paulo | Nora, Luisa Czamanski | gold, Green Published, Green Submitted | EXPRESSION;FILAMENTOUS FUNGUS;PROTEIN | Nora, Luisa Czamanski; Goncales, Relber Aguiar; Martins-Santana, Leonardo; Ferreira, Beatriz Henriques; Rodrigues, Fernando; Silva-Rocha, Rafael; | null | Univ Minho, Sch Hlth Sci, Life & Hlth Sci Res Inst ICVS, Braga, Portugal;Univ Sao Paulo, Fac Med Ribeiao Preto, Dept Biol Celular & Mol Biol & Bioagentes Patogen, Syst & Synthet Biol Lab, Ribeirao Preto, SP, Brazil;Univ Sao Paulo, Fac Med Ribeirao Preto, Dept Biol Celular & Mol Biol & Bioagentes Patogen, Immunochem & Glycobiol Lab, Ribeirao Preto, SP, Brazil | Univ Minho, Sch Hlth Sci, Life & Hlth Sci Res Inst ICVS, Braga, Portugal;Univ Sao Paulo, Fac Med Ribeiao Preto, Dept Biol Celular & Mol Biol & Bioagentes Patogen, Syst & Synthet Biol Lab, Ribeirao Preto, SP, Brazil;Univ Sao Paulo, Fac Med Ribeirao Preto, Dept Biol Celular & Mol Biol & Bioagentes Patogen, Immunochem & Glycobiol Lab, Ribeirao Preto, SP, Brazil | 1678-4685 | Agrobacterium tumefaciens;fungi;Synthetic biology;transformation;Vector | 2 | 1985;1992;1998;2000;2003;2007;2008;2012;2013;2014;2016;2017 | 9 | Univ Sao Paulo, Fac Med Ribeiao Preto, DepT Biol Celular & Mol Biol & Bioagentes Patogen, Av Banderiantes 3900, BR-14049900 Ribeirao Preto, SP, Brazil | Genet. Mol. Biol. | Silva-Rocha, Rafael | SOC BRASIL GENETICA | ,;:;a;added;Agrobacterium;allowing;also;alternate;an;and;another;applicable;ATMT;available;B;be;binary;borders;broad-host;by;can;cloning;collection;consist;containing;developed;different;efficient;EGFP;few;filamentous;flanked;fluorescent;for;four;fungal;fungi;fungus;gene;hence;Hygromicin;in;left;lutzii;mCherry;minimal;minimalist;modified;modular;module;molecular;multiple;of;one;or;origin;Paracoccidioides;pathogenic;plasmid;pLUO;present;primers;promoters;proteins;range;readily;recognition;reliable;replication;reporter;resistance;right;RK2;several;site;species;steps;still;synthetic;terminator;the;these;they;through;to;tool;transcription;transformation;tumefaciens;using;validated;vectors;versions;was;we;were;yeast | Univ Sao Paulo | We present a collection of minimalist binary vectors for transformation through ATMT applicable to several fungi species. pLUO plasmid binary vectors consist of a reporter module containing fluorescent proteins, mCherry or eGFP, flanked by a multiple cloning site and a transcription terminator site. They also present a synthetic gene allowing resistance to Hygromicin B flanked by alternate promoters, one for yeast and another for filamentous fungi. Left and right borders were added for Agrobacterium tumefaciens recognition, and a minimal broad-host range RK2 replication origin. Transformation was validated in the pathogenic fungus Paracoccidioides lutzii. Hence, we developed an efficient and reliable molecular tool for fungal transformation: minimalist, synthetic, modular, and available in four different versions, and these can still be readily modified using a few primers and few cloning steps. | AAT-7094-2020;H-4929-2012;JVZ-1542-2024;T-5299-2018 | EXPRESSION;FILAMENTOUS FUNGUS;PROTEIN | 0 | null | Agrobacterium tumefaciens;fungi;Synthetic biology;transformation;vectors | 4 | AGROBACTERIUM-TUMEFACIENS;EXPRESSION;FILAMENTOUS FUNGUS;fungi;PROTEIN;Synthetic biology;TRANSFORMATION;VECTORS | WOS:000483927900010 | Univ Minho, Braga, Portugal;Univ Sao Paulo, Ribeirao Preto SP, Brazil | Brazil;Portugal | 2,019 | null | 0000-0001-6319-631X;0000-0001-8436-9398;0000-0002-1497-7440;0000-0002-3037-3663;0000-0002-5074-023X | null | null | English | null | ACS SYNTH BIOL;ANNU REV MICROBIOL;BIOTECHNOL ADV;CURR GENOMICS;FUNGAL GENET BIOL;GENE;HDB FUNGAL BIOTECHNO;MED MYCOL;METHODS MOL BIOL;MOL MICROBIOL;NAT PROTOC;NUCLEIC ACIDS RES;PLASMID;PLOS ONE | Ferreira, Beatriz Henriques;Goncales, Relber Aguiar;Martins-Santana, Leonardo;Nora, Luisa Czamanski;Rodrigues, Fernando;Silva-Rocha, Rafael | 2024-03-11
ER | Almeida, A J;Amores, G R;Benedetti, I M;Bhat, M K;Christianson, T W;Fernández-Abalos, J M;Glass, N L;He, R L;Leigh J.;Menino Joao, F;Michielse, C B;Pasin, F;Silva-Rocha, R;Teixeira, M D;Ward, O P;Yanischperron, C | IU9VF | Ribeirao Preto SP, Brazil | 9 | null | 2 | null | 31,259,357 | Ferreira, Beatriz Henriques;Goncales, Relber Aguiar;Martins-Santana, Leonardo;Nora, Luisa Czamanski;Rodrigues, Fernando;Silva-Rocha, Rafael | GENET MOL BIOL | Braga, Portugal;Ribeirao Preto SP, Brazil |
Lam, C C K;Mohammad, N B;Truong, K | 10.1021/acs.biochem.8b01081 | null | 1155 16TH ST, NW, WASHINGTON, DC 20036 USA | 5qv1z3b1t3m584n32d6bi7359d1a4c48333n | Synthetic Biology Approaches in Immunology | Univ Toronto | null | Truong, K (corresponding author), Univ Toronto, Edward S Rogers Sr Dept Elect & Comp Engn, 10 Kings Coll Circle, Toronto, ON M5S 3G4, Canada.;Truong, K (corresponding author), Univ Toronto, Inst Biomat & Biomed Engn, 164 Coll St, Toronto, ON M5S 3G9, Canada. | SI | Lam, Candice Chee Ka;Mohammad, Niema Binth;Truong, Kevin | Biochemistry & Molecular Biology | null | WOS | Truong, K | Univ Toronto, Toronto ON, Canada | 58 | approaches;biology;Immunology;in;synthetic | 1 | Truong, Kevin | AMER CHEMICAL SOC | Univ Toronto, Edward S Rogers Sr Dept Elect & Comp Engn, 10 Kings Coll Circle, Toronto, ON M5S 3G4, Canada;Univ Toronto, Inst Biomat & Biomed Engn, 164 Coll St, Toronto, ON M5S 3G9, Canada;Univ Toronto, Inst Biomat & Biomed Engn, 164 Coll St, Toronto, ON M5S 3G9, Canada.; Truong, K (corresponding author), Univ Toronto, Edward S Rogers Sr Dept Elect & Comp Engn, 10 Kings Coll Circle, Toronto, ON M5S 3G4, Canada | Article | Univ Toronto | WASHINGTON | null | null | Univ Toronto | null | Truong, K (corresponding author), Univ Toronto, Inst Biomat & Biomed Engn, 164 Coll St, Toronto, ON M5S 3G9, Canada.; Truong, K (corresponding author), Univ Toronto, Edward S Rogers Sr Dept Elect & Comp Engn, 10 Kings Coll Circle, Toronto, ON M5S 3G4, Canada. | 1491 | Lam, Candice Chee Ka;Mohammad, Niema Binth;Truong, Kevin | 16 | 2 | 462,097,900,008 | null | Canada | BIOCHEMISTRY | Canada | null | null | Univ Toronto, Inst Biomat & Biomed Engn, 164 Coll St, Toronto, ON M5S 3G9, Canada | 0006-2960 | Lam, C C K;Mohammad, N B;Truong, K | MAR 19 | kevin.truong@utoronto.ca | Immunology;synthetic biology approaches | 3 | J | Biochemistry & Molecular Biology | ability;abundance;apoptosis;breakthroughs;cells;circulation;complex systems inside cells;control;DESIGN;development;disease sites;DNA sequence;engineering chimeric receptors;engineering new cell functions;expandable cell types (e.g. stem cells;GENE SYNTHESIS;guide;immune rejection;immune responses;Immunology;implantation;interest;mammalian cells;mechanisms;natural;novel functions;novel therapeutic interventions;patients;possible;problems;proteins;pursuit;recent developments;safety concerns;SAFETY SWITCH;secretion;specificity;synthetic biologists;synthetic biology approaches;synthetic genes;synthetic immunology;synthetic immunology,it;T cells);T-CELLS;therapeutic effect;therapeutic life ends;therapeutic proteins;therapy;thought;TOXICITY;wide range | Mohammad, N B | APOPTOSIS;DESIGN;Proteins;SAFETY SWITCH;T-CELLS;THERAPY;TOXICITY | 1484 | [Mohammad, Niema Binth; Lam, Candice Chee Ka; Truong, Kevin] Univ Toronto, Inst Biomat & Biomed Engn, 164 Coll St, Toronto, ON M5S 3G9, Canada. [Truong, Kevin] Univ Toronto, Edward S Rogers Sr Dept Elect & Comp Engn, 10 Kings Coll Circle, Toronto, ON M5S 3G4, Canada. | null | ability;abundance;breakthroughs;cells;circulation;complex systems inside cells;control;development;disease sites;DNA sequence;engineering chimeric receptors;engineering new cell functions;expandable cell types (e.g. stem cells;gene synthesis;guide;immune rejection;immune responses;immunology;implantation;interest;mammalian cells;mechanisms;natural;novel functions;novel therapeutic interventions;patients;possible;problems;pursuit;recent developments;safety concerns;secretion;specificity;synthetic biologists;synthetic genes;synthetic immunology;synthetic immunology,it;T cells);therapeutic effect;therapeutic life ends;therapeutic proteins;thought;wide range | 10.1002/bit.26523;10.1016/j.bbrc.2015.08.085;10.1016/j.ceca.2010.08.009;10.1016/j.ceca.2012.12.005;10.1016/j.cell.2016.01.012;10.1016/j.cell.2016.09.011;10.1016/j.cell.2017.03.012;10.1016/j.chembiol.2009.02.005;10.1016/j.chembiol.2011.09.014;10.1016/j.chembiol.2017.05.008;10.1016/j.copbio.2012.01.003;10.1016/j.expneurol.2018.03.005;10.1016/j.jmb.2005.10.076;10.1016/j.molcel.2017.10.033;10.1016/j.tibtech.2014.10.006;10.1016/j.ymthe.2018.03.001;10.1021/acssynbio.6b00310;10.1021/acssynbio.7b00076;10.1021/acssynbio.7b00323;10.1021/sb3000172;10.1038/nature10358;10.1038/nature14121;10.1038/nchembio.2179;10.1038/nchembio.477;10.1038/nrmicro3239;10.1038/s41467-018-05855-5;10.1038/s41591-018-0201-9;10.1038/s41598-018-22252-6;10.1038/sj.onc.1205280;10.1039/c7ib00203c;10.1056/NEJMoa1003466;10.1056/NEJMoa1106152;10.1056/NEJMoa1709919;10.1073/pnas.1602070113;10.1080/2162402X.2018.1480300;10.1089/hum.2010.050;10.1097/CJI.0b013e3182829903;10.1126/sciadv.1701620;10.1126/science.aat0271;10.1126/scitranslmed.3002842;10.1126/scitranslmed.3005930;10.1146/annurev-immunol-051116-052302;10.1172/jci.insight.92865;10.1182/blood-2004-11-4564;10.1182/blood-2005-08-3503;10.1182/blood-2013-03-490565;10.1200/JCO.2015.33.15_SUPPL.7010;10.1242/jcs.206979;10.18632/oncotarget.15733;10.3233/RNN-160678;10.3892/mmr.2017.7310;[10.1038/nchembio.1979, 10.1038/NCHEMBIO.1979] | Univ Toronto | Lam, C C K;Mohammad, N B;Truong, K | Mohammad, N B: Univ Toronto, Inst Biomat & Biomed Engn, 164 Coll St, Toronto, ON M5S 3G9, Canada | null | null | 52 | null | Canada | Univ Toronto | Mohammad, Niema Binth | null | APOPTOSIS;DESIGN;PROTEINS;SAFETY SWITCH;T-CELLS;THERAPY;TOXICITY | Mohammad, Niema Binth; Lam, Candice Chee Ka; Truong, Kevin; | null | Univ Toronto, Edward S Rogers Sr Dept Elect & Comp Engn, 10 Kings Coll Circle, Toronto, ON M5S 3G4, Canada;Univ Toronto, Inst Biomat & Biomed Engn, 164 Coll St, Toronto, ON M5S 3G9, Canada | Univ Toronto, Edward S Rogers Sr Dept Elect & Comp Engn, 10 Kings Coll Circle, Toronto, ON M5S 3G4, Canada;Univ Toronto, Inst Biomat & Biomed Engn, 164 Coll St, Toronto, ON M5S 3G9, Canada | null | null | 11 | 2002;2005;2006;2009;2010;2011;2012;2013;2014;2015;2016;2017;2018 | 2 | Univ Toronto, Edward S Rogers Sr Dept Elect & Comp Engn, 10 Kings Coll Circle, Toronto, ON M5S 3G4, Canada;Univ Toronto, Inst Biomat & Biomed Engn, 164 Coll St, Toronto, ON M5S 3G9, Canada | Biochemistry | Truong, Kevin | AMER CHEMICAL SOC | (e.g.;,;a;ability;abundance;actually;after;allowed;and;any;avoid;be;been;before;biologists;breakthroughs;but;by;can;cell;cells;cells);chimeric;circulation;complex;concerns;control;create;customize;derived;design;development;developments;disease;DNA;effect;enabling;ends;engineered;engineering;expandable;explored;expressing;feasible;for;from;functions;gene;genes;grown;guide;has;have;however;if;immune;immunology;immunology,it;implantation;in;induce;inside;interest;interventions;intractable;is;it;kill;life;mammalian;many;may;mechanisms;natural;necessitates;new;novel;now;of;or;over;patients;possibility;possible;predominantly;previously;problems;proteins;pursuit;range;recent;receptors;rejection;responses;safety;secretion;sequence;sites;specificity;stem;still;synthesis;synthetic;systems;T;tackle;target;that;the;their;then;therapeutic;these;this;thought;through;to;types;wide;with | Univ Toronto | Breakthroughs in gene synthesis has allowed synthetic biologists the ability to design any DNA sequence of interest, enabling the possibility to create complex systems inside cells with novel functions to tackle problems in immunology. Synthetic immunology of mammalian cells expressing natural or synthetic genes can guide and induce immune responses in patients. Through recent developments in engineering chimeric receptors, it is now feasible to customize control over engineered cells to target the disease sites with specificity. These cells can avoid immune rejection if derived from expandable cell types (e.g., stem cells or T cells) and then can be grown in abundance before implantation. However, safety concerns of engineered cells in circulation necessitates the development of a wide range of mechanisms to kill cells after their therapeutic life ends. This therapeutic effect is still predominantly the secretion of therapeutic proteins, but novel therapeutic interventions have been explored by synthetic biologists. In the pursuit of engineering new cell functions for synthetic immunology,it is possible that many problems previously thought intractable may actually be possible. | null | APOPTOSIS;DESIGN;PROTEIN;SAFETY SWITCH;T-CELLS;THERAPY;TOXICITY | 2 | null | null | 8 | APOPTOSIS;DESIGN;PROTEIN;SAFETY SWITCH;T-CELLS;THERAPY;TOXICITY | WOS:000462097900008 | Univ Toronto, Toronto ON, Canada | Canada | 2,019 | null | 0000-0002-9520-2144 | null | null | English | null | ACS SYNTH BIOL;ANNU REV IMMUNOL;BIOCHEM BIOPH RES CO;BIOTECHNOL BIOENG;BLOOD;CELL;CELL CALCIUM;CELL CHEM BIOL;CHEM BIOL;CURR OPIN BIOTECH;EXP NEUROL;HUM GENE THER;INTEGR BIOL-UK;J CELL SCI;J IMMUNOTHER;J MOL BIOL;JCI INSIGHT;Journal of Clinical Oncology;MOL CELL;MOL MED REP;MOL THER;NAT CHEM BIOL;NAT COMMUN;NAT MED;NAT REV MICROBIOL;NATURE;NEW ENGL J MED;ONCOGENE;ONCOIMMUNOLOGY;ONCOTARGET;P NATL ACAD SCI USA;RESTOR NEUROL NEUROS;SCI ADV;SCI REP-UK;SCI TRANSL MED;SCIENCE;TRENDS BIOTECHNOL | Lam, Candice Chee Ka;Mohammad, Niema Binth;Truong, Kevin | 2024-03-11
ER | [Anonymous];Al Mosabbir, A;Anderson, J C;Berger, C;Breitbach, C J;Brentjens, R J;Cameron, D E;Chan, C T Y;Chen, X J;Cho, J H;Chowdhury, S;Daniel, K;Di Stasi, A;Geering, B;Grace, P M;Hodi, F S;Jordan, R E;Kalos, M;Kamata, M;Karlsson, M;Langut, Y;Li, G L;Linette, G P;Liu, K I;Mandell, D J;Mills, E;Morgan, R A;Morsut, L;Mosabbir, A A;Park, J H;Pierini, A;Qudrat, A;Roybal, K T;Ruella, M;Shin, J;Spiegel, D A;Stavrou, M;Stewart, A N;Stirling, F;Straathof, K C;Toda, S;Tomicic, M T;Weber, W | HQ0PQ | Toronto ON, Canada;Toronto ON, Canada. | 3 | null | 1 | null | 30,481,004 | Lam, Candice Chee Ka;Mohammad, Niema Binth;Truong, Kevin | BIOCHEMISTRY-US | Toronto ON, Canada |
Rondon, R E;Wilson, C J | 10.1021/acssynbio.8b00324 | null | 1155 16TH ST, NW, WASHINGTON, DC 20036 USA | 2k3h3e4t632hx722gk2f2k3e01y6p5b5hy38 | Engineering a New Class of Anti-Lacl Transcription Factors with Alternate DNA Recognition | Georgia Inst Technol | null | Wilson, CJ (corresponding author), Georgia Inst Technol, Sch Chem & Biomol Engn, 311 Ferst Dr, Atlanta, GA 30332 USA. | null | Rondon, Ronald E;Wilson, Corey J | Biochemical Research Methods | NSF [MCB 1747439, CBET 1804639, CBET 1844289] | WOS | Wilson, C J | Georgia Inst Technol, Atlanta, GA USA | 8 | a;Alternate;Anti-Lacl;class;DNA;engineering;Factors;new;of;recognition;transcription;with | 1 | null | AMER CHEMICAL SOC | Georgia Inst Technol, Sch Chem & Biomol Engn, 311 Ferst Dr, Atlanta, GA 30332 USA | Article | Georgia Inst Technol | WASHINGTON | null | null | Georgia Inst Technol | NSF | Wilson, CJ (corresponding author), Georgia Inst Technol, Sch Chem & Biomol Engn, 311 Ferst Dr, Atlanta, GA 30332 USA. | 317 | Rondon, Ronald E;Wilson, Corey J | 25 | 1 | 459,367,000,014 | NSF [MCB 1747439, CBET 1804639, CBET 1844289] | USA | ACS SYNTHETIC BIOLOGY | USA | null | null | Georgia Inst Technol, Sch Chem & Biomol Engn, 311 Ferst Dr, Atlanta, GA 30332 USA | 2161-5063 | Rondon, R E;Wilson, C J | FEB | corey.wilson@chbe.gatech.edu | Alternate DNA Recognition;Anti-Lacl Transcription Factors;New Class | 2 | J | Biochemistry & Molecular Biology | 46 antilacs;46 I-ADR(A);alternate DNA binding function (I-ADR(A);alternate DNA recognition;alternate DNA recognition (ADR);anti-LacI (antilac) function (I-YQR(A);Anti-Lacl Transcription Factors;antilacs;archetypal transcription;bespoke I-ADR(A) bind orthogonally;BINDING;cells;collection;complementary synthetic operator DNA sequences;computational capacity;control;control two distinct fluorescent outputs;demonstration;DESIGN;disparate non-natural operator DNA sequences;engineered transcription factors;EXPANSION;full orthogonality;Gene circuits;gene expression;gene expression (apo ligand);gene outputs;gene suppression;I-ADR(A) gene regulators;I-ADR(A) transcription factors;I-ADR(A) transcription factors will;inverse;inverted function;IPTG;IPTG binding results;laboratory evolution;LacI;LacI (I-YQR(+);lactose repressor;ligand isopropyl beta-d-1-thiogalactopyranoside (IPTG);modularly via;native LacI topology;new class;nine alternate allosteric regulatory cores;number;one;operator O-1;operon;phenotypically;promoter(s);REPRESSOR;scalable increase;six alternate DNA binding domains;study;SWITCH;synthetic genetic networks;synthetic genetic toggle switches;systematic pairing;transcription factors);two nonsynonymous unit pair operations;unique transcription factors (or systems;via;wild-type I-YQR(+) function;workhorse | Rondon, R E | alternate DNA recognition;antilacs;BINDING;CELLS;DESIGN;engineered transcription factors;OPERON;REPRESSOR;SWITCH | 307 | [Rondon, Ronald E.; Wilson, Corey J.] Georgia Inst Technol, Sch Chem & Biomol Engn, 311 Ferst Dr, Atlanta, GA 30332 USA. | This work was supported by NSF Awards MCB 1747439, CBET 1804639, and CBET 1844289 to CJW. We would like to thank Andrew Short and Namratha Vedire for contributing to the cover art. | 46 antilacs;46 I-ADR(A);alternate DNA binding function (I-ADR(A);alternate DNA recognition (ADR);anti-LacI (antilac) function (I-YQR(A);archetypal transcription;bespoke I-ADR(A) bind orthogonally;binding;collection;complementary synthetic operator DNA sequences;computational capacity;control;control two distinct fluorescent outputs;demonstration;disparate non-natural operator DNA sequences;expansion;full orthogonality;gene circuits;gene expression;gene expression (apo ligand);gene outputs;gene suppression;I-ADR(A) gene regulators;I-ADR(A) transcription factors;I-ADR(A) transcription factors will;inverse;inverted function;IPTG;IPTG binding results;laboratory evolution;lacI;LacI (I-YQR(+);lactose repressor;ligand isopropyl beta-d-1-thiogalactopyranoside (IPTG);modularly via;native LacI topology;new class;nine alternate allosteric regulatory cores;number;one;operator O-1;phenotypically;promoter(s);scalable increase;six alternate DNA binding domains;study;synthetic genetic networks;synthetic genetic toggle switches;systematic pairing;transcription factors);two nonsynonymous unit pair operations;unique transcription factors (or systems;via;wild-type I-YQR(+) function;workhorse | 10.1002/j.1460-2075.1989.tb03500.x;10.1002/pro.389;10.1002/wnan.1461;10.1007/s00018-006-6296-z;10.1016/0022-2836(79)90333-4;10.1016/j.cbpa.2013.10.003;10.1016/j.cell.2011.06.035;10.1016/j.copbio.2006.09.001;10.1016/j.copbio.2010.07.005;10.1016/j.jmb.2009.06.039;10.1021/acssynbio.6b00048;10.1021/bi00238a024;10.1038/35002125;10.1038/35002131;10.1038/msb.2010.42;10.1038/nature03508;10.1038/nature07389;10.1038/nature07616;10.1038/nbt.1591;10.1038/nbt.2411;10.1038/nbt980;10.1073/pnas.0402940101;10.1073/pnas.71.6.2314;10.1073/pnas.74.3.966;10.1073/pnas.80.22.6785;10.1093/nar/25.6.1203;10.1093/protein/gzp051;10.1093/protein/gzt013;[10.1038/nmeth.2515, 10.1038/NMETH.2515] | Georgia Inst Technol | Rondon, R E;Wilson, C J | Rondon, R E: Georgia Inst Technol, Sch Chem & Biomol Engn, 311 Ferst Dr, Atlanta, GA 30332 USA | null | CBET 1804639;CBET 1844289;MCB 1747439 | 30 | null | USA | Georgia Inst Technol | Rondon, Ronald E | hybrid | BINDING;CELLS;DESIGN;OPERON;REPRESSOR;SWITCH | Rondon, Ronald E.; Wilson, Corey J.; | null | Georgia Inst Technol, Sch Chem & Biomol Engn, 311 Ferst Dr, Atlanta, GA 30332 USA | Georgia Inst Technol, Sch Chem & Biomol Engn, 311 Ferst Dr, Atlanta, GA 30332 USA | null | alternate DNA recognition;antilac;engineered transcription factors | 2 | 1974;1977;1979;1980;1983;1989;1991;1997;2000;2004;2005;2006;2007;2008;2009;2010;2011;2012;2013;2017 | 16 | Georgia Inst Technol, Sch Chem & Biomol Engn, 311 Ferst Dr, Atlanta, GA 30332 USA | ACS Synth. Biol. | Wilson, Corey J | AMER CHEMICAL SOC | (ADR);(antilac);(apo;(I-ADR(A);(I-YQR(+);(I-YQR(A);(IPTG);(or;,;46;a;achieved;allosteric;also;alternate;an;and;anti-LacI;antilacs;archetypal;are;been;bespoke;beta-d-1-thiogalactopyranoside;bind;binding;by;can;capacity;circuits;class;collection;complementary;composed;computational;confer;construction;control;cores;demonstration;designed;disparate;distinct;DNA;domains;engineered;evolution;expansion;expression;facilitate;factor;factors;factors);finally;fluorescent;full;function;gene;genetic;has;here;I-ADR(A);I-YQR(+);identified;in;increase;induced;interact;inverse;inverted;IPTG;is;isopropyl;laboratory;lacI;lactose;ligand;ligand);many;modularly;more;native;naturally;networks;new;nine;non-natural;nonsynonymous;number;O-1;occurring;of;one;operations;operator;or;Orthogonal;orthogonality;orthogonally;outputs;over;pair;pairing;phenotypically;possess;presence;promoter(s);recently;recognition;regulate;regulators;regulatory;represses;repressor;resulting;results;scalable;sequences;simultaneously;six;study;suppress;suppression;switches;synthetic;systematic;systems;that;the;this;to;toggle;topology;transcription;two;unique;unit;upon;used;via;was;way;we;were;where;wild-type;will;with;workhorse | Georgia Inst Technol | The lactose repressor, LacI (I-YQR(+)), is an archetypal transcription factor that has been a workhorse in many synthetic genetic networks. LacI represses gene expression (apo ligand) and is induced upon binding of the ligand isopropyl beta-d-1-thiogalactopyranoside (IPTG). Recently, laboratory evolution was used to confer inverted function in the native LacI topology resulting in anti-LacI (antilac) function (I-YQR(A)), where IPTG binding results in gene suppression. Here we engineered 46 antilacs with alternate DNA binding function (I-ADR(A)). Phenotypically, I-ADR(A) transcription factors are the inverse of wild-type I-YQR(+) function and possess alternate DNA recognition (ADR). This collection of bespoke I-ADR(A) bind orthogonally to disparate non-natural operator DNA sequences and suppress gene expression in the presence of IPTG. This new class of I-ADR(A) gene regulators were designed modularly via the systematic pairing of nine alternate allosteric regulatory cores with six alternate DNA binding domains that interact with complementary synthetic operator DNA sequences. The 46 I-ADR(A) identified in this study are also orthogonal to the naturally occurring operator O-1. Finally, a demonstration of full orthogonality was achieved via the construction of synthetic genetic toggle switches composed of two nonsynonymous unit pair operations that control two distinct fluorescent outputs. This new class of I-ADR(A) transcription factors will facilitate the expansion of the computational capacity of engineered gene circuits, via the scalable increase in the control over the number of gene outputs by way of the expansion of the number of unique transcription factors (or systems of transcription factors) that can simultaneously regulate one or more promoter(s). | null | BINDING;CELLS;DESIGN;OPERON;REPRESSOR;SWITCH | 3 | null | alternate DNA recognition;antilacs;engineered transcription factors | 21 | alternate DNA recognition;antilac;BINDING;CELLS;DESIGN;engineered transcription factors;OPERON;REPRESSOR;SWITCH | WOS:000459367000014 | Georgia Inst Technol, Atlanta, GA USA | USA | 2,019 | null | null | null | null | English | null | ACS SYNTH BIOL;BIOCHEMISTRY-US;CELL;CELL MOL LIFE SCI;CURR OPIN BIOTECH;CURR OPIN CHEM BIOL;EMBO J;J BIOL CHEM;J MOL BIOL;MOL SYST BIOL;NAT BIOTECHNOL;NAT METHODS;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;P NATL ACAD SCI-BIOL;PROTEIN ENG DES SEL;PROTEIN SCI;WIRES NANOMED NANOBI | Rondon, Ronald E;Wilson, Corey J | 2024-03-11
ER | Bahl, C P;Bashor, C J;Brenowitz, M;Chen, Y J;Clancy, K;Daber, R;Davey, J A;Elowitz, M B;Fung, E;Gardner, T S;Kobayashi, H;Kramer, B P;Lu, T K;Lutz, R;Meyer, S;Milk, L;Nielsen, A A K;Ogorman, R B;Pfahl, M;Poelwijk, F J;Reznikoff, W S;Richards, D H;Sadler, J R;Sartorius, J;Stricker, J;Tigges, M;Voigt, C A;Wilson, C J;Zhan, J A | HM3IM | Atlanta, GA USA | 17 | null | 1 | null | 30,601,657 | Rondon, Ronald E;Wilson, Corey J | ACS SYNTH BIOL | Atlanta, GA USA |
Damavandi, M S;Ghaznini, K;Mansury, D;Tanhaeian, A | 10.1186/s13568-018-0729-6 | 6 | CAMPUS, 4 CRINAN ST, LONDON, N1 9XW, ENGLAND | 213j1nt6u676b3t3s3m2x3cm35622561101g6v | Expression in eukaryotic cells and purification of synthetic gene encoding enterocin P: a bacteriocin with broad antimicrobial spectrum | Ferdowsi Univ Mashhad | null | Ghaznini, K (corresponding author), Mashhad Univ Med Sci, Antimicrobial Resistance Res Ctr, Mashhad, Iran.;Mansury, D (corresponding author), Varastegan Inst Med Sci, Dept Med Lab Sci, Mashhad, Iran. | null | Damavandi, Mohammad Sadegh;Ghaznini, Kiarash;Mansury, Davood;Tanhaeian, Abbas | Biotechnology & Applied Microbiology | Department of Medical Laboratory Sciences, Varastegan Institute for Medical Sciences [11]; Department of Biotechnology and Plant Breeding, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran | WOS | Ghaznini, K;Mansury, D | Ferdowsi Univ Mashhad, Mashhad, Iran;Isfahan Univ Med Sci, Esfahan, Iran;Mashhad Univ Med Sci, Mashhad, Iran;Varastegan Inst Med Sci, Mashhad, Iran | 9 | :;a;and;Antimicrobial;Bacteriocin;Broad;Cells;encoding;Enterocin;Eukaryotic;expression;gene;in;of;P;purification;spectrum;synthetic;with | 1 | Damavandi, Mohammad Sadegh;Mansury, Davood | SPRINGEROPEN | Ferdowsi Univ Mashhad, Dept Biotechnol & Plant Breeding, Fac Agr, Mashhad, Iran;Isfahan Univ Med Sci, Sch Med, Dept Microbiol, Esfahan, Iran;Mashhad Univ Med Sci, Antimicrobial Resistance Res Ctr, Mashhad, Iran;Varastegan Inst Med Sci, Dept Med Lab Sci, Mashhad, Iran;Varastegan Inst Med Sci, Dept Med Lab Sci, Mashhad, Iran.; Ghaznini, K (corresponding author), Mashhad Univ Med Sci, Antimicrobial Resistance Res Ctr, Mashhad, Iran | Article | Mashhad Univ Med Sci;Varastegan Inst Med Sci | LONDON | null | null | Ferdowsi Univ Mashhad;Isfahan Univ Med Sci;Mashhad Univ Med Sci;Varastegan Inst Med Sci | Department of Biotechnology and Plant Breeding, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran;Department of Medical Laboratory Sciences, Varastegan Institute for Medical Sciences | Mansury, D (corresponding author), Varastegan Inst Med Sci, Dept Med Lab Sci, Mashhad, Iran.; Ghaznini, K (corresponding author), Mashhad Univ Med Sci, Antimicrobial Resistance Res Ctr, Mashhad, Iran. | null | Damavandi, Mohammad Sadegh;Ghaznini, Kiarash;Mansury, Davood;Tanhaeian, Abbas | 12 | 4 | 455,201,600,001 | Department of Biotechnology and Plant Breeding, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran;Department of Medical Laboratory Sciences, Varastegan Institute for Medical Sciences [11] | Iran | AMB EXPRESS | Iran;Iran.; | null | null | Ferdowsi Univ Mashhad, Dept Biotechnol & Plant Breeding, Fac Agr, Mashhad, Iran | 2191-0855 | Damavandi, M S;Ghaznini, K;Mansury, D;Tanhaeian, A | JAN 7 | ab_tanhaeian@yahoo.com;GhazviniK@mums.ac.ir;mansourid921@mums.ac.ir | bacteriocin;broad antimicrobial spectrum;eukaryotic cells;expression;purification;synthetic gene encoding enterocin P | 4 | J | Biotechnology & Applied Microbiology | affinity chromatography;antimicrobial activities;antimicrobial peptides;attractive therapeutic candidate;BACTERIA;Bacteriocin;Bacteriocins;broad antimicrobial activities;broad antimicrobial activity;broad antimicrobial spectrum;Chinese hamster ovary (CHO) cells;CHO cell;CHO cells;class II bacteriocin member;decreasing;Enterocin P;enterocin P (EntP);EntP;eukaryotic cells;expression;FUNCTIONAL EXPRESSION;high salt medium;high temperatures;HOST-DEFENSE PEPTIDES;human plasma;infectious diseases;known mature amino acid sequence;multidrug-resistant bacteria;multidrug-resistant bacterial infections;multidrug-resistant pathogens;multidrug-resistant strains;nosocomial infections;numerous bacteria;offer alternative therapeutic strategies;pathogenic species;protein expression vector pcDNA3.1(+);PURIFICATION;recombinant EntP;recombinant EntP inhibited growth;recombinant plasmid;recombinant protein;resistance;small antimicrobial peptides;stability;stable;synthetic gene encoding enterocin P;synthetic gene matching CHO cell codon usage;treatment;treatment options;variety | Tanhaeian, A | Antimicrobial peptides;Bacteriocin;CHO cell;Enterocin P;EXPRESSION;HOST-DEFENSE PEPTIDES;resistance | null | [Tanhaeian, Abbas] Ferdowsi Univ Mashhad, Dept Biotechnol & Plant Breeding, Fac Agr, Mashhad, Iran. [Damavandi, Mohammad Sadegh] Isfahan Univ Med Sci, Sch Med, Dept Microbiol, Esfahan, Iran. [Mansury, Davood] Varastegan Inst Med Sci, Dept Med Lab Sci, Mashhad, Iran. [Ghaznini, Kiarash] Mashhad Univ Med Sci, Antimicrobial Resistance Res Ctr, Mashhad, Iran. | The financial support of the Department of Medical Laboratory Sciences, Varastegan Institute for Medical Sciences (Grant No. 11) and Department of Biotechnology and Plant Breeding, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran are gratefully acknowledged. | affinity chromatography;antimicrobial activities;attractive therapeutic candidate;bacteria;bacteriocins;broad antimicrobial activities;broad antimicrobial activity;Chinese hamster ovary (CHO) cells;CHO cells;class II bacteriocin member;decreasing;enterocin P (EntP);EntP;functional expression;high salt medium;high temperatures;human plasma;infectious diseases;known mature amino acid sequence;multidrug-resistant bacteria;multidrug-resistant bacterial infections;multidrug-resistant pathogens;multidrug-resistant strains;nosocomial infections;numerous bacteria;offer alternative therapeutic strategies;pathogenic species;protein expression vector pcDNA3.1(+);recombinant EntP;recombinant EntP inhibited growth;recombinant plasmid;recombinant protein;small antimicrobial peptides;stability;stable;synthetic gene matching CHO cell codon usage;treatment;treatment options;variety | 10.1002/anie.201506818;10.1007/s00018-011-0710-x;10.1007/s00253-011-3758-5;10.1007/s00726-014-1833-9;10.1016/j.bej.2011.05.012;10.1016/j.copbio.2014.06.010;10.1016/j.ijfoodmicro.2005.03.021;10.1016/j.jiph.2016.08.007;10.1016/j.micpath.2017.11.039;10.1016/j.micpath.2018.04.035;10.1016/j.pep.2005.05.012;10.1021/bi036018e;10.1038/nmeth.3213;10.1038/nprot.2010.5;10.1038/nrmicro2536;10.1038/nrmicro2937;10.1038/s41522-018-0053-6;10.1074/jbc.R112.354688;10.1080/03009734.2016.1195900;10.1093/infdis/jiq029;10.1093/jac/dkr260;10.1111/j.1574-6976.2007.00064.x;10.1128/AAC.00252-13;10.1128/AAC.02395-14;10.1128/AAC.42.9.2206;10.1128/AEM.02206-09;10.1128/AEM.02264-09;10.1128/AEM.02559-07;10.1128/AEM.62.8.2897-2903.1996;10.1128/MMBR.00016-05;10.1186/1471-2180-14-109;10.2174/1389203053027494;10.3390/ijms12095971;10.3390/ph6050579;[10.1128/mBio.01932-17, 10.1128/mbio.01932-17] | Ferdowsi Univ Mashhad | Damavandi, M S;Ghaznini, K;Mansury, D;Tanhaeian, A | Tanhaeian, A: Ferdowsi Univ Mashhad, Dept Biotechnol & Plant Breeding, Fac Agr, Mashhad, Iran | Damavandi, Mohammad Sadegh;Mansury, Davood | 11 | 37 | null | Iran | Ferdowsi Univ Mashhad;Isfahan Univ Med Sci;Mashhad Univ Med Sci;Varastegan Inst Med Sci | Tanhaeian, Abbas | Green Published, gold | HOST-DEFENSE PEPTIDES;RESISTANCE | Tanhaeian, Abbas; Damavandi, Mohammad Sadegh; Mansury, Davood; Ghaznini, Kiarash; | null | Ferdowsi Univ Mashhad, Dept Biotechnol & Plant Breeding, Fac Agr, Mashhad, Iran;Isfahan Univ Med Sci, Sch Med, Dept Microbiol, Esfahan, Iran;Mashhad Univ Med Sci, Antimicrobial Resistance Res Ctr, Mashhad, Iran;Varastegan Inst Med Sci, Dept Med Lab Sci, Mashhad, Iran | Ferdowsi Univ Mashhad, Dept Biotechnol & Plant Breeding, Fac Agr, Mashhad, Iran;Isfahan Univ Med Sci, Sch Med, Dept Microbiol, Esfahan, Iran;Mashhad Univ Med Sci, Antimicrobial Resistance Res Ctr, Mashhad, Iran;Varastegan Inst Med Sci, Dept Med Lab Sci, Mashhad, Iran | null | antimicrobial peptide;Bacteriocins;CHO cells;Enterocin P;expression | null | 1996;1998;1999;2004;2005;2006;2007;2008;2010;2011;2012;2013;2014;2015;2016;2017;2018 | 9 | Mashhad Univ Med Sci, Antimicrobial Resistance Res Ctr, Mashhad, Iran;Varastegan Inst Med Sci, Dept Med Lab Sci, Mashhad, Iran | AMB Express | Ghaznini, Kiarash | SPRINGEROPEN | (CHO);(EntP);,;a;acid;activities;activity;addition;affinity;alternative;amino;an;and;antimicrobial;are;at;attractive;bacteria;bacterial;bacteriocin;bacteriocins;both;broad;by;candidate;cause;cell;cells;Chinese;CHO;chromatography;class;cloned;cloning;codon;combat;cultured;decreasing;demonstrated;designed;diseases;due;emergence;enterocin;EntP;evaluated;expression;for;from;functional;gene;Gram-negative;Gram-positive;growth;hamster;high;human;II;in;including;infections;infectious;inhibited;into;it;known;make;matching;mature;medium;member;multidrug-resistant;nosocomial;numerous;of;offer;often;on;options;ovary;P;particularly;pathogenic;pathogens;pcDNA3.1(+);peptides;plasma;plasmid;produced;protein;purified;recombinant;salt;sequence;small;species;stability;stable;strains;strategies;synthetic;temperatures;that;the;therapeutic;to;transformed;treatment;usage;variety;vector;was;we;were;with | Mashhad Univ Med Sci;Varastegan Inst Med Sci | Due to the emergence of multidrug-resistant bacteria, treatment options for infectious diseases are decreasing. Bacteriocins are small antimicrobial peptides produced by numerous bacteria that offer alternative therapeutic strategies to combat multidrug-resistant bacterial infections. We evaluated the cloning, functional expression, and antimicrobial activities of enterocin P (EntP), a class II bacteriocin member, in Chinese hamster ovary (CHO) cells. A synthetic gene matching CHO cell codon usage was designed from the known mature amino acid sequence of EntP and cloned into the protein expression vector pcDNA3.1(+). CHO cells were transformed with the recombinant plasmid and cultured, and the recombinant protein was purified by affinity chromatography. Antimicrobial activities of the recombinant EntP were evaluated on Gram-positive, Gram-negative, and multidrug-resistant pathogens. Recombinant EntP inhibited growth of a variety of bacteria, including pathogenic species known to cause nosocomial infections, often with multidrug-resistant strains. In addition, recombinant EntP demonstrated broad antimicrobial activities in both high salt medium and human plasma and was stable at high temperatures. The broad antimicrobial activity and stability of EntP make it an attractive therapeutic candidate, particularly for treatment of multidrug-resistant bacterial infections. | H-6234-2016;Y-2879-2019 | HOST-DEFENSE PEPTIDES;RESISTANCE | 1 | null | Antimicrobial peptides;Bacteriocin;CHO cell;Enterocin P;expression | 9 | Antimicrobial peptides;Bacteriocins;CHO-CELLS;Enterocin P;EXPRESSION;HOST-DEFENSE PEPTIDES;resistance | WOS:000455201600001 | Ferdowsi Univ Mashhad, Mashhad, Iran;Isfahan Univ Med Sci, Esfahan, Iran;Mashhad Univ Med Sci, Mashhad, Iran;Varastegan Inst Med Sci, Mashhad, Iran | Iran | 2,019 | null | 0000-0002-2582-8838;0000-0003-0664-2007 | null | null | English | null | AMINO ACIDS;ANGEW CHEM INT EDIT;ANTIMICROB AGENTS CH;APPL ENVIRON MICROB;APPL MICROBIOL BIOT;BIOCHEM ENG J;BIOCHEMISTRY-US;BMC MICROBIOL;CELL MOL LIFE SCI;CURR OPIN BIOTECH;CURR PROTEIN PEPT SC;FEMS MICROBIOL REV;INT J FOOD MICROBIOL;INT J MOL SCI;J ANTIMICROB CHEMOTH;J BIOL CHEM;J INFECT DIS;J INFECT PUBLIC HEAL;MBIO;METH MOL B;MICROB PATHOGENESIS;MICROBIOL MOL BIOL R;NAT METHODS;NAT PROTOC;NAT REV MICROBIOL;NPJ BIOFILMS MICROBI;PHARMACEUTICALS;PROTEIN EXPRES PURIF;UPSALA J MED SCI | Damavandi, Mohammad Sadegh;Ghaznini, Kiarash;Mansury, Davood;Tanhaeian, Abbas | 2024-03-11
ER | Basanta, A;Beaulieu, L;Bowdish, D M E;Butler, M;Cantisani, M;Chellat, M F;Chiang, C Y;Chu, H L;Cotter, P D;De Kwaadsteniet, M;Drider, D;Franz, C M A P;Frieri, M;Hou, Z;Hu, C B;Jack, R W;Jamasbi, E;Jasovsky, D;Kaur, K;Kim, J Y;Krishnamoorthy, R;Lai, T F;Mathur, H;Micenková, L;Montalbán-López, M;Park, S C;Rehaiem, A;Roy, A;Sanchez, J;Shabir, U;Turner, J;Wayne P.;White, A R;Wilkins, M R;Willing, B P;Yang, J Y;Yeung, A T Y | HG7UU | Mashhad, Iran;Mashhad, Iran. | 10 | null | 4 | null | 30,617,751 | Damavandi, Mohammad Sadegh;Ghaznini, Kiarash;Mansury, Davood;Tanhaeian, Abbas | AMB EXPRESS | Esfahan, Iran;Mashhad, Iran |
Meza-Gutierrez, F;Simsek, D;Toczyski, D P | 10.1016/bs.mie.2018.12.020 | null | 525 B STREET, SUITE 1900, SAN DIEGO, CA 92101-4495 USA | 60vm2su3l72433p6u6p1s1y2o381o455h3q2f | A genetic approach to study polyubiquitination in <i>Saccharomyces cerevisiae</i> | Univ Calif San Francisco | Methods in Enzymology | Toczyski, DP (corresponding author), Univ Calif San Francisco, Dept Biochem, Helen Diller Family Comprehens Canc Ctr, San Francisco, CA 94143 USA. | null | Meza-Gutierrez, Fernando;Simsek, Deniz;Toczyski, David Paul | Biochemical Research Methods;Biochemistry & Molecular Biology | NIGMS NIH HHS [R35 GM118104] Funding Source: Medline | WOS | Toczyski, D P | Amgen Inc, San Francisco, CA USA;Univ Calif San Francisco, San Francisco, CA USA | 618 | <i>Saccharomyces;a;approach;cerevisiae</i>;genetic;in;polyubiquitination;study;to | 1 | null | ELSEVIER ACADEMIC PRESS INC | Amgen Inc, San Francisco, CA USA;Univ Calif San Francisco, Dept Biochem, Helen Diller Family Comprehens Canc Ctr, San Francisco, CA 94143 USA | Review; Book Chapter | Univ Calif San Francisco | SAN DIEGO | null | null | Amgen Inc;Univ Calif San Francisco | NIGMS NIH HHS | Toczyski, DP (corresponding author), Univ Calif San Francisco, Dept Biochem, Helen Diller Family Comprehens Canc Ctr, San Francisco, CA 94143 USA. | 72 | Meza-Gutierrez, Fernando;Simsek, Deniz;Toczyski, David Paul | 3 | 2 | 500,702,000,004 | NIGMS NIH HHS [R35 GM118104] Funding Source: Medline | USA | UBIQUITIN AND UBIQUITIN-LIKE PROTEIN MODIFIERS | USA | null | null | Univ Calif San Francisco, Dept Biochem, Helen Diller Family Comprehens Canc Ctr, San Francisco, CA 94143 USA | 0076-6879 | Meza-Gutierrez, F;Simsek, D;Toczyski, D P | null | david.toczyski@ucsf.edu | <i>Saccharomyces cerevisiae</i>;genetic approach;polyubiquitination | 3 | S | Biochemistry & Molecular Biology | 63;<i>Saccharomyces cerevisiae</i>;BIOLOGY;chain types;CHAINS;complex;DNA-REPAIR;four loci;genetic approach;high efficiency;KINASE;lysines 48;methods;mutant;ORGANIZATION;PARKIN;polyubiquitin chains;polyubiquitination;poorly characterized;RESOLUTION;REVEAL;seven lysines;several alterations;SK1 strain background;sporulates;standard protocols;synthetic genetic analysis;ubiquitin;UBIQUITIN CHAINS;ubiquitin mutants;use;viability;well;yeast;yeast Saccharomyces cerevisiae | Meza-Gutierrez, F | COMPLEX;DNA-REPAIR;KINASE;MUTANT;ORGANIZATION;PARKIN;RESOLUTION;REVEAL;UBIQUITIN CHAINS;YEAST | 49 | [Meza-Gutierrez, Fernando; Toczyski, David Paul] Univ Calif San Francisco, Dept Biochem, Helen Diller Family Comprehens Canc Ctr, San Francisco, CA 94143 USA. [Simsek, Deniz] Amgen Inc, San Francisco, CA USA. | null | 63;biology;chain types;chains;four loci;high efficiency;lysines 48;methods;polyubiquitin chains;poorly characterized;seven lysines;several alterations;SK1 strain background;sporulates;standard protocols;synthetic genetic analysis;ubiquitin;ubiquitin mutants;use;viability;well;yeast Saccharomyces cerevisiae | 10.1002/j.1460-2075.1987.tb02384.x;10.1002/yea.1806;10.1007/BF00330984;10.1016/j.cell.2005.08.031;10.1016/j.cell.2009.01.041;10.1016/j.cell.2013.07.033;10.1016/j.celrep.2013.05.007;10.1016/j.molcel.2007.11.015;10.1016/j.molcel.2010.07.001;10.1016/j.molcel.2012.05.028;10.1016/j.molcel.2014.03.035;10.1016/j.molcel.2014.09.007;10.1016/S0076-6879(10)70009-4;10.1016/S0092-8674(00)00126-4;10.1038/35085597;10.1038/nature00991;10.1038/nature05649;10.1038/nature12566;10.1038/ncb2012;10.1038/ng1674;10.1038/nprot.2008.211;10.1038/nrm3099;10.1038/nsmb1295;10.1073/pnas.0710061104;10.1073/pnas.1506593112;10.1074/jbc.M110.149633;10.1074/jbc.M114.563031;10.1074/jbc.M308540200;10.1083/jcb.200810114;10.1093/nar/gkn923;10.1101/gad.215681.113;10.1126/science.1065810;10.1126/science.1091317;10.1126/science.1180823;10.1126/science.aaf1420;10.1128/MCB.14.8.5501;10.1128/MCB.23.24.9251-9261.2003;10.1146/annurev-biochem-060210-093619;10.1146/annurev.genet.39.073003.114751;10.1186/gb-2006-7-7-r63;10.1242/jcs.183954;10.1371/journal.pgen.0020195;10.1534/genetics.104.029033;10.1534/genetics.112.140467 | Univ Calif San Francisco | Meza-Gutierrez, F;Simsek, D;Toczyski, D P | Meza-Gutierrez, F: Univ Calif San Francisco, Dept Biochem, Helen Diller Family Comprehens Canc Ctr, San Francisco, CA 94143 USA | simsek, DENİZ | R35 GM118104 | 46 | 978-0-12-816359-7 | USA | Amgen Inc;Univ Calif San Francisco | Meza-Gutierrez, Fernando | Green Accepted | COMPLEX;DNA-REPAIR;KINASE;MUTANT;ORGANIZATION;PARKIN;RESOLUTION;REVEAL;UBIQUITIN CHAINS;YEAST | Meza-Gutierrez, Fernando; Simsek, Deniz; Toczyski, David Paul; | null | Amgen Inc, San Francisco, CA USA;Univ Calif San Francisco, Dept Biochem, Helen Diller Family Comprehens Canc Ctr, San Francisco, CA 94143 USA | Amgen Inc, San Francisco, CA USA;Univ Calif San Francisco, Dept Biochem, Helen Diller Family Comprehens Canc Ctr, San Francisco, CA 94143 USA | null | null | null | 1984;1987;1994;1995;2000;2001;2002;2003;2004;2005;2006;2007;2009;2010;2011;2012;2013;2014;2015;2016 | 0 | Univ Calif San Francisco, Dept Biochem, Helen Diller Family Comprehens Canc Ctr, San Francisco, CA 94143 USA | Methods Enzymol. | Toczyski, David Paul | ELSEVIER ACADEMIC PRESS INC | ,;48;63;a;all;alterations;analysis;and;are;associated;background;be;biology;by;cerevisiae;chain;chains;characterized;could;described;do;efficiency;encoded;examine;for;formed;four;generate;genetic;has;here;high;in;including;is;loci;lysines;methodology;methods;more;mutants;necessitating;not;of;other;outline;polyubiquitin;poorly;protocols;Saccharomyces;seven;several;SK1;sporulates;standard;strain;studied;support;synthetic;that;the;those;through;to;types;ubiquitin;use;used;using;very;viability;we;well;which;while;with;yeast | Univ Calif San Francisco | Ubiquitin has seven lysines, all of which are used to generate polyubiquitin chains in the yeast Saccharomyces cerevisiae. While the biology associated with chains formed through lysines 48 and 63 is well studied, other chain types are more poorly characterized. We outline a methodology for using synthetic genetic analysis to examine ubiquitin mutants. Ubiquitin is encoded by four loci, necessitating several alterations to standard protocols, including the use of the SK1 strain background, which sporulates with very high efficiency. The methods described here could be used to examine other ubiquitin mutants, including those that do not support viability. | P-8986-2019 | COMPLEX;DNA-REPAIR;KINASE;MUTANTS;ORGANIZATION;PARKIN;RESOLUTION;REVEALS;UBIQUITIN CHAINS;YEAST | 1 | null | null | 24 | YEAST;COMPLEX;DNA-REPAIR;KINASE;MUTANTS;ORGANIZATION;PARKIN;RESOLUTION;REVEALS;UBIQUITIN CHAINS | WOS:000500702000004 | Amgen Inc, San Francisco, CA USA;Univ Calif San Francisco, San Francisco, CA USA | USA | 2,019 | null | null | null | Hochstrasser, M | English | null | ANNU REV BIOCHEM;ANNU REV GENET;CELL;CELL REP;EMBO J;GENE DEV;GENETICS;GENOME BIOL;J BIOL CHEM;J CELL BIOL;J CELL SCI;METHOD ENZYMOL;METHODS MOL BIOL;MOL CELL;MOL CELL BIOL;MOL GEN GENET;NAT CELL BIOL;NAT GENET;NAT PROTOC;NAT REV MOL CELL BIO;NAT STRUCT MOL BIOL;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PLOS GENET;SCIENCE;YEAST | Meza-Gutierrez, Fernando;Simsek, Deniz;Toczyski, David Paul | 2024-03-11
ER | Akutsu, M;Ben-Ari, G;Bin, W;Birsa, N;Boeke, J D;Braberg, H;Christensen, D E;Collins, S R;Costanzo, M;Dammer, E B;Deng, L;Deutschbauer, A M;Dixon, S J;Finley, D;Geisler, S;Grabbe, C;Haber, J E;Hanna, J;Harper, J W;Hoege, C;Huang, D W;Lauwers, E;Macgurn, J A;Manzanillo, P S;Matsumoto, M L;Nishikawa, H;Ordureau, A;Ozkaynak, E;Partow, S;Ryan, C J;Sarin, S;Schuldiner, M;Spence, J;Tong Amy Hin Yan;Tong, A H Y;Wang, C;Xu, P;Yuan, W C;Zhou, H L | BO1KG | San Francisco, CA USA | 0 | null | 2 | null | 30,850,062 | Meza-Gutierrez, Fernando;Simsek, Deniz;Toczyski, David Paul | METHOD ENZYMOL | San Francisco, CA USA |
Martínez-González, L;Morales-Domínguez, J F;Pérez-Juárez, F S;Quezada-Rivera, J J;Soria-Guerra, R E;Valdes-Rodríguez, S E;Vasco-Méndez, N L | null | null | 871 CORONADO CENTER DR, SUTE 200, HENDERSON, NV 89052 USA | 6f6s582q6n6f2l3x665f3j6d4s4b2d5sc4gs36 | Heterologous expression of bacteriocin E-760 in <i>Chlamydomonas reinhardtii</i> and functional analysis | Univ Autonoma Aguascalientes | null | Morales-Domínguez, JF (corresponding author), Univ Autonoma Aguascalientes, Dept Quim, Univ 940,Ciudad Univ, Aguascalientes 20131, Ags, Mexico. | null | Martinez-Gonzalez, L;Morales-Dominguez, J F;Perez-Juarez, F S;Quezada-Rivera, J J;Soria-Guerra, R E;Valdes-Rodriguez, S E;Vasco-Mendez, N L | Plant Sciences | CONACYT [401222]; Autonomous University of Aguascalientes [PIBT16-1] | WOS | Morales-Domínguez, J F | Inst Politecn Nacl, Gto, Mexico;Univ Autonoma Aguascalientes, Ags, Mexico;Univ Autonoma San Luis Potosi, Slp, Mexico | 88 | <i>Chlamydomonas;Analysis;and;Bacteriocin;E-760;expression;functional;Heterologous;in;of;reinhardtii</i> | 1 | Martinez, Luzmila;Martinez-Gonzalez, Luis Javier;Quezada-Rivera, Jesus Josafath;SORIA, RUTH;Valdes Rodriguez, Silvia | TECH SCIENCE PRESS | Inst Politecn Nacl, Ctr Invest & Estudios Avanzados, Dept Biotecnol & Bioquim, Cinvestav Unidad Irapuato, Km 9-6 Libramiento Nort Carr, Irapuato 36824, Gto, Mexico;Univ Autonoma Aguascalientes, Dept Quim, Univ 940,Ciudad Univ, Aguascalientes 20131, Ags, Mexico;Univ Autonoma San Luis Potosi, Fac Ciencias Quim, San Luis Potosi 78290, Slp, Mexico | Article | Univ Autonoma Aguascalientes | HENDERSON | null | null | Inst Politecn Nacl;Univ Autonoma Aguascalientes;Univ Autonoma San Luis Potosi | Autonomous University of Aguascalientes;CONACYT | Morales-Domínguez, JF (corresponding author), Univ Autonoma Aguascalientes, Dept Quim, Univ 940,Ciudad Univ, Aguascalientes 20131, Ags, Mexico. | 35 | Martinez-Gonzalez, L;Morales-Dominguez, J F;Perez-Juarez, F S;Quezada-Rivera, J J;Soria-Guerra, R E;Valdes-Rodriguez, S E;Vasco-Mendez, N L | 2 | 3 | 482,804,000,004 | Autonomous University of Aguascalientes [PIBT16-1];CONACYT [401222] | Mexico | PHYTON-INTERNATIONAL JOURNAL OF EXPERIMENTAL BOTANY | Mexico | null | null | Univ Autonoma Aguascalientes, Dept Quim, Univ 940,Ciudad Univ, Aguascalientes 20131, Ags, Mexico | 0031-9457 | Martínez-González, L;Morales-Domínguez, J F;Pérez-Juárez, F S;Quezada-Rivera, J J;Soria-Guerra, R E;Valdes-Rodríguez, S E;Vasco-Méndez, N L | null | jfmoral@correo.uaa.mx | <i>Chlamydomonas reinhardtii</i>;bacteriocin E-760;functional analysis;heterologous expression | 7 | J | Plant Sciences | 0.07 U log;0.14 (Non-induced culture;0.34 U log;0.36 U log;0.36% (Induced culture;0.48 U log;10 minutes;2 U log;35 degrees C;<i>Chlamydomonas reinhardtii</i>;activity;Agrobacterium tumefaciens;alternative;Antibacterial activity;antibacterial agent;antimicrobial peptides;antimicrobial peptides (AMPs);bacteria (bacteriocins);Bacteriocin E-760;C. reinhardtii;chimeric protein coding;Chlamydomonas reinhardtii;CHLOROPLAST;culture medium temperature;E-760;ELISA assay;Enterococcus faecium;expression;function;functional analysis;GENETIC-TRANSFORMATION;genome;genus Enterococcus sp;Gram-positive bacteria;GREEN-ALGA;heterologous expression;hygromycin;IC);increment;inhibitory activity;insulin;Klebsiella pneumoniae;Log inactivation;mass production;multidrug resistant;NIC);Nuclear transformation;nucleus;nucleus transformation;PCR;production;production level;PROTEIN;Pseudomonas aeruginosa;recombinant E-760;recombinant protein;recombinant route;results;stable expression platform;Staphylococcus aureus;Streptococcus agalactiae;study;synthetic gene E-760;synthetic gene E-760S;TAP medium;total soluble proteins (TSP);transgenic line;transgenic strain;use;viable option | Quezada-Rivera, J J | Antibacterial activity;Antimicrobial peptides;Bacteriocin E-760;Chlamydomonas reinhardtii;CHLOROPLAST;GENETIC-TRANSFORMATION;GREEN-ALGA;heterologous expression;INSULIN;Log inactivation;Nuclear transformation;PROTEIN | 25 | [Quezada-Rivera, J. J.; Vasco-Mendez, N. L.; Morales-Dominguez, J. F.] Univ Autonoma Aguascalientes, Dept Quim, Univ 940,Ciudad Univ, Aguascalientes 20131, Ags, Mexico. [Soria-Guerra, R. E.; Perez-Juarez, F. S.; Martinez-Gonzalez, L.] Univ Autonoma San Luis Potosi, Fac Ciencias Quim, San Luis Potosi 78290, Slp, Mexico. [Valdes-Rodriguez, S. E.] Inst Politecn Nacl, Ctr Invest & Estudios Avanzados, Dept Biotecnol & Bioquim, Cinvestav Unidad Irapuato, Km 9-6 Libramiento Nort Carr, Irapuato 36824, Gto, Mexico. | The authors want to thank CONACYT for the doctoral scholarship number 401222. This project was supported by the Autonomous University of Aguascalientes with grant number PIBT16-1. | 0.07 U log;0.14 (Non-induced culture;0.34 U log;0.36 U log;0.36% (Induced culture;0.48 U log;10 minutes;2 U log;35 degrees C;activity;Agrobacterium tumefaciens;alternative;antibacterial activity;antibacterial agent;antimicrobial peptides (AMPs);bacteria (bacteriocins);bacteriocin E-760;C. reinhardtii;chimeric protein coding;culture medium temperature;E-760;ELISA assay;Enterococcus faecium;expression;function;genome;genus Enterococcus sp;Gram-positive bacteria;hygromycin;IC);increment;inhibitory activity;Klebsiella pneumoniae;mass production;multidrug resistant;NIC);nucleus;nucleus transformation;PCR;production;production level;Pseudomonas aeruginosa;recombinant E-760;recombinant protein;recombinant route;results;stable expression platform;Staphylococcus aureus;Streptococcus agalactiae;study;synthetic gene E-760;synthetic gene E-760S;TAP medium;total soluble proteins (TSP);transgenic line;transgenic strain;use;viable option | 10.1002/9781118567166.CH27;10.1002/jcc.20084;10.1007/4735_2007_0225;10.1007/978-1-4419-7692-5_10;10.1007/s10811-018-1393-6;10.1007/s11103-015-0425-8;10.1007/s11240-012-0261-3;10.1007/s12033-013-9720-2;10.1007/s12602-009-9021-z;10.1016/0003-2697(76)90527-3;10.1016/j.bbamem.2016.01.005;10.1016/j.meatsci.2016.04.004;10.1016/j.peptides.2012.09.020;10.1016/j.plantsci.2003.11.012;10.1021/bi9619987;10.1038/ismej.2013.43;10.1038/msb.2011.75;10.1038/nbt1098-934;10.1038/nrmicro1273;10.1038/nrmicro2937;10.1038/s41598-017-02868-w;10.1038/srep15835;10.1093/nar/gkv416;10.1093/nar/gkw329;10.1111/j.1365-2672.2012.05338.x;10.1111/j.1365-313X.2008.03746.x;10.1111/j.1467-7652.2005.00159.x;10.1111/j.1467-7652.2010.00503.x;10.1126/science.1143609;10.1128/AAC.01569-06;10.1134/S1021443713030163;10.1155/2014/867381;10.1155/2015/767183;10.1155/2016/8060847;10.1186/1471-2180-7-89;10.12703/P5-51;10.13040/IJPSR.0975-8232.2(6).1467-72;10.1385/1-59259-890-0:571;10.1385/MB:20:2:131;10.13918/j.issn.2095-8137.2015.1.41;10.1590/S0103-90162008000100014;10.3724/SP.J.1206.2010.00671;[10.1093/nar/gkh131, 10.1093/nar/gkw1099] | Univ Autonoma Aguascalientes | Martínez-González, L;Morales-Domínguez, J F;Pérez-Juárez, F S;Quezada-Rivera, J J;Soria-Guerra, R E;Valdes-Rodríguez, S E;Vasco-Méndez, N L | Quezada-Rivera, J J: Univ Autonoma Aguascalientes, Dept Quim, Univ 940,Ciudad Univ, Aguascalientes 20131, Ags, Mexico | Martinez-Gonzalez, Luis Javier;QUEZADA RIVERA, JESUS JOSAFATH | 401222;PIBT16-1 | 47 | null | Mexico | Inst Politecn Nacl;Univ Autonoma Aguascalientes;Univ Autonoma San Luis Potosi | Quezada-Rivera, J J | gold | ANTIMICROBIAL PEPTIDES;CHLOROPLAST;GENETIC-TRANSFORMATION;GREEN-ALGA;INSULIN;PROTEIN | Quezada-Rivera, J. J.; Soria-Guerra, R. E.; Perez-Juarez, F. S.; Martinez-Gonzalez, L.; Valdes-Rodriguez, S. E.; Vasco-Mendez, N. L.; Morales-Dominguez, J. F.; | null | Inst Politecn Nacl, Ctr Invest & Estudios Avanzados, Dept Biotecnol & Bioquim, Cinvestav Unidad Irapuato, Km 9-6 Libramiento Nort Carr, Irapuato 36824, Gto, Mexico;Univ Autonoma Aguascalientes, Dept Quim, Univ 940,Ciudad Univ, Aguascalientes 20131, Ags, Mexico;Univ Autonoma San Luis Potosi, Fac Ciencias Quim, San Luis Potosi 78290, Slp, Mexico | Inst Politecn Nacl, Ctr Invest & Estudios Avanzados, Dept Biotecnol & Bioquim, Cinvestav Unidad Irapuato, Km 9-6 Libramiento Nort Carr, Irapuato 36824, Gto, Mexico;Univ Autonoma Aguascalientes, Dept Quim, Univ 940,Ciudad Univ, Aguascalientes 20131, Ags, Mexico;Univ Autonoma San Luis Potosi, Fac Ciencias Quim, San Luis Potosi 78290, Slp, Mexico | 1851-5657 | Antibacterial activity;Bacteriocin E-760;Chlamydomonas reinhardtii;heterologous expression;Log inactivation;Nuclear transformation | 1 | 1976;1990;1993;1997;1998;2001;2002;2004;2005;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016;2017;2018 | 3 | Univ Autonoma Aguascalientes, Dept Quim, Univ 940,Ciudad Univ, Aguascalientes 20131, Ags, Mexico | Phyton-Int. J. Exp. Bot. | Morales-Dominguez, J F | TECH SCIENCE PRESS | (AMPs);(bacteriocins);(Induced;(Non-induced;(TSP);,;0.07;0.14;0.34;0.36;0.36%;0.48;10;2;35;;;a;activity;aeruginosa;against;agalactiae;agent;Agrobacterium;also;alternative;an;and;antibacterial;antimicrobial;as;assay;at;aureus;bacteria;bacterial;bacteriocin;be;been;by;C;C.;can;chimeric;coding;combating;culture;degrees;demonstrate;E-760;E-760S;ELISA;Enterococcus;evaluated;expression;faecium;for;from;function;gene;genome;genus;Gram-negative;Gram-positive;has;hygromycin;IC);identified;in;increased;increment;inhibitory;inserted;into;is;isolated;it;its;Klebsiella;level;line;log;mass;medium;minutes;multidrug;NIC);nucleus;of;option;PCR;peptides;platform;pneumoniae;possess;possesses;potentially;production;protein;proteins;Pseudomonas;quantified;recombinant;reinhardtii;resistant;results;route;shown;soluble;sp;stable;Staphylococcus;strain;strains;streptococcus;study;synthesized;synthetic;TAP;temperature;that;the;their;these;this;to;total;transformation;transgenic;tumefaciens;U;use;used;using;viable;was;well;with | Univ Autonoma Aguascalientes | The use of antimicrobial peptides (AMPs) synthesized by bacteria (bacteriocins) is an alternative for combating multidrug resistant bacterial strains and their production by recombinant route is a viable option for their mass production. The bacteriocin E-760 isolated from the genus Enterococcus sp. has been shown to possess inhibitory activity against Gram-negative and Gram-positive bacteria. In this study, the expression of a chimeric protein coding for E-760 in the nucleus of C. reinhardtii was evaluated, as well as, its antibacterial activity. The synthetic gene E-760S was inserted into the genome of C. reinhardtii using Agrobacterium tumefaciens. A transgenic line was identified in TAP medium with hygromycin and also by PCR. The increment in the culture medium temperature of the transgenic strain at 35 degrees C for 10 minutes, increased the production level of the recombinant protein from 0.14 (Non-induced culture, NIC) to 0.36% (Induced culture, IC) of total soluble proteins (TSP); this was quantified by an ELISA assay. Recombinant E-760 possesses activity against Staphylococcus aureus in 0.34 U log, Streptococcus agalactiae in 0.48 U log, Enterococcus faecium in 0.36 U log, Pseudomonas aeruginosa in 2 U log and for Klebsiella pneumoniae, the activity was 0.07 U log. These results demonstrate that the nucleus transformation of C. reinhardtii can function as a stable expression platform for the production of the synthetic gene E-760 and it can potentially be used as an antibacterial agent. | ITV-0083-2023;L-6136-2014 | ANTIMICROBIAL PEPTIDES;CHLOROPLAST;GENETIC-TRANSFORMATION;GREEN-ALGA;INSULIN;PROTEIN | 1 | null | Antibacterial activity;Bacteriocin E-760;Chlamydomonas reinhardtii;heterologous expression;Log inactivation;Nuclear transformation | 11 | Antibacterial activity;Antimicrobial peptides;Bacteriocin E-760;CHLAMYDOMONAS-REINHARDTII;CHLOROPLAST;GENETIC-TRANSFORMATION;GREEN-ALGA;heterologous expression;INSULIN;Log inactivation;Nuclear transformation;PROTEIN | WOS:000482804000004 | Inst Politecn Nacl, Gto, Mexico;Univ Autonoma Aguascalientes, Ags, Mexico;Univ Autonoma San Luis Potosi, Slp, Mexico | Mexico | 2,019 | null | 0000-0001-9942-6156;0000-0002-6801-4906;0000-0002-8519-6545;0000-0003-2202-0662;0000-0003-3133-9982 | null | null | English | null | ANAL BIOCHEM;ANTIMICROB AGENTS CH;BBA-BIOMEMBRANES;BIOCHEMISTRY-US;BIOMED RES INT;BIOTECHNIQUES;BMC MICROBIOL;GENETICS;INT J PHARM SCI RES;INT J PHOTOENERGY;ISME J;J APPL MICROBIOL;J APPL PHYCOL;J COMPUT CHEM;MEAT SCI;MOL BIOTECHNOL;MOL SYST BIOL;Molecular cloning;NAT BIOTECHNOL;NAT REV MICROBIOL;NUCLEIC ACIDS RES;PEPTIDES;PLANT BIOTECHNOL J;PLANT CELL TISS ORG;PLANT J;PLANT MOL BIOL;PLANT SCI;PROBIOTICS ANTIMICRO;PROG BIOCHEM BIOPHYS;RUSS J PLANT PHYSL+;SCI REP-UK;SCIENCE;Technical report;The Proteomics Protocols Handbook;Zoological Research | Martinez-Gonzalez, L;Morales-Dominguez, J F;Perez-Juarez, F S;Quezada-Rivera, J J;Soria-Guerra, R E;Valdes-Rodriguez, S E;Vasco-Mendez, N L | 2024-03-11
ER | Apweiler, R;Arakawa, T;Arbulu, S;Bailey, T L;Barahimipour, R;Barrera D.J.;Belguesmia, Y;Bradford, M M;Campos-Quevedo, N;Cotter, P D;Dunahay, T G;Ebenhan, T;Garcidueñas-Piña, C;Gasteiger E.;Hammami, R;Hassan, M;Kang, S;Koop Hans-Ulrich;Kumar, S V;Kyriakou, P K;Lamiable, A;Line, J E;Liu Cun-Bao;Mello-Farias Paulo Celso De;Merchant, S S;Mesa-Pereira, B;Mu, F Y;Neupert, J;Newman, S M;Nissen-Meyer, J;Nykiforuk, C L;Parachin, N S;Pettersen, E F;Pratheesh, P T;Rasala, B A;Renukadevi, K P;Salas-Montantes, C J;Sambrook J.;Sievers, F;Tillotson Glenn, S;Who (World Health Organization);Wieprecht, T;Woraprayote, W;Xie, B;Zakharchenko, N S;Zhang, G G | IT4BO | Ags, Mexico | 3 | null | 3 | null | null | Martinez-Gonzalez, L;Morales-Dominguez, J F;Perez-Juarez, F S;Quezada-Rivera, J J;Soria-Guerra, R E;Valdes-Rodriguez, S E;Vasco-Mendez, N L | PHYTON-INT J EXP BOT | Ags, Mexico;Gto, Mexico;SLP, Mexico |
Bouchard, G;Dance, C R;Gaussier, É;Trouillon, T | 10.1613/jair.1.11305 | null | USC INFORMATION SCIENCES INST, 4676 ADMIRALITY WAY, MARINA DEL REY, CA 90292-6695 USA | 72582s6t5f225w3s5b1c1i1f626ty61672m3f5v | On Inductive Abilities of Latent Factor Models for Relational Learning | Univ Grenoble Alpes | null | Trouillon, T (corresponding author), Univ Grenoble Alpes, 700 Ave Cent, F-38401 St Martin Dheres, France. | null | Bouchard, Guillaume;Dance, Christopher R;Gaussier, Eric;Trouillon, Theo | Computer Science, Artificial Intelligence | Association Nationale de la Recherche et de la Technologie through the CIFRE grant [2014/0121] | WOS | Trouillon, T | Facebook, London, England;NAVER LABS Europe, Meylan, France;Univ Grenoble Alpes, St Martin Dheres, France | 64 | Abilities;factor;for;Inductive;Latent;learning;MODELS;of;on;Relational | 2 | Bouchard, Guillaume | AI ACCESS FOUNDATION | Facebook, 1 Rathbone Sq, London WT1 1FB, England;NAVER LABS Europe, 6 Chemin Maupertuis, F-38240 Meylan, France;Univ Grenoble Alpes, 700 Ave Cent, F-38401 St Martin Dheres, France | Article | Univ Grenoble Alpes | MARINA DEL REY | null | null | Facebook;NAVER LABS Europe;Univ Grenoble Alpes | Association Nationale de la Recherche et de la Technologie through the CIFRE grant | Trouillon, T (corresponding author), Univ Grenoble Alpes, 700 Ave Cent, F-38401 St Martin Dheres, France. | 53 | Bouchard, Guillaume;Dance, Christopher R;Gaussier, Eric;Trouillon, Theo | 1 | 3 | 466,976,900,002 | Association Nationale de la Recherche et de la Technologie through the CIFRE grant [2014/0121] | France;UK | JOURNAL OF ARTIFICIAL INTELLIGENCE RESEARCH | France | null | null | Univ Grenoble Alpes, 700 Ave Cent, F-38401 St Martin Dheres, France | 1076-9757 | Bouchard, G;Dance, C R;Gaussier, É;Trouillon, T | null | chris.dance@naverlabs.com;eric.gaussier@imag.fr;gbouchard@fb.com;theo.trouillon@imag.fr | Inductive Abilities;Latent Factor Models;Relational Learning | 4 | J | Computer Science | atomic properties;binary relations;class;common inter-relational inference;comparative end;exhibit first;existing models;experimental results;experimental survey;improved;Inductive Abilities;insight;Latent Factor Models;modeling multi-relational knowledge graphs;models works;new research directions;Relational Learning;simple;state-of-the-art models;strengths;synthetic genealogies;vectorial nature;weaknesses | Trouillon, T | null | 21 | [Trouillon, Theo; Gaussier, Eric] Univ Grenoble Alpes, 700 Ave Cent, F-38401 St Martin Dheres, France. [Dance, Christopher R.] NAVER LABS Europe, 6 Chemin Maupertuis, F-38240 Meylan, France. [Bouchard, Guillaume] Facebook, 1 Rathbone Sq, London WT1 1FB, England. | This work was supported in part by the Association Nationale de la Recherche et de la Technologie through the CIFRE grant 2014/0121. | atomic properties;binary relations;class;common inter-relational inference;comparative end;exhibit first;existing models;experimental results;experimental survey;improved;inductive abilities;insight;latent factor models;modeling multi-relational knowledge graphs;models works;new research directions;simple;state-of-the-art models;strengths;synthetic genealogies;vectorial nature;weaknesses | 10.1002/SAPM192761164];10.1007/978-3-662-44848-9_28;10.1007/BF02310791;10.1007/BF03037227;10.1007/s00493-007-2160-5;10.1007/s00778-015-0394-1;10.1007/s10994-006-5833-1;10.1007/s10994-013-5335-x;10.1016/0743-1066(94)90035-3;10.1016/S0304-3975(96)00128-4;10.1017/S0269888900006147;10.1017/S1471068410000116;10.1109/ICASSP.2015.7178992;10.1109/ICICIP.2013.6568119;10.1109/JPROC.2015.2483592;10.1109/MC.2009.263;10.1134/S0036023613040165;10.1137/07070111X;10.1145/1376616.1376746;10.1145/1401890.1401944];10.1145/174644.174647;10.1145/1968.1972;10.1145/2623330.2623623;10.1613/jair.5013;10.18653/V1/D16-1146, 10.18653/v1/d16-1146];10.3115/v1/N15-1118;10.5555/3104482.3104584;10.7551/mitpress/7432.003.0009 | Univ Grenoble Alpes | Bouchard, G;Dance, C R;Gaussier, É;Trouillon, T | Trouillon, T: Univ Grenoble Alpes, 700 Ave Cent, F-38401 St Martin Dheres, France | null | 2014/0121 | 70 | null | France | Facebook;NAVER LABS Europe;Univ Grenoble Alpes | Trouillon, Theo | Green Submitted, gold | null | Trouillon, Theo; Gaussier, Eric; Dance, Christopher R.; Bouchard, Guillaume; | null | Facebook, 1 Rathbone Sq, London WT1 1FB, England;NAVER LABS Europe, 6 Chemin Maupertuis, F-38240 Meylan, France;Univ Grenoble Alpes, 700 Ave Cent, F-38401 St Martin Dheres, France | Facebook, 1 Rathbone Sq, London WT1 1FB, England;NAVER LABS Europe, 6 Chemin Maupertuis, F-38240 Meylan, France;Univ Grenoble Alpes, 700 Ave Cent, F-38401 St Martin Dheres, France | 1943-5037 | null | null | 1545;1927;1934;1970;1984;1986;1992;1993;1994;1995;1997;1998;1999;2001;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016;2017 | 9 | Univ Grenoble Alpes, 700 Ave Cent, F-38401 St Martin Dheres, France | J. Artif. Intell. Res. | Bouchard, Guillaume | AI ACCESS FOUNDATION | ,;a;abilities;about;also;an;and;are;as;assess;atomic;based;be;binary;but;by;class;common;comparative;conduct;create;directions;each;end;exhibit;existing;experimental;factor;fail;first;for;genealogies;get;graphs;hard;how;improve;improved;increasingly;inductive;inference;insight;inter-relational;interpret;is;it;knowledge;latent;means;might;model;modeling;models;multi-relational;nature;new;not;of;on;only;popular;properties;propose;purely;relations;research;results;simple;so;state-of-the-art;strengths;survey;synthetic;tasks;that;the;their;then;these;they;this;through;to;towards;understand;vectorial;we;weaknesses;well;where;why;works | Univ Grenoble Alpes | Latent factor models are increasingly popular for modeling multi-relational knowledge graphs. By their vectorial nature, it is not only hard to interpret why this class of models works so well, but also to understand where they fail and how they might be improved. We conduct an experimental survey of state-of-the-art models, not towards a purely comparative end, but as a means to get insight about their inductive abilities. To assess the strengths and weaknesses of each model, we create simple tasks that exhibit first, atomic properties of binary relations, and then, common inter-relational inference through synthetic genealogies. Based on these experimental results, we propose new research directions to improve on existing models. | null | null | 0 | null | null | 33 | null | WOS:000466976900002 | Facebook, London, England;NAVER LABS Europe, Meylan, France;Univ Grenoble Alpes, St Martin Dheres, France | France;UK | 2,019 | null | 0009-0006-5332-0923 | null | null | English | null | 6 INT SEM WEB C BUS;AAAI C ART INT;AAAI CONF ARTIF INTE;AAAI SPRING S CIT;ACL WORKSH CONT VECT;ADV NEURAL INFORM PR;Advances in neural information processing systems;AI MAG;ARTIS MAGN SIVE REGU;ARXIV PREPRINT ARXIV;C COGN SCI SOC;C EMPIRICAL METHODS;C UNC ART INT;COMBINATORICA;COMMUN ACM;COMPUTER;Conference on learning theory;EUROPEAN CHAPTER ASS;GODEL;Inductive logic programming;INT C INT C MACHINE;INT C LEARNING REPRE;INT CONF ACOUST SPEE;INT WORKSH STAT REL;Introduction to Statistical Relational Learning;J ACM;J ARTIF INTELL RES;J LOGIC PROGRAM;J MACH LEARN RES;J MACHINE LEARNING R;JOINT C LEX COMP SEM;Knowledge Engineering Review;MACH LEARN;NAIVE SET THEORY;NATURE STAT LEAMING;NEW GENERAT COMPUT;P IEEE;P NIPS;PR MACH LEARN RES;PROC ACM SIGMOD INT;Proceedings of the Twenty-Fifth International Joint Conference on Artificial Intelligence;PSYCHOMETRIKA;SIAM REV;T ASSOC COMPUT LING;THEOR COMPUT SCI;THEOR PRACT LOG PROG;UCLA WORKING PAPERS;VLDB J;WORKSH AUT KNOWL BAS;WORKSH SEM PARS ACL;WORKSH VECT SPAC MOD | Bouchard, Guillaume;Dance, Christopher R;Gaussier, Eric;Trouillon, Theo | 2024-03-11
ER | [Anonymous];Aaronson, S;Alon Noga.;Auer, S;Bollacker K. D.;Bordes A.;Bordes Antoine;Bottou, L;Bouchard Guillaume;Bowman S. R.;Cardano G.;Carroll, J D;Davis, R;Demeester T.;Dong, X L;Duchi, J;Dzeroski S.;Friedman, N;Galárraga, L;Garcia-Duran Alberto;García-Durán, A;Grefenstette E.;Halmos Paul R.;Hamaguchi, T;Harshman, R A;Heckerman D.;Hinton G. E.;Hitchcock F. L.;Kearns, M;Kersting K.;Kolda, T G;Koren, Y;Lanthaler M.;Lewis M.;Linial, N;Lisi, F A;Ma, Y;Minervini P.;Muggleton, S;Ngo, L;Nickel M.;Nickel, M;Popper K.;Richardson, M;Riedel S.;Rocktaschel T.;Rocktaschel Tim;Singh Sameer;Smolensky P.;Socher R.;Sutskever I.;Trouillon T.;Trouillon Theo;Trouillon, T;Valiant, L G;Vapnik V.;Verga P.;Wang W.Y.;Welbl Johannes;Wellman M. P.;Yang B. | HW8YF | St Martin Dheres, France | 10 | null | 3 | null | null | Bouchard, Guillaume;Dance, Christopher R;Gaussier, Eric;Trouillon, Theo | J ARTIF INTELL RES | London, England;Meylan, France;St Martin Dheres, France |
de Greef, T F A;Dubuc, E;Huck, W T S;Pieters, P A;van der Linden, A J;van Sluijs, B;Yelleswarapu, M | 10.1021/acssynbio.8b00300 | null | 1155 16TH ST, NW, WASHINGTON, DC 20036 USA | 1i736n71f1l284d5y121a2z561ho6h526d6t6i | Sigma Factor-Mediated Tuning of Bacterial Cell-Free Synthetic Genetic Oscillators | Radboud Univ Nijmegen | null | de Greef, TFA (corresponding author), Eindhoven Univ Technol, Computat Biol Grp, Dept Biomed Engn, Inst Complex Mol Syst, POB 513, NL-5600 MB Eindhoven, Netherlands.;Huck, WTS (corresponding author), Radboud Univ Nijmegen, Inst Mol & Mat, Heyendaalseweg 135, NL-6525 AJ Nijmegen, Netherlands. | null | de Greef, Tom F A;Dubuc, Emilien;Huck, Wilhelm T S;Pieters, Pascal A;van der Linden, Ardjan J;van Sluijs, Bob;Yelleswarapu, Maaruthy | Biochemical Research Methods | TOPPUNT grant from The Netherlands Organization for Scientific Research (NWO); European Research Council, ERC [677313 BioCircuit]; NWO-VIDI grant from The Netherlands Organization for Scientific Research (NWO) [723.016.003]; Ministry of Education, Culture and Science (Gravity programs) [024.001.035, 024.003.013] | WOS | de Greef, T F A;Huck, W T S | Eindhoven Univ Technol, Eindhoven, Netherlands;Radboud Univ Nijmegen, Nijmegen, Netherlands | 7 | Bacterial;Cell-Free;Factor-Mediated;genetic;of;Oscillators;sigma;synthetic;Tuning | 1 | Pieters, Pascal | AMER CHEMICAL SOC | Eindhoven Univ Technol, Computat Biol Grp, Dept Biomed Engn, Inst Complex Mol Syst, POB 513, NL-5600 MB Eindhoven, Netherlands;Radboud Univ Nijmegen, Inst Mol & Mat, Heyendaalseweg 135, NL-6525 AJ Nijmegen, Netherlands;Radboud Univ Nijmegen, Inst Mol & Mat, Heyendaalseweg 135, NL-6525 AJ Nijmegen, Netherlands.; de Greef, TFA (corresponding author), Eindhoven Univ Technol, Computat Biol Grp, Dept Biomed Engn, Inst Complex Mol Syst, POB 513, NL-5600 MB Eindhoven, Netherlands | Article | Eindhoven Univ Technol;Radboud Univ Nijmegen | WASHINGTON | null | null | Eindhoven Univ Technol;Radboud Univ Nijmegen | European Research Council, ERC;Ministry of Education, Culture and Science (Gravity programs);NWO-VIDI grant from the Netherlands Organization for Scientific Research (NWO);TOPPUNT grant from The Netherlands Organization for Scientific Research (NWO) | Huck, WTS (corresponding author), Radboud Univ Nijmegen, Inst Mol & Mat, Heyendaalseweg 135, NL-6525 AJ Nijmegen, Netherlands.; de Greef, TFA (corresponding author), Eindhoven Univ Technol, Computat Biol Grp, Dept Biomed Engn, Inst Complex Mol Syst, POB 513, NL-5600 MB Eindhoven, Netherlands. | 2887 | de Greef, Tom F A;Dubuc, Emilien;Huck, Wilhelm T S;Pieters, Pascal A;van der Linden, Ardjan J;van Sluijs, Bob;Yelleswarapu, Maaruthy | 22 | 2 | 454,568,100,020 | European Research Council, ERC [677313 BioCircuit];Ministry of Education, Culture and Science (Gravity programs) [024.001.035, 024.003.013];NWO-VIDI grant from the Netherlands Organization for Scientific Research (NWO) [723.016.003];TOPPUNT grant from The Netherlands Organization for Scientific Research (NWO) | Netherlands | ACS SYNTHETIC BIOLOGY | Netherlands | null | null | Radboud Univ Nijmegen, Inst Mol & Mat, Heyendaalseweg 135, NL-6525 AJ Nijmegen, Netherlands | 2161-5063 | de Greef, T F A;Dubuc, E;Huck, W T S;Pieters, P A;van der Linden, A J;van Sluijs, B;Yelleswarapu, M | DEC | t.f.a.d.greef@tue.nl;w.huck@science.ru.nl | Bacterial Cell-Free Synthetic Genetic Oscillators;sigma Factor-Mediated Tuning | 7 | J | Biochemistry & Molecular Biology | activator-repressor motif;associated sigma factors;Bacterial Cell-Free Synthetic Genetic Oscillators;BINDING;BIOLOGY;cell-free systems;cell-free transcription-translation;competing sigma factors;competition;competition-induced regulation;coupling two oscillators;E. coli;E. coli-based cell-free system;evolutionary algorithm;exhibit complex temporal behavior;experimental data;expression;functional modulation;GENETIC ELEMENTS;genetic oscillator;key regulatory model parameters;kinetic model;microfluidic flow reactors;MODELS;modification;native transcriptional machinery;network properties;OSCILLATOR;passive transcriptional regulation;platform;RNA-POLYMERASE;RNAP;scarce;sigma Factor-Mediated Tuning;sigma factors;simplified prototyping environment;steady-state conditions;study synthetic networks;synthetic biology;toolbox;well characterized toolbox | Yelleswarapu, M | BINDING;BIOLOGY;cell-free systems;COMPETITION;competition-induced regulation;EXPRESSION;MODELS;OSCILLATOR;PLATFORM;RNA-POLYMERASE;sigma factors;Synthetic biology;TOOLBOX | 2879 | [Yelleswarapu, Maaruthy; van Sluijs, Bob; Huck, Wilhelm T. S.] Radboud Univ Nijmegen, Inst Mol & Mat, Heyendaalseweg 135, NL-6525 AJ Nijmegen, Netherlands. [van der Linden, Ardjan J.; Pieters, Pascal A.; Dubuc, Emilien; de Greef, Tom F. A.] Eindhoven Univ Technol, Computat Biol Grp, Dept Biomed Engn, Inst Complex Mol Syst, POB 513, NL-5600 MB Eindhoven, Netherlands. | We thank Frank H. T. Nelissen, Hans A. Heus and Evan Spruijt for helpful discussions and Roel Maas for his help with experiments. W.T.S.H. was supported by a TOPPUNT grant from The Netherlands Organization for Scientific Research (NWO). T.d.G was supported by the European Research Council, ERC (project no. 677313 BioCircuit) and NWO-VIDI grant from The Netherlands Organization for Scientific Research (NWO, 723.016.003), and funding from the Ministry of Education, Culture and Science (Gravity programs, 024.001.035 and 024.003.013). | activator-repressor motif;associated sigma factors;cell-free transcription-translation;competing sigma factors;coupling two oscillators;E. coli;E. coli-based cell-free system;evolutionary algorithm;exhibit complex temporal behavior;experimental data;functional modulation;genetic elements;genetic oscillator;key regulatory model parameters;kinetic model;microfluidic flow reactors;modification;native transcriptional machinery;network properties;oscillator;passive transcriptional regulation;RNAP;scarce;simplified prototyping environment;steady-state conditions;study synthetic networks;well characterized toolbox | 10.1016/j.biochi.2013.11.025;10.1016/j.celrep.2016.07.061;10.1016/j.cels.2018.01.011;10.1016/j.mbs.2012.01.001;10.1016/j.mib.2016.07.009;10.1016/j.molcel.2005.10.015;10.1016/j.molcel.2017.12.007;10.1016/S0092-8674(00)80566-8;10.1021/acssynbio.5b00296;10.1021/acssynbio.6b00361;10.1021/sb200016s;10.1021/sb400131a;10.1021/sb400203p;10.1038/35002125;10.1038/35002131;10.1038/nature03508;10.1038/nature04640;10.1038/nature07389;10.1038/nature12051;10.1038/nrm2530;10.1038/nrm2698;10.1039/c2ib00102k;10.1046/j.1365-2958.1998.00990.x;10.1073/pnas.0600828103;10.1073/pnas.0800663105;10.1073/pnas.1311166110;10.1073/pnas.1710620114;10.1093/bioinformatics/btp358;10.1093/nar/28.18.3497;10.1093/nar/gkl462;10.1093/nar/gkq117;10.1093/nar/gky010;10.1101/gr.1207003;10.1103/PhysRevLett.108.018102;10.1126/science.1255550;10.1186/1754-1611-4-9;10.1186/s12918-017-0499-9;10.1371/journal.pcbi.1003845;10.3791/50762;10.7554/eLife.09771;[10.1038/NCHEM.2644, 10.1038/nchem.2644] | Radboud Univ Nijmegen | de Greef, T F A;Dubuc, E;Huck, W T S;Pieters, P A;van der Linden, A J;van Sluijs, B;Yelleswarapu, M | Yelleswarapu, M: Radboud Univ Nijmegen, Inst Mol & Mat, Heyendaalseweg 135, NL-6525 AJ Nijmegen, Netherlands | de Greef, Tom F. A.;Huck, Wilhelm T.S. | 024.001.035;024.003.013;677313 BioCircuit;723.016.003 | 43 | null | Netherlands | Eindhoven Univ Technol;Radboud Univ Nijmegen | Yelleswarapu, Maaruthy | Green Published, hybrid | BINDING;BIOLOGY;COMPETITION;EXPRESSION;MODELS;PLATFORM;RNA-POLYMERASE;TOOLBOX | Yelleswarapu, Maaruthy; van der Linden, Ardjan J.; van Sluijs, Bob; Pieters, Pascal A.; Dubuc, Emilien; de Greef, Tom F. A.; Huck, Wilhelm T. S.; | null | Eindhoven Univ Technol, Computat Biol Grp, Dept Biomed Engn, Inst Complex Mol Syst, POB 513, NL-5600 MB Eindhoven, Netherlands;Radboud Univ Nijmegen, Inst Mol & Mat, Heyendaalseweg 135, NL-6525 AJ Nijmegen, Netherlands | Eindhoven Univ Technol, Computat Biol Grp, Dept Biomed Engn, Inst Complex Mol Syst, POB 513, NL-5600 MB Eindhoven, Netherlands;Radboud Univ Nijmegen, Inst Mol & Mat, Heyendaalseweg 135, NL-6525 AJ Nijmegen, Netherlands | null | cell-free systems;competition-induced regulation;oscillations;Sigma factor;Synthetic biology | 12 | 1998;1999;2000;2003;2005;2006;2008;2009;2010;2012;2013;2014;2015;2016;2017;2018 | 24 | Eindhoven Univ Technol, Computat Biol Grp, Dept Biomed Engn, Inst Complex Mol Syst, POB 513, NL-5600 MB Eindhoven, Netherlands;Radboud Univ Nijmegen, Inst Mol & Mat, Heyendaalseweg 135, NL-6525 AJ Nijmegen, Netherlands | ACS Synth. Biol. | Huck, Wilhelm T S | AMER CHEMICAL SOC | ,;:;a;activator-repressor;algorithm;allowing;an;and;are;associated;behavior;by;cell-free;characterized;coli;coli-based;competing;complex;conditions;coupling;data;design;despite;driven;E.;elements;environment;evolutionary;examples;exhibit;experimental;factors;flow;functional;genetic;has;here;implemented;in;investigated;its;key;kinetic;machinery;means;microfluidic;model;modification;modulation;motif;native;network;networks;of;optimized;oscillator;oscillators;parameters;passive;presence;present;properties;prototyping;provides;quantify;rapidly;reactors;regulation;regulatory;RNAP;scarce;sigma;simplified;steady-state;study;synthetic;system;temporal;that;the;to;toolbox;transcription-translation;transcriptional;two;under;using;utilizes;was;we;well;with | Eindhoven Univ Technol;Radboud Univ Nijmegen | Cell-free transcription-translation provides a simplified prototyping environment to rapidly design and study synthetic networks. Despite the presence of a well characterized toolbox of genetic elements, examples of genetic networks that exhibit complex temporal behavior are scarce. Here, we present a genetic oscillator implemented in an E. coli-based cell-free system under steady-state conditions using microfluidic flow reactors. The oscillator has an activator-repressor motif that utilizes the native transcriptional machinery of E. coli: the RNAP and its associated sigma factors. We optimized a kinetic model with experimental data using an evolutionary algorithm to quantify the key regulatory model parameters. The functional modulation of the RNAP was investigated by coupling two oscillators driven by competing sigma factors, allowing the modification of network properties by means of passive transcriptional regulation. | B-1471-2012;I-8124-2014 | BINDING;BIOLOGY;COMPETITION;EXPRESSION;MODEL;PLATFORM;RNA-POLYMERASE;TOOLBOX | 1 | null | cell-free systems;competition-induced regulation;oscillator;sigma factors;Synthetic biology | 17 | BINDING;BIOLOGY;cell-free systems;COMPETITION;competition-induced regulation;EXPRESSION;MODEL;OSCILLATIONS;PLATFORM;RNA-POLYMERASE;SIGMA-FACTOR;Synthetic biology;TOOLBOX | WOS:000454568100020 | Eindhoven Univ Technol, Eindhoven, Netherlands;Radboud Univ Nijmegen, Nijmegen, Netherlands | Netherlands | 2,018 | null | 0000-0003-2032-0100 | null | null | English | null | ACS SYNTH BIOL;BIOCHIMIE;BIOINFORMATICS;BMC SYST BIOL;CELL;CELL REP;CELL SYST;CURR OPIN MICROBIOL;ELIFE;GENOME RES;INTEGR BIOL-UK;J Biol Eng;JOVE-J VIS EXP;MATH BIOSCI;MOL CELL;MOL MICROBIOL;NAT CHEM;NAT REV MOL CELL BIO;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PHYS REV LETT;PLOS COMPUT BIOL;SCI TRANSL MED;SCIENCE | de Greef, Tom F A;Dubuc, Emilien;Huck, Wilhelm T S;Pieters, Pascal A;van der Linden, Ardjan J;van Sluijs, Bob;Yelleswarapu, Maaruthy | 2024-03-11
ER | Adamala, K P;Angelici, B;Bervoets, I;Borkowski, O;Caschera, F;Dunlap, J C;Elowitz, M B;Farewell, A;Fung, E;Garamella, J;Gardner, T S;Grigorova, I L;Iskakova, M B;Karzbrun, E;Kim, P M;Maeda, H;Marshall, R;Mauri, M;Mooney, R A;Niederholtmeyer, H;Novák, B;O'Brien, E L;Paddon, C J;Park, J;Purnick, P E M;Qian, Y L;Raue, A;Ro, D K;Rondelez, Y;Shao, J;Shin Jonghyeon;Shin, J;Siegal-Gaskins, D;Smith, R W;Stricker, J;Stögbauer, T;Sun, Z Z;Tayar, A M;Weber, W;Xie, Z | HF9NG | Eindhoven, Netherlands;Nijmegen, Netherlands. | 30 | null | 2 | null | 30,408,412 | de Greef, Tom F A;Dubuc, Emilien;Huck, Wilhelm T S;Pieters, Pascal A;van der Linden, Ardjan J;van Sluijs, Bob;Yelleswarapu, Maaruthy | ACS SYNTH BIOL | Eindhoven, Netherlands;Nijmegen, Netherlands |
Cassey, P;Prowse, T A A;Ross, J V;Thomas, P Q;Wilkins, K E | 10.1016/j.mbs.2018.09.005 | null | 360 PARK AVE SOUTH, NEW YORK, NY 10010-1710 USA | 5gg5n5q6d2j626h2w3i54r5x2iz634t5go5y | Pest demography critically determines the viability of synthetic gene drives for population control | Univ Adelaide | null | Prowse, TAA (corresponding author), Univ Adelaide, Sch Math Sci, Adelaide, SA 5005, Australia. | null | Cassey, Phillip;Prowse, Thomas A A;Ross, Joshua V;Thomas, Paul Q;Wilkins, Kym E | Biology;Mathematical & Computational Biology | Safe Genes Program of the USA Defence Advanced Research Projects Agency [DARPA-16-59-SAFE-FP-005] | WOS | Prowse, T A A | Univ Adelaide, SA, Australia | 305 | control;critically;demography;determines;Drives;for;gene;of;pest;population;synthetic;the;viability | 1 | Cassey, Phillip;Prowse, Thomas;Ross, Joshua | ELSEVIER SCIENCE INC | Univ Adelaide, Ctr Appl Conservat Sci, Adelaide, SA 5005, Australia;Univ Adelaide, Robinson Res Inst, Adelaide, SA 5005, Australia;Univ Adelaide, Sch Biol Sci, Adelaide, SA 5005, Australia;Univ Adelaide, Sch Math Sci, Adelaide, SA 5005, Australia;Univ Adelaide, Sch Med, Adelaide, SA 5005, Australia | Article | Univ Adelaide | NEW YORK | null | null | Univ Adelaide | Safe Genes Program of the USA Defence Advanced Research Projects Agency | Prowse, TAA (corresponding author), Univ Adelaide, Sch Math Sci, Adelaide, SA 5005, Australia. | 169 | Cassey, Phillip;Prowse, Thomas A A;Ross, Joshua V;Thomas, Paul Q;Wilkins, Kym E | 26 | 5 | 447,476,600,015 | Safe Genes Program of the USA Defence Advanced Research Projects Agency [DARPA-16-59-SAFE-FP-005] | Australia | MATHEMATICAL BIOSCIENCES | Australia | null | null | Univ Adelaide, Sch Math Sci, Adelaide, SA 5005, Australia | 0025-5564 | Cassey, P;Prowse, T A A;Ross, J V;Thomas, P Q;Wilkins, K E | NOV | thomas.prowse@adelaide.edu.au | pest demography;population control;synthetic gene drives;viability | 5 | J | Life Sciences & Biomedicine - Other Topics;Mathematical & Computational Biology | 10%;birth-death model;capacity);control;controlling invasive rodents;CRISPR;CRISPR-based gene drives;demographic assumptions;demography;deterministic;developmental genes;DNA sequence;effect;efficiency;ERADICATION;evolution;expected progression;EXTINCTION;fertility;Gene drive;gene drives;gene-drive suppression;gene-strategies;HOMOLOGOUS RECOMBINATION;HOUSE MICE;inheritance;initial gene-drive introduction (up;invasive alien species;Invasive species;islands;lacking;little impact;low population density);MANIPULATE;mass-action reproduction results;MATERNAL NUTRITION;mating system;model outcomes;novel solution;optimistic eradication outcomes;pest demography;Pest eradication;polygynous breeding;polygyny;population;population control;Population modelling;population outcomes;population suppression;POPULATIONS;production;real-world applications;realistic assumption;reproductive Allee effect (reduced reproductive rates;resistance;resistant alleles;robust assessment;self-replication errors;SEX-RATIO;size;strength;suppression drives;synthetic biology;synthetic gene drives;technology's viability;TROJAN Y-CHROMOSOME;two different gene-drive strategies;two-sex;viability;WILD | Wilkins, K E | CRISPR;ERADICATION;EVOLUTION;EXTINCTION;Gene drive;HOUSE MICE;Invasive species;MANIPULATE;MATERNAL NUTRITION;Mating system;Pest eradication;Population modelling;resistance;SEX-RATIO;Synthetic biology;TROJAN Y-CHROMOSOME;WILD | 160 | [Wilkins, Kym E.; Prowse, Thomas A. A.; Ross, Joshua V.] Univ Adelaide, Sch Math Sci, Adelaide, SA 5005, Australia. [Cassey, Phillip] Univ Adelaide, Ctr Appl Conservat Sci, Adelaide, SA 5005, Australia. [Cassey, Phillip] Univ Adelaide, Sch Biol Sci, Adelaide, SA 5005, Australia. [Thomas, Paul Q.] Univ Adelaide, Robinson Res Inst, Adelaide, SA 5005, Australia. [Thomas, Paul Q.] Univ Adelaide, Sch Med, Adelaide, SA 5005, Australia. | This study was partially funded by the Safe Genes Program of the USA Defence Advanced Research Projects Agency (Grant DARPA-16-59-SAFE-FP-005 to PC & PQT). | 10%;birth-death model;capacity);control;controlling invasive rodents;CRISPR-based gene drives;demographic assumptions;demography;deterministic;developmental genes;DNA sequence;effect;efficiency;eradication;evolution;expected progression;fertility;gene drives;gene-drive suppression;gene-strategies;homologous recombination;inheritance;initial gene-drive introduction (up;invasive alien species;islands;lacking;little impact;low population density);mass-action reproduction results;model outcomes;novel solution;optimistic eradication outcomes;pest demography;pest eradication;polygynous breeding;polygyny;population;population outcomes;population suppression;populations;production;real-world applications;realistic assumption;reproductive Allee effect (reduced reproductive rates;resistance;resistant alleles;robust assessment;self-replication errors;size;strength;suppression drives;synthetic gene drives;technology's viability;two different gene-drive strategies;two-sex;viability | 10.1002/ecs2.1589;10.1006/jtbi.2002.3084;10.1007/s10144-009-0152-6;10.1007/s10530-013-0475-2;10.1007/s10530-013-0476-1;10.1016/0270-0255(83)90031-3;10.1016/j.jtbi.2005.11.032;10.1016/S0167-8809(00)00178-X;10.1016/S0169-5347(99)01683-3;10.1038/252297a0;10.1038/ncomms12485;10.1038/ncomms12986;10.1038/nrg.2015.34;10.1038/s41598-017-02744-7;10.1038/s41598-017-10633-2;10.1073/pnas.0330808100;10.1073/pnas.1521077112;10.1073/pnas.1611064114;10.1073/pnas.1720354115;10.1080/23299460.2017.1415587;10.1098/rsbl.2015.0623;10.1098/rspb.2002.2319;10.1098/rspb.2013.2549;10.1098/rspb.2017.0799;10.1098/rstb.1986.0081;10.1101/104877];10.1101/115618;10.1111/eva.12583;10.1111/geb.12228;10.1111/j.1523-1739.2007.00755.x;10.1111/mec.14215;10.1126/sciadv.1601964;10.1186/s12936-017-1932-7;10.1371/journal.pgen.1006796;10.15252/embr.201541337;10.1530/jrf.0.0780587;10.1530/jrf.0.1050193;10.1534/genetics.116.197285;10.1534/genetics.116.197632;10.17226/23405;10.1890/070151;10.3897/neobiota.29.6959;10.4172/2155-9627.1000266];10.7554/eLife.03401 | Univ Adelaide | Cassey, P;Prowse, T A A;Ross, J V;Thomas, P Q;Wilkins, K E | Wilkins, K E: Univ Adelaide, Sch Math Sci, Adelaide, SA 5005, Australia | Ross, Joshua V | DARPA-16-59-SAFE-FP-005 | 51 | null | Australia | Univ Adelaide | Wilkins, Kym E | hybrid | ERADICATION;EVOLUTION;EXTINCTION;HOUSE MICE;MANIPULATE;MATERNAL NUTRITION;RESISTANCE;SEX-RATIO;TROJAN Y-CHROMOSOME;WILD | Wilkins, Kym E.; Prowse, Thomas A. A.; Cassey, Phillip; Thomas, Paul Q.; Ross, Joshua V.; | null | Univ Adelaide, Ctr Appl Conservat Sci, Adelaide, SA 5005, Australia;Univ Adelaide, Robinson Res Inst, Adelaide, SA 5005, Australia;Univ Adelaide, Sch Biol Sci, Adelaide, SA 5005, Australia;Univ Adelaide, Sch Math Sci, Adelaide, SA 5005, Australia;Univ Adelaide, Sch Med, Adelaide, SA 5005, Australia | Univ Adelaide, Ctr Appl Conservat Sci, Adelaide, SA 5005, Australia;Univ Adelaide, Robinson Res Inst, Adelaide, SA 5005, Australia;Univ Adelaide, Sch Biol Sci, Adelaide, SA 5005, Australia;Univ Adelaide, Sch Math Sci, Adelaide, SA 5005, Australia;Univ Adelaide, Sch Med, Adelaide, SA 5005, Australia | 1879-3134 | CRISPR;Gene drive;Invasive species;Mating system;Pest eradication;Population modelling;Synthetic biology | null | 1974;1983;1986;1995;1999;2001;2002;2003;2004;2006;2007;2008;2009;2013;2014;2015;2016;2017;2018 | 16 | Univ Adelaide, Sch Math Sci, Adelaide, SA 5005, Australia | Math. Biosci. | Ross, Joshua V | ELSEVIER SCIENCE INC | (reduced;(up;,;10%;;;a;adequately;affect;alien;Allee;alleles;also;although;and;applications;assessed;assessment;assumed;assumption;assumptions;at;be;before;bias;birth-death;both;breeding;by;can;capacity);carrying;compared;comprise;control;controlling;could;CRISPR-based;critical;currently;demographic;demography;density);deterministic;developmental;different;DNA;drives;due;effect;efficiency;eradication;errors;evolution;expected;failed;fertility;following;for;further;gene;gene-drive;gene-strategies;genes;had;highly;homologous;how;however;impact;impacts;in;included;increasing;inheritance;initial;introduction;invasive;investigate;is;islands;lacking;little;low;mass-action;model;more;novel;of;offer;on;optimistic;or;outcomes;overly;own;pest;polygynous;polygyny;population;populations;positioned;positively;production;progression;rates;real-world;realistic;recombination;replicated;reproduction;reproductive;resistance;resistant;results;robust;rodents;self-replication;sensitive;sequence;show;silence;since;size;solution;species;strategies;strength;suppression;synthetic;targeted;technology's;that;the;their;they;this;threatens;through;to;two;two-sex;understanding;unless;used;viability;was;we;were;when | Univ Adelaide | Synthetic gene drives offer a novel solution for the control of invasive alien species. CRISPR-based gene drives can positively bias their own inheritance, and comprise a DNA sequence that is replicated by homologous recombination. Since gene drives can be positioned to silence fertility or developmental genes, they could be used for population suppression. However, the production of resistant alleles following self-replication errors threatens the technology's viability for pest eradication in real-world applications. Further, a robust assessment of how pest demography impacts the expected progression of gene drives through populations is currently lacking. We used a deterministic, two-sex, birth-death model to investigate how demographic assumptions affect the efficiency of suppression drives for controlling invasive rodents on islands, for two different gene-drive strategies. We show that mass-action reproduction results in overly optimistic eradication outcomes when compared to the more realistic assumption of polygynous breeding. When polygyny was assumed, both gene-strategies failed due to the evolution of resistance unless a reproductive Allee effect (reduced reproductive rates at low population density) was also included; although model outcomes were highly sensitive to the strength of this effect. Increasing the size of the initial gene-drive introduction (up to 10% of carrying capacity) had little impact on population outcomes. Understanding the demography of a population targeted for eradication is critical before the viability of gene-drive suppression can be adequately assessed. | C-2761-2009 | ERADICATION;EVOLUTION;EXTINCTION;HOUSE MICE;MANIPULATION;MATERNAL NUTRITION;RESISTANCE;SEX-RATIO;TROJAN Y-CHROMOSOME;WILD | 0 | null | CRISPR;Gene drive;Invasive species;Mating system;Pest eradication;Population modelling;Synthetic biology | 10 | CRISPR;ERADICATION;EVOLUTION;EXTINCTION;Gene drive;HOUSE MICE;Invasive species;MANIPULATION;MATERNAL NUTRITION;Mating system;Pest eradication;Population modelling;resistance;SEX-RATIO;Synthetic biology;TROJAN Y-CHROMOSOME;WILD | WOS:000447476600015 | UNIV ADELAIDE, SA, AUSTRALIA | Australia | 2,018 | null | 0000-0002-2626-0172;0000-0002-4093-767X;0000-0002-9918-8167 | null | null | English | null | AGR ECOSYST ENVIRON;BIOD INTR SPEC S AUS;BIOL INVASIONS;BIOL LETTERS;BioRxiv;CONSERV BIOL;COUNTING COST IMPACT;DAISY CHAIN GENE DRI;ECOSPHERE;ELIFE;EMBO REP;ERADICATIONS VERTEBR;EVOL APPL;FACT SHEET INV SPEC;FRONT ECOL ENVIRON;GENE DRIVES HORIZON;GENETICS;GLOBAL ECOL BIOGEOGR;J REPROD FERTIL;J RESPONSIBLE INNOV;J THEOR BIOL;MALARIA J;MATH MODELLING;MOL ECOL;NAT COMMUN;NAT REV GENET;NATURE;NEOBIOTA;P NATL ACAD SCI USA;P ROY SOC B-BIOL SCI;PHILOS T ROY SOC B;PLOS GENET;POPUL ECOL;SCI ADV;SCI REP-UK;SYNTH BIOL;SYNTH GEN DRIV AUSTR;TRENDS ECOL EVOL | Cassey, Phillip;Prowse, Thomas A A;Ross, Joshua V;Thomas, Paul Q;Wilkins, Kym E | 2024-03-11
ER | Australian Academy Of Science;Backus, G A;Beaghton, A;Bellard, C;Boukal, D S;Bradshaw, C J A;Burt, A;Caplan, A L;Champer, J;Courchamp, F;Crowl, T A;Department Of The Environment And Heritage;Dhole, S;Early, R;Eckhoff, P A;Esvelt, K M;Gantz, V M;Gemmell, N J;Gregory S.;Gutierrez, J B;Hoffmann, B D;Howald, G;Kramer, A M;Manser, A;Marshall, J M;Mcleod, R;Meikle, D B;Min J.;Min John.;National Academies Of Sciences Engineering And Medicine;Nentwig W.;Noble, C;Pimentel, D;Prowse, T A A;Rivers, J P W;Rosen, K H;Rosenfeld, C S;Smidler A.;Teem, J L;Thompson, P B;Unckless, R L;Usher, M B;Vella, M R;Yunta E. | GX1KQ | SA, Australia | 18 | null | 1 | null | 30,219,282 | Cassey, Phillip;Prowse, Thomas A A;Ross, Joshua V;Thomas, Paul Q;Wilkins, Kym E | MATH BIOSCI | SA, AUSTRALIA |
Cai, Y Z;Dai, J B;Schindler, D | 10.1016/j.cbpa.2018.04.002 | null | THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, OXON, ENGLAND | 2r4v5k3e33d5i3i5m5l435n584g5564715k4n5r | Synthetic genomics: a new venture to dissect genome fundamentals and engineer new functions | Univ Manchester | null | Cai, YZ (corresponding author), Chinese Acad Sci, Shenzhen Inst Adv Technol, Inst Synthet Biol, Ctr Synthet Genom, Shenzhen 518055, Peoples R China.;Cai, YZ (corresponding author), Univ Manchester, Manchester Inst Biotechnol, 131 Princess St, Manchester M1 7DN, Lancs, England. | null | Cai, Yizhi;Dai, Junbiao;Schindler, Daniel | Biochemistry & Molecular Biology;Biophysics | Biotechnology and Biological Sciences Research Council [BB/P02114X/1]; University of Manchester President's Award for Research Excellence; National Natural Science Foundation of China [31471254, 31725002]; Bureau of International Cooperation, Chinese Academy of Sciences [172644KYSB20170042]; BBSRC [BB/M005690/1, BB/M005690/2, BB/M025640/1, BB/P02114X/1] Funding Source: UKRI; EPSRC [EP/P017401/1] Funding Source: UKRI | WOS | Cai, Y Z | Chinese Acad Sci, Shenzhen, Peoples R China;Univ Manchester, Lancs, England | 46 | :;a;and;dissect;engineer;functions;fundamentals;genome;genomics;new;synthetic;to;venture | 2 | Cai, Yizhi;Dai, Junbiao;Schindler, Daniel | ELSEVIER SCI LTD | Chinese Acad Sci, Shenzhen Inst Adv Technol, Inst Synthet Biol, Ctr Synthet Genom, Shenzhen 518055, Peoples R China;Univ Manchester, Manchester Inst Biotechnol, 131 Princess St, Manchester M1 7DN, Lancs, England;Univ Manchester, Manchester Inst Biotechnol, 131 Princess St, Manchester M1 7DN, Lancs, England.; Cai, YZ (corresponding author), Chinese Acad Sci, Shenzhen Inst Adv Technol, Inst Synthet Biol, Ctr Synthet Genom, Shenzhen 518055, Peoples R China | Review | Chinese Acad Sci;Univ Manchester | OXFORD | null | null | Chinese Acad Sci;Univ Manchester | BBSRC;Biotechnology and Biological Sciences Research Council;Bureau of International Cooperation, Chinese Academy of Sciences;EPSRC;National Natural Science Foundation of China;University of Manchester President's Award for Research Excellence | Cai, YZ (corresponding author), Univ Manchester, Manchester Inst Biotechnol, 131 Princess St, Manchester M1 7DN, Lancs, England.; Cai, YZ (corresponding author), Chinese Acad Sci, Shenzhen Inst Adv Technol, Inst Synthet Biol, Ctr Synthet Genom, Shenzhen 518055, Peoples R China. | 62 | Cai, Yizhi;Dai, Junbiao;Schindler, Daniel | 15 | 2 | 449,131,300,010 | BBSRC [BB/M005690/1, BB/M005690/2, BB/M025640/1, BB/P02114X/1] Funding Source: UKRI;Biotechnology and Biological Sciences Research Council [BB/P02114X/1];Bureau of International Cooperation, Chinese Academy of Sciences [172644KYSB20170042];EPSRC [EP/P017401/1] Funding Source: UKRI;National Natural Science Foundation of China [31471254, 31725002];University of Manchester President's Award for Research Excellence | China;UK | CURRENT OPINION IN CHEMICAL BIOLOGY | China;UK | null | null | Univ Manchester, Manchester Inst Biotechnol, 131 Princess St, Manchester M1 7DN, Lancs, England | 1367-5931 | Cai, Y Z;Dai, J B;Schindler, D | OCT | yizhi.cai@manchester.ac.uk | engineer new functions;genome fundamentals;new venture;synthetic genomics | 3 | J | Biochemistry & Molecular Biology;Biophysics | 10 000 bps;1970s;assembly;available;CHEMICAL-SYNTHESIS;custom made DNA;diversity;DNA;DNA synthesis;DNA-reading projects;efficiency;engineer new functions;engineer novel biological functions;few weeks;first synthetic gene;functionalities;genome fundamentals;large-scale projects;made-to-order DNA sequence synthesis;magnitude;new paradigms;new venture;past years;price;researchers;several orders;similar effects;steep drop;synthetic chromosomes;synthetic DNA;synthetic genomics;synthetic genomics opens;technologies;today;turnaround times;vivo | Schindler, D | CHEMICAL-SYNTHESIS;DIVERSITY | 56 | [Schindler, Daniel; Cai, Yizhi] Univ Manchester, Manchester Inst Biotechnol, 131 Princess St, Manchester M1 7DN, Lancs, England. [Dai, Junbiao; Cai, Yizhi] Chinese Acad Sci, Shenzhen Inst Adv Technol, Inst Synthet Biol, Ctr Synthet Genom, Shenzhen 518055, Peoples R China. | The work in the UK is funded through a Biotechnology and Biological Sciences Research Council grant (BB/P02114X/1), and the University of Manchester President's Award for Research Excellence to YC. This work is also supported by the National Natural Science Foundation of China (31471254 and 31725002) and partially supported by the Bureau of International Cooperation, Chinese Academy of Sciences (172644KYSB20170042) to JD. | 10 000 bps;1970s;assembly;available;custom made DNA;DNA;DNA synthesis;DNA-reading projects;efficiency;engineer novel biological functions;few weeks;first synthetic gene;functionalities;genome fundamentals;large-scale projects;made-to-order DNA sequence synthesis;magnitude;new paradigms;past years;price;researchers;several orders;similar effects;steep drop;synthetic chromosomes;synthetic DNA;synthetic genomics opens;technologies;today;turnaround times;vivo | 10.1016/j.pt.2004.11.010;10.1016/j.virusres.2009.02.009;10.1038/227027a0;10.1038/nature10403;10.1038/nmeth.1515;10.1073/pnas.0808116105;10.1073/pnas.1110889108;10.1073/pnas.1715365114;10.1073/pnas.2237126100;10.1073/pnas.74.12.5463;10.1089/hs.2017.0061;10.1093/femsre/fuv030;10.1101/gr.193433.115;10.1111/1751-7915.12384;10.1126/science.1072266;10.1126/science.1151721;10.1126/science.1190719;10.1126/science.1249252;10.1126/science.2999980;10.1126/science.328.5981.958;10.1126/science.aad6253;10.1126/science.aaf3639;10.1126/science.aaf3981;10.1126/science.aaf4557;10.1126/science.aaf4597;10.1126/science.aaf4704;10.1126/science.aaf4706;10.1126/science.aaf4791;10.1126/science.aaf6850;10.1371/journal.ppat.0030010 | Univ Manchester | Cai, Y Z;Dai, J B;Schindler, D | Schindler, D: Univ Manchester, Manchester Inst Biotechnol, 131 Princess St, Manchester M1 7DN, Lancs, England | Cai, Yizhi;Dai, Junbiao;Schindler, Daniel | 172644KYSB20170042;31471254;31725002;BB/M005690/1;BB/M005690/2;BB/M025640/1;BB/P02114X/1;EP/P017401/1 | 35 | null | UK | Chinese Acad Sci;Univ Manchester | Schindler, Daniel | Green Submitted, Green Published, hybrid | CHEMICAL-SYNTHESIS;DIVERSITY | Schindler, Daniel; Dai, Junbiao; Cai, Yizhi; | null | Chinese Acad Sci, Shenzhen Inst Adv Technol, Inst Synthet Biol, Ctr Synthet Genom, Shenzhen 518055, Peoples R China;Univ Manchester, Manchester Inst Biotechnol, 131 Princess St, Manchester M1 7DN, Lancs, England | Chinese Acad Sci, Shenzhen Inst Adv Technol, Inst Synthet Biol, Ctr Synthet Genom, Shenzhen 518055, Peoples R China;Univ Manchester, Manchester Inst Biotechnol, 131 Princess St, Manchester M1 7DN, Lancs, England | 1879-0402 | null | null | 1970;1977;1985;1992;2002;2003;2005;2007;2008;2009;2010;2011;2014;2015;2016;2017 | 22 | Chinese Acad Sci, Shenzhen Inst Adv Technol, Inst Synthet Biol, Ctr Synthet Genom, Shenzhen 518055, Peoples R China;Univ Manchester, Manchester Inst Biotechnol, 131 Princess St, Manchester M1 7DN, Lancs, England | Curr. Opin. Chem. Biol. | Cai, Yizhi | ELSEVIER SCI LTD | ,;000;10;1970s;a;advances;and;are;assembly;available;biological;bps;by;capacity;characterize;chromosomes;commercially;custom;DNA;DNA-reading;drop;effects;efficiency;enables;engineer;few;first;for;functionalities;functions;fundamentals;gene;genome;genomics;has;in;increased;large-scale;made;made-to-order;magnitude;more;new;novel;observed;of;opens;orders;over;paradigms;past;perform;price;projects;researchers;resulted;sequence;sequences;sequencing;several;similar;since;steep;study;synthesis;synthesized;synthetic;technologies;than;the;their;this;times;to;today;turnaround;underpin;up;vivo;was;weeks;were;which;with;write;years | Chinese Acad Sci;Univ Manchester | Since the first synthetic gene was synthesized in 1970s, the efficiency and the capacity of made-to-order DNA sequence synthesis has increased by several orders of magnitude. Advances in DNA synthesis and assembly over the past years has resulted in a steep drop in price for custom made DNA. Similar effects were observed in DNA sequencing technologies which underpin DNA-reading projects. Today, synthetic DNA sequences with more than 10 000 bps and turnaround times of a few weeks are commercially available. This enables researchers to perform large-scale projects to write synthetic chromosomes and characterize their functionalities in vivo. Synthetic genomics opens up new paradigms to study the genome fundamentals and engineer novel biological functions. | A-3550-2010;AAB-8328-2021;JRX-6098-2023 | CHEMICAL-SYNTHESIS;DIVERSITY | 3 | null | null | 7 | CHEMICAL-SYNTHESIS;DIVERSITY | WOS:000449131300010 | Chinese Acad Sci, Shenzhen, Peoples R China;Univ Manchester, Lancs, England | China;UK | 2,018 | null | 0000-0001-7423-6540;0000-0002-5299-4700;0000-0003-1663-2865 | null | null | English | null | BioRxiv;BIOTECHNOLOGY;CISC VIS NETW IND GL;FEMS MICROBIOL REV;GENOME RES;HEALTH SECUR;MICROB BIOTECHNOL;NAT METHODS;NATURE;P NATL ACAD SCI US;P NATL ACAD SCI USA;PLOS PATHOG;SCIENCE;TRENDS PARASITOL;VIRUS RES | Cai, Yizhi;Dai, Junbiao;Schindler, Daniel | 2024-03-11
ER | Agarwal, K L;Annaluru, N;Arslan, D;Becker, M M;Boeke, J D;Cello, J;Danchin, A;Dymond, J S;Finsterbusch, T;Gibson, D G;Henriquez, F L;Hutchison, C A;Jain M.;Klein R. M.;Koblentz, G D;Lee, Y N;Mercy, G;Mitchell, L A;Oldfield, L M;Ostrov, N;Pennisi, E;Richardson, S M;Saiki, R K;Sanger, F;Schindler, D;Shen, Y;Smith, H O;Wu, Y;Xie, Z X;Zhang, W M | GZ1MD | Lancs, England.;Shenzhen, Peoples R China | 23 | null | 2 | null | 29,751,161 | Cai, Yizhi;Dai, Junbiao;Schindler, Daniel | CURR OPIN CHEM BIOL | Lancs, England;Shenzhen, Peoples R China |
Date, M;Haruna, K;Iraha, F;Mukai, T;Ohtake, K;Sakamoto, K;Takahashi, M;Yokoyama, K | 10.1021/acssynbio.8b00157 | null | 1155 16TH ST, NW, WASHINGTON, DC 20036 USA | 351a2u743455g582x2d5j6v16za5h625r5k61 | Engineering an Automaturing Transglutaminase with Enhanced Thermostability by Genetic Code Expansion with Two Codon Reassignments | RIKEN | null | Sakamoto, K (corresponding author), RIKEN, Div Struct & Synthet Biol, Ctr Life Sci Technol CLST, 1-7-22 Suehiro Cho, Yokohama, Kanagawa 2300045, Japan.;Sakamoto, K (corresponding author), RIKEN, Lab Nonnat Amino Acid Technol, Ctr Biosyst Dynam Res BDR, 1-7-22 Suehiro Cho, Yokohama, Kanagawa 2300045, Japan. | null | Date, Masayo;Haruna, Ken-ichi;Iraha, Fumie;Mukai, Takahito;Ohtake, Kazumasa;Sakamoto, Kensaku;Takahashi, Mihoko;Yokoyama, Keiichi | Biochemical Research Methods | JSPS KAKENHI [26291035, 16K21631]; Grants-in-Aid for Scientific Research [16K21631, 26291035] Funding Source: KAKEN | WOS | Sakamoto, K | Ajinomoto Co Inc, Kanagawa, Japan;RIKEN, Kanagawa, Japan;Rikkyo Univ, Tokyo, Japan | 7 | an;Automaturing;by;Code;codon;engineering;enhanced;Expansion;genetic;Reassignments;Thermostability;Transglutaminase;two;with | 1 | null | AMER CHEMICAL SOC | Ajinomoto Co Inc, Inst Innovat, Kawasaki Ku, 1-1 Suzuki Cho, Kawasaki, Kanagawa 2108681, Japan;RIKEN, Div Struct & Synthet Biol, Ctr Life Sci Technol CLST, 1-7-22 Suehiro Cho, Yokohama, Kanagawa 2300045, Japan;RIKEN, Div Struct & Synthet Biol, Ctr Life Sci Technol CLST, 1-7-22 Suehiro Cho, Yokohama, Kanagawa 2300045, Japan.; Sakamoto, K (corresponding author), RIKEN, Lab Nonnat Amino Acid Technol, Ctr Biosyst Dynam Res BDR, 1-7-22 Suehiro Cho, Yokohama, Kanagawa 2300045, Japan;RIKEN, Lab Nonnat Amino Acid Technol, Ctr Biosyst Dynam Res BDR, 1-7-22 Suehiro Cho, Yokohama, Kanagawa 2300045, Japan;Rikkyo Univ, Coll Sci, Dept Life Sci, Toshima Ku, 3-34-1 Nishi Ikebukuro, Tokyo 1718501, Japan | Article | RIKEN | WASHINGTON | null | null | Ajinomoto Co Inc;Div Struct & Synthet Biol;RIKEN;Rikkyo Univ | Grants-in-Aid for Scientific Research;JSPS KAKENHI | Sakamoto, K (corresponding author), RIKEN, Div Struct & Synthet Biol, Ctr Life Sci Technol CLST, 1-7-22 Suehiro Cho, Yokohama, Kanagawa 2300045, Japan.; Sakamoto, K (corresponding author), RIKEN, Lab Nonnat Amino Acid Technol, Ctr Biosyst Dynam Res BDR, 1-7-22 Suehiro Cho, Yokohama, Kanagawa 2300045, Japan. | 2176 | Date, Masayo;Haruna, Ken-ichi;Iraha, Fumie;Mukai, Takahito;Ohtake, Kazumasa;Sakamoto, Kensaku;Takahashi, Mihoko;Yokoyama, Keiichi | 21 | 4 | 445,711,300,021 | Grants-in-Aid for Scientific Research [16K21631, 26291035] Funding Source: KAKEN;JSPS KAKENHI [26291035, 16K21631] | Japan | ACS SYNTHETIC BIOLOGY | Japan | null | null | RIKEN, Div Struct & Synthet Biol, Ctr Life Sci Technol CLST, 1-7-22 Suehiro Cho, Yokohama, Kanagawa 2300045, Japan | 2161-5063 | Date, M;Haruna, K;Iraha, F;Mukai, T;Ohtake, K;Sakamoto, K;Takahashi, M;Yokoyama, K | SEP | kensaku.sakamoto@riken.jp | Automaturing Transglutaminase;Enhanced Thermostability;Genetic Code Expansion;Two Codon Reassignments | 8 | J | Biochemistry & Molecular Biology | 146;15 tyrosine residues;171;217;3-chloro-L-tyrosine;3-chlorotyrosine;3-chlorotyrosines;310;34;60 degrees C.;62;75;a-hydroxy acid analogue;AGG codon;alkaline conditions (pH 11.0);AlocKOH;ALPHA-HYDROXY ACID;AMINO-ACIDS;Automaturing Transglutaminase;autonomous maturation;chlorotyrosine;end;Enhanced Thermostability;enzyme;enzymes;Escherichia coli strain;ESCHERICHIA-COLI;ester bond;first amino acid;Genetic Code Expansion;GLUTAMICUM;half-life 5.1-fold;hydroxy acid;in-frame UAG codons;IN-VIVO;incorporated two types;increase thermostability;industrial enzyme;main chain;MICROBIAL TRANSGLUTAMINASE;microbial transglutaminase (MTG);MTG;MTG variant;MTG variants;multiple codon reassignments;N-epsilon-allyloxycarbonyl-L-lysine (AlocKOH);N-terminal inhibitory peptide;neutral effects;neutral ones;novel designs;one;positions 20;positions 24;present study;PRO-TRANSGLUTAMINASE;pyrrolysyl-tRNA synthetase;recognition;response;results;SELF-CLEAVAGE;self-cleaved;seven substitutions;stabilized variant;Streptoverti-cillium mobaraense;STREPTOVERTICILLIUM-MOBARAENSE TRANSGLUTAMINASE;synthetic components;synthetic genetic code;synthetic genetic codes;thermostabilized MTG;TRANSFER-RNA-SYNTHETASE;Two Codon Reassignments;two stabilizing chlorinations;two substitutions;utility;wild alpha-type enzyme | Ohtake, K | AGG codon;ALPHA-HYDROXY ACID;AMINO-ACIDS;chlorotyrosine;ESCHERICHIA-COLI;GLUTAMICUM;hydroxy acid;IN-VIVO;MICROBIAL TRANSGLUTAMINASE;PRO-TRANSGLUTAMINASE;pyrrolysyl-tRNA synthetase;RECOGNITION;SELF-CLEAVAGE;STREPTOVERTICILLIUM-MOBARAENSE TRANSGLUTAMINASE;TRANSFER-RNA-SYNTHETASE | 2170 | [Ohtake, Kazumasa; Mukai, Takahito; Iraha, Fumie; Takahashi, Mihoko; Sakamoto, Kensaku] RIKEN, Div Struct & Synthet Biol, Ctr Life Sci Technol CLST, 1-7-22 Suehiro Cho, Yokohama, Kanagawa 2300045, Japan. [Ohtake, Kazumasa; Takahashi, Mihoko; Sakamoto, Kensaku] RIKEN, Lab Nonnat Amino Acid Technol, Ctr Biosyst Dynam Res BDR, 1-7-22 Suehiro Cho, Yokohama, Kanagawa 2300045, Japan. [Haruna, Ken-ichi; Date, Masayo; Yokoyama, Keiichi] Ajinomoto Co Inc, Inst Innovat, Kawasaki Ku, 1-1 Suzuki Cho, Kawasaki, Kanagawa 2108681, Japan. [Mukai, Takahito] Rikkyo Univ, Coll Sci, Dept Life Sci, Toshima Ku, 3-34-1 Nishi Ikebukuro, Tokyo 1718501, Japan. | This work was supported in part by JSPS KAKENHI Grants 26291035 to K.S. and 16K21631 to K.O. | 146;15 tyrosine residues;171;217;3-chloro-L-tyrosine;3-chlorotyrosine;3-chlorotyrosines;310;34;60 degrees C.;62;75;a-hydroxy acid analogue;AGG codon;alkaline conditions (pH 11.0);AlocKOH;autonomous maturation;end;enzyme;enzymes;Escherichia coli strain;ester bond;first amino acid;half-life 5.1-fold;in-frame UAG codons;incorporated two types;increase thermostability;industrial enzyme;main chain;microbial transglutaminase (MTG);MTG;MTG variant;MTG variants;multiple codon reassignments;N-epsilon-allyloxycarbonyl-L-lysine (AlocKOH);N-terminal inhibitory peptide;neutral effects;neutral ones;novel designs;one;positions 20;positions 24;present study;response;results;self-cleaved;seven substitutions;stabilized variant;Streptoverti-cillium mobaraense;synthetic components;synthetic genetic code;synthetic genetic codes;thermostabilized MTG;two codon reassignments;two stabilizing chlorinations;two substitutions;utility;wild alpha-type enzyme | 10.1002/anie.200704074;10.1007/s00726-011-1015-y;10.1016/j.bbrc.2008.04.164;10.1016/j.bbrc.2011.07.020;10.1016/j.chembiol.2008.10.004;10.1016/j.enzmictec.2003.08.004;10.1016/j.enzmictec.2006.10.036;10.1016/j.jbiotec.2008.06.005;10.1016/j.jmb.2008.02.045;10.1016/j.jmb.2008.11.059;10.1016/j.str.2009.01.008;10.1016/S1046-5928(02)00536-3;10.1021/acs.bioconjchem.5b00602;10.1021/cb300020s;10.1021/jacs.5b04681;10.1038/nchembio.657;10.1038/srep09699;10.1038/srep09762;10.1074/jbc.M203933200;10.1093/nar/gkq707;10.1093/nar/gkv787;10.1111/j.1365-2621.2002.tb08819.x;10.1126/science.1205822;10.1128/AEM.69.1.358-366.2003;10.1128/AEM.69.5.3011-3014.2003;10.1529/biophysj.105.064485 | RIKEN | Date, M;Haruna, K;Iraha, F;Mukai, T;Ohtake, K;Sakamoto, K;Takahashi, M;Yokoyama, K | Ohtake, K: RIKEN, Div Struct & Synthet Biol, Ctr Life Sci Technol CLST, 1-7-22 Suehiro Cho, Yokohama, Kanagawa 2300045, Japan | Sakamoto, Kensaku | 16K21631;26291035 | 27 | null | Japan | Ajinomoto Co Inc;RIKEN;Rikkyo Univ | Ohtake, Kazumasa | null | ALPHA-HYDROXY ACID;AMINO-ACIDS;ESCHERICHIA-COLI;GLUTAMICUM;IN-VIVO;MICROBIAL TRANSGLUTAMINASE;PRO-TRANSGLUTAMINASE;RECOGNITION;STREPTOVERTICILLIUM-MOBARAENSE TRANSGLUTAMINASE;TRANSFER-RNA-SYNTHETASE | Ohtake, Kazumasa; Mukai, Takahito; Iraha, Fumie; Takahashi, Mihoko; Haruna, Ken-ichi; Date, Masayo; Yokoyama, Keiichi; Sakamoto, Kensaku; | null | Ajinomoto Co Inc, Inst Innovat, Kawasaki Ku, 1-1 Suzuki Cho, Kawasaki, Kanagawa 2108681, Japan;RIKEN, Div Struct & Synthet Biol, Ctr Life Sci Technol CLST, 1-7-22 Suehiro Cho, Yokohama, Kanagawa 2300045, Japan;RIKEN, Lab Nonnat Amino Acid Technol, Ctr Biosyst Dynam Res BDR, 1-7-22 Suehiro Cho, Yokohama, Kanagawa 2300045, Japan;Rikkyo Univ, Coll Sci, Dept Life Sci, Toshima Ku, 3-34-1 Nishi Ikebukuro, Tokyo 1718501, Japan | Ajinomoto Co Inc, Inst Innovat, Kawasaki Ku, 1-1 Suzuki Cho, Kawasaki, Kanagawa 2108681, Japan;RIKEN, Div Struct & Synthet Biol, Ctr Life Sci Technol CLST, 1-7-22 Suehiro Cho, Yokohama, Kanagawa 2300045, Japan;RIKEN, Lab Nonnat Amino Acid Technol, Ctr Biosyst Dynam Res BDR, 1-7-22 Suehiro Cho, Yokohama, Kanagawa 2300045, Japan;Rikkyo Univ, Coll Sci, Dept Life Sci, Toshima Ku, 3-34-1 Nishi Ikebukuro, Tokyo 1718501, Japan | null | self-cleavage;AGG codon;chlorotyrosine;hydroxy acid;pyrrolysyl-tRNA synthetase | 9 | 1991;2002;2003;2004;2005;2007;2008;2009;2010;2011;2012;2015;2016 | 22 | RIKEN, Div Struct & Synthet Biol, Ctr Life Sci Technol CLST, 1-7-22 Suehiro Cho, Yokohama, Kanagawa 2300045, Japan;RIKEN, Lab Nonnat Amino Acid Technol, Ctr Biosyst Dynam Res BDR, 1-7-22 Suehiro Cho, Yokohama, Kanagawa 2300045, Japan | ACS Synth. Biol. | Sakamoto, Kensaku | AMER CHEMICAL SOC | (AlocKOH);(MTG);(pH;,;11.0);146;15;171;20;217;24;3-chloro-L-tyrosine;3-chlorotyrosine;3-chlorotyrosines;310;34;5.1-fold;60;62;75;a;a-hydroxy;achieving;acid;AGG;alkaline;AlocKOH;alpha-type;amino;an;analogue;and;at;autonomous;be;bond;both;by;C.;chain;chlorinations;code;codes;codon;codons;coli;combined;components;conditions;contain;containing;degrees;designs;developing;each;effects;efficiently;end;engineered;enhance;enzyme;enzymes;Escherichia;ester;exhibited;exhibiting;first;for;found;from;further;genetic;half-life;have;in;in-frame;incorporated;incorporating;increase;industrial;inhibitory;into;longer;main;maturation;microbial;mobaraense;modified;most;MTG;multiple;N-epsilon-allyloxycarbonyl-L-lysine;N-terminal;neutral;next;novel;of;one;ones;peptide;positions;present;previously;reassignments;residues;response;results;self-cleaved;separately;seven;simultaneously;specified;stabilized;stabilizing;strain;Streptoverti-cillium;study;substitute;substitutions;suggested;synthesizing;synthetic;than;that;the;then;thermostability;thermostabilized;these;this;thus;to;transglutaminase;two;types;tyrosine;UAG;under;used;useful;utility;variant;variants;was;we;were;while;wild;with;would | RIKEN | In the present study, we simultaneously incorporated two types of synthetic components into microbial transglutaminase (MTG) from Streptoverti-cillium mobaraense to enhance the utility of this industrial enzyme. The first amino acid, 3-chloro-L-tyrosine, was incorporated into MTG in response to in-frame UAG codons to substitute for the 15 tyrosine residues separately. The two substitutions at positions 20 and 62 were found to each increase thermostability of the enzyme, while the seven substitutions at positions 24, 34, 75, 146, 171, 217, and 310 exhibited neutral effects. Then, these two stabilizing chlorinations were combined with one of the neutral ones, and the most stabilized variant was found to contain 3-chlorotyrosines at positions 20, 62, and 171, exhibiting a half-life 5.1-fold longer than that of the wild alpha-type enzyme at 60 degrees C. Next, this MTG variant was further modified by incorporating the a-hydroxy acid analogue of N-epsilon-allyloxycarbonyl-L-lysine (AlocKOH), specified by the AGG codon, at the end of the N-terminal inhibitory peptide. We used an Escherichia coli strain previously engineered to have a synthetic genetic code with two codon reassignments for synthesizing MTG variants containing both 3-chlorotyrosine and AlocKOH. The ester bond, thus incorporated into the main chain, efficiently self-cleaved under alkaline conditions (pH 11.0), achieving the autonomous maturation of the thermostabilized MTG. The results suggested that synthetic genetic codes with multiple codon reassignments would be useful for developing the novel designs of enzymes. | N-7496-2015 | ALPHA-HYDROXY ACID;AMINO-ACIDS;ESCHERICHIA-COLI;GLUTAMICUM;IN-VIVO;MICROBIAL TRANSGLUTAMINASE;PRO-TRANSGLUTAMINASE;RECOGNITION;STREPTOVERTICILLIUM-MOBARAENSE TRANSGLUTAMINASE;TRANSFER-RNA SYNTHETASE | 1 | null | AGG codon;chlorotyrosine;hydroxy acid;pyrrolysyl-tRNA synthetase;self-cleavage | 13 | SELF-CLEAVAGE;ESCHERICHIA-COLI;AGG CODONS;ALPHA-HYDROXY ACID;AMINO-ACIDS;chlorotyrosine;GLUTAMICUM;hydroxy acids;IN-VIVO;MICROBIAL TRANSGLUTAMINASE;PRO-TRANSGLUTAMINASE;pyrrolysyl-tRNA synthetase;RECOGNITION;STREPTOVERTICILLIUM-MOBARAENSE TRANSGLUTAMINASE;TRANSFER-RNA SYNTHETASE | WOS:000445711300021 | Ajinomoto Co Inc, Kanagawa, Japan;RIKEN, Kanagawa, Japan;Rikkyo Univ, Tokyo, Japan | Japan | 2,018 | null | null | null | null | English | null | ACS CHEM BIOL;AMINO ACIDS;ANGEW CHEM INT EDIT;APPL ENVIRON MICROB;BIOCHEM BIOPH RES CO;BIOCONJUGATE CHEM;BIOPHYS J;CHEM BIOL;ENZYME MICROB TECH;J AM CHEM SOC;J BIOL CHEM;J BIOTECHNOL;J FOOD SCI;J MOL BIOL;NAT CHEM BIOL;NUCLEIC ACIDS RES;PROTEIN EXPRES PURIF;SCI REP-UK;SCIENCE;STRUCTURE | Date, Masayo;Haruna, Ken-ichi;Iraha, Fumie;Mukai, Takahito;Ohtake, Kazumasa;Sakamoto, Kensaku;Takahashi, Mihoko;Yokoyama, Keiichi | 2024-03-11
ER | Bindman, N A;Brinda, K V;Buettner, K;Cortez, J;Date, M;De Jong, G A H;Guo, J T;Isaacs, F J;Johnson, D B F;Kashiwagi, T;Kikuchi, Y;Kobayashi, T;Li, Y M;Marx, C K;Mukai, T;Ohtake, K;Sakamoto, K;Varshney, U;Yamaguchi, A;Yanagisawa, T;Yokoyama, K | GU9XT | Kanagawa, Japan;Kanagawa, Japan. | 23 | null | 3 | null | 30,063,837 | Date, Masayo;Haruna, Ken-ichi;Iraha, Fumie;Mukai, Takahito;Ohtake, Kazumasa;Sakamoto, Kensaku;Takahashi, Mihoko;Yokoyama, Keiichi | ACS SYNTH BIOL | Kanagawa, Japan;Tokyo, Japan |
Chupalov, A;Li, J;Marchisio, M A;Xu, Z L | 10.1186/s13036-018-0101-z | 11 | CAMPUS, 4 CRINAN ST, LONDON N1 9XW, ENGLAND | 3k6r24c1n6g375s5i2k2j275yp4w84v6iw70 | Anti- CRISPR-based biosensors in the yeast <i>S</i>. <i>cerevisiae</i> | Life Technol Corp | null | Marchisio, MA (corresponding author), Sch Life Sci & Technol, 2 Yikuang St, Harbin 150080, Heilongjiang, Peoples R China. | null | Chupalov, Aleksandr;Li, Jing;Marchisio, Mario Andrea;Xu, Zengliang | Biochemical Research Methods;Biotechnology & Applied Microbiology | National Natural Science Foundation of China [31571373] | WOS | Marchisio, M A | Sch Life Sci & Technol, Heilongjiang, Peoples R China | 12 | <i>S</i>;anti-;biosensors;CRISPR-based;i>cerevisiae</i>;in;the;yeast | 1 | Marchisio, Mario Andrea | BMC | Sch Life Sci & Technol, 2 Yikuang St, Harbin 150080, Heilongjiang, Peoples R China | Article | Life Technol Corp | LONDON | null | null | Sch Life Sci & Technol | National Natural Science Foundation of China | Marchisio, MA (corresponding author), Sch Life Sci & Technol, 2 Yikuang St, Harbin 150080, Heilongjiang, Peoples R China. | null | Chupalov, Aleksandr;Li, Jing;Marchisio, Mario Andrea;Xu, Zengliang | 43 | 1 | 440,452,800,001 | National Natural Science Foundation of China [31571373] | China | JOURNAL OF BIOLOGICAL ENGINEERING | China | null | null | Sch Life Sci & Technol, 2 Yikuang St, Harbin 150080, Heilongjiang, Peoples R China | 1754-1611 | Chupalov, A;Li, J;Marchisio, M A;Xu, Z L | AUG 1 | marchisio@hit.edu.cn | anti- CRISPR-based biosensors;i>cerevisiae</i>;Yeast <i>S</i> | 4 | J | Biochemistry & Molecular Biology;Biotechnology & Applied Microbiology | ACRIIA4;activity;anti- CRISPR-based biosensors;anti-CRISPR;anti-CRISPR proteins;anti-CRISPR proteins (LmAcrIIA4;anti-CRISPR-based biosensors;anti-CRISPR-based synthetic gene circuits;anti-CRISPR-dSpCas9;background;BACTERIA;bacterial CRISPR-Cas defense system;beta-estradiol;BINDING;biosensors;clarified;conclusions;control;dependent;DESIGN;diverse functions;DNA;dSpCas9;dSpCas9-Mxi1;effective dSpCas9 suppressors;efficiency;efficient inhibitors;ENHANCEMENT;Escherichia coli;expression cassette;FLUORESCENCE;fluorescence expression;galactose;genes;gRNA;gRNA complex;gRNA interaction;gRNA system;Guide RNA;GUIDE RNAS;i>cerevisiae</i>;IN-VIVO;increase;induction;INHIBITION;LmAcrIIA2;LmAcrIIA4;mammalian cells;new components;non-negligible negative effects;nuclease-deficient version dSpCas9;phages;powerful means;produced;proteins;protospacer adjacent motif (PAM) recognition site;reaction;reports;results;ribozyme-gRNA-ribozyme;S. Cerevisiae;Saccharomyces cerevisiae;SACCHAROMYCES-CEREVISIAE;SpCas9;StAcrIIA5;StAcrIIA5);structures;synthetic biology;systems;TERMINATORS;Yeast <i>S</i>;yeast cell growth;yeast cells;yeast constitutive ADH1 promoter;yeast S. cerevisiae synthetic biosensors;yeast synthetic gene circuits | Li, J | ACRIIA4;anti-CRISPR;biosensors;DESIGN;dSpCas9;GENES;Guide RNA;IN-VIVO;INHIBITION;Proteins;SACCHAROMYCES-CEREVISIAE;Synthetic biology;SYSTEMS;TERMINATORS | null | [Li, Jing; Xu, Zengliang; Chupalov, Aleksandr; Marchisio, Mario Andrea] Sch Life Sci & Technol, 2 Yikuang St, Harbin 150080, Heilongjiang, Peoples R China. | We acknowledge financial support by the National Natural Science Foundation of China, grant number 31571373. | activity;anti-CRISPR proteins;anti-CRISPR proteins (LmAcrIIA4;anti-CRISPR-based biosensors;anti-CRISPR-based synthetic gene circuits;anti-CRISPR-dSpCas9;background;bacteria;bacterial CRISPR-Cas defense system;beta-estradiol;binding;clarified;conclusions;control;dependent;diverse functions;DNA;dSpCas9-Mxi1;effective dSpCas9 suppressors;efficiency;efficient inhibitors;enhancement;Escherichia coli;expression cassette;fluorescence;fluorescence expression;galactose;gRNA;gRNA complex;gRNA interaction;gRNA system;guide RNAs;increase;induction;LmAcrIIA2;LmAcrIIA4;mammalian cells;new components;non-negligible negative effects;nuclease-deficient version dSpCas9;phages;powerful means;produced;protospacer adjacent motif (PAM) recognition site;reaction;reports;results;ribozyme-gRNA-ribozyme;S. Cerevisiae;Saccharomyces cerevisiae;SpCas9;StAcrIIA5;StAcrIIA5);structures;yeast cell growth;yeast cells;yeast constitutive ADH1 promoter;yeast S. cerevisiae synthetic biosensors;yeast synthetic gene circuits | 10.1002/yea.1130;10.1016/0378-1119(93)90681-R;10.1016/j.biocel.2010.11.012;10.1016/j.cell.2014.09.029;10.1016/j.cell.2016.12.009;10.1016/j.cell.2017.07.037;10.1016/j.molcel.2017.05.024;10.1016/j.molcel.2017.09.002;10.1021/acssynbio.5b00162;10.1021/acssynbio.7b00163;10.1021/sb400081r;10.1021/sb5003357;10.1038/nature15254;10.1038/nature22377;10.1038/ncomms15459;10.1038/nrg3197;10.1038/s41564-017-0004-7;10.1093/bioinformatics/btu743;10.1093/nar/29.9.e45;10.1093/nar/gkp687;10.1093/nar/gkt135;10.1093/nar/gkt1402;10.1093/nar/gku616;10.1099/mic.0.000635;10.1111/jipb.12152;10.1126/sciadv.1701620;10.1186/1471-2105-10-106;10.1186/1754-1611-8-6;10.1186/s13036-016-0040-5;10.1186/s13059-016-0900-9;10.1371/journal.pcbi.1001083;10.1371/journal.pone.0003647;10.1534/g3.111.001917 | Sch Life Sci & Technol | Chupalov, A;Li, J;Marchisio, M A;Xu, Z L | Li, J: Sch Life Sci & Technol, 2 Yikuang St, Harbin 150080, Heilongjiang, Peoples R China | Marchisio, Mario Andrea | 31571373 | 36 | null | China | Sch Life Sci & Technol | Li, Jing | Green Published, gold | ACRIIA4;DESIGN;GENES;GUIDE RNA;IN-VIVO;INHIBITION;PROTEINS;SACCHAROMYCES-CEREVISIAE;SYSTEMS;TERMINATORS | Li, Jing; Xu, Zengliang; Chupalov, Aleksandr; Marchisio, Mario Andrea; | null | Sch Life Sci & Technol, 2 Yikuang St, Harbin 150080, Heilongjiang, Peoples R China | Sch Life Sci & Technol, 2 Yikuang St, Harbin 150080, Heilongjiang, Peoples R China | null | anti-CRISPR;Biosensor;dSpCas9;Guide RNA;Synthetic biology | null | 1993;2001;2002;2004;2008;2009;2011;2012;2013;2014;2015;2016;2017;2018 | 22 | Sch Life Sci & Technol, 2 Yikuang St, Harbin 150080, Heilongjiang, Peoples R China | J. Biol. Eng. | Marchisio, Mario Andrea | BMC | ";(LmAcrIIA4;(PAM);,;:;a;achieved;activity;ADH1;adjacent;an;and;anti-CRISPR;anti-CRISPR-based;anti-CRISPR-dSpCas9;are;as;background;bacteria;bacterial;based;be;been;best;beta-estradiol;binding;biosensors;by;cassette;cell;cells;cerevisiae;circuits;clarified;coli;complex;components;conclusions;constitutive;constructed;control;could;CRISPR-Cas;date;defense;demonstrates;dependent;determined;diverse;DNA;dSpCas9;dSpCas9-Mxi1;effective;effects;efficiency;efficient;employed;engineered;enhancement;Escherichia;expressed;expression;fluorescence;found;from;functions;galactose;gene;gRNA;growth;guide;had;have;hence;in;increase;induction;inhibitors;interact;interaction;into;its;LmAcrIIA2;LmAcrIIA4;mammalian;means;measured;modulate;motif;negative;new;no;non-negligible;nuclease-deficient;occlude;of;on;only;or;particular;performance;performed;phages;powerful;preventing;previously;produced;promoter;proteins;protospacer;reaction;recently;recognition;reports;represent;results;ribozyme-gRNA-ribozyme;RNAs;S.;Saccharomyces;shown;site;SpCas9;StAcrIIA5;StAcrIIA5);strongly;structures;such;suppressors;synthetic;system;tested;that;the;their;there;thereby;this;to;under;upon;using;version;was;we;well;were;whereas;which;with;work;yeast | Sch Life Sci & Technol | Background: Anti-CRISPR proteins are expressed by phages as a reaction to the bacterial CRISPR-Cas defense system. Recently, the structures of anti-CRISPR proteins have been determined, and their diverse functions have been clarified. Anti-CRISPR proteins such as LmAcrIIA2 and LmAcrIIA4 interact with the SpCas9: gRNA system and occlude the protospacer adjacent motif (PAM) recognition site, thereby preventing SpCas9: gRNA from binding to the DNA. Hence, anti-CRISPR proteins represent a powerful means to control and modulate the activity of SpCas9 and its nuclease-deficient version dSpCas9. LmAcrIIA2 and LmAcrIIA4 have been shown to be efficient inhibitors of SpCas9 in Escherichia coli, Saccharomyces cerevisiae, and mammalian cells. To date, there have been no reports of anti-CRISPR-based synthetic gene circuits engineered into yeast cells. Results: We constructed in the yeast S. cerevisiae synthetic biosensors based on the anti-CRISPR-dSpCas9: gRNA interaction. Upon induction with galactose or beta-estradiol, anti-CRISPR proteins (LmAcrIIA4, LmAcrIIA2, and StAcrIIA5) produced an enhancement in fluorescence expression by preventing the dSpCas9-Mxi1: gRNA complex from binding to the DNA. We found that LmAcrIIA2 performed as well as LmAcrIIA4 in S. cerevisiae, whereas StAcrIIA5, which had previously been tested in bacteria only, had non-negligible negative effects on yeast cell growth. The efficiency of anti-CRISPR-based biosensors was strongly dependent on the means by which the guide RNAs were produced. The best performance, as measured by the increase in fluorescence, was achieved using a "ribozyme-gRNA-ribozyme" expression cassette under the control of the yeast constitutive ADH1 promoter. Conclusions: This work demonstrates that anti-CRISPR proteins are effective dSpCas9 suppressors in yeast cells. In particular, LmAcrIIA2 and LmAcrIIA4 could be employed as new components of yeast synthetic gene circuits. | ABE-8451-2020 | ACRIIA4;DESIGN;GENE;GUIDE RNA;IN-VIVO;INHIBITION;PROTEIN;SACCHAROMYCES-CEREVISIAE;SYSTEM;TERMINATION | 4 | null | anti-CRISPR;biosensors;dSpCas9;Guide RNA;Synthetic biology | 14 | SACCHAROMYCES-CEREVISIAE;ACRIIA4;anti-CRISPR;Biosensor;DESIGN;dSpCas9;GENE;Guide RNA;IN-VIVO;INHIBITION;PROTEIN;Synthetic biology;SYSTEM;TERMINATION | WOS:000440452800001 | Sch Life Sci & Technol, Heilongjiang, Peoples R China | China | 2,018 | null | 0000-0002-5102-1069 | null | null | English | null | ACS SYNTH BIOL;BIOINFORMATICS;BMC BIOINFORMATICS;CELL;GENE;GENOME BIOL;INT J BIOCHEM CELL B;J Biol Eng;J INTEGR PLANT BIOL;METHOD ENZYMOL;MICROBIOL-SGM;MOL CELL;MOL CLONING;NAT COMMUN;NAT MICROBIOL;NAT REV GENET;NATURE;NUCLEIC ACIDS RES;PLOS COMPUT BIOL;PLOS ONE;RNA BIOL;SCI ADV;YEAST | Chupalov, Aleksandr;Li, Jing;Marchisio, Mario Andrea;Xu, Zengliang | 2024-03-11
ER | Basgall, E M;Benenson, Y;Bondy-Denomy, J;Chee, M K;Curran, K A;Deaner, M;Dicarlo, J E;Dong, D;Engler, C;Farzadfard, F;Gander, M W;Gao, Y B;Gibson, D G;Gietz, R D;Gilbert, L A;Hahne, F;Harrington, L B;Hynes, A P;Louvion, J F;Marchisio, M A;Maxwell, K L;Mcisaac, R S;Naito, Y;Ottoz, D S M;Pfaffl, M W;Rauch, B J;Sambrook J.;Schwartz, C M;Sheff, M A;Shin, J;Smith, J D;Song, W J;Yang, H | GO9UH | Heilongjiang, Peoples R China | 25 | null | 1 | null | 30,123,320 | Chupalov, Aleksandr;Li, Jing;Marchisio, Mario Andrea;Xu, Zengliang | J BIOL ENG | Heilongjiang, Peoples R China |
Bray, E R;Burnstein, K L;Copello, V A;D'Urso, G;Heidman, L;Magani, F;Martinez, M J;Peacock, S O;Wiley, D J;Zhao, N | 10.15252/msb.20188202 | e8202 | 111 RIVER ST, HOBOKEN 07030-5774, NJ USA | 686b3b1l6me4m136q3i4l361c6f32195o3j4241 | Identification of an oncogenic network with prognostic and therapeutic value in prostate cancer | Univ Miami | null | Burnstein, KL (corresponding author), SCCC, Miami, FL 33136 USA.;Burnstein, KL (corresponding author), Univ Miami, Miller Sch Med, Dept Mol & Cellular Pharmacol, Miami, FL 33136 USA. | null | Bray, Eric R;Burnstein, Kerry L;Copello, Valeria A;D'Urso, Gennaro;Heidman, Laine;Magani, Fiorella;Martinez, Maria J;Peacock, Stephanie O;Wiley, David J;Zhao, Ning | Biochemistry & Molecular Biology | NIH [CA132200]; NIH predoctoral fellowship [F30AG038275]; Women's Cancer Association; Sylvester Comprehensive Cancer Center | WOS | Burnstein, K L | SCCC, Miami, FL USA;Univ Miami, Miami, FL USA | 14 | an;and;cancer;Identification;in;network;of;oncogenic;prognostic;prostate;therapeutic;value;with | 1 | Copello, Valeria;Zhao, Ning | WILEY | SCCC, Miami, FL 33136 USA;Univ Miami, Miller Sch Med, Dept Mol & Cellular Pharmacol, Miami, FL 33136 USA;Univ Miami, Miller Sch Med, Dept Mol & Cellular Pharmacol, Miami, FL 33136 USA.; Burnstein, KL (corresponding author), SCCC, Miami, FL 33136 USA;Univ Miami, Miller Sch Med, Dept Neurol Surg, Miami Project Cure Paralysis, Miami, FL 33136 USA;Univ Miami, Miller Sch Med, Sheila & David Fuente Grad Program Canc Biol, Miami, FL 33136 USA | Article | Univ Miami;SCCC | HOBOKEN | null | null | Miami;SCCC;Univ Miami | NIH;NIH predoctoral fellowship;Sylvester Comprehensive Cancer Center;Women's Cancer Association | Burnstein, KL (corresponding author), Univ Miami, Miller Sch Med, Dept Mol & Cellular Pharmacol, Miami, FL 33136 USA.; Burnstein, KL (corresponding author), SCCC, Miami, FL 33136 USA. | null | Bray, Eric R;Burnstein, Kerry L;Copello, Valeria A;D'Urso, Gennaro;Heidman, Laine;Magani, Fiorella;Martinez, Maria J;Peacock, Stephanie O;Wiley, David J;Zhao, Ning | 3 | 4 | 444,544,200,005 | NIH [CA132200];NIH predoctoral fellowship [F30AG038275];Sylvester Comprehensive Cancer Center;Women's Cancer Association | USA | MOLECULAR SYSTEMS BIOLOGY | USA;USA.; | null | null | Univ Miami, Miller Sch Med, Sheila & David Fuente Grad Program Canc Biol, Miami, FL 33136 USA | 1744-4292 | Bray, E R;Burnstein, K L;Copello, V A;D'Urso, G;Heidman, L;Magani, F;Martinez, M J;Peacock, S O;Wiley, D J;Zhao, N | AUG | KBurnstein@med.miami.edu | Identification;oncogenic network;prognostic;prostate cancer;therapeutic value | 10 | J | Biochemistry & Molecular Biology | ABIRATERONE;accurate prognosis;ACTIVE ANDROGEN RECEPTOR;androgen receptor splice variants;approach;AR activity;AR variant-driven gene module;AR variants;castration resistance;constitutively active androgen receptor (AR) splice variant-driven pathways;drive cancer progression;effective therapy;ENZALUTAMIDE RESISTANCE;experimental AR variant transcriptome analyses;expression;FEEDBACK LOOP;gene co-expression network analysis;gene hub;gene set;genes;growth;high-throughput synthetic genetic array screen;human PC progression;human prostate samples;IDENTIFICATION;identified;identifying critical pathways governing disease progression;identifying genes;intractable mechanism;large independent PC patient cohorts;members;meta-analysis;mitotic gene signature;module;novel gene discovery strategy;novel systems-level gene discovery strategy;oncogenic;oncogenic network;PC;pharmacologic inhibition;prognostic;PROGRESSION;prostate cancer;prostate cancer (PC) therapeutic resistance;representative;Schizosaccharomyces pombe;seven AR variant-regulated genes;seven genes predicted poor disease-free survival;SPLICE VARIANTS;strategy;strong prognostic;synergistically decreased PC cell proliferation;systems biology;therapeutic potential;therapeutic value;upregulated;weighted gene co-expression network analysis;yeast synthetic genetic array | Magani, F | ABIRATERONE;ACTIVE ANDROGEN RECEPTOR;androgen receptor splice variants;castration resistance;ENZALUTAMIDE RESISTANCE;EXPRESSION;FEEDBACK LOOP;GENES;GROWTH;mitotic gene signature;PROGRESSION;SPLICE VARIANTS;systems biology;weighted gene co-expression network analysis;yeast synthetic genetic array | null | [Magani, Fiorella; Copello, Valeria A.; Peacock, Stephanie O.] Univ Miami, Miller Sch Med, Sheila & David Fuente Grad Program Canc Biol, Miami, FL 33136 USA. [Magani, Fiorella; Martinez, Maria J.; Zhao, Ning; Copello, Valeria A.; Heidman, Laine; Peacock, Stephanie O.; Wiley, David J.; D'Urso, Gennaro; Burnstein, Kerry L.] Univ Miami, Miller Sch Med, Dept Mol & Cellular Pharmacol, Miami, FL 33136 USA. [Bray, Eric R.] Univ Miami, Miller Sch Med, Dept Neurol Surg, Miami Project Cure Paralysis, Miami, FL 33136 USA. [Burnstein, Kerry L.] SCCC, Miami, FL 33136 USA. | We are grateful to Drs. Sawsan Khuri, Tan Ince, Enrique Mesri, Irina Agoulnik, Sandra Lemmon, Priyamvada Rai, and Nagi Ayad for helpful advice; to Mr. Dimitri Nader for assistance with experiments; to Ms. Meenakkshy Manoharan for help with the manuscript preparation; and to Ms. Ann M. Greene for editing the manuscript. This research was conducted using the resources of the University of Miami Center for Computational Science (CCS) and the Onco-genomics Shared Resource of Sylvester Comprehensive Cancer Center. Research performed in this manuscript was supported by NIH Grant CA132200 (KLB), NIH predoctoral fellowship F30AG038275 (SOP), Women's Cancer Association (KLB), and by developmental and shared equipment funds from the Sylvester Comprehensive Cancer Center. | accurate prognosis;approach;AR activity;AR variant-driven gene module;AR variants;constitutively active androgen receptor (AR) splice variant-driven pathways;drive cancer progression;effective therapy;experimental AR variant transcriptome analyses;expression;gene co-expression network analysis;gene hub;gene set;high-throughput synthetic genetic array screen;human PC progression;human prostate samples;identified;identifying critical pathways governing disease progression;identifying genes;intractable mechanism;large independent PC patient cohorts;members;meta-analysis;module;novel gene discovery strategy;novel systems-level gene discovery strategy;oncogenic;PC;pharmacologic inhibition;prostate cancer (PC) therapeutic resistance;representative;Schizosaccharomyces pombe;seven AR variant-regulated genes;seven genes predicted poor disease-free survival;strategy;strong prognostic;synergistically decreased PC cell proliferation;therapeutic potential;upregulated | 10.1001/jama.2015.6036;10.1002/humu.21138;10.1002/pros.22901;10.1016/0065-2571(84)90007-4;10.1016/j.ccell.2015.06.004;10.1016/j.ccr.2005.10.001;10.1016/j.eururo.2017.11.038;10.1016/j.neuron.2016.01.034;10.1016/j.tem.2010.01.002;10.1016/S1470-2045(10)70295-3;10.1021/jm960666x;10.1038/ng.3419;10.1038/ng1570;10.1038/nrurol.2015.13;10.1038/onc.2013.206;10.1038/srep07654;10.1038/srep16018;10.1056/NEJMoa1315815;10.1073/pnas.0604193103;10.1073/pnas.0806261105;10.1073/pnas.1012443107;10.1074/jbc.M112.352930;10.1074/jbc.M112.370783;10.1093/bioinformatics/btw788;10.1093/carcin/bgp261;10.1093/nar/gkv262;10.1093/nar/gkx1306;10.1111/iju.13137;10.1111/j.2042-7158.2012.01567.x;10.1126/science.1132939;10.1126/scitranslmed.3003180;10.1158/0008-5472.CAN-08-0594;10.1158/0008-5472.CAN-08-3795;10.1158/0008-5472.CAN-10-2585;10.1158/0008-5472.CAN-11-3892;10.1158/0008-5472.CAN-12-3630;10.1158/0008-5472.CAN-15-0381;10.1158/1078-0432.CCR-09-0911;10.1158/1078-0432.CCR-13-3296;10.1158/1541-7786.MCR-13-0545;10.1158/2159-8290.CD-12-0095;10.1186/1471-2105-9-559;10.1186/1471-2164-14-95;10.1200/JCO.2008.17.2882;10.1200/JCO.2016.70.1961;10.1210/en.2017-00109;10.1210/me.2012-1165;10.12688/f1000research.4188.1;10.1371/journal.pone.0002568;10.1371/journal.pone.0019059;10.1371/journal.pone.0025822;10.1371/journal.pone.0142327;10.1593/neo.101324;10.1621/nrs.06001;10.18632/oncotarget.1802;10.18632/oncotarget.4105;10.18632/oncotarget.5585;10.2202/1544-6115.1128;10.3109/0284186X.2010.531284;10.3892/mmr.2012.956;10.3892/or_00000600;10.6026/97320630008855;[10.3322/caac.21387, 10.3322/caac.21654, 10.3322/caac.21551, 10.3322/caac.21254, 10.3322/caac.21601, 10.3322/caac.20006, 10.3322/caac.21332, 10.3322/caac.20073] | Univ Miami | Bray, E R;Burnstein, K L;Copello, V A;D'Urso, G;Heidman, L;Magani, F;Martinez, M J;Peacock, S O;Wiley, D J;Zhao, N | Magani, F: Univ Miami, Miller Sch Med, Sheila & David Fuente Grad Program Canc Biol, Miami, FL 33136 USA | null | CA132200;F30AG038275 | 64 | null | USA | SCCC;Univ Miami | Magani, Fiorella | Green Published, gold | ABIRATERONE;ACTIVE ANDROGEN RECEPTOR;ENZALUTAMIDE RESISTANCE;EXPRESSION;FEEDBACK LOOP;GENES;GROWTH;PROGRESSION;SPLICE VARIANTS;SYSTEMS BIOLOGY | Magani, Fiorella; Bray, Eric R.; Martinez, Maria J.; Zhao, Ning; Copello, Valeria A.; Heidman, Laine; Peacock, Stephanie O.; Wiley, David J.; D'Urso, Gennaro; Burnstein, Kerry L.; | null | SCCC, Miami, FL 33136 USA;Univ Miami, Miller Sch Med, Dept Mol & Cellular Pharmacol, Miami, FL 33136 USA;Univ Miami, Miller Sch Med, Dept Neurol Surg, Miami Project Cure Paralysis, Miami, FL 33136 USA;Univ Miami, Miller Sch Med, Sheila & David Fuente Grad Program Canc Biol, Miami, FL 33136 USA | SCCC, Miami, FL 33136 USA;Univ Miami, Miller Sch Med, Dept Mol & Cellular Pharmacol, Miami, FL 33136 USA;Univ Miami, Miller Sch Med, Dept Neurol Surg, Miami Project Cure Paralysis, Miami, FL 33136 USA;Univ Miami, Miller Sch Med, Sheila & David Fuente Grad Program Canc Biol, Miami, FL 33136 USA | null | androgen receptor splice variants;castration resistance;mitotic gene signature;weighted gene co-expression network analysis;yeast synthetic genetic array | 8 | 1984;1991;1997;2005;2006;2008;2009;2010;2011;2012;2013;2014;2015;2016;2017;2018;2021 | 22 | SCCC, Miami, FL 33136 USA;Univ Miami, Miller Sch Med, Dept Mol & Cellular Pharmacol, Miami, FL 33136 USA | Mol. Syst. Biol. | Burnstein, Kerry L | WILEY | (AR);(PC);,;a;accurate;active;activity;also;an;analyses;analysis;and;androgen;applicable;approach;AR;array;as;broadly;by;cancer;cell;clinically;co-expression;cohorts;combined;constitutively;critical;decreased;developed;discovery;disease;disease-free;drive;during;effective;enhance;essential;experimental;expression;filtered;focused;for;functionally;gene;genes;genetic;governing;high-throughput;hub;human;identified;identifying;in;independent;inhibition;interacted;interacting;intractable;is;large;mechanism;members;meta-analysis;module;network;novel;of;on;oncogenic;pathways;patient;PC;performed;pharmacologic;pombe;poor;potential;potently;predicted;prognosis;prognostic;progression;proliferation;prostate;receptor;relevant;representative;resistance;samples;Schizosaccharomyces;screen;set;seven;splice;strategy;strong;survival;synergistically;synthetic;systems-level;that;the;therapeutic;therapy;this;transcriptome;unbiased;upregulated;using;variant;variant-driven;variant-regulated;variants;was;we;weighted;with | SCCC;Univ Miami | Identifying critical pathways governing disease progression is essential for accurate prognosis and effective therapy. We developed a broadly applicable and novel systems-level gene discovery strategy. This approach focused on constitutively active androgen receptor (AR) splice variant-driven pathways as representative of an intractable mechanism of prostate cancer (PC) therapeutic resistance. We performed a meta-analysis of human prostate samples using weighted gene co-expression network analysis combined with experimental AR variant transcriptome analyses. An AR variant-driven gene module that is upregulated during human PC progression was identified. We filtered this module by identifying genes that functionally interacted with AR variants using a high-throughput synthetic genetic array screen in Schizosaccharomyces pombe. This strategy identified seven AR variant-regulated genes that also enhance AR activity and drive cancer progression. Expression of the seven genes predicted poor disease-free survival in large independent PC patient cohorts. Pharmacologic inhibition of interacting members of the gene set potently and synergistically decreased PC cell proliferation. This unbiased and novel gene discovery strategy identified a clinically relevant, oncogenic, interacting gene hub with strong prognostic and therapeutic potential in PC. | null | ABIRATERONE;ACTIVE ANDROGEN RECEPTOR;ENZALUTAMIDE RESISTANCE;EXPRESSION;FEEDBACK LOOPS;GENE;GROWTH;PROGRESS;SPLICE VARIANTS;SYSTEMS BIOLOGY | 0 | null | androgen receptor splice variants;castration resistance;mitotic gene signature;weighted gene co-expression network analysis;yeast synthetic genetic array | 15 | ABIRATERONE;ACTIVE ANDROGEN RECEPTOR;androgen receptor splice variants;castration resistance;ENZALUTAMIDE RESISTANCE;EXPRESSION;FEEDBACK LOOPS;GENE;GROWTH;mitotic gene signature;PROGRESS;SPLICE VARIANTS;systems biology;weighted gene co-expression network analysis;yeast synthetic genetic array | WOS:000444544200005 | SCCC, Miami, FL USA;Univ Miami, Miami, FL USA | USA | 2,018 | null | 0000-0001-6514-234X;0000-0002-7035-4467 | null | null | English | null | ACTA ONCOL;Adv Enzyme Regul;BIOINFORMATICS;BIOINFORMATION;BMC BIOINFORMATICS;BMC GENOMICS;CA-CANCER J CLIN;CANCER CELL;CANCER DISCOV;CANCER RES;CARCINOGENESIS;CLIN CANCER RES;ENDOCRINOLOGY;EUR UROL;HUM MUTAT;INT J UROL;J BIOL CHEM;J CLIN ONCOL;J MED CHEM;J PHARM PHARMACOL;JAMA-J AM MED ASSOC;LANCET ONCOL;METHOD ENZYMOL;MOL CANCER RES;MOL ENDOCRINOL;MOL MED REP;NAT GENET;NAT REV UROL;NEOPLASIA;NEURON;NEW ENGL J MED;Nucl Recept Signal;NUCLEIC ACIDS RES;ONCOGENE;ONCOL REP;ONCOTARGET;P NATL ACAD SCI USA;PLOS ONE;PROSTATE;SCI REP-UK;SCI TRANSL MED;SCIENCE;STAT APPL GENET MOL;TRENDS ENDOCRIN MET | Bray, Eric R;Burnstein, Kerry L;Copello, Valeria A;D'Urso, Gennaro;Heidman, Laine;Magani, Fiorella;Martinez, Maria J;Peacock, Stephanie O;Wiley, David J;Zhao, Ning | 2024-03-11
ER | Antonarakis, E S;Arredouani, M S;Balk Steven, P;Bjartell, A;Cao, B;Cerami, E;Chan, S C;Chandran, V;Chen, S Y;Chia, K M;Chou, T C;Cooperberg, M R;Cuzick, J;Dehm, S M;Dixon, S J;Goodwin, J F;Guo, Z Y;Havlicek, L;He, Y D;Ho, Y;Hu, R;Hörnberg, E;Imamura, Y;Jia, Z Y;Kadarmideen, H N;Karacosta, L G;Karantanos, T;Knudsen, K E;Kong, D J;Kreeger, P K;Lamb, J;Langfelder, P;Li, H L;Li, Y M;Liu, C F;Lu, J;Luo, J;Marcias, G;Mendiratta, P;Moreno, S;Mortensen, M M;Peacock, S O;Pomerantz, M M;Prensner, J R;Qu, Y Y;Rands, C M;Rhodes, D R;Satake, H;Schaefer-Klein, J L;Shafi, A A;Siegel, R L;Tacar, O;Traka, M;Vaarala, M H;Varambally, S;Watson, P A;Wiley David, J;Xu, D;Yu, Y J;Zhang, B;Zhang, X B;Zhu, L | GT5JR | Miami, FL USA;Miami, FL USA. | 23 | null | 2 | null | 30,108,134 | Bray, Eric R;Burnstein, Kerry L;Copello, Valeria A;D'Urso, Gennaro;Heidman, Laine;Magani, Fiorella;Martinez, Maria J;Peacock, Stephanie O;Wiley, David J;Zhao, Ning | MOL SYST BIOL | Miami, FL USA |
Kiani, S;Menn, D J;Pradhan, S;Wang, X | 10.1021/acssynbio.8b00153 | null | 1155 16TH ST, NW, WASHINGTON, DC 20036 USA | 4v1r4w641a5o4l2q3p3o375376e2z421w1x1c55 | Fluorescent Guide RNAs Facilitate Development of Layered Pol II-Driven CRISPR Circuits | Arizona State Univ | null | Kiani, S; Wang, X (corresponding author), Arizona State Univ, Sch Biol & Hlth Syst Engn, Tempe, AZ 85281 USA. | null | Kiani, Samira;Menn, David J;Pradhan, Swechchha;Wang, Xiao | Biochemical Research Methods | ASU Dean's Fellowship; NIH [GM106081]; ASU School of Biological and Health Systems Engineering | WOS | Kiani, S;Wang, X | Arizona State Univ, Tempe, AZ USA | 7 | circuits;CRISPR;Development;Facilitate;fluorescent;guide;II-Driven;Layered;of;Pol;RNAs | 1 | Kiani, Samira;Pradhan, Swechchha;Wang, Xiao | AMER CHEMICAL SOC | Arizona State Univ, Sch Biol & Hlth Syst Engn, Tempe, AZ 85281 USA;X (corresponding author), Arizona State Univ, Sch Biol & Hlth Syst Engn, Tempe, AZ 85281 USA | Article | Arizona State Univ | WASHINGTON | null | null | Arizona State Univ | ASU Dean's Fellowship;ASU School of Biological and Health Systems Engineering;NIH | Kiani, S; Wang, X (corresponding author), Arizona State Univ, Sch Biol & Hlth Syst Engn, Tempe, AZ 85281 USA. | 1936 | Kiani, Samira;Menn, David J;Pradhan, Swechchha;Wang, Xiao | 17 | 1 | 442,454,500,010 | ASU Dean's Fellowship;ASU School of Biological and Health Systems Engineering;NIH [GM106081] | USA | ACS SYNTHETIC BIOLOGY | USA | null | null | Arizona State Univ, Sch Biol & Hlth Syst Engn, Tempe, AZ 85281 USA | 2161-5063 | Kiani, S;Menn, D J;Pradhan, S;Wang, X | AUG | samira.kiani@asu.edu;xiaowang@asu.edu | development;fluorescent Guide RNAs;Layered Pol II-Driven CRISPR Circuits | 4 | J | Biochemistry & Molecular Biology | affecting gRNA functionality;approach;circuit modification;complex CRISPR-based synthetic gene networks;computational biology;corresponding network behavior;CRISPR;development;evolution;expression;fgRNA;fluorescent gRNA (fgRNA);fluorescent Guide RNAs;gene networks;genetic circuit;gRNA;hurdles;improvement;IN-VITRO;information necessary;insight;interspaced short palindromic repeat (CRISPR) guide RNA (gRNA) expression;Layered Pol II-Driven CRISPR Circuits;MAMMALIAN-CELLS;MESSENGER-RNA;need;network function;networks;NUCLEAR EXPORT;overall function;Pol II-driven CRISPR circuits;Pol II-regulated gRNA expression;PROMOTER;PROTEIN;RNA Polymerase II (Pol II) promoters will aid;studying gRNA dynamics;synthetic biology;synthetic CRISPR network dynamics;tools;transcriptional cascade | Menn, D J | computational biology;CRISPR;EVOLUTION;EXPRESSION;fgRNA;gene networks;genetic circuit;IN-VITRO;MAMMALIAN-CELLS;MESSENGER-RNA;NUCLEAR EXPORT;PROMOTER;PROTEIN;Synthetic biology;transcriptional cascade | 1929 | [Menn, David J.; Pradhan, Swechchha; Kiani, Samira; Wang, Xiao] Arizona State Univ, Sch Biol & Hlth Syst Engn, Tempe, AZ 85281 USA. | We thank K. Haynes and M. Ebrahimkhani for helpful suggestions and discussion. D.M. was supported by the ASU Dean's Fellowship. This study was financially supported by an NIH grant (GM106081) (to X.W.) and the ASU School of Biological and Health Systems Engineering (S.K.). | affecting gRNA functionality;approach;circuit modification;complex CRISPR-based synthetic gene networks;corresponding network behavior;fluorescent gRNA (fgRNA);gRNA;hurdles;improvement;information necessary;insight;interspaced short palindromic repeat (CRISPR) guide RNA (gRNA) expression;need;network function;networks;overall function;Pol II-driven CRISPR circuits;Pol II-regulated gRNA expression;RNA Polymerase II (Pol II) promoters will aid;studying gRNA dynamics;synthetic CRISPR network dynamics;tools | 10.1002/j.1460-2075.1991.tb04901.x;10.1016/j.ceb.2004.03.013;10.1016/j.cell.2013.06.044;10.1016/j.cell.2014.11.052;10.1016/j.chembiol.2014.10.008;10.1016/j.molcel.2014.04.022;10.1016/S0014-5793(01)02482-6;10.1021/ja410819x;10.1021/ja508478x;10.1021/sb400081r;10.1023/A:1008103730027;10.1038/35014651;10.1038/mt.2008.144;10.1038/nbt.2808;10.1038/nbt.3526;10.1038/nbt739;10.1038/ncomms15459;10.1038/NMETH.1253;10.1073/pnas.0408507102;10.1073/pnas.1305423110;10.1073/pnas.1420294112;10.1093/emboj/21.7.1800;10.1093/molbev/msr143;10.1093/nar/23.12.2259;10.1111/jipb.12152;10.1126/science.1172005;10.1126/science.1207339;10.1126/science.7792603;10.1128/JVI.79.15.9933-9944.2005;10.1128/MCB.01673-13;10.1155/2013/270805;10.1261/rna.5250403;10.1371/journal.pcbi.0030057;10.15252/msb.20145735;10.4161/rna.8.3.15190;10.7554/eLife.23702;[10.1038/NMETH.2969, 10.1038/nmeth.2969];[10.1038/NMETH.3312, 10.1038/nmeth.3312];[10.1038/NMETH.3433, 10.1038/nmeth.3433] | Arizona State Univ | Kiani, S;Menn, D J;Pradhan, S;Wang, X | Menn, D J: Arizona State Univ, Sch Biol & Hlth Syst Engn, Tempe, AZ 85281 USA | Wang, Xiao | GM106081 | 39 | null | USA | Arizona State Univ | Menn, David J | null | EVOLUTION;EXPRESSION;GENE NETWORKS;IN-VITRO;MAMMALIAN-CELLS;MESSENGER-RNA;NUCLEAR EXPORT;PROMOTER;PROTEIN;TRANSCRIPTIONAL CASCADE | Menn, David J.; Pradhan, Swechchha; Kiani, Samira; Wang, Xiao; | null | Arizona State Univ, Sch Biol & Hlth Syst Engn, Tempe, AZ 85281 USA | Arizona State Univ, Sch Biol & Hlth Syst Engn, Tempe, AZ 85281 USA | null | computational biology;CRISPR;fgRNA;Genetic circuits;Synthetic biology | 8 | 1991;1995;2000;2001;2002;2003;2004;2005;2007;2008;2009;2011;2012;2013;2014;2015;2016;2017 | 6 | Arizona State Univ, Sch Biol & Hlth Syst Engn, Tempe, AZ 85281 USA | ACS Synth. Biol. | Wang, Xiao | AMER CHEMICAL SOC | (CRISPR);(fgRNA);(gRNA);(Pol;,;a;address;affecting;aid;and;approach;behavior;circuit;circuits;clustered;complex;construction;corresponding;CRISPR;CRISPR-based;directly;dynamics;efficient;employed;enables;expression;fluorescent;for;from;function;functionality;gene;generates;gRNA;guide;hurdles;II;ii);II-driven;II-regulated;improvement;in;information;insight;interspaced;into;modification;necessary;need;network;networks;of;optimizing;overall;palindromic;Pol;polymerase;promoters;properly;provides;quantitatively;regularly;remaining;repeat;require;RNA;short;show;study;studying;synthetic;that;the;these;this;to;tools;visualize;we;will;without;yet | Arizona State Univ | Efficient clustered regularly interspaced short palindromic repeat (CRISPR) guide RNA (gRNA) expression from RNA Polymerase II (Pol II) promoters will aid in construction of complex CRISPR-based synthetic gene networks. Yet, we require tools to properly visualize gRNA directly to quantitatively study the corresponding network behavior. To address this need, we employed a fluorescent gRNA (fgRNA) to visualize synthetic CRISPR network dynamics without affecting gRNA functionality. We show that studying gRNA dynamics directly enables circuit modification and improvement of network function in Pol II-driven CRISPR circuits. This approach generates information necessary for optimizing the overall function of these networks and provides insight into the hurdles remaining in Pol II-regulated gRNA expression. | A-8414-2008 | EVOLUTION;EXPRESSION;GENE NETWORKS;IN-VITRO;MAMMALIAN-CELLS;MESSENGER-RNA;NUCLEAR EXPORT;PROMOTER;PROTEIN;TRANSCRIPTIONAL CASCADE | 0 | null | computational biology;CRISPR;fgRNA;Genetic circuit;Synthetic biology | 15 | computational biology;CRISPR;EVOLUTION;EXPRESSION;fgRNA;gene networks;Genetic circuits;IN-VITRO;MAMMALIAN-CELLS;MESSENGER-RNA;NUCLEAR EXPORT;PROMOTER;PROTEIN;Synthetic biology;transcriptional cascade | WOS:000442454500010 | Arizona State Univ, Tempe, AZ USA | USA | 2,018 | null | 0000-0001-7550-5108;0000-0002-4056-0155;0000-0003-2695-1501 | null | null | English | null | ACS SYNTH BIOL;BIOMED RES INT;CELL;CHEM BIOL;CURR OPIN CELL BIOL;CYTOTECHNOLOGY;ELIFE;EMBO J;FEBS LETT;J AM CHEM SOC;J INTEGR PLANT BIOL;J VIROL;MOL BIOL EVOL;MOL CELL;MOL CELL BIOL;MOL SYST BIOL;MOL THER;NAT BIOTECHNOL;NAT COMMUN;NAT METHODS;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PLOS COMPUT BIOL;RNA;RNA BIOL;SCIENCE | Kiani, Samira;Menn, David J;Pradhan, Swechchha;Wang, Xiao | 2024-03-11
ER | Becskei, A;Brockmann, R;Chavez, A;Farzadfard, F;Filonov, G S;Friedland, A E;Fu, Y F;Gander, M W;Gao, Y B;Giering, J C;Gilbert, L A;Gossen, M;Grieger, J C;Hector, R E;Hooshangi, S;Kiani, S;Lin, Z G;Lloyd, D R;Ma, H H;Ma, M;Nehlin, J O;Nielsen, A A;Nissim, L;Nott, A;Paige, J S;Przybilski, R;Raj, A;Shechner, D M;Song, W J;Thompson, J D;Vinciguerra, P;Wu, F Q;Wu, M;Xia, H B;Xie, K B;Zalatan, J G;Zenklusen, D;Zhang, B | GR2ZC | Tempe, AZ USA | 6 | null | 1 | null | 30,021,068 | Kiani, Samira;Menn, David J;Pradhan, Swechchha;Wang, Xiao | ACS SYNTH BIOL | Tempe, AZ USA |
Fussenegger, M;Xie, M Q | 10.1038/s41580-018-0024-z | null | MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND | 3v1l32631gt6ry566w1r5k56w2x2b86s3r6e | Designing cell function: assembly of synthetic gene circuits for cell biology applications | Swiss Fed Inst Technol | null | Fussenegger, M (corresponding author), Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland.;Fussenegger, M (corresponding author), Univ Basel, Fac Sci, Basel, Switzerland. | null | Fussenegger, Martin;Xie, Mingqi | Cell Biology | European Research Council (ERC ProNet) [321381]; Swiss National Centre of Competence in Research (NCCR) Molecular Systems Engineering; European Research Council (ERC) [321381] Funding Source: European Research Council (ERC) | WOS | Fussenegger, M | Swiss Fed Inst Technol, Basel, Switzerland;Univ Basel, Basel, Switzerland | 19 | :;applications;Assembly;biology;cell;circuits;Designing;for;function;gene;of;synthetic | 1 | null | NATURE PUBLISHING GROUP | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland;Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland.; Fussenegger, M (corresponding author), Univ Basel, Fac Sci, Basel, Switzerland;Univ Basel, Fac Sci, Basel, Switzerland | Review | Swiss Fed Inst Technol;Univ Basel | LONDON | null | null | Swiss Fed Inst Technol;Univ Basel | European Research Council (ERC ProNet);European Research Council (ERC);Swiss National Centre of Competence in Research (NCCR) Molecular Systems Engineering | Fussenegger, M (corresponding author), Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland.; Fussenegger, M (corresponding author), Univ Basel, Fac Sci, Basel, Switzerland. | 525 | Fussenegger, Martin;Xie, Mingqi | 208 | 2 | 439,404,000,008 | European Research Council (ERC ProNet) [321381];European Research Council (ERC) [321381] Funding Source: European Research Council (ERC);Swiss National Centre of Competence in Research (NCCR) Molecular Systems Engineering | Switzerland | NATURE REVIEWS MOLECULAR CELL BIOLOGY | Switzerland | null | null | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland | 1471-0072 | Fussenegger, M;Xie, M Q | AUG | fussenegger@bsse.ethz.ch | Assembly;cell biology applications;designing cell function;synthetic gene circuits | 2 | J | Cell Biology | applied life sciences;assembled genetic circuits;assembly;BACTERIA DETECT;biomedicine;biotechnology industry;blood transfusion therapies;cell biology applications;cell engineering;CHIMERIC-ANTIGEN-RECEPTOR;complex problems;control;converting cells;designing cell function;discipline;DRIVE SYSTEM;early breakthroughs;ectopic (over) expression;engineering application-driven biological functionalities;environmental sciences;high spatiotemporal precision;human cell functions;intractable diseases;larger-scale;living therapeutics;LOGIC COMPUTATION;MAMMALIAN-CELLS;nature;OPTICAL CONTROL;personalized medicine;regenerative medicine;revolutionary impact;single sets;SINGLE-CELL;synthetic biology;synthetic gene circuits;T-CELLS;toggle switch;transcription factor;TRANSGENES;will open new possibilities | Xie, M Q | BACTERIA DETECT;CHIMERIC-ANTIGEN-RECEPTOR;DRIVE SYSTEM;LOGIC COMPUTATION;MAMMALIAN-CELLS;OPTICAL CONTROL;SINGLE-CELL;T-CELLS;toggle switch;transcription factor | 507 | [Xie, Mingqi; Fussenegger, Martin] Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland. [Fussenegger, Martin] Univ Basel, Fac Sci, Basel, Switzerland. | The authors apologize to colleagues for work that they were unable to cite owing to space constraints. They thank H. Wang for critical comments on the manuscript. Synthetic biology research in the laboratory of M.F. is supported by the European Research Council (ERC ProNet advanced grant no. 321381) and by the Swiss National Centre of Competence in Research (NCCR) Molecular Systems Engineering. | applied life sciences;assembled genetic circuits;biomedicine;biotechnology industry;blood transfusion therapies;cell engineering;complex problems;control;converting cells;discipline;early breakthroughs;ectopic (over) expression;engineering application-driven biological functionalities;environmental sciences;high spatiotemporal precision;human cell functions;intractable diseases;larger-scale;living therapeutics;nature;personalized medicine;regenerative medicine;revolutionary impact;single sets;synthetic biology;transgenes;will open new possibilities | 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| BACTERIA DETECT;CHIMERIC-ANTIGEN-RECEPTOR;DRIVE SYSTEM;LOGIC COMPUTATION;MAMMALIAN-CELLS;OPTICAL CONTROL;SINGLE-CELL;T-CELLS;TOGGLE SWITCH;TRANSCRIPTION FACTOR | Xie, Mingqi; Fussenegger, Martin; | null | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland;Univ Basel, Fac Sci, Basel, Switzerland | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland;Univ Basel, Fac Sci, Basel, Switzerland | 1471-0080 | null | 8 | 1998;2000;2001;2003;2004;2005;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016;2017;2018 | 147 | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland;Univ Basel, Fac Sci, Basel, Switzerland | Nat. Rev. Mol. Cell Biol. | Fussenegger, Martin | NATURE PUBLISHING GROUP | (over);,;a;advance;already;and;application-driven;applied;assembled;based;biological;biology;biomedicine;biotechnology;blood;breakthroughs;by;cell;cells;circuits;combat;complex;control;converting;discipline;diseases;early;ectopic;employing;engineered;engineering;environmental;evolved;expression;for;functionalities;functions;genetic;had;have;high;hitherto;human;impact;in;industry;into;intractable;is;larger-scale;life;living;medicine;more;nature;new;not;now;of;on;open;order;personalized;possibilities;precision;problems;programme;rationally;regenerative;require;revolutionary;Sciences;sets;single;solve;spatiotemporal;synthetic;that;the;therapeutics;therapies;this;to;transfusion;transgenes;various;we;were;which;will;with | Swiss Fed Inst Technol;Univ Basel | Synthetic biology is the discipline of engineering application-driven biological functionalities that were not evolved by nature. Early breakthroughs of cell engineering, which were based on ectopic (over) expression of single sets of transgenes, have already had a revolutionary impact on the biotechnology industry, regenerative medicine and blood transfusion therapies. Now, we require larger-scale, rationally assembled genetic circuits engineered to programme and control various human cell functions with high spatiotemporal precision in order to solve more complex problems in applied life sciences, biomedicine and environmental sciences. This will open new possibilities for employing synthetic biology to advance personalized medicine by converting cells into living therapeutics to combat hitherto intractable diseases. | null | BACTERIA DETECT;CHIMERIC-ANTIGEN-RECEPTOR;DRIVE SYSTEM;LOGIC COMPUTATION;MAMMALIAN-CELLS;OPTICAL CONTROL;SINGLE-CELL;T-CELLS;TOGGLE SWITCH;TRANSCRIPTION FACTORS | 9 | null | null | 19 | BACTERIA DETECT;CHIMERIC ANTIGEN RECEPTOR;DRIVE SYSTEM;LOGIC COMPUTATION;MAMMALIAN-CELLS;OPTICAL CONTROL;SINGLE-CELL;T-CELLS;toggle switch;transcription factor | WOS:000439404000008 | Swiss Fed Inst Technol, Basel, Switzerland;Univ Basel, Basel, Switzerland | Switzerland | 2,018 | null | null | null | null | English | null | ACS CHEM BIOL;ACS SYNTH BIOL;ANGEW CHEM INT EDIT;ANNU REV BIOCHEM;ANNU REV CHEM BIOMOL;ANNU REV PHARMACOL;BIOTECHNIQUES;BIOTECHNOL BIOENG;BLOOD;BMC BIOL;BMC SYST BIOL;CELL;CELL REP;CELL STEM CELL;CHEM BIOL;CLIN CANCER RES;CSH PERSPECT BIOL;CURR OPIN BIOTECH;CURR OPIN CHEM BIOL;EMBO REP;GENE DEV;J BIOL CHEM;J Biol Eng;J CELL BIOL;J CELL SCI;J CONTROL RELEASE;J HEPATOL;LAB CHIP;METAB ENG;MOL CELL;MOL SYST BIOL;MOL THER-NUCL ACIDS;NANO LETT;NAT BIOMED ENG;NAT BIOTECHNOL;NAT CELL BIOL;NAT CHEM BIOL;NAT COMMUN;NAT MED;NAT METHODS;NAT NANOTECHNOL;NAT REV CANCER;NAT REV DRUG DISCOV;NAT REV IMMUNOL;NAT REV MOL CELL BIO;NAT STRUCT MOL BIOL;NATURE;NEW ENGL J MED;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;SCI REP-UK;SCI TRANSL MED;SCIENCE;TRENDS BIOTECHNOL;WIRES SYST BIOL MED | Fussenegger, Martin;Xie, Mingqi | 2024-03-11
ER | Ajikumar, P K;Ariyachet, C;Atkinson, M R;Atsumi, S;Ausländer, D;Ausländer, S;Bacchus, W;Baeumler, T A;Bai, P;Barker, N;Barnea, G;Basu, S;Beisel, C L;Beyer, H M;Bonger, K M;Bonnet, J;Borrero, J;Briner, A E;Bugaj, L J;Burrill, D R;Chakravarti, D;Chan, C T Y;Chappell, J;Chen, B H;Chen, D;Chen, Y;Chilov, D;Chung, S;Copeland, M F;Courbet, A;Covert, M W;Culler, S J;Danino, T;Deans, T L;Di Stasi, A;Din, M O;Dominguez, A A;Eichenberger, M;Eil, R;Elowitz, M B;Esvelt, K M;Farzadfard, F;Fedorov, V D;Fesnak, A D;Finley, D;Fire, A;Folcher, M;Frieda, K L;Fukuda, N;Fung, E;Fux, C;Gaber, R;Galanie, S;Gardner, T S;Garg, A;Gootenberg, J S;Grada, Z;Graf, T;Greber, D;Green, A A;Griss, R;Hammond, A;Heng, B C;Hughes, R M;Hussain, F;Imanishi, M;Ipsaro, J J;Janse, D M;Kahn, M;Kalhor, R;Karlsson, M;Kashida, S;Kawano, F;Keeley, M B;Kemmer, C;Khalil, A S;Klebanoff, C A;Kobayashi, H;Kojima, R;Kolar, K;Kotula, J W;Kramer, B P;Lapique, N;Leisner, M;Lescroart, F;Levskaya, A;Lienert, F;Lim, W A;Liu, C L;Liu, Y C;Livet, J;Macian, F;Maude, S L;Menzel, A;Metcalfe, C;Minty, J J;Mishra, D;Mondragón-Palomino, O;Moon, E K;Moon, T S;Morsut, L;Myhrvold, C;Müller, K;Müller, M;Neddermann, P;Nielsen, J;Nihongaki, Y;Niopek, D;Nishimura, K;Nissim, L;Paddon, C J;Paek, K Y;Pagliuca, F W;Pardee, K;Park, J S;Perli, S D;Porter, D L;Prindle, A;Prochazka, L;Regot, S;Renicke, C;Riglar, D T;Rinaudo, K;Roybal, K T;Ruegg, T L;Ryback, B M;Rössger, K;Saeidi, N;Sandri, M;Saxena, P;Schena, A;Schukur, L;Schwarz, K A;Sedlmayer, F;Shao, J W;Siuti, P;Skjoedt, M L;Slomovic, S;Spiltoir, J I;Stanton, B C;Stricker, J;Strickland, D;Swofford, C A;Takahashi, K;Tamsir, A;Teague, B P;Thakore, P I;Tigges, M;Toettcher, J E;Torikai, H;Van Etten, J;Wang, W;Wang, Y H;Weber, W;Wehr, M C;Weinberg, B H;Whitaker, W R;Widmaier, D M;Win, M N;Windbichler, N;Wong, A;Wright, C M;Wu, C Y;Wu, Y I;Wurm, F M;Xie, M;Xie, Z;Yang, L;Yang, X R;Yao, G;Ye, H F;You, L C;Zalatan, J G;Zhou, Q;Zhu, S Y | GN8IV | Basel, Switzerland;Basel, Switzerland. | 171 | null | 2 | null | 29,858,606 | Fussenegger, Martin;Xie, Mingqi | NAT REV MOL CELL BIO | Basel, Switzerland |
Cecchi, R J;Chan, Y L;Chavez, A;CHURCH, G M;Collins, J J;Davidsohn, N;Ebrahimkhani, M R;Guo, X G;Kiani, S;Kuo, C C;Lance-Byrne, A;Lewis, N E;Lim, E T;Menn, D;Milanova, D;Pradhan, S;Sharma, S;Tung, A;Tuttle, M;Yeo, N C | 10.1038/s41592-018-0048-5 | null | MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND | 112f4c6u46483l6y5b472g253i6e1j5q73y2s6e | An enhanced CRISPR repressor for targeted mammalian gene regulation | Harvard Univ | null | Chavez, A (corresponding author), Columbia Univ Coll Phys & Surg, Dept Pathol & Cell Biol, 630 W 168th St, New York, NY 10032 USA.;Church, GM (corresponding author), Harvard Med Sch, Dept Genet, Boston, MA 02115 USA.;Church, GM (corresponding author), Harvard Univ, Wyss Inst Biol Inspired Engn, Cambridge, MA 02138 USA.;Kiani, S (corresponding author), Arizona State Univ, Ira A Fulton Sch Engn, Sch Biol & Hlth Syst Engn, Tempe, AZ 85287 USA. | null | Cecchi, Ryan J;Chan, Yingleong;Chavez, Alejandro;Church, George M;Collins, James J;Davidsohn, Noah;Ebrahimkhani, Mo R;Guo, Xiaoge;Kiani, Samira;Kuo, Chih-Chung;Lance-Byrne, Alissa;Lewis, Nathan E;Lim, Elaine T;Menn, David;Milanova, Denitsa;Pradhan, Swechchha;Sharma, Sumana;Tung, Angela;Tuttle, Marcelle;Yeo, Nan Cher | Biochemical Research Methods | NIH [RM1 HG008525, P50 HG005550]; National Cancer Institute [5T32CA009216-34]; Burroughs Wellcome Fund (Career Award for Medical Scientists); NIGMS [R35 GM119850]; Novo Nordisk Foundation [NNF10CC1016517]; DARPA (Young Faculty Award) [D16AP00047]; Arizona State University Fulton Schools of Engineering startup fund; Paul G. Allen Frontiers Group | WOS | Chavez, A;Church, G M;Kiani, S | Arizona State Univ, Tempe, AZ USA;Broad Inst MIT & Harvard, Cambridge, MA USA;Columbia Univ Coll Phys & Surg, New York, NY USA;Harvard Med Sch, Boston, MA USA;Harvard Univ, Cambridge, MA USA;Mayo Clin, Phoenix, AZ USA;MIT, Cambridge, MA USA;Univ Calif San Diego, San Diego, CA USA;Wellcome Trust Sanger Inst, Cambridge, England | 15 | an;CRISPR;enhanced;for;gene;mammalian;regulation;repressor;targeted | 2 | Cecchi, Ryan;church, george;Ebrahimkhani, Mo R.;Kiani, Samira;Lewis, Nathan;Lim, Teng-Ting;Pradhan, Swechchha;Sharma, Sumana;Tuttle, Marcelle;Yeo, Nan Cher | NATURE PUBLISHING GROUP | Arizona State Univ, Ira A Fulton Sch Engn, Sch Biol & Hlth Syst Engn, Tempe, AZ 85287 USA;Broad Inst MIT & Harvard, Cambridge, MA 02142 USA;Columbia Univ Coll Phys & Surg, Dept Pathol & Cell Biol, 630 W 168th St, New York, NY 10032 USA;Harvard Med Sch, Dept Genet, Boston, MA 02115 USA;Harvard Univ, Wyss Inst Biol Inspired Engn, Cambridge, MA 02138 USA;Harvard Univ, Wyss Inst Biol Inspired Engn, Cambridge, MA 02138 USA.; Church, GM (corresponding author), Harvard Med Sch, Dept Genet, Boston, MA 02115 USA.; Chavez, A (corresponding author), Columbia Univ Coll Phys & Surg, Dept Pathol & Cell Biol, 630 W 168th St, New York, NY 10032 USA.; Kiani, S (corresponding author), Arizona State Univ, Ira A Fulton Sch Engn, Sch Biol & Hlth Syst Engn, Tempe, AZ 85287 USA;Mayo Clin, Coll Med & Sci, Div Gastroenterol & Hematol, Phoenix, AZ USA;MIT, Dept Biol Engn, 77 Massachusetts Ave, Cambridge, MA 02139 USA;MIT, Inst Med Engn & Sci, 77 Massachusetts Ave, Cambridge, MA 02139 USA;MIT, Synthet Biol Ctr, 77 Massachusetts Ave, Cambridge, MA 02139 USA;Univ Calif San Diego, Dept Bioengn, San Diego, CA 92103 USA;Univ Calif San Diego, Dept Pediat, San Diego, CA 92103 USA;Univ Calif San Diego, Novo Nordisk Fdn, Ctr Biosustainabil, San Diego, CA 92103 USA;Wellcome Trust Sanger Inst, Cell Surface Signalling Lab, Cambridge, England | Article | Arizona State Univ;Columbia Univ Coll Phys & Surg;Harvard Med Sch;Harvard Univ | LONDON | null | null | Arizona State Univ;Broad Inst MIT & Harvard;Columbia Univ Coll Phys & Surg;Harvard Med Sch;Harvard Univ;Mayo Clin;MIT;Univ Calif San Diego;Wellcome Trust Sanger Inst | Arizona State University Fulton Schools of Engineering startup fund;Burroughs Wellcome Fund (Career Award for Medical Scientists);DARPA (Young Faculty Award);National Cancer Institute;NIGMS;NIH;Novo Nordisk Foundation;Paul G. Allen Frontiers Group | Church, GM (corresponding author), Harvard Univ, Wyss Inst Biol Inspired Engn, Cambridge, MA 02138 USA.; Church, GM (corresponding author), Harvard Med Sch, Dept Genet, Boston, MA 02115 USA.; Chavez, A (corresponding author), Columbia Univ Coll Phys & Surg, Dept Pathol & Cell Biol, 630 W 168th St, New York, NY 10032 USA.; Kiani, S (corresponding author), Arizona State Univ, Ira A Fulton Sch Engn, Sch Biol & Hlth Syst Engn, Tempe, AZ 85287 USA. | + | Cecchi, Ryan J;Chan, Yingleong;Chavez, Alejandro;Church, George M;Collins, James J;Davidsohn, Noah;Ebrahimkhani, Mo R;Guo, Xiaoge;Kiani, Samira;Kuo, Chih-Chung;Lance-Byrne, Alissa;Lewis, Nathan E;Lim, Elaine T;Menn, David;Milanova, Denitsa;Pradhan, Swechchha;Sharma, Sumana;Tung, Angela;Tuttle, Marcelle;Yeo, Nan Cher | 83 | 13 | 440,334,000,022 | Arizona State University Fulton Schools of Engineering startup fund;Burroughs Wellcome Fund (Career Award for Medical Scientists);DARPA (Young Faculty Award) [D16AP00047];National Cancer Institute [5T32CA009216-34];NIGMS [R35 GM119850];NIH [RM1 HG008525, P50 HG005550];Novo Nordisk Foundation [NNF10CC1016517];Paul G. Allen Frontiers Group | UK;USA | NATURE METHODS | USA;USA.; | null | null | Harvard Univ, Wyss Inst Biol Inspired Engn, Cambridge, MA 02138 USA | 1548-7091 | Cecchi, R J;Chan, Y L;Chavez, A;CHURCH, G M;Collins, J J;Davidsohn, N;Ebrahimkhani, M R;Guo, X G;Kiani, S;Kuo, C C;Lance-Byrne, A;Lewis, N E;Lim, E T;Menn, D;Milanova, D;Pradhan, S;Sharma, S;Tung, A;Tuttle, M;Yeo, N C | AUG | ac4304@cumc.columbia.edu;gchurch@genetics.med.harvard.edu;samira.kiani@asu.edu | enhanced CRISPR repressor;mammalian gene regulation | 20 | J | Biochemistry & Molecular Biology | C-terminal fusion;Cas9;coding;CPG-BINDING PROTEIN;designed bipartite repressor domain;DNA METHYLATION;dual guide RNA library screens;enabling new architectures;ENDONUCLEASE;enhanced CRISPR repressor;expression;genome;HISTONE DEACETYLASE;HUMAN-CELLS;improved Cas9 repressor;inefficiencies;KRAB-MeCP2;mammalian gene regulation;MECP2;noncoding genes;nuclease-dead Cas9;programmable transcriptional repressor;results;RNA-guided endonuclease Cas9;single;synthetic genetic circuits;system's superiority;target genes;target-gene;TRANSCRIPTIONAL REPRESSION;utility | Yeo, N C | CAS9;CPG-BINDING PROTEIN;DNA METHYLATION;ENDONUCLEASE;EXPRESSION;GENOME;HISTONE DEACETYLASE;HUMAN-CELLS;MECP2;TRANSCRIPTIONAL REPRESSION | 611 | [Yeo, Nan Cher; Lance-Byrne, Alissa; Chan, Yingleong; Milanova, Denitsa; Guo, Xiaoge; Tung, Angela; Cecchi, Ryan J.; Tuttle, Marcelle; Lim, Elaine T.; Davidsohn, Noah; Collins, James J.; Church, George M.] Harvard Univ, Wyss Inst Biol Inspired Engn, Cambridge, MA 02138 USA. [Yeo, Nan Cher; Chan, Yingleong; Milanova, Denitsa; Guo, Xiaoge; Lim, Elaine T.; Davidsohn, Noah; Church, George M.] Harvard Med Sch, Dept Genet, Boston, MA 02115 USA. [Chavez, Alejandro] Columbia Univ Coll Phys & Surg, Dept Pathol & Cell Biol, 630 W 168th St, New York, NY 10032 USA. [Menn, David; Pradhan, Swechchha; Ebrahimkhani, Mo R.; Kiani, Samira] Arizona State Univ, Ira A Fulton Sch Engn, Sch Biol & Hlth Syst Engn, Tempe, AZ 85287 USA. [Kuo, Chih-Chung; Lewis, Nathan E.] Univ Calif San Diego, Dept Bioengn, San Diego, CA 92103 USA. [Kuo, Chih-Chung; Lewis, Nathan E.] Univ Calif San Diego, Novo Nordisk Fdn, Ctr Biosustainabil, San Diego, CA 92103 USA. [Sharma, Sumana] Wellcome Trust Sanger Inst, Cell Surface Signalling Lab, Cambridge, England. [Ebrahimkhani, Mo R.] Mayo Clin, Coll Med & Sci, Div Gastroenterol & Hematol, Phoenix, AZ USA. [Collins, James J.] MIT, Inst Med Engn & Sci, 77 Massachusetts Ave, Cambridge, MA 02139 USA. [Collins, James J.] MIT, Synthet Biol Ctr, 77 Massachusetts Ave, Cambridge, MA 02139 USA. [Collins, James J.] MIT, Dept Biol Engn, 77 Massachusetts Ave, Cambridge, MA 02139 USA. [Collins, James J.] Broad Inst MIT & Harvard, Cambridge, MA 02142 USA. [Lewis, Nathan E.] Univ Calif San Diego, Dept Pediat, San Diego, CA 92103 USA. | This work was supported by the NIH (grants RM1 HG008525 and P50 HG005550 to G.M.C.), the National Cancer Institute (grant 5T32CA009216-34 to A.C.), the Burroughs Wellcome Fund (Career Award for Medical Scientists to A.C.), NIGMS (R35 GM119850 to N.E.L.), the Novo Nordisk Foundation (NNF10CC1016517 to N.E.L.), DARPA (Young Faculty Award D16AP00047 to S.K.), the Arizona State University Fulton Schools of Engineering startup fund (S.K.), and the Paul G. Allen Frontiers Group (J.J.C.). HEK293T cells were a gift from P. Mali (University of California, San Diego, San Diego, CA, USA). psPAX2 was a gift from D. Trono (Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland). pCMV-VSV-G was a gift from B. Weinberg (Massachusetts Institute of Technology, Boston, MA, USA). The plasmid containing a single gRNA library targeting essential genes was a gift from R. Bernards (The Netherlands Cancer Institute, Amsterdam, the Netherlands). | C-terminal fusion;coding;designed bipartite repressor domain;dual guide RNA library screens;enabling new architectures;improved Cas9 repressor;inefficiencies;KRAB-MeCP2;noncoding genes;nuclease-dead Cas9;programmable transcriptional repressor;results;RNA-guided endonuclease Cas9;single;synthetic genetic circuits;system's superiority;target genes;target-gene;utility | 10.1006/meth.2001.1262;10.1016/j.cell.2013.02.022;10.1016/j.cell.2013.04.025;10.1016/j.cell.2013.06.044;10.1016/j.cell.2014.09.029;10.1016/j.cell.2014.09.039;10.1016/j.cell.2014.11.052;10.1016/j.stem.2016.01.022;10.1016/S0921-8777(99)00072-5;10.1038/30764;10.1038/561;10.1038/nature12466;10.1038/nature13166;10.1038/nature14136;10.1038/nature16526;10.1038/nbt.2501;10.1038/nbt.2507;10.1038/nbt.2800;10.1038/nbt.2808;10.1038/nbt.2889;10.1038/nbt.2916;10.1038/nbt.3536;10.1038/nmeth.4225;10.1038/onc.2014.470;10.1073/pnas.1431624100;10.1073/pnas.93.26.15299;10.1074/jbc.M209923200;10.1093/nar/24.24.4859;10.1093/nar/gkl1035;10.1093/nar/gkt135;10.1093/nar/gkw1112;10.1101/gad.10.16.2067;10.1101/gr.179044.114;10.1101/sqb.1998.63.435;10.1126/science.1225829;10.1126/science.1231143;10.1126/science.1232033;10.1126/science.1246981;10.1126/science.1247005;10.1126/science.1257601;10.1126/science.aaf1420;10.1128/MCB.00512-15;10.1146/annurev.genet.39.073003.114751;10.1186/s13059-014-0554-4;10.18632/oncotarget.4875;10.4161/cc.22581;[10.1038/NMETH.2969, 10.1038/nmeth.2969];[10.1038/NMETH.3312, 10.1038/nmeth.3312];[10.1038/NMETH.3733, 10.1038/nmeth.3733];[10.1038/nmeth.3871, 10.1038/NMETH.3871] | Harvard Univ | Cecchi, R J;Chan, Y L;Chavez, A;CHURCH, G M;Collins, J J;Davidsohn, N;Ebrahimkhani, M R;Guo, X G;Kiani, S;Kuo, C C;Lance-Byrne, A;Lewis, N E;Lim, E T;Menn, D;Milanova, D;Pradhan, S;Sharma, S;Tung, A;Tuttle, M;Yeo, N C | Yeo, N C: Harvard Univ, Wyss Inst Biol Inspired Engn, Cambridge, MA 02138 USA | Kuo, Chihchung;Lewis, Nathan | 5T32CA009216-34;D16AP00047;NNF10CC1016517;P50 HG005550;R35 GM119850;RM1 HG008525 | 51 | null | USA | Arizona State Univ;Broad Inst MIT & Harvard;Columbia Univ Coll Phys & Surg;Harvard Med Sch;Harvard Univ;Mayo Clin;MIT;Univ Calif San Diego;Wellcome Trust Sanger Inst | Yeo, Nan Cher | Green Submitted, Green Accepted | CAS9;CPG-BINDING PROTEIN;DNA METHYLATION;ENDONUCLEASE;EXPRESSION;GENOME;HISTONE DEACETYLASE;HUMAN-CELLS;MECP2;TRANSCRIPTIONAL REPRESSION | Yeo, Nan Cher; Chavez, Alejandro; Lance-Byrne, Alissa; Chan, Yingleong; Menn, David; Milanova, Denitsa; Kuo, Chih-Chung; Guo, Xiaoge; Sharma, Sumana; Tung, Angela; Cecchi, Ryan J.; Tuttle, Marcelle; Pradhan, Swechchha; Lim, Elaine T.; Davidsohn, Noah; Ebrahimkhani, Mo R.; Collins, James J.; Lewis, Nathan E.; Kiani, Samira; Church, George M.; | null | Arizona State Univ, Ira A Fulton Sch Engn, Sch Biol & Hlth Syst Engn, Tempe, AZ 85287 USA;Broad Inst MIT & Harvard, Cambridge, MA 02142 USA;Columbia Univ Coll Phys & Surg, Dept Pathol & Cell Biol, 630 W 168th St, New York, NY 10032 USA;Harvard Med Sch, Dept Genet, Boston, MA 02115 USA;Harvard Univ, Wyss Inst Biol Inspired Engn, Cambridge, MA 02138 USA;Mayo Clin, Coll Med & Sci, Div Gastroenterol & Hematol, Phoenix, AZ USA;MIT, Dept Biol Engn, 77 Massachusetts Ave, Cambridge, MA 02139 USA;MIT, Inst Med Engn & Sci, 77 Massachusetts Ave, Cambridge, MA 02139 USA;MIT, Synthet Biol Ctr, 77 Massachusetts Ave, Cambridge, MA 02139 USA;Univ Calif San Diego, Dept Bioengn, San Diego, CA 92103 USA;Univ Calif San Diego, Dept Pediat, San Diego, CA 92103 USA;Univ Calif San Diego, Novo Nordisk Fdn, Ctr Biosustainabil, San Diego, CA 92103 USA;Wellcome Trust Sanger Inst, Cell Surface Signalling Lab, Cambridge, England | Arizona State Univ, Ira A Fulton Sch Engn, Sch Biol & Hlth Syst Engn, Tempe, AZ 85287 USA;Broad Inst MIT & Harvard, Cambridge, MA 02142 USA;Columbia Univ Coll Phys & Surg, Dept Pathol & Cell Biol, 630 W 168th St, New York, NY 10032 USA;Harvard Med Sch, Dept Genet, Boston, MA 02115 USA;Harvard Univ, Wyss Inst Biol Inspired Engn, Cambridge, MA 02138 USA;Mayo Clin, Coll Med & Sci, Div Gastroenterol & Hematol, Phoenix, AZ USA;MIT, Dept Biol Engn, 77 Massachusetts Ave, Cambridge, MA 02139 USA;MIT, Inst Med Engn & Sci, 77 Massachusetts Ave, Cambridge, MA 02139 USA;MIT, Synthet Biol Ctr, 77 Massachusetts Ave, Cambridge, MA 02139 USA;Univ Calif San Diego, Dept Bioengn, San Diego, CA 92103 USA;Univ Calif San Diego, Dept Pediat, San Diego, CA 92103 USA;Univ Calif San Diego, Novo Nordisk Fdn, Ctr Biosustainabil, San Diego, CA 92103 USA;Wellcome Trust Sanger Inst, Cell Surface Signalling Lab, Cambridge, England | 1548-7105 | null | 8 | 1996;1998;2000;2001;2003;2007;2009;2012;2013;2014;2015;2016;2017 | 246 | Arizona State Univ, Ira A Fulton Sch Engn, Sch Biol & Hlth Syst Engn, Tempe, AZ 85287 USA;Columbia Univ Coll Phys & Surg, Dept Pathol & Cell Biol, 630 W 168th St, New York, NY 10032 USA;Harvard Med Sch, Dept Genet, Boston, MA 02115 USA;Harvard Univ, Wyss Inst Biol Inspired Engn, Cambridge, MA 02138 USA | Nat. Methods | Church, George M | NATURE PUBLISHING GROUP | ,;a;an;and;architectures;based;be;bipartite;but;C-terminal;can;Cas9;circuits;coding;converted;demonstrate;describe;designed;domain;dual;enabling;endonuclease;fusion;genes;genetic;guide;have;here;improved;improving;in;inefficiencies;into;its;KRAB-MeCP2;library;limited;new;noncoding;nuclease-dead;of;on;programmable;rationally;repressing;repressor;results;RNA;RNA-guided;screens;series;silencing;simultaneously;single;superiority;synthetic;system's;target;target-gene;the;to;transcriptional;utility;we | Arizona State Univ;Columbia Univ Coll Phys & Surg;Harvard Med Sch;Harvard Univ | The RNA-guided endonuclease Cas9 can be converted into a programmable transcriptional repressor, but inefficiencies in target-gene silencing have limited its utility. Here we describe an improved Cas9 repressor based on the C-terminal fusion of a rationally designed bipartite repressor domain, KRAB-MeCP2, to nuclease-dead Cas9. We demonstrate the system's superiority in silencing coding and noncoding genes, simultaneously repressing a series of target genes, improving the results of single and dual guide RNA library screens, and enabling new architectures of synthetic genetic circuits. | ABE-7290-2020;X-4576-2019 | CAS9;CPG-BINDING PROTEIN;DNA METHYLATION;ENDONUCLEASE;EXPRESSION;GENOME;HISTONE DEACETYLASES;HUMAN-CELLS;MECP2;TRANSCRIPTIONAL REPRESSION | 3 | null | null | 11 | CAS9;CPG-BINDING PROTEIN;DNA METHYLATION;ENDONUCLEASE;EXPRESSION;GENOME;HISTONE DEACETYLASE;HUMAN-CELLS;MECP2;TRANSCRIPTIONAL REPRESSION | WOS:000440334000022 | Arizona State Univ, Tempe, AZ USA;Broad Inst MIT & Harvard, Cambridge, MA USA;Columbia Univ Coll Phys & Surg, New York, NY USA;Harvard Med Sch, Boston, MA USA;Harvard Univ, Cambridge, MA USA;Mayo Clin, Phoenix, AZ USA;MIT, Cambridge, MA USA;Univ Calif San Diego, San Diego, CA USA;Wellcome Trust Sanger Inst, Cambridge, England | UK;USA | 2,018 | null | 0000-0001-5753-6779;0000-0001-6232-9969;0000-0001-7550-5108;0000-0001-7700-3654;0000-0002-6354-4115;0000-0003-0598-2181;0000-0003-2695-1501;0000-0003-3651-0654;0009-0005-1246-8879;0009-0009-5463-1215 | null | null | English | null | ANNU REV GENET;BioRxiv;CELL;CELL CYCLE;CELL STEM CELL;COLD SPRING HARB SYM;GENE DEV;GENOME BIOL;GENOME RES;J BIOL CHEM;METHODS;MOL CELL BIOL;MUTAT RES-DNA REPAIR;NAT BIOTECHNOL;NAT GENET;NAT METHODS;NATURE;NUCLEIC ACIDS RES;ONCOGENE;ONCOTARGET;P NATL ACAD SCI USA;SCIENCE | Cecchi, Ryan J;Chan, Yingleong;Chavez, Alejandro;Church, George M;Collins, James J;Davidsohn, Noah;Ebrahimkhani, Mo R;Guo, Xiaoge;Kiani, Samira;Kuo, Chih-Chung;Lance-Byrne, Alissa;Lewis, Nathan E;Lim, Elaine T;Menn, David;Milanova, Denitsa;Pradhan, Swechchha;Sharma, Sumana;Tung, Angela;Tuttle, Marcelle;Yeo, Nan Cher | 2024-03-11
ER | Budd, M E;Chavez, A;Cho, S W;Cong, L;Costanzo, M;Dicarlo, J E;Dixon, S J;Evers, B;Friedman, J R;Fu, Y F;Gilbert, L A;Hwang, W Y;Imamura, O;Jinek, M;Jones, P L;Kiani, S;Kim, S S;Kimura, H;Kleinstiver, B P;Koike-Yusa, H;Konermann, S;Kuscu, C;La Russa, M F;Li, F Y;Li, W;Livak, K J;Mali, P;Mandegar, M A;Menche, J;Moosmann, P;Nan, X S;Polstein, L R;Popuri, V;Qi, L S;Sajesh, B V;Shalem, O;Shao S.;Shen, J P;Stepper, P;Stolzenburg, S;Tanenbaum, M E;Thakore, P I;Wade, P A;Wang, H Y;Wang, T;Wu, X B;Zalatan, J G;Zhou, Y X | GO8JG | Boston, MA USA.;Cambridge, MA USA.;New York, NY USA.;Tempe, AZ USA | 298 | null | 9 | null | 30,013,045 | Cecchi, Ryan J;Chan, Yingleong;Chavez, Alejandro;Church, George M;Collins, James J;Davidsohn, Noah;Ebrahimkhani, Mo R;Guo, Xiaoge;Kiani, Samira;Kuo, Chih-Chung;Lance-Byrne, Alissa;Lewis, Nathan E;Lim, Elaine T;Menn, David;Milanova, Denitsa;Pradhan, Swechchha;Sharma, Sumana;Tung, Angela;Tuttle, Marcelle;Yeo, Nan Cher | NAT METHODS | Boston, MA USA;Cambridge, England;Cambridge, MA USA;New York, NY USA;Phoenix, AZ USA;San Diego, CA USA;Tempe, AZ USA |
Arzumanyan, G A;Gabriel, K N;Javanpour, A A;Liu, C C;Ravikumar, A | 10.1021/acssynbio.8b00195 | null | 1155 16TH ST, NW, WASHINGTON, DC 20036 USA | 4x3f1k58172m474oz3u152i5i4u3o1w4v1g2a3u | Mutually Orthogonal DNA Replication Systems <i>In Vivo</i> | Univ Calif Irvine | null | Liu, CC (corresponding author), Univ Calif Irvine, Dept Biomed Engn, Irvine, CA 92697 USA.;Liu, CC (corresponding author), Univ Calif Irvine, Dept Chem, Irvine, CA 92697 USA.;Liu, CC (corresponding author), Univ Calif Irvine, Dept Mol Biol & Biochem, Irvine, CA 92697 USA. | null | Arzumanyan, Garri A;Gabriel, Kristin N;Javanpour, Alex A;Liu, Chang C;Ravikumar, Arjun | Biochemical Research Methods | National Science Foundation [MCB1545158]; Defense Advanced Research Projects Agency [HR0011-15-2-0031]; National Institutes of Health [1DP2GM119163-01]; Direct For Biological Sciences [1545158] Funding Source: National Science Foundation; Div Of Molecular and Cellular Bioscience [1545158] Funding Source: National Science Foundation | WOS | Liu, C C | Univ Calif Irvine, Irvine, CA USA | 7 | <i>in;DNA;mutually;Orthogonal;Replication;systems;vivo</i> | 1 | Ambrosini, Kristin;Liu, Chang | AMER CHEMICAL SOC | Univ Calif Irvine, Dept Biomed Engn, Irvine, CA 92697 USA;Univ Calif Irvine, Dept Biomed Engn, Irvine, CA 92697 USA.; Liu, CC (corresponding author), Univ Calif Irvine, Dept Mol Biol & Biochem, Irvine, CA 92697 USA.; Liu, CC (corresponding author), Univ Calif Irvine, Dept Chem, Irvine, CA 92697 USA;Univ Calif Irvine, Dept Chem, Irvine, CA 92697 USA;Univ Calif Irvine, Dept Mol Biol & Biochem, Irvine, CA 92697 USA | Article | Univ Calif Irvine | WASHINGTON | null | null | Univ Calif Irvine | Defense Advanced Research Projects Agency;Direct For Biological Sciences;Div Of Molecular and Cellular Bioscience;National Institutes of Health;National Science Foundation | Liu, CC (corresponding author), Univ Calif Irvine, Dept Biomed Engn, Irvine, CA 92697 USA.; Liu, CC (corresponding author), Univ Calif Irvine, Dept Mol Biol & Biochem, Irvine, CA 92697 USA.; Liu, CC (corresponding author), Univ Calif Irvine, Dept Chem, Irvine, CA 92697 USA. | 1729 | Arzumanyan, Garri A;Gabriel, Kristin N;Javanpour, Alex A;Liu, Chang C;Ravikumar, Arjun | 43 | 3 | 439,761,800,010 | Defense Advanced Research Projects Agency [HR0011-15-2-0031];Direct For Biological Sciences [1545158] Funding Source: National Science Foundation;Div Of Molecular and Cellular Bioscience [1545158] Funding Source: National Science Foundation;National Institutes of Health [1DP2GM119163-01];National Science Foundation [MCB1545158] | USA | ACS SYNTHETIC BIOLOGY | USA;USA.; | null | null | Univ Calif Irvine, Dept Biomed Engn, Irvine, CA 92697 USA | 2161-5063 | Arzumanyan, G A;Gabriel, K N;Javanpour, A A;Liu, C C;Ravikumar, A | JUL | ccl@uci.edu | Orthogonal DNA Replication Systems <i>In Vivo</i> | 5 | J | Biochemistry & Molecular Biology | cell-based continuous evolution;custom genes;demonstration;DNA replication;error-prone TP-DNAP2s;FLUCTUATION ANALYSIS;genetic recording;genomic replication;in vivo mutagenesis;KILLER SYSTEM;KLUYVEROMYCES-LACTIS;large;linear plasmids;mutation rate;MUTATION-RATE;new applications;orthogonal DNA replication system;orthogonal DNA replication systems;Orthogonal DNA Replication Systems <i>In Vivo</i>;orthogonal replication;pGKL1 replication;pGKL2;pGKL2 replication;pGKL2/TP-DNAP2 plasmid/DNA polymerase pair;Polymerase Engineering;properties;protein primed replication;Saccharomyces cerevisiae;second orthogonal replication system;supporting;synthetic biology;synthetic genetic polymers;TP-DNAP1;TP-DNAP2;tunable error rates;two;vivo continuous evolution;yeast;yeast cytoplasmically localized pGKL1/TP-DNAP1 plasmid/DNA polymerase pair | Arzumanyan, G A | DNA replication;FLUCTUATION ANALYSIS;in vivo mutagenesis;KILLER SYSTEM;KLUYVEROMYCES-LACTIS;linear plasmids;MUTATION-RATE;orthogonal replication;polymerase engineering;protein primed replication;SYNTHETIC GENETIC POLYMERS;YEAST | 1722 | [Arzumanyan, Garri A.; Ravikumar, Arjun; Javanpour, Alex A.; Liu, Chang C.] Univ Calif Irvine, Dept Biomed Engn, Irvine, CA 92697 USA. [Gabriel, Kristin N.; Liu, Chang C.] Univ Calif Irvine, Dept Mol Biol & Biochem, Irvine, CA 92697 USA. [Liu, Chang C.] Univ Calif Irvine, Dept Chem, Irvine, CA 92697 USA. | We thank members of our group for helpful discussions and suggestions. This research was funded by the National Science Foundation (MCB1545158), the Defense Advanced Research Projects Agency (HR0011-15-2-0031), and the National Institutes of Health (1DP2GM119163-01). | cell-based continuous evolution;custom genes;demonstration;error-prone TP-DNAP2s;genetic recording;genomic replication;large;mutation rate;new applications;orthogonal DNA replication system;orthogonal DNA replication systems;pGKL1 replication;pGKL2;pGKL2 replication;pGKL2/TP-DNAP2 plasmid/DNA polymerase pair;properties;Saccharomyces cerevisiae;second orthogonal replication system;supporting;synthetic biology;TP-DNAP1;TP-DNAP2;tunable error rates;two;vivo continuous evolution;yeast cytoplasmically localized pGKL1/TP-DNAP1 plasmid/DNA polymerase pair | 10.1002/cbic.201000215;10.1002/cbic.201500157;10.1002/yea.320060102;10.1007/7171_2007_095;10.1007/BF00120324;10.1007/BF00351695;10.1007/s10709-016-9904-3;10.1016/B978-0-12-385120-8.00015-2;10.1016/j.jmb.2004.02.018;10.1016/S0076-6879(05)09012-9;10.1038/nature13314;10.1038/nature13982;10.1038/nprot.2007.13;10.1038/nrg2626;10.1093/bioinformatics/btp253;10.1093/nar/25.17.3389;10.1093/nar/gkh726;10.1101/gr.2.1.28;10.1126/science.1217622;10.1126/science.aag0511;10.1371/journal.pgen.1002282;10.1534/genetics.107.071506;10.7554/eLife.03703;[10.1038/NCHEMBIO.1439, 10.1038/nchembio.1439] | Univ Calif Irvine | Arzumanyan, G A;Gabriel, K N;Javanpour, A A;Liu, C C;Ravikumar, A | Arzumanyan, G A: Univ Calif Irvine, Dept Biomed Engn, Irvine, CA 92697 USA | null | 1545158;1DP2GM119163-01;HR0011-15-2-0031;MCB1545158 | 26 | null | USA | Univ Calif Irvine | Arzumanyan, Garri A | Green Accepted | FLUCTUATION ANALYSIS;KILLER SYSTEM;KLUYVEROMYCES-LACTIS;MUTATION-RATE;SYNTHETIC GENETIC POLYMERS;YEAST | Arzumanyan, Garri A.; Gabriel, Kristin N.; Ravikumar, Arjun; Javanpour, Alex A.; Liu, Chang C.; | null | Univ Calif Irvine, Dept Biomed Engn, Irvine, CA 92697 USA;Univ Calif Irvine, Dept Chem, Irvine, CA 92697 USA;Univ Calif Irvine, Dept Mol Biol & Biochem, Irvine, CA 92697 USA | Univ Calif Irvine, Dept Biomed Engn, Irvine, CA 92697 USA;Univ Calif Irvine, Dept Chem, Irvine, CA 92697 USA;Univ Calif Irvine, Dept Mol Biol & Biochem, Irvine, CA 92697 USA | null | DNA replication;in vivo mutagenesis;linear plasmids;orthogonal replication;polymerase engineering;protein primed replication | 7 | 1990;1992;1997;2004;2005;2006;2007;2008;2009;2010;2011;2012;2014;2015;2016;2018 | 20 | Univ Calif Irvine, Dept Biomed Engn, Irvine, CA 92697 USA;Univ Calif Irvine, Dept Chem, Irvine, CA 92697 USA;Univ Calif Irvine, Dept Mol Biol & Biochem, Irvine, CA 92697 USA | ACS Synth. Biol. | Liu, Chang C | AMER CHEMICAL SOC | ,;a;an;and;applications;at;be;biology;both;by;can;cell-based;cerevisiae;continuous;custom;cytoplasmically;demonstration;DNA;drastically;enable;encoded;engineered;error;error-prone;evolution;expressed;forms;from;genes;genetic;genomic;here;in;increased;influencing;is;large;localized;mutation;mutually;new;of;Orthogonal;pair;pGKL1;pGKL1/TP-DNAP1;pGKL2;pGKL2/TP-DNAP2;plasmid/DNA;polymerase;properties;rate;rates;recording;replication;report;Saccharomyces;second;should;show;supporting;synthetic;system;systems;that;the;thereby;this;to;TP-DNAP1;TP-DNAP2;TP-DNAP2s;tunable;two;vivo;we;whose;with;without;yeast | Univ Calif Irvine | The yeast cytoplasmically localized pGKL1/TP-DNAP1 plasmid/DNA polymerase pair forms an orthogonal DNA replication system whose mutation rate can be drastically increased without influencing genomic replication, thereby supporting in vivo continuous evolution. Here, we report that the pGKL2/TP-DNAP2 plasmid/DNA polymerase pair forms a second orthogonal replication system. We show that custom genes can be encoded and expressed from pGKL2, that error-prone TP-DNAP2s can be engineered, and that pGKL2 replication by TP-DNAP2 is both orthogonal to genomic replication in Saccharomyces cerevisiae and mutually orthogonal with pGKL1 replication by TP-DNAP1. This demonstration of two mutually orthogonal DNA replication systems with tunable error rates and properties should enable new applications in cell-based continuous evolution, genetic recording, and synthetic biology at large. | null | FLUCTUATION ANALYSIS;KILLER SYSTEM;KLUYVEROMYCES-LACTIS;MUTATION-RATE;SYNTHETIC GENETIC POLYMERS;YEAST | 2 | null | DNA replication;in vivo mutagenesis;linear plasmids;orthogonal replication;polymerase engineering;protein primed replication | 15 | YEAST;DNA-REPLICATION;FLUCTUATION ANALYSIS;in vivo mutagenesis;KILLER SYSTEM;KLUYVEROMYCES-LACTIS;linear plasmids;Mutation rate;orthogonal replication;polymerase engineering;protein primed replication;SYNTHETIC GENETIC POLYMERS | WOS:000439761800010 | Univ Calif Irvine, Irvine, CA USA | USA | 2,018 | null | 0000-0002-3290-2880;0000-0002-9518-0483 | null | null | English | null | BIOINFORMATICS;BioRxiv;CHEMBIOCHEM;CURR GENET;ELIFE;GENETICA;GENETICS;J MOL BIOL;METHOD ENZYMOL;NAT CHEM BIOL;NAT PROTOC;NAT REV GENET;NATURE;NUCLEIC ACIDS RES;PCR Methods Appl;PLOS GENET;SCIENCE;YEAST | Arzumanyan, Garri A;Gabriel, Kristin N;Javanpour, Alex A;Liu, Chang C;Ravikumar, Arjun | 2024-03-11
ER | Altschul, S F;Amberg Dc.;Cadwell R, C;Foster, P L;Gibson, D G;Gietz, R D;Hall, B M;Herr, A J;Klassen Roland;Kranaster, R;Lang, G I;Malyshev, D A;Metzker, M L;Mysiak, M E;Perli, S D;Pinheiro, V B;Ravikumar, A;Rodríguez, I;Ryan, O W;Sarkar, S;Schaffrath, R;Stark, M J R;Taylor, A I;Zheng, Q | GO1ZR | Irvine, CA USA;Irvine, CA USA. | 31 | null | 1 | null | 29,969,238 | Arzumanyan, Garri A;Gabriel, Kristin N;Javanpour, Alex A;Liu, Chang C;Ravikumar, Arjun | ACS SYNTH BIOL | Irvine, CA USA |
Brophy, J A N;Dinneny, J R;Larue, T | 10.1016/j.semcdb.2017.08.051 | null | 24-28 OVAL RD, LONDON NW1 7DX, ENGLAND | 2ly643r4b150193u3hxd613i54n5j2st2i | Understanding and engineering plant form | Carnegie Inst Sci | null | Dinneny, JR (corresponding author), Carnegie Inst Sci, Dept Plant Biol, 290 Panama St, Stanford, CA 94305 USA. | null | Brophy, Jennifer A N;Dinneny, Jose R;LaRue, Therese | Cell Biology;Developmental Biology | U.S. Department of Energy's Biological and Environmental Research program [DE-SC0008769]; National Science Foundation Graduate Research Fellowship; National Institutes of Health Predoctoral Training Grant [T32GM007276]; U.S. Department of Energy (DOE) [DE-SC0008769] Funding Source: U.S. Department of Energy (DOE) | WOS | Dinneny, J R | Carnegie Inst Sci, Stanford, CA USA;Stanford Univ, Stanford, CA USA | 79 | and;engineering;form;plant;understanding | 1 | null | ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD | Carnegie Inst Sci, Dept Plant Biol, 290 Panama St, Stanford, CA 94305 USA;Stanford Univ, Dept Biol, Stanford, CA 94305 USA | Review | Carnegie Inst Sci | LONDON | null | null | Carnegie Inst Sci;Stanford Univ | National Institutes of Health Predoctoral Training Grant;National Science Foundation Graduate Research Fellowship;U.S. Department of Energy (DOE);U.S. Department of Energy's Biological and Environmental Research program | Dinneny, JR (corresponding author), Carnegie Inst Sci, Dept Plant Biol, 290 Panama St, Stanford, CA 94305 USA. | 77 | Brophy, Jennifer A N;Dinneny, Jose R;LaRue, Therese | 14 | 2 | 433,227,500,008 | National Institutes of Health Predoctoral Training Grant [T32GM007276];National Science Foundation Graduate Research Fellowship;U.S. Department of Energy (DOE) [DE-SC0008769] Funding Source: U.S. Department of Energy (DOE);U.S. Department of Energy's Biological and Environmental Research program [DE-SC0008769] | USA | SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY | USA | null | null | Carnegie Inst Sci, Dept Plant Biol, 290 Panama St, Stanford, CA 94305 USA | 1084-9521 | Brophy, J A N;Dinneny, J R;Larue, T | JUL | jdinneny@carnegiescience.edu | engineering plant form;understanding | 3 | J | Cell Biology;Developmental Biology | agriculture;altered forms;ARABIDOPSIS-THALIANA;Authors;C 2017;CELL-PROLIFERATION;comprehensive understanding;computer models;development;DNA REPLICONS;economic value;Elsevier Ltd;engineer plants;engineering;engineering plant form;fitness;GENE-EXPRESSION;growth;identifying genes;important determinant;iterative rounds;knowledge;MAIZE;modern techniques;novel plant forms;pathways;plant form;plant's form;plants;potential;potential role;prerequisite;process;review strategies;ROOT-SYSTEM ARCHITECTURE;SELECTION;SHOOT MERISTEMLESS;single genes;synthetic biology;synthetic genetic circuits;transcription factor;transgene;understanding;understanding development | Brophy, J A N | ARABIDOPSIS-THALIANA;CELL-PROLIFERATION;DNA REPLICONS;GENE-EXPRESSION;MAIZE;ROOT-SYSTEM ARCHITECTURE;SHOOT MERISTEMLESS;Synthetic biology;transcription factor;TRANSGENE | 68 | [Brophy, Jennifer A. N.; Dinneny, Jose R.] Carnegie Inst Sci, Dept Plant Biol, 290 Panama St, Stanford, CA 94305 USA. [LaRue, Therese] Stanford Univ, Dept Biol, Stanford, CA 94305 USA. | We thank members of the Dinneny lab, and anonymous reviewers for helpful comments during the preparation of this work. Funding was provided by the U.S. Department of Energy's Biological and Environmental Research program (Grant DE-SC0008769 to J.R.D.), the National Science Foundation Graduate Research Fellowship (T.L.) and the National Institutes of Health Predoctoral Training Grant (T32GM007276 to T.L.). Jose Dinneny is also supported in this work as an HHMI-Simons Faculty Scholar. | agriculture;altered forms;comprehensive understanding;computer models;development;economic value;engineer plants;engineering;fitness;growth;identifying genes;important determinant;iterative rounds;knowledge;modern techniques;novel plant forms;pathways;plant form;plant's form;plants;potential;potential role;prerequisite;process;review strategies;selection;single genes;synthetic genetic circuits;understanding development | 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10.1038/nmeth.2404];[10.1038/nmeth.2515, 10.1038/NMETH.2515];[10.1038/NMETH.2926, 10.1038/nmeth.2926];[10.1038/NMETH.3659, 10.1038/nmeth.3659] | Carnegie Inst Sci | Brophy, J A N;Dinneny, J R;Larue, T | Brophy, J A N: Carnegie Inst Sci, Dept Plant Biol, 290 Panama St, Stanford, CA 94305 USA | Dinneny, Jose R | DE-SC0008769;T32GM007276 | 194 | null | USA | Carnegie Inst Sci;Stanford Univ | Brophy, Jennifer A N | hybrid | ARABIDOPSIS-THALIANA;CELL-PROLIFERATION;DNA REPLICONS;GENE-EXPRESSION;MAIZE;ROOT-SYSTEM ARCHITECTURE;SHOOT MERISTEMLESS;SYNTHETIC BIOLOGY;TRANSCRIPTION FACTOR;TRANSGENE | Brophy, Jennifer A. N.; LaRue, Therese; Dinneny, Jose R.; | null | Carnegie Inst Sci, Dept Plant Biol, 290 Panama St, Stanford, CA 94305 USA;Stanford Univ, Dept Biol, Stanford, CA 94305 USA | Carnegie Inst Sci, Dept Plant Biol, 290 Panama St, Stanford, CA 94305 USA;Stanford Univ, Dept Biol, Stanford, CA 94305 USA | null | null | null | 1970;1971;1972;1973;1986;1991;1992;1994;1995;1996;1997;1998;1999;2000;2001;2002;2003;2004;2005;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016;2017 | 7 | Carnegie Inst Sci, Dept Plant Biol, 290 Panama St, Stanford, CA 94305 USA | Semin. Cell Dev. Biol. | Dinneny, Jose R | ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD | ,;a;about;agriculture;altered;an;and;are;as;be;been;changing;circuits;comprehensive;computer;design;determinant;development;discuss;economic;effectively;emphasize;engineer;engineering;fitness;for;form;forms;generate;genes;genetic;growth;has;here;highlighted;historically;identifying;important;in;into;involved;is;iterative;its;knowledge;models;modern;more;needed;novel;of;or;pathways;plant;plant's;plants;potential;prerequisite;process;producing;requiring;review;role;rounds;selection;single;slow;strategies;synthetic;techniques;that;the;their;to;tools;translating;understanding;value;we;will;with | Carnegie Inst Sci | A plant's form is an important determinant of its fitness and economic value. Here, we review strategies for producing plants with altered forms. Historically, the process of changing a plant's form has been slow in agriculture, requiring iterative rounds of growth and selection. We discuss modern techniques for identifying genes involved in the development of plant form and tools that will be needed to effectively design and engineer plants with altered forms. Synthetic genetic circuits are highlighted for their potential to generate novel plant forms. We emphasize understanding development as a prerequisite to engineering and discuss the potential role of computer models in translating knowledge about single genes or pathways into a more comprehensive understanding of development. | J-8312-2012 | ARABIDOPSIS-THALIANA;CELL-PROLIFERATION;DNA REPLICONS;GENE-EXPRESSION;MAIZE;ROOT-SYSTEM ARCHITECTURE;SHOOT MERISTEMLESS;SYNTHETIC BIOLOGY;TRANSCRIPTION FACTORS;TRANSGENES | 0 | null | null | 10 | ARABIDOPSIS-THALIANA;CELL-PROLIFERATION;DNA REPLICONS;GENE-EXPRESSION;MAIZE;ROOT-SYSTEM ARCHITECTURE;SHOOT MERISTEMLESS;Synthetic biology;transcription factor;transgenic | WOS:000433227500008 | Carnegie Inst Sci, Stanford, CA USA;Stanford Univ, Stanford, CA USA | USA | 2,018 | null | null | null | null | English | null | ACS SYNTH BIOL;AM J BOT;AM NAT;ANN BOT-LONDON;ANNU PLANT REV;ANNU REV ECOL SYST;ANNU REV PLANT BIOL;Arabidopsis Book;BBA-GENE STRUCT EXPR;BioRxiv;BMC PLANT BIOL;BMC Plant Biology;CELL;CELL BIOSCI;COLLOID SURFACE B;CROP SCI;CSH PERSPECT BIOL;CSH Protoc;CURR BIOL;CURR OPIN BIOTECH;CURR OPIN CHEM BIOL;CURR OPIN MICROBIOL;CURR OPIN PLANT BIOL;DEV BIOL;DEVELOPMENT;ELIFE;EMBO J;ENVIRON SCI TECHNOL;EVOLUTION PLANT FORM;FEBS LETT;FRONT PLANT SCI;FUNCT ECOL;GENE DEV;GENETICS;GENOME BIOL;HORTIC RES-ENGLAND;J BIOSCI BIOENG;J EXP BOT;J HUM EVOL;J INTEGR PLANT BIOL;J R SOC INTERFACE;MAYDICA;METHODS MOL BIOL;MOL BREEDING;MOL CELLS;MOL SYST BIOL;NAT BIOTECHNOL;NAT CHEM BIOL;NAT COMMUN;NAT GENET;NAT METHODS;NAT REV GENET;NAT REV MICROBIOL;NAT REV MOL CELL BIO;NATURE;NEW PHYTOL;NUCLEIC ACIDS RES;ORNAMENTAL PLANT BIO;P NATL ACAD SCI USA;PHILOS T R SOC B;PLANT CELL;PLANT CELL ENVIRON;PLANT CELL REP;PLANT J;PLANT METHODS;PLANT MOL BIOL;PLANT MOL BIOL REP;PLANT PHYSIOL;PLANT SCI;PLANT SOIL;PLANT TRANSFORMATION;PLANTA;PLOS BIOL;PLOS ONE;SCI AM;SCI REP-UK;SCIENCE;SHAPE LIFE GENES;Syst Synth Biol;TRANSGENIC RES;TRENDS BIOTECHNOL;TRENDS ECOL EVOL;TRENDS GENET;TRENDS PLANT SCI;VADOSE ZONE J;WASTED AM IS LOSING | Brophy, Jennifer A N;Dinneny, Jose R;LaRue, Therese | 2024-03-11
ER | Abad, U;Aida, M;Allen, G;Altpeter, F;Ambrose B. A.;Anderson, J T;Antunes, M S;Araus, J L;Baltes, N J;Basu Supratim;Basu, S;Bergmann, D C;Blount, B A;Bommert, P;Bowman, J L;Brand, U;Brooks, C;Brophy, J A N;Buendía-Monreal, M;Byrne, M E;Cambray, G;Casal, J J;Cattolico, R A;Cermák, T;Charrier, B;Chen, L;Chen, Y J;Clark, S E;Clausnitzer, V;Coen, E S;Collard, B C Y;Cosgrove Daniel, J;Craine, J M;Curtin, S J;Daniell, H;Day, C D;De Dorlodot, S;De Rybel, B;De Smet, I;Depicker, A;Dinh Thanh Theresa;Doebley, J;Dorweiler, J E;Draper, J;Dubrovsky, J G;Dun, E A;Dunbabin, V M;Duncan, W G;Dutt, M;Duvick, D N;Elowitz, M B;Fahlgren, N;Falster, D S;Fletcher, L C;Fourcaud, T;Fritz Georg;Fukaki, H;Gatz, C;Gaudin, A C M;Gelvin, S B;Gil-Humanes, J;Graham M.W.;Grover Abhinav;Guan, X;Gunders D.;Guseman, J M;Guye, P;Gómez, J F;Hay, A;Hooshangi, S;Huang, D Q;Huang, P;Il Je, B;Javaux, M;Jusiak, B;Kast, E J;Kearns, C A;Kimura S.;Korte, A;Koyama, T;Krizek, B A;Laplaze, L;Le Cunff, L;Lee, J T;Lee, J Y;Lepetit, M;Liang, Y;Lienert, F;Lim, C J;Liu, W S;Lobell, D B;Lobet, G;Lowe, K;Lucks, J B;Lungley, D R;Lynch, J P;Malamy, J E;Malzahn, A;Martin, L B B;Mccaw, M E;Meijón, M;Mironov, V;Mizukami, Y;Mohan, C;Moon, T S;Moore, R;Moreno-Risueno, M A;Mourrain, P;Mutalik, V K;Nielsen, A A;Nielsen, A A K;Nitz, I;O'Malley, R C;Ogura, T;Ohno, S;Pablo M.;Paddon, C J;Pagès, L;Panchy, N;Pautler, M;Pelaz, S;Peleman, J D;Peng, J R;Pierre-Jerome, E;Piotrzkowski, N;Porco, S;Prindle, A;Prusinkiewicz, P;Purcell, O;Purugganan, M D;Qin, L X;Que, Q D;Raff R. A.;Rajeevkumar, S;Reitz, L P;Roquet, N;Rosas, U;Rosier, B J H M;Schaumberg, K A;Schena, M;Scheres Ben;Schmidt, J E;Schmitt, J;Schnepf, A;Schwab, R;Scofield, S;Sebastian, J;Shao, H B;Shen, S S;Simon Anna, J;Sohka, T;Soyk, S;Stanton, B C;Stoger, E;Stricker, J;Stroud, H;Tam, T H Y;Tandon, J P;Teague, B P;Till Bradley J.;Tiwari, M;Toplak N.;Topp, C N;Trang, P T K;Uga, Y;Van Der Meer, J R;Van Norman, J M;Vanneste, S;Voytas, D F;Wang, R;Wang, R L;Wang, Y P;Waterhouse, P M;Wilde, R J;Wood, R;Wright, S I;Zhan, A;Zhang, Y;Zhao, Y D;Zurek, P R | GH2JF | Stanford, CA USA | 9 | null | 2 | null | 28,864,344 | Brophy, Jennifer A N;Dinneny, Jose R;LaRue, Therese | SEMIN CELL DEV BIOL | Stanford, CA USA |
Burns, J R;Howorka, S;Pugh, G C | 10.1038/s41570-018-0015-9 | null | MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND | 16146g5g161tfd6q3g262t16e5v112p6s6r38 | Comparing proteins and nucleic acids for next-generation biomolecular engineering | UCL | null | Howorka, S (corresponding author), UCL, Inst Struct & Mol Biol, Dept Chem, London, England. | null | Burns, Jonathan R;Howorka, Stefan;Pugh, Genevieve C | Chemistry, Multidisciplinary | EPSRC [EP/N009282/1]; BBSRC [BB/M025373/1, BB/N017331/1]; Leverhulme Trust [RPG-2017-015]; Oxford Nanopore Technologies; BBSRC [BB/N017331/1, BB/M025373/1] Funding Source: UKRI | WOS | Howorka, S | UCL, London, England | 2 | acids;and;biomolecular;comparing;engineering;for;next-generation;Nucleic;Proteins | 1 | null | NATURE PUBLISHING GROUP | UCL, Inst Struct & Mol Biol, Dept Chem, London, England | Review | UCL | LONDON | null | null | Inst Struct & Mol Biol;UCL | BBSRC;EPSRC;Leverhulme Trust;Oxford Nanopore Technologies | Howorka, S (corresponding author), UCL, Inst Struct & Mol Biol, Dept Chem, London, England. | 130 | Burns, Jonathan R;Howorka, Stefan;Pugh, Genevieve C | 155 | 1 | 438,549,000,006 | BBSRC [BB/M025373/1, BB/N017331/1];BBSRC [BB/N017331/1, BB/M025373/1] Funding Source: UKRI;EPSRC [EP/N009282/1];Leverhulme Trust [RPG-2017-015];Oxford Nanopore Technologies | UK | NATURE REVIEWS CHEMISTRY | UK | null | null | UCL, Inst Struct & Mol Biol, Dept Chem, London, England | 2397-3358 | Burns, J R;Howorka, S;Pugh, G C | JUL | s.howorka@ucl.ac.uk | comparing proteins;next-generation biomolecular engineering;nucleic acids | 3 | J | Chemistry | application;attention;BACTERIAL S-LAYERS;biomedicine;biomolecules;biotechnology;BISPECIFIC ANTIBODIES;comparing protein engineering;comparing proteins;COMPUTATIONAL DESIGN;different biopolymers;different structural properties;directed evolution;DNA;DNA nanotechnology;DNA ORIGAMI NANOSTRUCTURES;DNA/RNA;emerging areas;function;functional nanostructures;given molecular structure;hybrid materials;IN-VITRO SELECTION;materials sciences;molecular architectures;nanoscale engineering;nanostructures;next-generation biomolecular engineering;nucleic acids;PLASMONIC NANOSTRUCTURES;possible designs;PROTEIN;proteins;REPEAT-PROTEIN;research;review;RNA;SINGLE-STRANDED-DNA;synthetic biology research;synthetic genetic polymers;synthetic routes;traction;use | Pugh, G C | BACTERIAL S-LAYERS;BISPECIFIC ANTIBODIES;COMPUTATIONAL DESIGN;directed evolution;DNA ORIGAMI NANOSTRUCTURES;IN-VITRO SELECTION;PLASMONIC NANOSTRUCTURES;REPEAT-PROTEIN;SINGLE-STRANDED-DNA;SYNTHETIC GENETIC POLYMERS | 113 | [Pugh, Genevieve C.; Burns, Jonathan R.; Howorka, Stefan] UCL, Inst Struct & Mol Biol, Dept Chem, London, England. | Supported the EPSRC (EP/N009282/1), the BBSRC (BB/M025373/1, BB/N017331/1), the Leverhulme Trust (RPG-2017-015) and Oxford Nanopore Technologies. The authors thank Keith Fox, Birte Hocker, and Derek Woolfson for critically reading the manuscript and suggesting improvements, and Katya Ahmad for calculating the van der Waals volumes of amino acids and nucleotides, and suggesting improvements for Box 1. | application;attention;biomedicine;biomolecules;biotechnology;comparing protein engineering;different biopolymers;different structural properties;DNA;DNA nanotechnology;DNA/RNA;emerging areas;function;functional nanostructures;given molecular structure;hybrid materials;materials sciences;molecular architectures;nanoscale engineering;nanostructures;nucleic acids;possible designs;protein;proteins;research;review;RNA;synthetic biology research;synthetic routes;traction;use | 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null | BB/M025373/1;BB/N017331/1;EP/N009282/1;RPG-2017-015 | 296 | null | UK | UCL | Pugh, Genevieve C | Green Submitted | BACTERIAL S-LAYERS;BISPECIFIC ANTIBODIES;COMPUTATIONAL DESIGN;DIRECTED EVOLUTION;DNA ORIGAMI NANOSTRUCTURES;IN-VITRO SELECTION;PLASMONIC NANOSTRUCTURES;REPEAT-PROTEIN;SINGLE-STRANDED-DNA;SYNTHETIC GENETIC POLYMERS | Pugh, Genevieve C.; Burns, Jonathan R.; Howorka, Stefan; | null | UCL, Inst Struct & Mol Biol, Dept Chem, London, England | UCL, Inst Struct & Mol Biol, Dept Chem, London, England | null | null | 7 | 1975;1981;1984;1985;1986;1988;1989;1990;1993;1994;1995;1996;1997;1998;1999;2000;2001;2003;2004;2005;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016;2017;2018 | 38 | UCL, Inst Struct & Mol Biol, Dept Chem, London, England | Nat. Rev. Chem. | Howorka, Stefan | NATURE PUBLISHING GROUP | ,;?;a;acids;advantages;and;application;architectures;are;areas;as;attention;attracting;best;biological;biology;biomedicine;biomolecules;biopolymers;biotechnology;built;by;comparing;composed;designs;different;DNA;DNA/RNA;emerging;engineering;evaluate;for;from;function;functional;gaining;given;highlight;hybrid;identify;in;is;many;materials;molecular;nanoscale;nanostructures;nanotechnology;nucleic;of;or;pioneered;possible;properties;protein;proteins;rapidly;relevant;research;review;RNA;routes;Sciences;structural;structure;such;suited;synthetic;that;the;this;traction;use;was;we;well;what;which;with;yet | UCL | Nanostructures built from biomolecules such as proteins, DNA and RNA are attracting attention in many areas of biological and materials sciences. Such nanoscale engineering was pioneered with proteins, yet the use of DNA is rapidly gaining traction. What are the advantages of the different biopolymers and which is best suited for a given molecular structure, function or application? In this Review, we evaluate the different structural properties of proteins and nucleic acids, as well as possible designs and synthetic routes for functional nanostructures. By comparing protein engineering and DNA nanotechnology, we highlight molecular architectures that are relevant in biotechnology, biomedicine and synthetic biology research, and identify emerging areas for research such as hybrid materials composed of protein and DNA/RNA. | null | BACTERIAL S-LAYERS;BISPECIFIC ANTIBODIES;COMPUTATIONAL DESIGN;DIRECTED EVOLUTION;DNA ORIGAMI NANOSTRUCTURES;IN-VITRO SELECTION;PLASMONIC NANOSTRUCTURES;REPEAT PROTEINS;SINGLE-STRANDED-DNA;SYNTHETIC GENETIC POLYMERS | 5 | null | null | 18 | BACTERIAL S-LAYERS;bispecific antibody;COMPUTATIONAL DESIGN;directed evolution;DNA ORIGAMI NANOSTRUCTURES;IN-VITRO SELECTION;PLASMONIC NANOSTRUCTURES;REPEAT PROTEINS;SINGLE-STRANDED-DNA;SYNTHETIC GENETIC POLYMERS | WOS:000438549000006 | UCL, London, England | UK | 2,018 | null | null | null | null | English | null | ACCOUNTS CHEM RES;ACS NANO;ANGEW CHEM INT EDIT;ANNU REV BIOCHEM;ANNU REV BIOMED ENG;ANNU REV BIOPHYS;ANNU REV CHEM BIOMOL;ANNU REV MICROBIOL;ANNU REV PHARMACOL;APPL ENVIRON MICROB;BIOCHEM SOC T;BIOCHEMISTRY-US;BIOPHYS J;CELL;CHEM COMMUN;CHEM REV;CHEM SOC REV;CHEMBIOCHEM;CURR OPIN BIOTECH;CURR OPIN CHEM BIOL;CURR OPIN STRUC BIOL;DRUG DISCOV TODAY;ELIFE;FEMS MICROBIOL REV;GENE;J AM CHEM SOC;J BIOL CHEM;J MATER CHEM;J MOL BIOL;J ORG CHEM;J STRUCT BIOL;MABS-AUSTIN;NANO LETT;NAT BIOTECHNOL;NAT CHEM;NAT CHEM BIOL;NAT COMMUN;NAT GENET;NAT MATER;NAT METHODS;NAT NANOTECHNOL;NAT REV DRUG DISCOV;NAT REV GENET;NAT REV MATER;NAT REV MICROBIOL;NAT REV MOL CELL BIO;NAT STRUCT MOL BIOL;NATURE;NEW ENGL J MED;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PROG MOL BIOL TRANSL;SCIENCE;SMALL;SOFT MATTER;STRUCTURE;TRENDS BIOCHEM SCI;TRENDS BIOTECHNOL | Burns, Jonathan R;Howorka, Stefan;Pugh, Genevieve C | 2024-03-11
ER | Acuna, G P;Agapakis, C M;Agarwal, N P;Alberts B.;Aldaye, F A;Alivisatos, A P;Amir, Y;Andersen, E S;Angelin, A;Atsumi, S;Attwood Teresak.;Ayub, M;Balchin, D;Ban, N;Baneyx, F;Baranova, E;Bargou, R;Bell, N A W;Benson, E;Better, M;Bhan, N;Binz, H K;Blomberg, R;Boder, E T;Boersma, A J;Boersma, Y L;Bombelli, F B;Bornscheuer, U T;Boulianne, G L;Brekke, O H;Brinkmann, U;Brodin, J D;Burgess, N C;Burns, J R;Burton, A J;Butterfield, G L;Carlson, J C;Castro, C E;Cech, T R;Chao, F A;Chen, I;Chen, T;Chen, Y J;Chen, Z;Chevalier, A;Chin, J W;Choi, J;Chudasama Vijay;Colin, P Y;Cuenoud, B;Currin, A;Czogalla, A;Damborsky, J;Davids, T;Dawson, P E;De Wildt, R M T;Delebecque, C J;Delpeyroux, F;Denard, C A;Derr, N D;Desantis, G;Dietz, H;Dobson, C M;Dodani, S C;Dolk, E;Douglas, S M;Driggers, E M;Dueber, J E;Dunn, K E;Durao, P;Edwardson, T G W;Ellefson, J W;Ellington, A D;Estell, D A;Fagan, R P;Fan, C G;Farías-Rico, J A;Fischlechner, M;Fisher, M A;Flavell, R R;Fletcher, J M;Fox, R J;Franquelim, H G;Frost, A;Frushicheva, M P;Fu, J L;Garces, F;Gartner, Z J;Geary, C;Gerling, T;Gibson, D G;Giger, L;Goodman, R P;Gopinath, A;Gotrik, M R;Gradisar, H;Griengl, H;Gross, G;Grossi, G;Grueninger, D;Guillard, S;Hamerscasterman, C;Hammer, S C;Han, D R;Harris, L J;He, M Y;He, Y;Henning-Knechtel, A;Hilvert, D;Hong, F;Horning, D P;Hosseinzadeh, P;Howorka, S;Huang, P S;Huber, T;Hung, A M;Hussack, G;Hänsel-Hertsch, R;Höcker, B;Iinuma, R;Ilk, N;Jeschek, M;Jiang, L;Johannes, L;Johnson-Buck, A;Jones, M R;Jones, P T;Jost, C;Jung, C;Jungmann, R;Kanekiyo, M;Kato, K;Ke, Y G;Keefe, A D;Kell, D B;Kerfeld, C A;Kershner, R J;Keys, T G;Khoury, G A;King, N P;Klinkova, A;Knudsen, J B;Kocabey, S;Kohler, G;Kontermann, R E;Korendovych, I V;Kotterman, M A;Kozlowski, L P;Kries, H;Kukwikila, M;Kuzyk, A;Küchler, A;Lai, Y T;Lane, M D;Langecker, M;Lee, D S;Lee, M J;Lee, Y J;Li, J;Lichman, B R;Linko, V;List, J;Liszka, M J;Liu, W Y;Low, H H;Lu, Y;Magnotti, E L;Mandell, D J;Manning, G S;Marold, J D;Martell, J D;Maruani, A;Marvin, D A;Matteucci, M D;Mcmahon, H T;Meng, H M;Meng, W J;Merski, M;Mirkin, C A;Missiakas, D;Modi, S;Mor-Vaknin, N;Muyldermans, S;Nam, Y S;Ng, E W M;Nimjee, S M;O'Maille, P E;O'Reilly, R K;Omabegho, T;Ozbay, E;Packer, M S;Padilla, J E;Park, K;Parmeggiani, F;Perrault, S D;Peter, B J;Pinheiro, A V;Pinheiro, V B;Plückthun, A;Ponce-Salvatierra, A;Porter, J L;Praetorius, F;Preiswerk, N;Prier, C K;Ramakers, B E I;Renata, H;Rinker, S;Rioz-Martínez, A;Rocklin, G J;Rodriguez, E A;Rosenbaum, L;Rothbauer, U;Rothemund, P W K;Ryadnov, M G;Röthlisberger, D;Saccà, B;Samanta, B;Savile, C K;Schiffels, D;Schluenzen, F;Schäffer, C;Seelig, B;Seeman, N C;Sharma, J;Shenton, W;Shih, W M;Shivalingam, A;Silverman, S K;Sleytr, U B;Spicer, C D;Spiess, C;Spruijt, E;Stanfield, R L;Steen, E J;Stemmer, W P C;Sun, W;Surana, S;Sutter, M;Suzuki, Y;Tan, S J;Tanaka, S;Tikhomirov, G;Tiller, K E;Tizei, P A G;Torring, T;Trinh, T;Tuerk, C;Turner, N J;Urvoas, A;Van Raaij, M J;Veneziano, R;Wagenbauer, K F;Wang, X X;Wei, B;Wells, J A;Wickham, S F J;Wilner, O I;Wilson, D S;Winfree, E;Winnacker, M;Wollman, A J M;Woo, S;Woolfson, D N;Wu, A M;Xu, C F;Xu, W M;Yan, H;Yang, Y;Yeates, T O;Yi, L;Yoshina-Ishii, C;Zhang, F;Zhang, Z;Zhao, Y H;Zhao, Z;Zheng, J P;Zheng, J W;Zhou, J H;Zolot, R S | GM9FE | London, England | 44 | null | 1 | null | null | Burns, Jonathan R;Howorka, Stefan;Pugh, Genevieve C | NAT REV CHEM | London, England |
Cai, D B;Chen, S W;Li, X Y;Wang, D;Wang, Q;Zhan, Y Y | 10.1128/AEM.00262-18 | e00262-18 | 1752 N ST NW, WASHINGTON, DC 20036-2904 USA | 5n5k4qt5yh1w662r2j652e2q32521473405g6t | Regulation of the Synthesis and Secretion of the Iron Chelator Cyclodipeptide Pulcherriminic Acid in <i>Bacillus licheniformis</i> | Huazhong Agr Univ | null | Chen, SW (corresponding author), Huazhong Agr Univ, Coll Life Sci & Technol, State Key Lab Agr Microbiol, Wuhan, Hubei, Peoples R China.;Chen, SW (corresponding author), Hubei Univ, Coll Life Sci, Hubei Collaborat Innovat Ctr Green Transformat Bi, Environm Microbial Technol Ctr Hubei Prov, Wuhan, Hubei, Peoples R China. | null | Cai, Dongbo;Chen, Shouwen;Li, Xiaoyun;Wang, Dong;Wang, Qin;Zhan, Yangyang | Biotechnology & Applied Microbiology;Microbiology | National Program on Key Basic Research Project (973 Program) [2015CB150505]; Science and Technology Program of Wuhan [20160201010086] | WOS | Chen, S W | Huazhong Agr Univ, Hubei, Peoples R China;Hubei Univ, Hubei, Peoples R China | 84 | <i>Bacillus;acid;and;Chelator;Cyclodipeptide;in;IRON;licheniformis</i>;of;Pulcherriminic;regulation;SECRETION;synthesis;the | 1 | null | AMER SOC MICROBIOLOGY | Huazhong Agr Univ, Coll Life Sci & Technol, State Key Lab Agr Microbiol, Wuhan, Hubei, Peoples R China;Huazhong Agr Univ, Coll Life Sci & Technol, State Key Lab Agr Microbiol, Wuhan, Hubei, Peoples R China.; Chen, SW (corresponding author), Hubei Univ, Coll Life Sci, Hubei Collaborat Innovat Ctr Green Transformat Bi, Environm Microbial Technol Ctr Hubei Prov, Wuhan, Hubei, Peoples R China;Hubei Univ, Coll Life Sci, Hubei Collaborat Innovat Ctr Green Transformat Bi, Environm Microbial Technol Ctr Hubei Prov, Wuhan, Hubei, Peoples R China | Article | Huazhong Agr Univ;Hubei Univ | WASHINGTON | null | null | Huazhong Agr Univ;Hubei Univ | National Program on Key Basic Research Project (973 Program);Science and Technology Program of Wuhan | Chen, SW (corresponding author), Huazhong Agr Univ, Coll Life Sci & Technol, State Key Lab Agr Microbiol, Wuhan, Hubei, Peoples R China.; Chen, SW (corresponding author), Hubei Univ, Coll Life Sci, Hubei Collaborat Innovat Ctr Green Transformat Bi, Environm Microbial Technol Ctr Hubei Prov, Wuhan, Hubei, Peoples R China. | null | Cai, Dongbo;Chen, Shouwen;Li, Xiaoyun;Wang, Dong;Wang, Qin;Zhan, Yangyang | 37 | 2 | 435,471,900,008 | National Program on Key Basic Research Project (973 Program) [2015CB150505];Science and Technology Program of Wuhan [20160201010086] | China | APPLIED AND ENVIRONMENTAL MICROBIOLOGY | China | null | null | Huazhong Agr Univ, Coll Life Sci & Technol, State Key Lab Agr Microbiol, Wuhan, Hubei, Peoples R China | 0099-2240 | Cai, D B;Chen, S W;Li, X Y;Wang, D;Wang, Q;Zhan, Y Y | JUL | me1212@126.com | <i>Bacillus licheniformis</i>;Iron Chelator Cyclodipeptide Pulcherriminic Acid;Regulation;SECRETION;synthesis | 6 | J | Biotechnology & Applied Microbiology;Microbiology | <i>Bacillus licheniformis</i>;AbrB;act;B. licheniformis;Bacillus licheniformis;BACTERIA;balance;BIOCONTROL;BIOFILM FORMATION;BIOLOGICAL-CONTROL;biosynthesis;biosynthesis window;broad variety;CDPS gene transcription;CDPS genes;CDPSs;CDPSs use aminoacyl tRNAs;cells;certain pathogens;clearer understanding;combined concentration;cyclodipeptide;cyclodipeptide pulcherriminic acid;cyclodipeptide scaffold;cyclodipeptide synthases (CDPSs);cyclodipeptide synthesis;cyclodipeptides;decisive factor;downregulating YvnA expression;eight;environment;excessive iron removal;expression;fate;genes;IDENTIFICATION;importance;INFORMATION;insights;insoluble iron-pulcherriminic acid complex;IRON;iron carrier;iron chelator;Iron Chelator Cyclodipeptide Pulcherriminic Acid;iron depletion;iron starvation;iron-limiting conditions;iron-limiting environments;iron-rich environment;knowledge;little;main regulator;mechanism;member;nature;nonribosomal peptide synthetases (NRPSs);NRPS-dependent pathways;pharmacological activities;present;producer cells;PROTEIN;pulcherriminic acid;pulcherriminic acid biosynthesis;pulcherriminic acid secretion;pulcherriminic acid synthase YvmC;pulcherriminic acid synthesis;pulcherriminic acid synthesis pathway;regulation;REGULATORY NETWORK;secretion;self-protection;SIDEROPHORES;similar approaches;study;Substrates;SUBTILIS;synthesis;three regulators;TRANSPORTER;transporter gene yvmA;two peptide bonds;unclear;YvmB;YvmB expression;yvmC-cypX synthetic gene cluster;YvnA;YvnA expression | Wang, D | AbrB;Bacillus licheniformis;BIOCONTROL;BIOFILM FORMATION;BIOLOGICAL-CONTROL;BIOSYNTHESIS;cyclodipeptide;GENES;IDENTIFICATION;iron depletion;PROTEIN;pulcherriminic acid;SIDEROPHORES;SUBTILIS;TRANSPORTER | null | [Wang, Dong; Chen, Shouwen] Huazhong Agr Univ, Coll Life Sci & Technol, State Key Lab Agr Microbiol, Wuhan, Hubei, Peoples R China. [Zhan, Yangyang; Cai, Dongbo; Li, Xiaoyun; Wang, Qin; Chen, Shouwen] Hubei Univ, Coll Life Sci, Hubei Collaborat Innovat Ctr Green Transformat Bi, Environm Microbial Technol Ctr Hubei Prov, Wuhan, Hubei, Peoples R China. | This work was supported by the National Program on Key Basic Research Project (973 Program; grant 2015CB150505) and the Science and Technology Program of Wuhan (grant 20160201010086). | AbrB;act;B. licheniformis;Bacillus licheniformis;bacteria;balance;biocontrol;biosynthesis window;broad variety;CDPS gene transcription;CDPS genes;CDPSs;CDPSs use aminoacyl tRNAs;cells;certain pathogens;clearer understanding;combined concentration;cyclodipeptide pulcherriminic acid;cyclodipeptide scaffold;cyclodipeptide synthases (CDPSs);cyclodipeptide synthesis;cyclodipeptides;decisive factor;downregulating YvnA expression;eight;environment;excessive iron removal;expression;fate;importance;information;insights;insoluble iron-pulcherriminic acid complex;iron;iron carrier;iron chelator;iron starvation;iron-limiting conditions;iron-limiting environments;iron-rich environment;knowledge;little;main regulator;mechanism;member;nature;nonribosomal peptide synthetases (NRPSs);NRPS-dependent pathways;pharmacological activities;present;producer cells;pulcherriminic acid;pulcherriminic acid biosynthesis;pulcherriminic acid secretion;pulcherriminic acid synthase YvmC;pulcherriminic acid synthesis;pulcherriminic acid synthesis pathway;regulation;regulatory network;secretion;self-protection;siderophores;similar approaches;study;substrates;three regulators;transporter gene yvmA;two peptide bonds;unclear;YvmB;YvmB expression;yvmC-cypX synthetic gene cluster;YvnA;YvnA expression | 10.1007/BF00011694;10.1007/BF00406050;10.1007/BF02602840;10.1007/s00253-012-4572-4;10.1007/s12010-017-2500-x;10.1016/j.resmic.2017.02.010;10.1016/j.tibs.2013.01.003;10.1016/j.tig.2015.09.001;10.1016/S0167-7012(98)00087-6;10.1021/bi100910y;10.1038/286885a0;10.1038/nrmicro1129;10.1039/b906679a;10.1039/c2np20010d;10.1046/j.1365-2958.1998.00961.x;10.1046/j.1365-2958.2002.02727.x;10.1046/j.1365-2958.2002.02885.x;10.1078/0723-2020-00045;10.1089/IND.2006.2.66;10.1093/jmcb/mjq021;10.1094/PHYTO.2004.94.11.1272;10.1099/00221287-107-2-319;10.1111/j.1365-2958.2004.04023.x;10.1111/j.1365-2958.2004.04440.x;10.1111/j.1365-2958.2005.04587.x;10.1111/j.1365-2958.2009.06955.x;10.1111/j.1462-2920.2012.02794.x;10.1128/AEM.01275-06;10.1128/AEM.02751-06;10.1128/AEM.07912-11;10.1128/AEM.59.1.74-82.1993;10.1128/JB.00464-08;10.1128/JB.00553-08;10.1128/JB.01081-07;10.1128/JB.181.23.7346-7355.1999;10.1128/JB.183.2.483-489.2001;10.1128/JB.187.6.2010-2019.2005;10.1128/mBio.01906-16;10.1128/MMBR.00012-07;10.1128/MMBR.66.2.223-249.2002;10.1146/annurev.micro.54.1.881;10.1186/s12866-016-0807-3;10.1186/s12934-017-0688-7;10.1371/journal.pone.0108642;10.3389/fmicb.2015.00785;10.3390/ijms150814610 | Huazhong Agr Univ | Cai, D B;Chen, S W;Li, X Y;Wang, D;Wang, Q;Zhan, Y Y | Wang, D: Huazhong Agr Univ, Coll Life Sci & Technol, State Key Lab Agr Microbiol, Wuhan, Hubei, Peoples R China | Chen, Shouwen;zhang, xu | 2015CB150505;20160201010086 | 47 | null | China | Huazhong Agr Univ;Hubei Univ | Wang, Dong | Green Published, Bronze | BIOCONTROL;BIOFILM FORMATION;BIOLOGICAL-CONTROL;BIOSYNTHESIS;GENES;IDENTIFICATION;PROTEIN;SIDEROPHORES;SUBTILIS;TRANSPORTER | Wang, Dong; Zhan, Yangyang; Cai, Dongbo; Li, Xiaoyun; Wang, Qin; Chen, Shouwen; | null | Huazhong Agr Univ, Coll Life Sci & Technol, State Key Lab Agr Microbiol, Wuhan, Hubei, Peoples R China;Hubei Univ, Coll Life Sci, Hubei Collaborat Innovat Ctr Green Transformat Bi, Environm Microbial Technol Ctr Hubei Prov, Wuhan, Hubei, Peoples R China | Huazhong Agr Univ, Coll Life Sci & Technol, State Key Lab Agr Microbiol, Wuhan, Hubei, Peoples R China;Hubei Univ, Coll Life Sci, Hubei Collaborat Innovat Ctr Green Transformat Bi, Environm Microbial Technol Ctr Hubei Prov, Wuhan, Hubei, Peoples R China | 1098-5336 | AbrB;Bacillus licheniformis;cyclodipeptide;iron depletion;pulcherriminic acid | 13 | 1967;1978;1980;1990;1993;1998;1999;2000;2001;2002;2004;2005;2006;2007;2008;2009;2010;2012;2013;2014;2015;2016;2017 | 27 | Huazhong Agr Univ, Coll Life Sci & Technol, State Key Lab Agr Microbiol, Wuhan, Hubei, Peoples R China;Hubei Univ, Coll Life Sci, Hubei Collaborat Innovat Ctr Green Transformat Bi, Environm Microbial Technol Ctr Hubei Prov, Wuhan, Hubei, Peoples R China | Appl. Environ. Microbiol. | Chen, Shouwen | AMER SOC MICROBIOLOGY | (CDPSs);(NRPSs);,;:;a;about;AbrB;acid;act;activities;also;aminoacyl;an;and;antagonizes;approaches;are;as;at;augment;B.;Bacillus;bacteria;balance;be;between;biocontrol;biological;biosynthesis;bonds;broad;but;by;can;cannot;carrier;causes;CDPS;CDPSs;cells;certain;chelator;clear;clearer;close;cluster;combined;complex;concentration;conditions;considered;cyclodipeptide;cyclodipeptides;decisive;determined;determines;developed;directly;do;downregulating;eight;environment;environments;excessive;exhibit;explains;expression;factor;fate;for;from;gene;genes;how;however;identified;importance;in;information;insights;insoluble;into;involved;iron;iron-limiting;iron-pulcherriminic;iron-rich;is;it;knowledge;known;licheniformis;little;main;may;mechanism;member;nature;negatively;network;nonribosomal;not;NRPS-dependent;of;on;only;other;our;pathogens;pathway;pathways;peptide;pharmacological;present;producer;provides;pulcherriminic;regulated;regulation;regulator;regulators;regulatory;remain;removal;removing;repressed;required;scaffold;secretion;self-protection;show;siderophores;similar;since;starvation;strikes;study;substrates;synthase;synthases;synthesis;synthesize;synthesized;synthetases;synthetic;that;the;this;three;to;transcription;transporter;tRNAs;two;unclear;under;understanding;use;used;variety;was;we;which;while;widespread;window;with;within;yvmA;YvmB;YvmC;yvmC-cypX;YvnA | Huazhong Agr Univ;Hubei Univ | The cyclodipeptide pulcherriminic acid synthesized by Bacillus licheniformis is an iron chelator that antagonizes certain pathogens by removing iron from the environment. But since the insoluble iron-pulcherriminic acid complex cannot act as an iron carrier as siderophores do, excessive synthesized pulcherriminic acid causes iron starvation for the producer cells. At present, the regulation of pulcherriminic acid synthesis and the mechanism by which B. licheniformis strikes a balance between biocontrol and self-protection from excessive iron removal remain unclear. This study provides insights into the regulatory network and explains the mechanism of pulcherriminic acid biosynthesis. The yvmC-cypX synthetic gene cluster was directly negatively regulated by three regulators: AbrB, YvnA, and YvmB. Within the regulatory network, YvnA expression was repressed not only by AbrB but also by iron-limiting environments, while YvmB expression was repressed by YvnA. The transporter gene yvmA is repressed by YvmB and is required for pulcherriminic acid secretion. The biosynthesis window is determined by the combined concentration of the three regulators in an iron-rich environment. Under iron-limiting conditions, cells close the pulcherriminic acid synthesis pathway by downregulating YvnA expression. IMPORTANCE The cyclodipeptides are widespread in nature and exhibit a broad variety of biological and pharmacological activities. The cyclodipeptide scaffold is synthesized by nonribosomal peptide synthetases (NRPSs) and cyclodipeptide synthases (CDPSs). At present, it is clear that CDPSs use aminoacyl tRNAs as substrates to synthesize the two peptide bonds, and the pulcherriminic acid synthase YvmC is a member of the eight identified CDPSs. However, little is known about the regulation of cyclodipeptide synthesis and secretion. In this study, we show that AbrB, which is considered to be the main regulator of NRPS-dependent pathways, is also involved in the regulation of CDPS genes. However, AbrB is not the decisive factor for pulcherriminic acid synthesis, as the expression of YvnA determines the fate of pulcherriminic acid synthesis. With this information on how CDPS gene transcription is regulated, a clearer understanding of cyclodipeptide synthesis can be developed for B. licheniformis. Similar approaches may be used to augment our knowledge on CDPSs in other bacteria. | D-6269-2018;JEO-4879-2023 | BIOCONTROL;BIOFILM FORMATION;BIOLOGICAL-CONTROL;BIOSYNTHESIS;GENE;IDENTIFICATION;PROTEIN;SIDEROPHORES;SUBTILIS;TRANSPORT | 3 | null | AbrB;Bacillus licheniformis;cyclodipeptide;iron depletion;pulcherriminic acid | 14 | AbrB;Bacillus licheniformis;BIOCONTROL;BIOFILM FORMATION;BIOLOGICAL-CONTROL;BIOSYNTHESIS;cyclodipeptide;GENE;IDENTIFICATION;iron depletion;PROTEIN;pulcherriminic acid;SIDEROPHORES;SUBTILIS;TRANSPORT | WOS:000435471900008 | Huazhong Agr Univ, Hubei, Peoples R China;Hubei Univ, Hubei, Peoples R China | China | 2,018 | null | null | null | null | English | null | ANNU REV MICROBIOL;APPL BIOCHEM BIOTECH;APPL ENVIRON MICROB;APPL MICROBIOL BIOT;ARCH MIKROBIOL;BIOCHEMISTRY-US;BMC MICROBIOL;CURR MICROBIOL;ENVIRON MICROBIOL;FRONT MICROBIOL;Ind Biotechnol;INT J MOL SCI;J BACTERIOL;J GEN MICROBIOL;J MICROBIOL METH;J MOL CELL BIOL;MBIO;MICROB CELL FACT;MICROBIOL MOL BIOL R;MOL MICROBIOL;NAT PROD REP;NAT REV MICROBIOL;NATURE;PHYTOPATHOLOGY;PLANT SOIL;PLOS ONE;RES MICROBIOL;SYST APPL MICROBIOL;TRENDS BIOCHEM SCI;TRENDS GENET;Z NATURFORSCH C | Cai, Dongbo;Chen, Shouwen;Li, Xiaoyun;Wang, Dong;Wang, Qin;Zhan, Yangyang | 2024-03-11
ER | Albano, M;Barber, M F;Behnsen, J;Belin, P;Brickman, T J;Cai, D B;Chet, I;Crosa, J H;Cryle, M J;Duitman, E H;Furrer, J L;Giessen, T W;Haas, D;Hamon, M A;Hider, R C;Hoa, T T;Hommais, F;Horiyama, T;Jacobsen, B J;Kearns, D B;Kloepper, J W;Kupfer, D G;Kurtzman, C P;Lan, L F;Lemanceau, P;Li, X Y;Meyer, J M;Miethke, M;Park, S Y;Perera, I C;Randazzo, P;Ratledge, C;Romeo, T;Sipiczki, M;Stein, T;Strauch, M A;Tang Mr.;Türkel, S;Wang, D;Weng, J;Xue, G P;Yan, N;Zheng, G L;Zhu, W M | GJ6CS | Hubei, Peoples R China;Hubei, Peoples R China. | 29 | null | 2 | null | 29,703,732 | Cai, Dongbo;Chen, Shouwen;Li, Xiaoyun;Wang, Dong;Wang, Qin;Zhan, Yangyang | APPL ENVIRON MICROB | Hubei, Peoples R China |
Hu, C Y;Lucks, J B;Takahashi, M K;Zhang, Y | 10.1021/acssynbio.7b00440 | null | 1155 16TH ST, NW, WASHINGTON, DC 20036 USA | 5man6r3d535a6f6w406406j3k6oq5y103q6e | Engineering a Functional Small RNA Negative Autoregulation Network with Model-Guided Design | Cornell Univ | null | Lucks, JB (corresponding author), Northwestern Univ, Sch Chem & Biol Engn, Evanston, IL 60208 USA. | null | Hu, Chelsea Y;Lucks, Julius B;Takahashi, Melissa K;Zhang, Yan | Biochemical Research Methods | NSF CAREER Award [1452441]; National Science Foundation Graduate Research Fellowship [DGE-1144153]; Searle Funds at The Chicago Community Trust; Direct For Biological Sciences; Div Of Molecular and Cellular Bioscience [1452441] Funding Source: National Science Foundation | WOS | Lucks, J B | Cornell Univ, Ithaca, NY USA;Georgia Inst Technol, Atlanta, GA USA;MIT, Cambridge, MA USA;Northwestern Univ, Evanston, IL USA | 7 | a;Autoregulation;design;engineering;functional;model-guided;Negative;network;RNA;small;with | 1 | Hu, Chelsea;Lucks, Julius;Takahashi, Melissa;Zhang, Yan | AMER CHEMICAL SOC | Cornell Univ, Robert F Smith Sch Chem & Biomol Engn, Ithaca, NY 14850 USA;Georgia Inst Technol, Sch Chem & Biomol Engn, Atlanta, GA 30332 USA;MIT, Inst Med Engn & Sci, 77 Massachusetts Ave, Cambridge, MA 02139 USA;Northwestern Univ, Sch Chem & Biol Engn, Evanston, IL 60208 USA | Article | Northwestern Univ | WASHINGTON | null | null | Cornell Univ;Georgia Inst Technol;MIT;Northwestern Univ | Direct For Biological Sciences;Div Of Molecular and Cellular Bioscience;National Science Foundation Graduate Research Fellowship;NSF CAREER award;Searle Funds at The Chicago Community Trust | Lucks, JB (corresponding author), Northwestern Univ, Sch Chem & Biol Engn, Evanston, IL 60208 USA. | 1518 | Hu, Chelsea Y;Lucks, Julius B;Takahashi, Melissa K;Zhang, Yan | 16 | 4 | 435,746,400,004 | Direct For Biological Sciences;Div Of Molecular and Cellular Bioscience [1452441] Funding Source: National Science Foundation;National Science Foundation Graduate Research Fellowship [DGE-1144153];NSF CAREER Award [1452441];Searle Funds at The Chicago Community Trust | USA | ACS SYNTHETIC BIOLOGY | USA | null | null | Cornell Univ, Robert F Smith Sch Chem & Biomol Engn, Ithaca, NY 14850 USA | 2161-5063 | Hu, C Y;Lucks, J B;Takahashi, M K;Zhang, Y | JUN | jblucks@northwestern.edu | Functional Small RNA Negative Autoregulation Network;Model-Guided Design | 4 | J | Biochemistry & Molecular Biology | ability;cellfree transcription-translation (TX-TL) reactions;computational model;core motifs;DYNAMIC-RANGE;Escherichia coli;FEEDBACK;Functional Small RNA Negative Autoregulation Network;GENE-EXPRESSION;increases;intrinsic noise;MEDIATED TRANSCRIPTIONAL ATTENUATION;model-guided design;NAR function;NAR network motifs;natural genetic networks;negative autoregulation;network response time;parameter sensitivity analysis;parameterization;platform;powerful components;predictable function;prototype sRNA NAR.;reducing network response time;regulators;repertoire;RNA regulators;RNA synthetic circuitry;sensitivity analysis;simple set;small RNAs (sRNAs);sophisticated RNA genetic networks;sRNA transcriptional network;stability;steady state signal;steady-state gene expression;successful network designs;synthetic biology toolbox;synthetic gene networks;transcriptional negative autoregulation (NAR) network;transcriptional sRNA regulator;TX-TL;VERSATILE | Hu, C Y | DYNAMIC-RANGE;FEEDBACK;GENE-EXPRESSION;INCREASES;INTRINSIC NOISE;MEDIATED TRANSCRIPTIONAL ATTENUATION;model-guided design;negative autoregulation;parameterization;PLATFORM;REGULATORS;RNA synthetic circuitry;sensitivity analysis;STABILITY;transcriptional sRNA regulator;VERSATILE | 1507 | [Hu, Chelsea Y.; Takahashi, Melissa K.; Zhang, Yan] Cornell Univ, Robert F Smith Sch Chem & Biomol Engn, Ithaca, NY 14850 USA. [Takahashi, Melissa K.] MIT, Inst Med Engn & Sci, 77 Massachusetts Ave, Cambridge, MA 02139 USA. [Zhang, Yan] Georgia Inst Technol, Sch Chem & Biomol Engn, Atlanta, GA 30332 USA. [Hu, Chelsea Y.; Lucks, Julius B.] Northwestern Univ, Sch Chem & Biol Engn, Evanston, IL 60208 USA. | This work was supported by an NSF CAREER Award (1452441 to J.B.L.), a National Science Foundation Graduate Research Fellowship (Grant No. DGE-1144153 to M.K.T.) and Searle Funds at The Chicago Community Trust (to J.B.L.). The authors gratefully acknowledge the gift of TX-TL extract and buffers used in this work from Vincent Noireaux's laboratory (University of Minnesota). The authors also thank Marshall Colville for early help in characterizing NAR circuitry, and Adam Silverman for helpful comments on this manuscript. | ability;cellfree transcription-translation (TX-TL) reactions;computational model;core motifs;Escherichia coli;NAR function;NAR network motifs;natural genetic networks;network response time;parameter sensitivity analysis;powerful components;predictable function;prototype sRNA NAR.;reducing network response time;regulators;repertoire;RNA regulators;simple set;small RNAs (sRNAs);sophisticated RNA genetic networks;sRNA transcriptional network;steady state signal;steady-state gene expression;successful network designs;synthetic biology toolbox;synthetic gene networks;transcriptional negative autoregulation (NAR) network;TX-TL | 10.1016/0092-8674(89)90300-0;10.1016/j.bpj.2009.02.064;10.1016/j.cbpa.2015.05.018;10.1016/j.cell.2013.02.022;10.1016/j.cell.2014.10.002;10.1016/j.cell.2016.04.059;10.1016/j.cels.2016.10.008;10.1016/j.molcel.2014.04.022;10.1016/j.ymeth.2015.05.020;10.1016/S0022-2836(02)00994-4;10.1021/acssynbio.5b00077;10.1021/acssynbio.5b00296;10.1021/bp9801143;10.1021/sb400206c;10.1038/252546a0;10.1038/35014651;10.1038/msb.2008.58;10.1038/msb.2013.27;10.1038/nature07389;10.1038/nbt1172;10.1038/nbt1413;10.1038/nbt986;10.1038/nchembio.1737;10.1038/ncomms12834;10.1038/ncomms15459;10.1038/ng1807;10.1038/nrm2530;10.1038/nsb959;10.1038/s41467-017-01082-6;10.1046/j.1365-2958.2000.01813.x;10.1049/sb:20045029;10.1063/1.2208927;10.1073/pnas.0736140100;10.1073/pnas.0804829105;10.1073/pnas.0809901106;10.1073/pnas.1015741108;10.1073/pnas.151588598;10.1073/pnas.96.11.6131;10.1093/nar/gks385;10.1093/nar/gkt452;10.1093/nar/gkx215;10.1098/rsif.2016.0380;10.1126/science.1070919;10.1126/science.1212209;10.1128/JB.184.10.2740-2747.2002;10.1186/1752-0509-2-6;10.1186/1752-0509-5-111;10.1371/journal.pone.0003647;10.3791/50762;[10.1038/nmeth.2515, 10.1038/NMETH.2515];[10.1038/NMETH.2969, 10.1038/nmeth.2969] | Cornell Univ | Hu, C Y;Lucks, J B;Takahashi, M K;Zhang, Y | Hu, C Y: Cornell Univ, Robert F Smith Sch Chem & Biomol Engn, Ithaca, NY 14850 USA | Lucks, Julius | 1452441;DGE-1144153 | 54 | null | USA | Cornell Univ;Georgia Inst Technol;MIT;Northwestern Univ | Hu, Chelsea Y | Green Submitted | DYNAMIC-RANGE;FEEDBACK;GENE-EXPRESSION;INCREASES;INTRINSIC NOISE;MEDIATED TRANSCRIPTIONAL ATTENUATION;PLATFORM;REGULATORS;STABILITY;VERSATILE | Hu, Chelsea Y.; Takahashi, Melissa K.; Zhang, Yan; Lucks, Julius B.; | null | Cornell Univ, Robert F Smith Sch Chem & Biomol Engn, Ithaca, NY 14850 USA;Georgia Inst Technol, Sch Chem & Biomol Engn, Atlanta, GA 30332 USA;MIT, Inst Med Engn & Sci, 77 Massachusetts Ave, Cambridge, MA 02139 USA;Northwestern Univ, Sch Chem & Biol Engn, Evanston, IL 60208 USA | Cornell Univ, Robert F Smith Sch Chem & Biomol Engn, Ithaca, NY 14850 USA;Georgia Inst Technol, Sch Chem & Biomol Engn, Atlanta, GA 30332 USA;MIT, Inst Med Engn & Sci, 77 Massachusetts Ave, Cambridge, MA 02139 USA;Northwestern Univ, Sch Chem & Biol Engn, Evanston, IL 60208 USA | null | model-guided design;negative autoregulation;parameterization;RNA synthetic circuitry;sensitivity analysis;transcriptional sRNA regulator | 6 | 1974;1989;1999;2000;2001;2002;2003;2004;2005;2006;2008;2009;2011;2012;2013;2014;2015;2016;2017 | 23 | Northwestern Univ, Sch Chem & Biol Engn, Evanston, IL 60208 USA | ACS Synth. Biol. | Lucks, Julius B | AMER CHEMICAL SOC | (NAR);(sRNAs);(TX-TL);,;a;ability;accurately;allow;analysis;and;are;autoregulation;biology;both;broadens;built;by;cellfree;coli;components;computational;construct;constructing;constructs;core;design;designs;Escherichia;expand;experiments;expression;for;from;function;gene;genetic;here;in;increasingly;into;known;model;motifs;NAR;NAR.;natural;negative;network;networks;of;our;out;parameter;powerful;predict;predictable;prototype;reactions;reduces;reducing;regulators;repertoire;response;RNA;RNAs;sensitivity;set;show;signal;simple;small;sophisticated;sRNA;state;steady;steady-state;successful;synthetic;that;the;these;this;time;to;toolbox;transcription-translation;transcriptional;transfer;TX-TL;us;use;using;we;with;work | Northwestern Univ | RNA regulators are powerful components of the synthetic biology toolbox. Here, we expand the repertoire of synthetic gene networks built from these regulators by constructing a transcriptional negative autoregulation (NAR) network out of small RNAs (sRNAs). NAR network motifs are core motifs of natural genetic networks, and are known for reducing network response time and steady state signal. Here we use cellfree transcription-translation (TX-TL) reactions and a computational model to design and prototype sRNA NAR. constructs. Using parameter sensitivity analysis, we design a simple set of experiments that allow us to accurately predict NAR function in TX-TL. We transfer successful network designs into Escherichia coli and show that our sRNA transcriptional network reduces both network response time and steady-state gene expression. This work broadens our ability to construct increasingly sophisticated RNA genetic networks with predictable function. | L-2801-2016 | DYNAMIC-RANGE;FEEDBACK;GENE-EXPRESSION;INCREASES;INTRINSIC NOISE;MEDIATED TRANSCRIPTIONAL ATTENUATION;PLATFORM;REGULATORS;STABILITY;VERSATILE | 1 | null | model-guided design;negative autoregulation;parameterization;RNA synthetic circuitry;sensitivity analysis;transcriptional sRNA regulator | 23 | DYNAMIC-RANGE;FEEDBACK;GENE-EXPRESSION;INCREASES;INTRINSIC NOISE;MEDIATED TRANSCRIPTIONAL ATTENUATION;model-guided design;negative autoregulation;parameterization;PLATFORM;REGULATOR;RNA synthetic circuitry;sensitivity analysis;STABILITY;transcriptional sRNA regulator;VERSATILE | WOS:000435746400004 | CORNELL UNIV, ITHACA, NY USA;Georgia Inst Technol, Atlanta, GA USA;MIT, Cambridge, MA USA;Northwestern Univ, Evanston, IL USA | USA | 2,018 | null | 0000-0002-0619-6505;0000-0002-2211-1778;0000-0003-0719-5456;0000-0003-4937-2924 | null | null | English | null | ACS SYNTH BIOL;BIOPHYS J;BIOTECHNOL PROGR;BMC SYST BIOL;CELL;CELL SYST;CHAOS;CURR OPIN CHEM BIOL;INTRO SYSTEMS BIOL;J BACTERIOL;J MOL BIOL;J R SOC INTERFACE;JOVE-J VIS EXP;MATH WORLD WOLFRAM W;METHODS;MOL CELL;MOL MICROBIOL;MOL SYST BIOL;NAT BIOTECHNOL;NAT CHEM BIOL;NAT COMMUN;NAT GENET;NAT METHODS;NAT REV MOL CELL BIO;NAT STRUCT BIOL;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PLOS ONE;SCIENCE;SOCIOLOGICAL SIGHTS;SYSTEMS BIOL | Hu, Chelsea Y;Lucks, Julius B;Takahashi, Melissa K;Zhang, Yan | 2024-03-11
ER | Alon, U;Bar-Even, A;Becskei, A;Brantl, S;Canton, B;Carothers, J M;Carrier, T A;Chappell, J;Chen, Y J;Cox, C D;Del Vecchio, D;Elowitz, M B;Engler, C;Felletti, M;Gadkar, K G;Gander, M W;Garamella, J;Grate, D;Green, A A;Hooshangi, S;Hu, C Y;Isaacs, F J;Khvorova, A;Kiani, S;Lucks, J B;Madar, D;Mehta, P;Millar N.;Nevozhay, D;Nissim, L;Novick, R P;Novák, B;Pardee, K;Pédelacq, J D;Qi, L S;Rosenfeld, N;Savageau, M A;Shimoga, V;Simpson, M L;Singh, A;Stekel, D J;Stricker, J;Sun, Z Z;Takahashi, M K;Thattai, M;Voliotis, M;Wang, Y H;Weisstein E. W.;Westbrook, A M | GJ9SY | Evanston, IL USA | 27 | null | 4 | null | 29,733,627 | Hu, Chelsea Y;Lucks, Julius B;Takahashi, Melissa K;Zhang, Yan | ACS SYNTH BIOL | Atlanta, GA USA;Cambridge, MA USA;Evanston, IL USA;Ithaca, NY USA |
Cozens, C;Dumbre, S;Groaz, E;Herdewijn, P;Jaziri, F;Liu, C;Marlière, P;Maréchal, A;Pezo, V;Pinheiro, V B;Rozenski, J | 10.1021/jacs.8b03447 | null | 1155 16TH ST, NW, WASHINGTON, DC 20036 USA | 5bk4w204f712y5x3g683916256s5o113c35m6h | Phosphonomethyl Oligonucleotides as Backbone-Modified Artificial Genetic Polymers | Katholieke Univ Leuven | null | Herdewijn, P (corresponding author), Katholieke Univ Leuven, Rega Inst Med Res, Med Chem, Herestr 49, B-3000 Louvain, Belgium.;Herdewijn, P (corresponding author), Univ Paris Saclay, CNRS, UEVE, iSSB,Genopole, 5 Rue Henri Desbrueres, F-91030 Evry, France.;Pinheiro, VB (corresponding author), UCL, Gower St, London WC1E 6BT, England.;Pinheiro, VB (corresponding author), Univ London, Birkbeck Coll, Inst Struct & Mol Biol, Malet St, London WC1E 7HX, England. | null | Cozens, Christopher;Dumbre, Shrinivas;Groaz, Elisabetta;Herdewijn, Piet;Jaziri, Faten;Liu, Chao;Marechal, Amandine;Marliere, Philippe;Pezo, Valerie;Pinheiro, Vitor B;Rozenski, Jef | Chemistry, Multidisciplinary | China Scholarship Council (CSC) [201306220065]; European Research Council under the European Union/ERC [ERC-2012-ADG 20120216/320683]; FWO Vlaanderen [G0A8816N]; ERASynBio (in vivo XNA); Hercules Foundation of the Flemish Government [20100225-7]; U.K. Biotechnology and Biosciences Research Council [BB/N01023X/1]; European Research Council [336936]; Medical Research Council U.K. [MR/M00936X/1]; European Research Council (ERC) [336936] Funding Source: European Research Council (ERC); BBSRC [BB/N01023X/1] Funding Source: UKRI; MRC [MR/M00936X/1] Funding Source: UKRI | WOS | Herdewijn, P;Pinheiro, V B | Katholieke Univ Leuven, Louvain, Belgium;UCL, London, England;Univ London, London, England;Univ Paris Saclay, Evry, France | 140 | Artificial;as;Backbone-Modified;genetic;oligonucleotides;phosphonomethyl;Polymers | 3 | Cozens, Christopher;Dumbre, Shrinivas;Groaz, Elisabetta;Herdewijn, Piet;Liu, Chao;MARECHAL, Amandine;Pinheiro, Vitor;Rozenski, Jef | AMER CHEMICAL SOC | Katholieke Univ Leuven, Rega Inst Med Res, Med Chem, Herestr 49, B-3000 Louvain, Belgium;Katholieke Univ Leuven, Rega Inst Med Res, Med Chem, Herestr 49, B-3000 Louvain, Belgium.; Pinheiro, VB (corresponding author), UCL, Gower St, London WC1E 6BT, England.; Herdewijn, P (corresponding author), Univ Paris Saclay, CNRS, UEVE, iSSB,Genopole, 5 Rue Henri Desbrueres, F-91030 Evry, France.; Pinheiro, VB (corresponding author), Univ London, Birkbeck Coll, Inst Struct & Mol Biol, Malet St, London WC1E 7HX, England;UCL, Gower St, London WC1E 6BT, England;Univ London, Birkbeck Coll, Inst Struct & Mol Biol, Malet St, London WC1E 7HX, England;Univ Paris Saclay, CNRS, UEVE, iSSB,Genopole, 5 Rue Henri Desbrueres, F-91030 Evry, France | Article | Katholieke Univ Leuven;UCL;Univ London;Univ Paris Saclay | WASHINGTON | null | null | Gower St;Katholieke Univ Leuven;UCL;Univ London;Univ Paris Saclay | BBSRC;China Scholarship Council (CSC);ERASynBio (in vivo XNA);European Research Council;European Research Council (ERC);European Research Council under the European Union/ERC;FWO Vlaanderen;Hercules Foundation of the Flemish Government;Medical Research Council U.K.;MRC;U.K. Biotechnology and Biosciences Research Council | Herdewijn, P (corresponding author), Katholieke Univ Leuven, Rega Inst Med Res, Med Chem, Herestr 49, B-3000 Louvain, Belgium.; Pinheiro, VB (corresponding author), UCL, Gower St, London WC1E 6BT, England.; Herdewijn, P (corresponding author), Univ Paris Saclay, CNRS, UEVE, iSSB,Genopole, 5 Rue Henri Desbrueres, F-91030 Evry, France.; Pinheiro, VB (corresponding author), Univ London, Birkbeck Coll, Inst Struct & Mol Biol, Malet St, London WC1E 7HX, England. | 6699 | Cozens, Christopher;Dumbre, Shrinivas;Groaz, Elisabetta;Herdewijn, Piet;Jaziri, Faten;Liu, Chao;Marechal, Amandine;Marliere, Philippe;Pezo, Valerie;Pinheiro, Vitor B;Rozenski, Jef | 43 | 4 | 434,101,100,026 | BBSRC [BB/N01023X/1] Funding Source: UKRI;China Scholarship Council (CSC) [201306220065];ERASynBio (in vivo XNA);European Research Council (ERC) [336936] Funding Source: European Research Council (ERC);European Research Council [336936];European Research Council under the European Union/ERC [ERC-2012-ADG 20120216/320683];FWO Vlaanderen [G0A8816N];Hercules Foundation of the Flemish Government [20100225-7];Medical Research Council U.K. [MR/M00936X/1];MRC [MR/M00936X/1] Funding Source: UKRI;U.K. Biotechnology and Biosciences Research Council [BB/N01023X/1] | Belgium;France;UK | JOURNAL OF THE AMERICAN CHEMICAL SOCIETY | Belgium.;;France;UK | null | null | Katholieke Univ Leuven, Rega Inst Med Res, Med Chem, Herestr 49, B-3000 Louvain, Belgium | 0002-7863 | Cozens, C;Dumbre, S;Groaz, E;Herdewijn, P;Jaziri, F;Liu, C;Marlière, P;Maréchal, A;Pezo, V;Pinheiro, V B;Rozenski, J | MAY 30 | piet.herdewijn@kuleuven.be;v.pinheiro@ucl.ac.uk | Backbone-Modified Artificial Genetic Polymers;phosphonomethyl Oligonucleotides | 11 | J | Chemistry | 17 X 10(-3) per base;3'-2' phosphonomethylthreosyl nucleic acid (tPhoNA);aggregate error rate;Backbone-Modified Artificial Genetic Polymers;biorthogonality;CHEMICAL SYNTHESIS;DEOXYTHREOSYL NUCLEOSIDE PHOSPHONATES;DNA duplexes;DNA-POLYMERASES;E. coli cellular machinery;ENZYMATIC-SYNTHESIS;essential;first report;functional XNAs;genetic information;HYBRID DUPLEXES;IN-VITRO;Introduction;isolation;limited potential;major hurdles;natural DNA processing enzymes;natural nucleic acids;novel tPhoNA synthetase enzyme;novel XNA genetic material;orthogonality;phosphate backbone moieties;phosphonate nucleic acids;phosphonomethyl Oligonucleotides;phosphorylated monomeric building blocks;prime candidate;replacement;reported XNA reverse transcriptase;routes;several synthetic;significant advance;STRUCTURAL BASIS;sugar;synthetic genetic material;synthetic genetics;THERMINATOR POLYMERASE;THREOSE NUCLEIC-ACID;TNA synthesis;tPhoNA;tPhoNA orthogonality;viable genetic material (with;viable genetic materials;vitro;vivo;vivo applications;vivo experiments;vivo XNA applications;xenobiotic nucleic acids (XNAs);XNA processing enzymes;XNA systems;XNAs | Liu, C | DEOXYTHREOSYL NUCLEOSIDE PHOSPHONATES;DNA-POLYMERASES;ENZYMATIC-SYNTHESIS;HYBRID DUPLEXES;IN-VITRO;STRUCTURAL BASIS;synthetic genetics;THERMINATOR POLYMERASE;THREOSE NUCLEIC-ACID;TNA SYNTHESIS | 6690 | [Liu, Chao; Rozenski, Jef; Dumbre, Shrinivas; Groaz, Elisabetta; Herdewijn, Piet] Katholieke Univ Leuven, Rega Inst Med Res, Med Chem, Herestr 49, B-3000 Louvain, Belgium. [Cozens, Christopher; Marechal, Amandine; Pinheiro, Vitor B.] UCL, Gower St, London WC1E 6BT, England. [Jaziri, Faten; Pezo, Valerie; Marliere, Philippe; Herdewijn, Piet] Univ Paris Saclay, CNRS, UEVE, iSSB,Genopole, 5 Rue Henri Desbrueres, F-91030 Evry, France. [Pinheiro, Vitor B.] Univ London, Birkbeck Coll, Inst Struct & Mol Biol, Malet St, London WC1E 7HX, England. | C.L. acknowledges the China Scholarship Council (CSC) for funding (grant 201306220065). The research leading to these results has received funding from the European Research Council under the European Union's Seventh Framework Program (FP7/2007-2013)/ERC (grant agreement no. ERC-2012-ADG 20120216/320683). We also thank FWO Vlaanderen (G0A8816N) and ERASynBio (in vivo XNA) for financial support. Mass spectrometry was conducted with the support of the Hercules Foundation of the Flemish Government (grant 20100225-7). We express our gratitude to Guy Schepers, Luc Baudemprez, and Lia Margamuljana for excellent technical assistance. V.B.P. and C.C. were supported by the U.K. Biotechnology and Biosciences Research Council (grant number BB/N01023X/1). V.B.P. was also supported by the European Research Council [ERC-2013-StG project 336936 (HNAepisome)]. A.M. was supported by the Medical Research Council U.K. (career development award MR/M00936X/1). | 17 X 10(-3) per base;3'-2' phosphonomethylthreosyl nucleic acid (tPhoNA);aggregate error rate;biorthogonality;chemical synthesis;DNA duplexes;E. coli cellular machinery;essential;first report;functional XNAs;genetic information;introduction;isolation;limited potential;major hurdles;natural DNA processing enzymes;natural nucleic acids;novel tPhoNA synthetase enzyme;novel XNA genetic material;orthogonality;phosphate backbone moieties;phosphonate nucleic acids;phosphorylated monomeric building blocks;prime candidate;replacement;reported XNA reverse transcriptase;routes;several synthetic;significant advance;sugar;synthetic genetic material;tPhoNA;tPhoNA orthogonality;viable genetic material (with;viable genetic materials;vitro;vivo;vivo applications;vivo experiments;vivo XNA applications;xenobiotic nucleic acids (XNAs);XNA processing enzymes;XNA systems;XNAs | 10.1002/anie.200603435;10.1002/anie.201100535;10.1002/anie.201303288;10.1002/anie.201508678;10.1002/anie.201601529;10.1002/bies.201200135;10.1002/cbdv.200900083;10.1002/cbic.200800494;10.1002/cbic.201402226;10.1002/cbic.201600338;10.1002/chem.201406392;10.1002/hlca.200290000;10.1016/j.chembiol.2012.10.011;10.1016/j.copbio.2017.04.004;10.1016/j.crvi.2003.10.004;10.1016/j.jmb.2005.06.015;10.1021/acs.jmedchem.6b01260;10.1021/acs.orglett.6b01167;10.1021/bi00034a013;10.1021/ja01464a034;10.1021/ja043045z;10.1021/ja075953c;10.1021/ja3118703;10.1021/jacs.6b09661;10.1038/nature13982;10.1038/nature24659;10.1038/ncomms11235;10.1038/nsb867;10.1038/s41467-017-02014-0;10.1039/c1ob05488k;10.1039/c5sc03474d;10.1039/c7ob01265a;10.1073/pnas.0704211104;10.1073/pnas.1120964109;10.1073/pnas.88.11.4690;10.1093/nar/30.2.605;10.1093/nar/gki840;10.1093/nar/gku125;10.1126/science.1217622;10.1126/science.290.5495.1347;10.1371/journal.pone.0188005;[10.1038/NCHEM.1241, 10.1038/nchem.1241] | Katholieke Univ Leuven | Cozens, C;Dumbre, S;Groaz, E;Herdewijn, P;Jaziri, F;Liu, C;Marlière, P;Maréchal, A;Pezo, V;Pinheiro, V B;Rozenski, J | Liu, C: Katholieke Univ Leuven, Rega Inst Med Res, Med Chem, Herestr 49, B-3000 Louvain, Belgium | Dumbre, Shrinivas;Liu, Chao;MARECHAL, Amandine;Pinheiro, Vitor | 20100225-7;201306220065;336936;BB/N01023X/1;ERC-2012-ADG 20120216/320683;G0A8816N;MR/M00936X/1 | 43 | null | Belgium | Katholieke Univ Leuven;UCL;Univ London;Univ Paris Saclay | Liu, Chao | Green Accepted | DEOXYTHREOSYL NUCLEOSIDE PHOSPHONATES;DNA-POLYMERASES;ENZYMATIC-SYNTHESIS;HYBRID DUPLEXES;IN-VITRO;STRUCTURAL BASIS;SYNTHETIC GENETICS;THERMINATOR POLYMERASE;THREOSE NUCLEIC-ACID;TNA SYNTHESIS | Liu, Chao; Cozens, Christopher; Jaziri, Faten; Rozenski, Jef; Marechal, Amandine; Dumbre, Shrinivas; Pezo, Valerie; Marliere, Philippe; Pinheiro, Vitor B.; Groaz, Elisabetta; Herdewijn, Piet; | null | Katholieke Univ Leuven, Rega Inst Med Res, Med Chem, Herestr 49, B-3000 Louvain, Belgium;UCL, Gower St, London WC1E 6BT, England;Univ London, Birkbeck Coll, Inst Struct & Mol Biol, Malet St, London WC1E 7HX, England;Univ Paris Saclay, CNRS, UEVE, iSSB,Genopole, 5 Rue Henri Desbrueres, F-91030 Evry, France | Katholieke Univ Leuven, Rega Inst Med Res, Med Chem, Herestr 49, B-3000 Louvain, Belgium;UCL, Gower St, London WC1E 6BT, England;Univ London, Birkbeck Coll, Inst Struct & Mol Biol, Malet St, London WC1E 7HX, England;Univ Paris Saclay, CNRS, UEVE, iSSB,Genopole, 5 Rue Henri Desbrueres, F-91030 Evry, France | 1520-5126 | null | 21 | 1961;1991;1995;2000;2001;2002;2003;2005;2007;2008;2009;2011;2012;2013;2014;2015;2016;2017 | 45 | Katholieke Univ Leuven, Rega Inst Med Res, Med Chem, Herestr 49, B-3000 Louvain, Belgium;UCL, Gower St, London WC1E 6BT, England;Univ London, Birkbeck Coll, Inst Struct & Mol Biol, Malet St, London WC1E 7HX, England;Univ Paris Saclay, CNRS, UEVE, iSSB,Genopole, 5 Rue Henri Desbrueres, F-91030 Evry, France | J. Am. Chem. Soc. | Herdewijn, Piet | AMER CHEMICAL SOC | (tPhoNA);(with;(XNAs);,;10(-3);17;3'-2';a;access;acid;acids;advance;affected;aggregate;although;an;and;applications;approximately;are;as;availability;backbone;base;be;been;biorthogonality;blocks;both;building;by;candidate;cellular;chemical;coli;compatible;demonstrated;destabilized;DNA;do;duplexes;E.;engineered;enzyme;enzymes;error;essential;established;experiments;first;for;functional;genetic;had;have;here;hurdles;in;information;interact;introduction;is;isolation;limited;machinery;major;material;materials;modified;moieties;monomeric;natural;not;novel;nucleic;of;only;or;orthogonality;our;particularly;per;phosphate;phosphonate;phosphonomethylthreosyl;phosphorylated;potential;previously;prime;processing;rate;remain;replacement;report;reported;represents;reverse;routes;several;showed;shown;significant;specialized;sugar;synthesis;synthetase;synthetic;systems;test;that;the;their;to;toward;tPhoNA;transcriptase;upon;very;viable;vitro;vivo;we;well;were;with;work;x;xenobiotic;XNA;XNAs | Katholieke Univ Leuven;UCL;Univ London;Univ Paris Saclay | Although several synthetic or xenobiotic nucleic acids (XNAs) have been shown to be viable genetic materials in vitro, major hurdles remain for their in vivo applications, particularly orthogonality. The availability of XNAs that do not interact with natural nucleic acids and are not affected by natural DNA processing enzymes, as well as specialized XNA processing enzymes that do not interact with natural nucleic acids, is essential. Here, we report 3'-2' phosphonomethylthreosyl nucleic acid (tPhoNA) as a novel XNA genetic material and a prime candidate for in vivo XNA applications. We established routes for the chemical synthesis of phosphonate nucleic acids and phosphorylated monomeric building blocks, and we demonstrated that DNA duplexes were destabilized upon replacement with tPhoNA. We engineered a novel tPhoNA synthetase enzyme and, with a previously reported XNA reverse transcriptase, demonstrated that tPhoNA is a viable genetic material (with an aggregate error rate of approximately 17 X 10(-3) per base) compatible with the isolation of functional XNAs. In vivo experiments to test tPhoNA orthogonality showed that the E. coli cellular machinery had only very limited potential to access genetic information in tPhoNA. Our work is the first report of a synthetic genetic material modified in both sugar and phosphate backbone moieties and represents a significant advance in biorthogonality toward the introduction of XNA systems in vivo. | AAB-5350-2019;AAF-7931-2020;GXV-5590-2022;O-5514-2017 | DEOXYTHREOSYL NUCLEOSIDE PHOSPHONATES;DNA-POLYMERASE;ENZYMATIC-SYNTHESIS;HYBRID DUPLEXES;IN-VITRO;STRUCTURAL BASIS;SYNTHETIC GENETICS;THERMINATOR POLYMERASE;THREOSE NUCLEIC-ACID;TNA SYNTHESIS | 0 | null | null | 10 | DEOXYTHREOSYL NUCLEOSIDE PHOSPHONATES;DNA-POLYMERASE;ENZYMATIC-SYNTHESIS;HYBRID DUPLEXES;IN-VITRO;STRUCTURAL BASIS;synthetic genetics;THERMINATOR POLYMERASE;THREOSE NUCLEIC-ACID;TNA SYNTHESIS | WOS:000434101100026 | Katholieke Univ Leuven, Louvain, Belgium;UCL, London, England;Univ London, London, England;Univ Paris Saclay, Evry, France | Belgium;France;UK | 2,018 | null | 0000-0001-9624-5536;0000-0002-1237-9586;0000-0002-7411-7821;0000-0002-8866-2265;0000-0003-2491-0028;0000-0003-3460-3806;0000-0003-3589-8503;0000-0003-4067-6921 | null | null | English | null | ANGEW CHEM INT EDIT;BIOCHEMISTRY-US;BIOESSAYS;CHEM BIODIVERS;CHEM BIOL;CHEM SCI;CHEM-EUR J;CHEMBIOCHEM;CR BIOL;CURR OPIN BIOTECH;HELV CHIM ACTA;J AM CHEM SOC;J MED CHEM;J MOL BIOL;NAT CHEM;NAT COMMUN;NAT STRUCT BIOL;NATURE;NUCLEIC ACIDS RES;NUCLEOS NUCLEOT;ORG BIOMOL CHEM;ORG LETT;P NATL ACAD SCI USA;PLOS ONE;SCIENCE | Cozens, Christopher;Dumbre, Shrinivas;Groaz, Elisabetta;Herdewijn, Piet;Jaziri, Faten;Liu, Chao;Marechal, Amandine;Marliere, Philippe;Pezo, Valerie;Pinheiro, Vitor B;Rozenski, Jef | 2024-03-11
ER | Bande, O;Chaput, J C;Chim, N;Cozens, C;Dunn, M R;Eremeeva, E;Fogg, M J;Gardner, A F;Herdewijn, P;Houlihan, G;Ichida, J K;Inoue, N;Kostov, O;Kropp, H M;Kuroita, T;Larsen, A C;Lesnik, E A;Liu, C;Marlière, P;Mehta, A P;Moffatt, J G;Pezo, V;Pinheiro, V B;Pochet, S;Páv, O;Reiman D.;Renders, M;Schöning, K U;Sípová, H;Taylor, A I;Tchou, J;Tsai, C H;Wu, T F;Yu, H Y;Zhang, Y | GI1AH | Evry, France.;London, England;London, England.;Louvain, Belgium. | 48 | null | 4 | null | 29,722,977 | Cozens, Christopher;Dumbre, Shrinivas;Groaz, Elisabetta;Herdewijn, Piet;Jaziri, Faten;Liu, Chao;Marechal, Amandine;Marliere, Philippe;Pezo, Valerie;Pinheiro, Vitor B;Rozenski, Jef | J AM CHEM SOC | Evry, France;London, England;Louvain, Belgium |
Beyer, H M;Chatelle, C;Engesser, R;Jones, A R;Ochoa-Fernandez, R;Schneider, N;Timmer, J;Weber, W;Zurbriggen, M D | 10.1021/acssynbio.7b00450 | null | 1155 16TH ST, NW, WASHINGTON, DC 20036 USA | 154ke553o5d3sm5p1ry623q6e582i304a6q26 | A Green-Light-Responsive System for the Control of Transgene Expression in Mammalian and Plant Cells | Univ Freiburg | null | Weber, W (corresponding author), Univ Freiburg, BIOSS Ctr Biol Signalling Studies, D-79104 Freiburg, Germany.;Weber, W (corresponding author), Univ Freiburg, Fac Biol, D-79104 Freiburg, Germany.;Weber, W (corresponding author), Univ Freiburg, SGBM Spemann Grad Sch Biol & Med, D-79104 Freiburg, Germany.;Zurbriggen, MD (corresponding author), Heinrich Heine Univ, iGRAD Plant Grad Sch, D-40225 Dusseldorf, Germany.;Zurbriggen, MD (corresponding author), Heinrich Heine Univ, Inst Synthet Biol, D-40225 Dusseldorf, Germany. | null | Beyer, Hannes M;Chatelle, Claire;Engesser, Raphael;Jones, Alex R;Ochoa-Fernandez, Rocio;Schneider, Nils;Timmer, Jens;Weber, Wilfried;Zurbriggen, Matias D | Biochemical Research Methods | Excellence Initiative of the German Federal Government [BIOSS EXC-294, CEPLAS EXC-1028, SGBM GSC-4, iGRAD-Plant GRK-1525]; Excellence Initiative of the German State Government [BIOSS EXC-294, CEPLAS EXC-1028, SGBM GSC-4, iGRAD-Plant GRK-1525]; DFG [WE 4733/4-1, SPP1926 Z259/2-1] | WOS | Weber, W;Zurbriggen, M D | Heinrich Heine Univ, Dusseldorf, Germany;Natl Phys Lab, Middx, England;Univ Freiburg, Freiburg, Germany;Univ Helsinki, Helsinki, Finland | 7 | a;and;Cells;control;expression;for;Green-Light-Responsive;in;mammalian;of;plant;system;the;transgene | 3 | Beyer, Hannes;Jones, Alex;Ochoa-Fernandez, Rocio;Weber, Wilfried | AMER CHEMICAL SOC | Heinrich Heine Univ, iGRAD Plant Grad Sch, D-40225 Dusseldorf, Germany;Heinrich Heine Univ, Inst Synthet Biol, D-40225 Dusseldorf, Germany;Natl Phys Lab, Teddington TW11 0LW, Middx, England;Univ Freiburg, BIOSS Ctr Biol Signalling Studies, D-79104 Freiburg, Germany;Univ Freiburg, Fac Biol, D-79104 Freiburg, Germany;Univ Freiburg, Fac Biol, D-79104 Freiburg, Germany.; Weber, W (corresponding author), Univ Freiburg, BIOSS Ctr Biol Signalling Studies, D-79104 Freiburg, Germany.; Weber, W (corresponding author), Univ Freiburg, SGBM Spemann Grad Sch Biol & Med, D-79104 Freiburg, Germany.; Zurbriggen, MD (corresponding author), Heinrich Heine Univ, Inst Synthet Biol, D-40225 Dusseldorf, Germany.; Zurbriggen, MD (corresponding author), Heinrich Heine Univ, iGRAD Plant Grad Sch, D-40225 Dusseldorf, Germany;Univ Freiburg, Inst Phys, D-79104 Freiburg, Germany;Univ Freiburg, SGBM Spemann Grad Sch Biol & Med, D-79104 Freiburg, Germany;Univ Helsinki, Inst Biotechnol, Helsinki, Finland | Article | Heinrich Heine Univ Dusseldorf;Univ Freiburg | WASHINGTON | null | null | Heinrich Heine Univ;Natl Phys Lab;Univ Freiburg;Univ Helsinki | DFG;Excellence Initiative of the German Federal Government;Excellence Initiative of the German State Government | Weber, W (corresponding author), Univ Freiburg, Fac Biol, D-79104 Freiburg, Germany.; Weber, W (corresponding author), Univ Freiburg, BIOSS Ctr Biol Signalling Studies, D-79104 Freiburg, Germany.; Weber, W (corresponding author), Univ Freiburg, SGBM Spemann Grad Sch Biol & Med, D-79104 Freiburg, Germany.; Zurbriggen, MD (corresponding author), Heinrich Heine Univ, Inst Synthet Biol, D-40225 Dusseldorf, Germany.; Zurbriggen, MD (corresponding author), Heinrich Heine Univ, iGRAD Plant Grad Sch, D-40225 Dusseldorf, Germany. | 1358 | Beyer, Hannes M;Chatelle, Claire;Engesser, Raphael;Jones, Alex R;Ochoa-Fernandez, Rocio;Schneider, Nils;Timmer, Jens;Weber, Wilfried;Zurbriggen, Matias D | 47 | 8 | 432,901,300,019 | DFG [WE 4733/4-1, SPP1926 Z259/2-1];Excellence Initiative of the German Federal Government [BIOSS EXC-294, CEPLAS EXC-1028, SGBM GSC-4, iGRAD-Plant GRK-1525];Excellence Initiative of the German State Government [BIOSS EXC-294, CEPLAS EXC-1028, SGBM GSC-4, iGRAD-Plant GRK-1525] | Finland;Germany;UK | ACS SYNTHETIC BIOLOGY | Germany | null | null | Univ Freiburg, Fac Biol, D-79104 Freiburg, Germany | 2161-5063 | Beyer, H M;Chatelle, C;Engesser, R;Jones, A R;Ochoa-Fernandez, R;Schneider, N;Timmer, J;Weber, W;Zurbriggen, M D | MAY | matias.zurbriggen@uni-duesseldorf.de;wilfried.weber@bioss.uni-freiburg.de | Control;Green-Light-Responsive System;Plant Cells;Transgene Expression | 9 | J | Biochemistry & Molecular Biology | 350-fold);A. thaliana protoplasts;activating light;AdoB12;applications;BINDING;CarH;cognate DNA operator sequence CarO;control;demonstrated gene repression;development;endogenous photoreceptors;environment;ever-increasing complexity;experimental validation;first synthetic light-responsive system;gene expression;gene expression dynamics;GENE-EXPRESSION;green light;green range;Green-Light-Responsive System;high reversibility;HYDROGELS;interference;light;light spectrum;light-responsive gene expression;light-sensitive bacterial transcription factor CarH;low leakiness;mammalian backgrounds;mammalian cell lines;mammalian cells;mathematical model;minimal activity;new opportunities;optogenetic approaches;optogenetic studies;optogenetics;orthogonal gene expression systems;particular interest;Perspectives;PHOTORECEPTORS;Plant Cells;plant photoreceptors;plants;receptor;response;showing high induction (up;SPACE;synthetic biology;synthetic gene networks;SYSTEM;system will;systems;systems characteristics;Thermus thermophilus;time;TRANSCOBALAMIN;TRANSGENE EXPRESSION;unprecedented resolution;will open | Chatelle, C | AdoB12;BINDING;CarH;ENVIRONMENT;GENE-EXPRESSION;green light;HYDROGELS;light-responsive gene expression;optogenetics;PHOTORECEPTORS;PLANTS;RECEPTOR;TRANSCOBALAMIN | 1349 | [Chatelle, Claire; Schneider, Nils; Beyer, Hannes M.; Weber, Wilfried] Univ Freiburg, Fac Biol, D-79104 Freiburg, Germany. [Chatelle, Claire; Engesser, Raphael; Schneider, Nils; Beyer, Hannes M.; Timmer, Jens; Weber, Wilfried] Univ Freiburg, BIOSS Ctr Biol Signalling Studies, D-79104 Freiburg, Germany. [Ochoa-Fernandez, Rocio; Beyer, Hannes M.; Weber, Wilfried] Univ Freiburg, SGBM Spemann Grad Sch Biol & Med, D-79104 Freiburg, Germany. [Engesser, Raphael; Timmer, Jens] Univ Freiburg, Inst Phys, D-79104 Freiburg, Germany. [Ochoa-Fernandez, Rocio; Zurbriggen, Matias D.] Heinrich Heine Univ, Inst Synthet Biol, D-40225 Dusseldorf, Germany. [Ochoa-Fernandez, Rocio; Zurbriggen, Matias D.] Heinrich Heine Univ, iGRAD Plant Grad Sch, D-40225 Dusseldorf, Germany. [Jones, Alex R.] Natl Phys Lab, Teddington TW11 0LW, Middx, England. [Beyer, Hannes M.] Univ Helsinki, Inst Biotechnol, Helsinki, Finland. | We would like to thank Susanne Knall, Elke Wehinger, and Reinhild Wurm for their excellent technical assistance and Montserrat Elias-Arnanz for fruitful discussions. This work was supported by the Excellence Initiative of the German Federal and State Governments (BIOSS EXC-294, CEPLAS EXC-1028, SGBM GSC-4, and iGRAD-Plant GRK-1525) as well as by DFG grants to WW (WE 4733/4-1) and MZ (SPP1926 Z259/2-1). | 350-fold);A. thaliana protoplasts;activating light;applications;cognate DNA operator sequence CarO;control;demonstrated gene repression;development;endogenous photoreceptors;ever-increasing complexity;experimental validation;first synthetic light-responsive system;gene expression;gene expression dynamics;green range;high reversibility;interference;light;light spectrum;light-sensitive bacterial transcription factor CarH;low leakiness;mammalian backgrounds;mammalian cell lines;mammalian cells;mathematical model;minimal activity;new opportunities;optogenetic approaches;optogenetic studies;orthogonal gene expression systems;particular interest;perspectives;plant cells;plant photoreceptors;response;showing high induction (up;space;synthetic biology;synthetic gene networks;system;system will;systems;systems characteristics;Thermus thermophilus;time;unprecedented resolution;will open | 10.1002/anie.201609229;10.1002/anie.201611998;10.1002/cbic.201700642;10.1007/978-1-4939-3512-3_9;10.1007/s00249-013-0897-x;10.1007/s10265-016-0792-5;10.1016/j.addr.2016.05.006;10.1016/j.biochi.2013.02.004;10.1016/j.conb.2015.01.013;10.1016/j.copbio.2010.07.006;10.1016/j.copbio.2017.06.010;10.1016/j.tibtech.2012.11.006;10.1016/S0378-1119(01)00824-1;10.1021/acssynbio.5b00004;10.1038/81208;10.1038/nature08446;10.1038/nature14950;10.1038/nbt731;10.1038/ncomms8907;10.1038/nmat2250;10.1038/nn.2113;10.1038/srep02052;10.1039/c3mb70579j;10.1039/c7pp00054e;10.1063/1.3528102;10.1073/pnas.0500345102;10.1073/pnas.0800663105;10.1073/pnas.1018972108;10.1073/pnas.1621350114;10.1073/pnas.89.12.5547;10.1093/bioinformatics/btp358;10.1093/bioinformatics/btv405;10.1093/nar/28.5.1120;10.1101/gad.2.6.718;10.1101/pdb.prot5439];10.1126/science.aaf4006;10.1146/annurev-biochem-061516-044500;10.1182/blood-2008-10-181750;10.1371/journal.pone.0137652;10.1515/hsz-2014-0199;10.3732/ajb.1200354;[10.1038/nchembio.1559, 10.1038/NCHEMBIO.1559] | Univ Freiburg | Beyer, H M;Chatelle, C;Engesser, R;Jones, A R;Ochoa-Fernandez, R;Schneider, N;Timmer, J;Weber, W;Zurbriggen, M D | Chatelle, C: Univ Freiburg, Fac Biol, D-79104 Freiburg, Germany | Jones, Alex;Ochoa-Fernandez, Rocio;Weber, Wilfried;Zurbriggen, Matias D | BIOSS EXC-294;CEPLAS EXC-1028;iGRAD-Plant GRK-1525;SGBM GSC-4;SPP1926 Z259/2-1;WE 4733/4-1 | 43 | null | Germany | Heinrich Heine Univ;Natl Phys Lab;Univ Freiburg;Univ Helsinki | Chatelle, Claire | null | BINDING;ENVIRONMENT;GENE-EXPRESSION;HYDROGELS;PHOTORECEPTORS;RECEPTOR;TRANSCOBALAMIN | Chatelle, Claire; Ochoa-Fernandez, Rocio; Engesser, Raphael; Schneider, Nils; Beyer, Hannes M.; Jones, Alex R.; Timmer, Jens; Zurbriggen, Matias D.; Weber, Wilfried; | null | Heinrich Heine Univ, iGRAD Plant Grad Sch, D-40225 Dusseldorf, Germany;Heinrich Heine Univ, Inst Synthet Biol, D-40225 Dusseldorf, Germany;Natl Phys Lab, Teddington TW11 0LW, Middx, England;Univ Freiburg, BIOSS Ctr Biol Signalling Studies, D-79104 Freiburg, Germany;Univ Freiburg, Fac Biol, D-79104 Freiburg, Germany;Univ Freiburg, Inst Phys, D-79104 Freiburg, Germany;Univ Freiburg, SGBM Spemann Grad Sch Biol & Med, D-79104 Freiburg, Germany;Univ Helsinki, Inst Biotechnol, Helsinki, Finland | Heinrich Heine Univ, iGRAD Plant Grad Sch, D-40225 Dusseldorf, Germany;Heinrich Heine Univ, Inst Synthet Biol, D-40225 Dusseldorf, Germany;Natl Phys Lab, Teddington TW11 0LW, Middx, England;Univ Freiburg, BIOSS Ctr Biol Signalling Studies, D-79104 Freiburg, Germany;Univ Freiburg, Fac Biol, D-79104 Freiburg, Germany;Univ Freiburg, Inst Phys, D-79104 Freiburg, Germany;Univ Freiburg, SGBM Spemann Grad Sch Biol & Med, D-79104 Freiburg, Germany;Univ Helsinki, Inst Biotechnol, Helsinki, Finland | null | AdoB12;CarH;green light;light-responsive gene expression;optogenetics;plants | 5 | 1988;1992;2000;2002;2005;2008;2009;2010;2011;2013;2014;2015;2016;2017;2018 | 47 | Heinrich Heine Univ, iGRAD Plant Grad Sch, D-40225 Dusseldorf, Germany;Heinrich Heine Univ, Inst Synthet Biol, D-40225 Dusseldorf, Germany;Univ Freiburg, BIOSS Ctr Biol Signalling Studies, D-79104 Freiburg, Germany;Univ Freiburg, Fac Biol, D-79104 Freiburg, Germany;Univ Freiburg, SGBM Spemann Grad Sch Biol & Med, D-79104 Freiburg, Germany | ACS Synth. Biol. | Weber, Wilfried | AMER CHEMICAL SOC | (up;,;350-fold);a;A.;activating;activity;along;and;applications;approaches;are;as;backgrounds;bacterial;based;biology;broadly;by;CarH;CarO;cell;cells;characteristics;cognate;complexity;control;demonstrated;describe;described;development;DNA;due;dynamics;enable;endogenous;engineered;ever-increasing;expect;experimental;expression;factor;finally;first;for;from;functional;gene;green;have;here;high;however;in;induction;interest;interference;into;its;leakiness;light;light-responsive;light-sensitive;limited;lines;low;mammalian;mathematical;minimal;model;networks;new;of;on;open;operator;opportunities;optogenetic;Orthogonal;particular;perspectives;photoreceptors;plant;precise;protoplasts;provide;quantitatively;range;repression;requires;resolution;responds;response;responsive;reversibility;sequence;showing;space;spectrum;still;studies;synthetic;system;systems;targeted;thaliana;that;the;thermophilus;Thermus;they;this;time;to;transcription;transferred;unprecedented;up;used;validation;various;was;we;well;which;while;will;with | Heinrich Heine Univ;Univ Freiburg | The ever-increasing complexity of synthetic gene networks and applications of synthetic biology requires precise and orthogonal gene expression systems. Of particular interest are systems responsive to light as they enable the control of gene expression dynamics with unprecedented resolution in space and time. While broadly used in mammalian backgrounds, however, optogenetic approaches in plant cells are still limited due to interference of the activating light with endogenous photoreceptors. Here, we describe the development of the first synthetic light-responsive system for the targeted control of gene expression in mammalian and plant cells that responds to the green range of the light spectrum in which plant photoreceptors have minimal activity. We first engineered a system based on the light-sensitive bacterial transcription factor CarH and its cognate DNA operator sequence CarO from Thermus thermophilus to control gene expression in mammalian cells. The system was functional in various mammalian cell lines, showing high induction (up to 350-fold) along with low leakiness, as well as high reversibility. We quantitatively described the systems characteristics by the development and experimental validation of a mathematical model. Finally, we transferred the system into A. thaliana protoplasts and demonstrated gene repression in response to green light. We expect that this system will provide new opportunities in applications based on synthetic gene networks and will open up perspectives for optogenetic studies in mammalian and plant cells. | AAY-1448-2020;AFQ-8212-2022;B-4732-2012;L-1778-2013 | BINDING;ENVIRONMENT;GENE-EXPRESSION;HYDROGELS;PHOTORECEPTOR;RECEPTOR;TRANSCOBALAMIN | 4 | null | AdoB12;CarH;green light;light-responsive gene expression;optogenetics;plants | 19 | AdoB12;BINDING;CarH;ENVIRONMENT;GENE-EXPRESSION;green light;HYDROGELS;light-responsive gene expression;optogenetics;PHOTORECEPTOR;PLANTS;RECEPTOR;TRANSCOBALAMIN | WOS:000432901300019 | Heinrich Heine Univ, Dusseldorf, Germany;Natl Phys Lab, Middx, England;Univ Freiburg, Freiburg, Germany;Univ Helsinki, Helsinki, Finland | Finland;Germany;UK | 2,018 | null | 0000-0001-6021-7824;0000-0001-8946-2700;0000-0002-6882-006X;0000-0003-4340-4446 | null | null | English | null | ACS SYNTH BIOL;ADV DRUG DELIVER REV;AM J BOT;ANGEW CHEM INT EDIT;ANNU REV BIOCHEM;BIOCHIMIE;BIOINFORMATICS;BIOL CHEM;BLOOD;CHAOS;CHEMBIOCHEM;COLD SPRING HARB PRO;CURR OPIN BIOTECH;CURR OPIN NEUROBIOL;EUR BIOPHYS J BIOPHY;GENE;GENE DEV;J PLANT RES;METHODS MOL BIOL;MOL BIOSYST;NAT BIOTECHNOL;NAT CHEM BIOL;NAT COMMUN;NAT MATER;NAT NEUROSCI;NATURE;NUCL ACIDS RES;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PHOTOCH PHOTOBIO SCI;PLOS ONE;SCI REP-UK;SCIENCE;TRENDS BIOTECHNOL | Beyer, Hannes M;Chatelle, Claire;Engesser, Raphael;Jones, Alex R;Ochoa-Fernandez, Rocio;Schneider, Nils;Timmer, Jens;Weber, Wilfried;Zurbriggen, Matias D | 2024-03-11
ER | Ausländer, S;Baumgärtel, K;Beyer, H M;Díez, A I;Ehrbar, M;Engesser R.;Fussenegger, M;Galvao, V C;Gossen, M;Jacobsen, D W;Jones, A R;Jost, M;Kainrath, S;Kojima, R;Kolar, K;Kong, S G;Kramer, B P;Kutta, R J;Levskaya, A;Müller, K;Ochoa-Fernandez, R;Olson, E J;Ortiz-Guerrero, J M;Padmanabhan, S;Quadros, E V;Rang, A;Raue, A;Redchuk, T A;Rio D.C.;Schlatter, S;Triezenberg, S J;Wang, R;Wang, Y H;Weber, W;Wend, S;Xie, M | GG7TR | Dusseldorf, Germany;Dusseldorf, Germany.;Freiburg, Germany. | 55 | null | 4 | null | 29,634,242 | Beyer, Hannes M;Chatelle, Claire;Engesser, Raphael;Jones, Alex R;Ochoa-Fernandez, Rocio;Schneider, Nils;Timmer, Jens;Weber, Wilfried;Zurbriggen, Matias D | ACS SYNTH BIOL | Dusseldorf, Germany;Freiburg, Germany;Helsinki, Finland;Middx, England |
Kurata, H;Maeda, K | 10.1016/j.jtbi.2017.12.014 | null | 24-28 OVAL RD, LONDON NW1 7DX, ENGLAND | 2136125s6d1c4f5n3g62116k1t2q5r86zg1x3b | Long negative feedback loop enhances period tunability of biological oscillators | Kyushu Inst Technol | null | Maeda, K (corresponding author), Kyushu Inst Technol, Dept Biosci & Bioinformat, 680-4 Kawazu, Iizuka, Fukuoka 8208502, Japan. | null | Kurata, Hiroyuki;Maeda, Kazuhiro | Biology;Mathematical & Computational Biology | Japan Society for the Promotion of Science [26870432, 16H02898]; Grants-in-Aid for Scientific Research [16H02898, 26870432] Funding Source: KAKEN | WOS | Maeda, K | Kyushu Inst Technol, Fukuoka, Japan | 440 | biological;enhances;feedback;long;loop;Negative;of;Oscillators;period;tunability | 1 | Kurata, Hiroyuki;Maeda, Kazuhiro | ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD | Kyushu Inst Technol, Biomed Informat R&D Ctr, 680-4 Kawazu, Iizuka, Fukuoka 8208502, Japan;Kyushu Inst Technol, Dept Biosci & Bioinformat, 680-4 Kawazu, Iizuka, Fukuoka 8208502, Japan;Kyushu Inst Technol, Frontier Res Acad Young Researchers, 1-1 Sensui Cho, Kitakyushu, Fukuoka 8048550, Japan | Article | Kyushu Inst Technol | LONDON | null | null | Kyushu Inst Technol | Grants-in-Aid for Scientific Research;Japan Society for the Promotion of Science | Maeda, K (corresponding author), Kyushu Inst Technol, Dept Biosci & Bioinformat, 680-4 Kawazu, Iizuka, Fukuoka 8208502, Japan. | 31 | Kurata, Hiroyuki;Maeda, Kazuhiro | 26 | 3 | 424,733,100,003 | Grants-in-Aid for Scientific Research [16H02898, 26870432] Funding Source: KAKEN;Japan Society for the Promotion of Science [26870432, 16H02898] | Japan | JOURNAL OF THEORETICAL BIOLOGY | Japan | null | null | Kyushu Inst Technol, Frontier Res Acad Young Researchers, 1-1 Sensui Cho, Kitakyushu, Fukuoka 8048550, Japan | 0022-5193 | Kurata, H;Maeda, K | MAR 7 | kmaeda@bio.kyutech.ac.jp;kurata@bio.kyutech.ac.jp | biological oscillators;long negative feedback loop;period tunability | 2 | J | Life Sciences & Biomedicine - Other Topics;Mathematical & Computational Biology | (period) tunability;additional positive feedback loops;amplitude;biological oscillations;biological oscillators;biological oscillators produce tunable oscillations;C 2017 Elsevier Ltd;cell cycles;CELL-CYCLE;Circadian clock;Circadian rhythm;CIRCUITS;clues;computational experiments;CYANOBACTERIA;dynamic range;FEEDBACK LOOP;first;GENE-EXPRESSION;heartbeats;hysteresis-based mechanism;long negative feedback loop;major role;MODEL;negative feedback loop;negative feedback oscillators;networks;non-tunable synthetic gene oscillator;one;ORGANISMS;OSCILLATIONS;oscillatory phenomena;period;period tunability;positive-plus-negative feedback oscillators;positive-plus-negative feedback oscillators produce tunable oscillations;produce tunable oscillations;prominent features;property;question;repressilator;RHYTHMS;rights reserved;ROBUST;sensitivity;significant changes;simulation;study;synthetic biologists;synthetic biology;systems biology;TEMPERATURE COMPENSATION;third;tunability;tunable gene oscillators;tunable oscillations;tunable oscillator;unexplored | Maeda, K | CELL-CYCLE;Circadian clock;Circadian rhythm;CIRCUITS;CYANOBACTERIA;FEEDBACK LOOP;GENE-EXPRESSION;MODEL;NETWORKS;repressilator;RHYTHMS;ROBUST;SENSITIVITY;SIMULATION;Synthetic biology;systems biology;TEMPERATURE COMPENSATION | 21 | [Maeda, Kazuhiro] Kyushu Inst Technol, Frontier Res Acad Young Researchers, 1-1 Sensui Cho, Kitakyushu, Fukuoka 8048550, Japan. [Maeda, Kazuhiro; Kurata, Hiroyuki] Kyushu Inst Technol, Dept Biosci & Bioinformat, 680-4 Kawazu, Iizuka, Fukuoka 8208502, Japan. [Kurata, Hiroyuki] Kyushu Inst Technol, Biomed Informat R&D Ctr, 680-4 Kawazu, Iizuka, Fukuoka 8208502, Japan. | This work was supported by Grant-in-Aid for Young Scientists(B) (26870432) and partially supported by Grant-in-Aid for Scientific Research (B) (16H02898) from Japan Society for the Promotion of Science. The super-computing resource was provided by Human Genome Center, Institute of Medical Science, University of Tokyo. We thank Dr. Yu Matsuoka and Dr. Midori Iida for critical reading of the manuscript. | (period) tunability;additional positive feedback loops;amplitude;biological oscillations;biological oscillators produce tunable oscillations;cell cycles;clues;computational experiments;dynamic range;first;heartbeats;hysteresis-based mechanism;major role;negative feedback loop;negative feedback oscillators;non-tunable synthetic gene oscillator;one;organisms;oscillations;oscillatory phenomena;period;positive-plus-negative feedback oscillators;positive-plus-negative feedback oscillators produce tunable oscillations;produce tunable oscillations;prominent features;property;question;repressilator;significant changes;study;synthetic biologists;third;tunability;tunable gene oscillators;tunable oscillations;tunable oscillator;unexplored | 10.1006/jtbi.2000.2038;10.1007/BF02460724;10.1007/s001140050704;10.1016/0065-2571(65)90067-1;10.1016/j.bpj.2014.02.039;10.1016/j.cell.2011.03.006;10.1016/j.cels.2017.06.013;10.1016/j.cub.2017.10.014;10.1016/j.febslet.2011.04.048;10.1016/j.gde.2010.08.006;10.1016/j.jtbi.2010.12.012;10.1016/j.mbs.2012.01.001;10.1016/j.molcel.2015.08.022;10.1016/S0092-8674(00)80566-8;10.1038/31960;10.1038/35002125;10.1038/417329a;10.1038/457271a;10.1038/msb.2012.62;10.1038/nature02533;10.1038/nature07389;10.1038/nature07616;10.1038/nature08753;10.1038/nature19841;10.1038/nbt.1591;10.1038/ncomms9587;10.1038/nrg1633;10.1038/nrg2697;10.1038/nrm2530;10.1049/iet-syb.2015.0090;10.1063/1.1345702;10.1073/pnas.1004720108;10.1083/jcb.201611002;10.1093/bib/bbt048;10.1098/rsif.2010.0183;10.1098/rspb.1995.0153;10.1101/gad.1696108;10.1103/PhysRevE.80.011926;10.1126/science.1156951;10.1126/science.1230996;10.1126/science.aaa3794;10.1126/scisignal.2000810;10.1145/1089014.1089020;10.1177/0748730402238239;10.1186/1752-0509-8-S5-S1;10.1186/cc2836;10.1186/gb-2012-13-2-240;10.1371/journal.pcbi.1000990;10.1371/journal.pcbi.1005298;10.1371/journal.pcbi.1005501;10.1371/journal.pone.0008083;10.1371/journal.pone.0030489;10.1371/journal.pone.0104761;10.1529/biophysj.106.081240 | Kyushu Inst Technol | Kurata, H;Maeda, K | Maeda, K: Kyushu Inst Technol, Frontier Res Acad Young Researchers, 1-1 Sensui Cho, Kitakyushu, Fukuoka 8048550, Japan | Maeda, Kazuhiro | 16H02898;26870432 | 57 | null | Japan | Kyushu Inst Technol | Maeda, Kazuhiro | null | CELL-CYCLE;CIRCADIAN CLOCK;CIRCUITS;CYANOBACTERIA;GENE-EXPRESSION;MODEL;NETWORKS;RHYTHMS;ROBUST;SYNTHETIC BIOLOGY | Maeda, Kazuhiro; Kurata, Hiroyuki; | null | Kyushu Inst Technol, Biomed Informat R&D Ctr, 680-4 Kawazu, Iizuka, Fukuoka 8208502, Japan;Kyushu Inst Technol, Dept Biosci & Bioinformat, 680-4 Kawazu, Iizuka, Fukuoka 8208502, Japan;Kyushu Inst Technol, Frontier Res Acad Young Researchers, 1-1 Sensui Cho, Kitakyushu, Fukuoka 8048550, Japan | Kyushu Inst Technol, Biomed Informat R&D Ctr, 680-4 Kawazu, Iizuka, Fukuoka 8208502, Japan;Kyushu Inst Technol, Dept Biosci & Bioinformat, 680-4 Kawazu, Iizuka, Fukuoka 8208502, Japan;Kyushu Inst Technol, Frontier Res Acad Young Researchers, 1-1 Sensui Cho, Kitakyushu, Fukuoka 8048550, Japan | 1095-8541 | Circadian rhythm;Feedback loop;repressilator;Sensitivity;Simulation;Synthetic biology;systems biology;Temperature compensation | null | 1965;1991;1995;1998;1999;2000;2001;2002;2004;2005;2006;2008;2009;2010;2011;2012;2013;2014;2015;2016;2017 | 8 | Kyushu Inst Technol, Dept Biosci & Bioinformat, 680-4 Kawazu, Iizuka, Fukuoka 8208502, Japan | J. Theor. Biol. | Kurata, Hiroyuki | ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD | (period);,;a;additional;amplitude;and;any;as;be;been;biological;biologists;by;called;can;cell;changes;clues;computational;computationally;confirmed;converted;correlated;cycles;demonstrated;design;dynamic;experiments;features;feedback;finally;first;found;gene;generate;has;heartbeats;how;however;hysteresis-based;in;into;is;it;known;largely;lengthening;long;loop;loops;major;mechanism;negative;non-tunable;of;one;organisms;oscillations;oscillator;oscillators;oscillatory;period;phenomena;play;positive;positive-plus-negative;positively;produce;prominent;property;provides;question;range;remains;reported;repressilator;role;second;showed;significant;some;study;such;synthetic;tackle;that;the;third;this;through;to;tunability;tunable;tuned;unexplored;using;we;with;without;work | Kyushu Inst Technol | Oscillatory phenomena play a major role in organisms. In some biological oscillations such as cell cycles and heartbeats, the period can be tuned without significant changes in the amplitude. This property is called (period) tunability, one of the prominent features of biological oscillations. However, how biological oscillators produce tunable oscillations remains largely unexplored. We tackle this question using computational experiments. It has been reported that positive-plus-negative feedback oscillators produce tunable oscillations through the hysteresis-based mechanism. First, in this study, we confirmed that positive-plus-negative feedback oscillators generate tunable oscillations. Second, we found that tunability is positively correlated with the dynamic range of oscillations. Third, we showed that long negative feedback oscillators without any additional positive feedback loops can produce tunable oscillations. Finally, we computationally demonstrated that by lengthening the negative feedback loop, the Repressilator, known as a non-tunable synthetic gene oscillator, can be converted into a tunable oscillator. This work provides synthetic biologists with clues to design tunable gene oscillators. | Y-3151-2019 | CELL-CYCLE;CIRCADIAN CLOCK;CIRCUITS;CYANOBACTERIA;GENE-EXPRESSION;MODEL;NETWORKS;RHYTHMS;ROBUST;SYNTHETIC BIOLOGY | 0 | null | Circadian rhythm;Feedback loop;repressilator;Sensitivity;Simulation;Synthetic biology;systems biology;Temperature compensation | 11 | CELL-CYCLE;Circadian clock;CIRCADIAN-RHYTHMS;CIRCUITS;CYANOBACTERIA;FEEDBACK LOOPS;GENE-EXPRESSION;MODEL;NETWORKS;repressilator;RHYTHMS;ROBUST;SENSITIVITY;SIMULATION;Synthetic biology;systems biology;TEMPERATURE COMPENSATION | WOS:000424733100003 | Kyushu Inst Technol, Fukuoka, Japan | Japan | 2,018 | null | 0000-0002-6038-1322;0000-0003-4254-2214 | null | null | English | null | ACM T MATH SOFTWARE;ADVANCE ENZYME REGULAT;B MATH BIOL;BIOPHYS J;BMC SYST BIOL;BRIEF BIOINFORM;CELL;CELL SYST;CHAOS;CRIT CARE;CURR BIOL;CURR OPIN GENET DEV;FEBS LETT;GENE DEV;GENOME BIOL;IET SYST BIOL;J BIOL RHYTHM;J CELL BIOL;J R SOC INTERFACE;J THEOR BIOL;MATH BIOSCI;MOL CELL;MOL SYST BIOL;NAT BIOTECHNOL;NAT COMMUN;NAT REV GENET;NAT REV MOL CELL BIO;NATURE;NATURWISSENSCHAFTEN;P NATL ACAD SCI USA;P ROY SOC B-BIOL SCI;PHYS REV E;PLOS COMPUT BIOL;PLOS ONE;SCI SIGNAL;SCIENCE;Studies in Nonlinearity | Kurata, Hiroyuki;Maeda, Kazuhiro | 2024-03-11
ER | [Anonymous];Ananthasubramaniam, B;Baum, K;Bell-Pedersen, D;Bewick, V;Cardillo G.;Chen, Y;Chen, Y Y;Csikász-Nagy, A;D'Alessandro, M;Danino, T;Dolmetsch, R E;Dunlap, J C;Elowitz, M B;Ferrell, J E;Forger, D B;Fujita, K A;Goldbeter, A;Goodwin Brian C.;Gore, J;Hasty, J;Hess, B;Hindmarsh, A C;Hogenesch, J B;Kim, J K;Kurata, H;Kurosawa, G;Lema, M A;Li, Z D;Lu, T K;Maeda, K;Marucci, L;Mathur, M;Mihalcescu, I;Mukherji, S;Novák, B;O'Brien, E L;Oikonomou, C;Panda, S;Potvin-Trottier, L;Purcell, O;Stricker, J;Strogatz S.;Swinburne, I A;Teng, S W;Thommen, Q;Thron, C D;Tian, X J;Tigges, M;Tsai, T Y C;Zhou, M | FV7AH | Fukuoka, Japan | 9 | null | 1 | null | 29,253,507 | Kurata, Hiroyuki;Maeda, Kazuhiro | J THEOR BIOL | Fukuoka, Japan |
Alexander, S C;Busby, K N;Devaraj, N K;Zhang, D Y;Zhou, C Y | 10.1002/anie.201710917 | null | POSTFACH 101161, 69451 WEINHEIM, GERMANY | 5w5dn2y1t3x2384w55251h6brq5n6b3k1s5d | Light-Activated Control of Translation by Enzymatic Covalent mRNA Labeling | Univ Calif San Diego | null | Devaraj, NK (corresponding author), Univ Calif San Diego, Dept Chem & Biochem, 9500 Gilman Dr, La Jolla, CA 92093 USA. | null | Alexander, Seth C;Busby, Kayla N;Devaraj, Neal K;Zhang, Dongyang;Zhou, Cun Yu | Chemistry, Multidisciplinary | U.S. Army Research Office through the MURI program [W911NF-13-1-0383]; National Institutes of Health [R01 GM123285-01, T32 GM112584-03] | WOS | Devaraj, N K | Univ Calif San Diego, La Jolla, CA USA | 57 | by;control;Covalent;enzymatic;Labeling;Light-Activated;mRNA;of;translation | 1 | Busby, Kayla | WILEY-V C H VERLAG GMBH | Univ Calif San Diego, Dept Chem & Biochem, 9500 Gilman Dr, La Jolla, CA 92093 USA | Article | Univ Calif San Diego | WEINHEIM | null | null | Univ Calif San Diego | National Institutes of Health;U.S. Army Research Office through the MURI program | Devaraj, NK (corresponding author), Univ Calif San Diego, Dept Chem & Biochem, 9500 Gilman Dr, La Jolla, CA 92093 USA. | 2826 | Alexander, Seth C;Busby, Kayla N;Devaraj, Neal K;Zhang, Dongyang;Zhou, Cun Yu | 51 | 1 | 426,490,700,008 | National Institutes of Health [R01 GM123285-01, T32 GM112584-03];U.S. Army Research Office through the MURI program [W911NF-13-1-0383] | USA | ANGEWANDTE CHEMIE-INTERNATIONAL EDITION | USA | null | null | Univ Calif San Diego, Dept Chem & Biochem, 9500 Gilman Dr, La Jolla, CA 92093 USA | 1433-7851 | Alexander, S C;Busby, K N;Devaraj, N K;Zhang, D Y;Zhou, C Y | MAR 5 | ndevaraj@ucsd.edu | Enzymatic Covalent mRNA;light-Activated Control;translation | 5 | J | Chemistry | 5' untranslated region (5' UTR);5' UTR;activation;bacterial tRNA guanine transglycosylase (TGT);biotechnological applications;cells;cellular protein expression;developing synthetic gene regulatory circuits;efficient approach;Enzymatic Covalent mRNA;enzymatic process;gene expression;GENE-EXPRESSION;groups;groups covalently;guanine nucleobase;INITIATION;light-Activated Control;method;modified mRNA (mod-mRNA) transcripts;mRNA;mRNA translation efficiency;OLIGONUCLEOTIDES;optogenetics;photocleavable;regeneration;RNA labeling;RNA modification;RNA transglycosylation;single-cell precision;SMALL-MOLECULE;specific 17-nucleotide motif (Tag);stability;strategy;successful spatiotemporal photo-regulation;synthetic pre-queuosine1 (preQ(1) derivatives;therapeutic discovery;therapeutically;translation;visible-light photocleavage;vitro transcribed mRNA (IVT-mRNA) | Zhang, D Y | CELLS;gene expression;GENE-EXPRESSION;INITIATION;OLIGONUCLEOTIDES;optogenetics;REGENERATION;RNA labeling;RNA modification;STABILITY | 2822 | [Zhang, Dongyang; Zhou, Cun Yu; Busby, Kayla N.; Alexander, Seth C.; Devaraj, Neal K.] Univ Calif San Diego, Dept Chem & Biochem, 9500 Gilman Dr, La Jolla, CA 92093 USA. | This work was supported by the U.S. Army Research Office through the MURI program under award W911NF-13-1-0383 and by the National Institutes of Health under award R01 GM123285-01 and T32 GM112584-03. | 5' untranslated region (5' UTR);5' UTR;activation;bacterial tRNA guanine transglycosylase (TGT);biotechnological applications;cellular protein expression;developing synthetic gene regulatory circuits;efficient approach;enzymatic process;gene expression;groups;groups covalently;guanine nucleobase;method;modified mRNA (mod-mRNA) transcripts;mRNA;mRNA translation efficiency;photocleavable;RNA transglycosylation;single-cell precision;small-molecule;specific 17-nucleotide motif (Tag);strategy;successful spatiotemporal photo-regulation;synthetic pre-queuosine1 (preQ(1) derivatives;therapeutic discovery;therapeutically;visible-light photocleavage;vitro transcribed mRNA (IVT-mRNA) | 10.1002/anie.201405355;10.1002/anie.201604107;10.1002/cbic.201402495;10.1016/0092-8674(95)90325-9;10.1016/j.cell.2009.01.042;10.1016/j.jconrel.2015.09.050;10.1016/j.stem.2010.10.002;10.1016/s0165-9936(04)00734-4;10.1016/S0968-0004(03)00051-3;10.1021/cb400293e;10.1021/ja5055862;10.1021/jacs.5b07286;10.1023/B:MICS.0000006846.13226.38;10.1038/mt.2008.200;10.1038/nbt.2682;10.1038/ng1089;10.1038/ng583;10.1038/nrd4278;10.1038/nrg2041;10.1038/nrg3724;10.1038/nrg887;10.1038/nrm2838;10.1039/b812058g;10.1093/nar/gkm1029;10.1093/nar/gks996;10.1093/nar/gkt806;10.1146/annurev-biochem-060308-103103;10.3390/pharmaceutics7030137;10.3791/51943;[10.1038/NMETH.1892, 10.1038/nmeth.1892] | Univ Calif San Diego | Alexander, S C;Busby, K N;Devaraj, N K;Zhang, D Y;Zhou, C Y | Zhang, D Y: Univ Calif San Diego, Dept Chem & Biochem, 9500 Gilman Dr, La Jolla, CA 92093 USA | Alexander, Seth C;Devaraj, Neal K | R01 GM123285-01;T32 GM112584-03;W911NF-13-1-0383 | 31 | null | USA | Univ Calif San Diego | Zhang, Dongyang | Green Accepted | CELLS;GENE-EXPRESSION;INITIATION;OLIGONUCLEOTIDES;REGENERATION;STABILITY | Zhang, Dongyang; Zhou, Cun Yu; Busby, Kayla N.; Alexander, Seth C.; Devaraj, Neal K.; | null | Univ Calif San Diego, Dept Chem & Biochem, 9500 Gilman Dr, La Jolla, CA 92093 USA | Univ Calif San Diego, Dept Chem & Biochem, 9500 Gilman Dr, La Jolla, CA 92093 USA | 1521-3773 | gene expression;optogenetics;RNA labeling;RNA modification | 11 | 1995;2001;2002;2003;2004;2007;2008;2009;2010;2012;2013;2014;2015;2016;2017 | 38 | Univ Calif San Diego, Dept Chem & Biochem, 9500 Gilman Dr, La Jolla, CA 92093 USA | Angew. Chem.-Int. Edit. | Devaraj, Neal K | WILEY-V C H VERLAG GMBH | (5';(IVT-mRNA);(mod-mRNA);(preQ(1);(Tag);(TGT);,;17-nucleotide;5';a;achieved;activation;an;and;applications;applied;approach;are;attached;bacterial;be;biotechnological;caging;can;cellular;chemically;circuits;conjugated;covalently;demonstrate;derivatives;developing;discovery;efficiency;efficient;enzymatic;exchanges;expression;for;gene;groups;guanine;in;method;modified;modular;motif;mRNA;nucleobase;of;our;photo-regulation;photocleavable;photocleavage;placed;pre-queuosine1;precision;process;protein;provides;reduce;region;regulatory;relevant;RNA;severely;single-cell;small-molecule;spatiotemporal;specific;strategically;strategy;successful;synthetic;the;therapeutic;therapeutically;these;this;through;to;transcribed;transcripts;transglycosylase;transglycosylation;translation;tRNA;untranslated;upon;using;UTR;UTR);visible-light;vitro;was;we;when;which;with | Univ Calif San Diego | Activation of cellular protein expression upon visible-light photocleavage of small-molecule caging groups covalently attached to the 5' untranslated region (5' UTR) of an mRNA was achieved. These photocleavable caging groups are conjugated to in vitro transcribed mRNA (IVT-mRNA) through RNA transglycosylation, an enzymatic process in which a bacterial tRNA guanine transglycosylase (TGT) exchanges a guanine nucleobase in a specific 17-nucleotide motif (Tag) for synthetic pre-queuosine1 (preQ(1)) derivatives. The caging groups severely reduce mRNA translation efficiency when strategically placed in the 5' UTR. Using this method, we demonstrate the successful spatiotemporal photo-regulation of gene expression with single-cell precision. Our method can be applied to therapeutically relevant chemically modified mRNA (mod-mRNA) transcripts. This strategy provides a modular and efficient approach for developing synthetic gene regulatory circuits, biotechnological applications, and therapeutic discovery. | B-4712-2014;E-5734-2011 | CELLS;GENE-EXPRESSION;INITIATION;OLIGONUCLEOTIDES;REGENERATION;STABILITY | 0 | null | gene expression;optogenetics;RNA labeling;RNA modification | 5 | CELLS;GENE-EXPRESSION;INITIATION;RNA labeling;OLIGONUCLEOTIDES;optogenetics;REGENERATION;RNA modification;STABILITY | WOS:000426490700008 | Univ Calif San Diego, La Jolla, CA USA | USA | 2,018 | null | 0000-0002-3360-9707 | null | null | English | null | ACS CHEM BIOL;ANGEW CHEM INT EDIT;ANNU REV BIOCHEM;CELL;CELL STEM CELL;CHEM COMMUN;CHEMBIOCHEM;J AM CHEM SOC;J CONTROL RELEASE;JOVE-J VIS EXP;Methods in Cell Science;MOL PHARM;MOL THER;NAT BIOTECHNOL;NAT GENET;NAT METHODS;NAT REV DRUG DISCOV;NAT REV GENET;NAT REV MOL CELL BIO;NUCLEIC ACIDS RES;PHARMACEUTICS;TRAC-TREND ANAL CHEM;TRENDS BIOCHEM SCI | Alexander, Seth C;Busby, Kayla N;Devaraj, Neal K;Zhang, Dongyang;Zhou, Cun Yu | 2024-03-11
ER | Alexander, S C;Ando Hideki;Ando, H;Avci-Adali, M;Curtis, D;Ehret F.;Elangovan, S;Fabian, M R;Fu, Y;Furuta, T;Govan, J M;Holstein, J M;Jackson, R J;Jaenisch, R;Karikó, K;Katayama, K;Lanctôt, C;Li, E;Luo, J;Ogasawara, S;Rosa, A;Sahin, U;Sonenberg, N;Tang, X;Uchida, S;Wang, X;Wilkie, G S;Wu, L;Yamazoe, S;Zangi, L | FY0HG | La Jolla, CA USA | 46 | null | 1 | null | 29,380,476 | Alexander, Seth C;Busby, Kayla N;Devaraj, Neal K;Zhang, Dongyang;Zhou, Cun Yu | ANGEW CHEM INT EDIT | La Jolla, CA USA |
Coleman, J R;Gould, N;Liu, H M;Machado, V;Papamichail, D;Papamichail, G | 10.1109/TCBB.2016.2542808 | null | 10662 LOS VAQUEROS CIRCLE, PO BOX 3014, LOS ALAMITOS, CA 90720-1314 USA | 5n2zpk2o495f4q2cxo396t2m4c6vb6c136v | Codon Context Optimization in Synthetic Gene Design | Coll New Jersey | null | Papamichail, D (corresponding author), Coll New Jersey, Dept Comp Sci, 2000 Pennington Rd, Ewing, NJ 08628 USA. | null | Coleman, J Robert;Gould, Nathan;Liu, Hongmei;Machado, Vitor;Papamichail, Dimitris;Papamichail, Georgios | Biochemical Research Methods;Computer Science, Interdisciplinary Applications;Mathematics, Interdisciplinary Applications;Statistics & Probability | US NSF [CCF-1418874]; MUSE program at The College of New Jersey; Division of Computing and Communication Foundations; Direct For Computer & Info Scie & Enginr [1418874] Funding Source: National Science Foundation | WOS | Papamichail, D | Coll New Jersey, Ewing, NJ USA;Farmingdale State Coll, Farmingdale, NY USA;New York Coll, Athens, Greece;Univ Miami, Miami, FL USA | 15 | codon;Context;design;gene;in;optimization;synthetic | 2 | null | IEEE COMPUTER SOC | Coll New Jersey, Dept Comp Sci, 2000 Pennington Rd, Ewing, NJ 08628 USA;Farmingdale State Coll, Dept Biol, Farmingdale, NY 11735 USA;New York Coll, Dept Informat, Amalias 38 Ave, Athens 10558, Greece;Univ Miami, Miller Sch Med, Dept Publ Hlth Sci, Div Biostat, Miami, FL 33136 USA | Article; Proceedings Paper | Coll New Jersey | LOS ALAMITOS | null | 1st International Conference on Algorithms for Computational Biology (AlCoB) | Coll New Jersey;Farmingdale State Coll;New York Coll;Univ Miami | Direct For Computer & Info Scie & Enginr;Division of Computing and Communication Foundations;MUSE program at The College of New Jersey;US NSF | Papamichail, D (corresponding author), Coll New Jersey, Dept Comp Sci, 2000 Pennington Rd, Ewing, NJ 08628 USA. | 459 | Coleman, J Robert;Gould, Nathan;Liu, Hongmei;Machado, Vitor;Papamichail, Dimitris;Papamichail, Georgios | 11 | 4 | 428,936,900,012 | Direct For Computer & Info Scie & Enginr [1418874] Funding Source: National Science Foundation;Division of Computing and Communication Foundations;MUSE program at The College of New Jersey;US NSF [CCF-1418874] | Greece;USA | IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS | USA | Tarragona, SPAIN | null | Coll New Jersey, Dept Comp Sci, 2000 Pennington Rd, Ewing, NJ 08628 USA | 1545-5963 | Rovira i Virgili Univ, Res Grp Math Linguist | MAR-APR | colemajr@farmingdale.edu;gouldn1@tcnj.edu;h.liu7@med.miami.edu;machadv1@tcnj.edu;papamicd@tcnj.edu;pmichael@ekdd.gr | codon Context Optimization;synthetic gene design | 6 | J | Biochemistry & Molecular Biology;Computer Science;Mathematics | affecting mRNA translational efficiency;another feature;appropriate context;ATTENUATION;BIAS;codon bias;codon context;codon context bias;codon context measures;codon Context Optimization;computational biology;computational complexity;computational gene design methods make possible;customization;de novo synthesis;design quality;designing novel;direct manipulation;DNA;dynamic programming;efficient heuristic gene recoding algorithms;existing methods;expression;features;genes;genome;INDEX;mRNA secondary structure;number;PAIRS;phenomenon;protein coding sequences;quantifiable guarantees;reasonable constraint models;SCALE;sequence;simulated annealing;statistical properties;study;synthetic biology;Synthetic gene design;tools;untested heuristics;USAGE;web-based tool | Papamichail, D | ATTENUATION;BIAS;computational biology;dynamic programming;EXPRESSION;GENOME;INDEX;NUMBER;PAIRS;SCALE;SEQUENCE;simulated annealing;Synthetic biology;USAGE | 452 | [Papamichail, Dimitris; Machado, Vitor; Gould, Nathan] Coll New Jersey, Dept Comp Sci, 2000 Pennington Rd, Ewing, NJ 08628 USA. [Liu, Hongmei] Univ Miami, Miller Sch Med, Dept Publ Hlth Sci, Div Biostat, Miami, FL 33136 USA. [Coleman, J. Robert] Farmingdale State Coll, Dept Biol, Farmingdale, NY 11735 USA. [Papamichail, Georgios] New York Coll, Dept Informat, Amalias 38 Ave, Athens 10558, Greece. | This work was supported by US NSF Grant CCF-1418874 and the MUSE program at The College of New Jersey. D. Papamichail is the corresponding author and can be reached at papamicd@tcnj.edu. | affecting mRNA translational efficiency;another feature;appropriate context;codon bias;codon context;codon context bias;codon context measures;codon context optimization;computational complexity;computational gene design methods make possible;customization;de novo synthesis;design quality;designing novel;direct manipulation;DNA;efficient heuristic gene recoding algorithms;existing methods;features;genes;mRNA secondary structure;phenomenon;protein coding sequences;quantifiable guarantees;reasonable constraint models;statistical properties;study;tools;untested heuristics;web-based tool | 10.1007/s00239-001-0051-8;10.1016/0022-2836(81)90003-6;10.1016/0378-1119(90)90491-9;10.1016/B978-0-12-385120-8.00003-6;10.1016/j.gene.2004.03.001;10.1016/j.tibtech.2004.04.006;10.1016/j.tibtech.2008.10.007;10.1016/j.virol.2015.07.012;10.1038/nbt.1568;10.1038/nbt.1636;10.1073/pnas.0404957101;10.1073/pnas.86.10.3699;10.1074/jbc.270.39.22801;10.1093/bioinformatics/18.8.1046;10.1093/bioinformatics/btg082;10.1093/bioinformatics/bts465;10.1093/bioinformatics/btu192;10.1093/infdis/jir010;10.1093/nar/14.13.5125;10.1093/nar/15.3.1281;10.1093/nar/30.5.1192;10.1093/nar/gkh834;10.1101/gr.1485203;10.1126/science.1155761;10.1126/science.1170160;10.1126/science.220.4598.671;10.1186/1471-2148-4-19;10.1186/gb-2005-6-3-r28;10.1214/ss/1177011077;10.1371/journal.pone.0007002;10.3389/fbioe.2014.00041;10.4049/jimmunol.1302007 | Coll New Jersey | Coleman, J R;Gould, N;Liu, H M;Machado, V;Papamichail, D;Papamichail, G | Papamichail, D: Coll New Jersey, Dept Comp Sci, 2000 Pennington Rd, Ewing, NJ 08628 USA | null | 1418874;CCF-1418874 | 34 | null | USA | Coll New Jersey;Farmingdale State Coll;New York Coll;Univ Miami | Papamichail, Dimitris | Green Submitted, hybrid | ATTENUATION;BIAS;EXPRESSION;GENOME;INDEX;NUMBER;PAIRS;SCALE;SEQUENCE;USAGE | Papamichail, Dimitris; Liu, Hongmei; Machado, Vitor; Gould, Nathan; Coleman, J. Robert; Papamichail, Georgios; | null | Coll New Jersey, Dept Comp Sci, 2000 Pennington Rd, Ewing, NJ 08628 USA;Farmingdale State Coll, Dept Biol, Farmingdale, NY 11735 USA;New York Coll, Dept Informat, Amalias 38 Ave, Athens 10558, Greece;Univ Miami, Miller Sch Med, Dept Publ Hlth Sci, Div Biostat, Miami, FL 33136 USA | Coll New Jersey, Dept Comp Sci, 2000 Pennington Rd, Ewing, NJ 08628 USA;Farmingdale State Coll, Dept Biol, Farmingdale, NY 11735 USA;New York Coll, Dept Informat, Amalias 38 Ave, Athens 10558, Greece;Univ Miami, Miller Sch Med, Dept Publ Hlth Sci, Div Biostat, Miami, FL 33136 USA | 1557-9964 | computational biology;dynamic programming;simulated annealing;Synthetic biology | 2 | 1964;1981;1983;1986;1987;1989;1990;1993;1995;2002;2003;2004;2005;2008;2009;2010;2011;2012;2014;2015 | 11 | Coll New Jersey, Dept Comp Sci, 2000 Pennington Rd, Ewing, NJ 08628 USA | IEEE-ACM Trans. Comput. Biol. Bioinform. | Papamichail, Georgios | IEEE COMPUTER SOC | ,;a;advances;affecting;algorithms;also;an;analyze;and;another;appropriate;as;better;bias;but;by;coding;codon;complexity;computational;constraint;context;customization;de;design;designing;direct;DNA;do;efficiency;efficient;effort;evaluating;exact;examine;existing;feature;features;for;gene;genes;guarantees;heuristic;heuristics;in;is;make;manipulation;measures;methods;models;mRNA;not;novel;novo;of;on;optimization;optimized;phenomenon;possible;present;properties;protein;provide;quality;quantifiable;reasonable;recoding;secondary;sequences;significantly;statistical;structure;study;such;synthesis;the;this;to;tool;tools;translational;under;understand;untested;utilize;we;Web-based | Coll New Jersey | Advances in de novo synthesis of DNA and computational gene design methods make possible the customization of genes by direct manipulation of features such as codon bias and mRNA secondary structure. Codon context is another feature significantly affecting mRNA translational efficiency, but existing methods and tools for evaluating and designing novel optimized protein coding sequences utilize untested heuristics and do not provide quantifiable guarantees on design quality. In this study we examine statistical properties of codon context measures in an effort to better understand the phenomenon. We analyze the computational complexity of codon context optimization and design exact and efficient heuristic gene recoding algorithms under reasonable constraint models. We also present a web-based tool for evaluating codon context bias in the appropriate context. | null | ATTENUATION;BIAS;EXPRESSION;GENOME;INDEX;NUMBERS;PAIR;SCALE;SEQUENCE;USAGE | 2 | JUL 01-03, 2014 | computational biology;dynamic programming;simulated annealing;Synthetic biology | 8 | ATTENUATION;BIAS;computational biology;dynamic programming;EXPRESSION;GENOME;INDEX;NUMBERS;PAIR;SCALE;SEQUENCE;simulated annealing;Synthetic biology;USAGE | WOS:000428936900012 | Coll New Jersey, Ewing, NJ USA;Farmingdale State Coll, Farmingdale, NY USA;New York Coll, Athens, Greece;Univ Miami, Miami, FL USA | Greece;USA | 2,018 | null | null | null | null | English | null | BIOINFORMATICS;BMC EVOL BIOL;Front Bioeng Biotechnol;GENE;GENETICS;GENOME BIOL;GENOME RES;J BIOL CHEM;J IMMUNOL;J INFECT DIS;J MOL BIOL;J MOL EVOL;LECT NOTES COMPUT SC;METHOD ENZYMOL;NAT BIOTECHNOL;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PLOS ONE;SCIENCE;STAT SCI;TRENDS BIOTECHNOL;VIROLOGY | Coleman, J Robert;Gould, Nathan;Liu, Hongmei;Machado, Vitor;Papamichail, Dimitris;Papamichail, Georgios | 2024-03-11
ER | Bertsimas, D;Boycheva, S;Chin, J X;Coleman, J R;Czar, M J;Dos Reis, M;Fedorov, A;Gao, L;Gaspar, P;Gould Nathan;Gustafsson, C;Gutman, G A;Hooper, S D;Ikemura, T;Irwin, B;Johnson, D S;Kimura, M;Kirkpatrick, S;Kudla, G;Lithwick, G;Marr, N;Moura, G;Mueller, S;Plotkin, J B;Salis, H M;Shah, A A;Sharp, P M;Suzuki, H;Wan, X F;Welch, M;Wright, F | GB3DZ | Ewing, NJ USA | 11 | null | 4 | null | 27,019,501 | Coleman, J Robert;Gould, Nathan;Liu, Hongmei;Machado, Vitor;Papamichail, Dimitris;Papamichail, Georgios | IEEE ACM T COMPUT BI | Athens, Greece;Ewing, NJ USA;Farmingdale, NY USA;Miami, FL USA |
Foo, M;Jo, H H;Kim, J K;Kim, P J;Kim, Y J;Somers, D E | 10.1038/s42003-018-0217-1 | 207 | 75 VARICK ST, 9TH FLR, NEW YORK, NY 10013-1917 USA | 1ta1s2a63d6u5a4a446v4b6g4t1e6g386v1z6v | Waveforms of molecular oscillations reveal circadian timekeeping mechanisms | Asia Pacific Ctr Theoret Phys | null | Kim, PJ (corresponding author), Abdus Salam Int Ctr Theoret Phys, I-34151 Trieste, Italy.;Kim, PJ (corresponding author), Hong Kong Baptist Univ, Ctr Quantitat Syst Biol, Kowloon, Hong Kong, Peoples R China.;Kim, PJ (corresponding author), Hong Kong Baptist Univ, Dept Biol, Kowloon, Hong Kong, Peoples R China.;Kim, PJ (corresponding author), Hong Kong Baptist Univ, Inst Computat & Theoret Studies, Kowloon, Hong Kong, Peoples R China. | null | Foo, Mathias;Jo, Hang-Hyun;Kim, Jae Kyoung;Kim, Pan-Jun;Kim, Yeon Jeong;Somers, David E | Biology;Multidisciplinary Sciences | National Research Foundation of Korea (NRF) - Ministry of Education [2015R1D1A1A01058958]; National Research Foundation of Korea (NRF) - Ministry of Science, ICT and Future Planning [N01160447]; National Institutes of Health [R01GM093285]; Next-Generation BioGreen21 Program (Systems and Synthetic Agrobiotech Center), Rural Development Administration, Republic of Korea [PJ01327305]; Hong Kong Baptist University, Research Committee, Start-up Grant for New Academics | WOS | Kim, P J | Aalto Univ, Espoo, Finland;Abdus Salam Int Ctr Theoret Phys, Trieste, Italy;Asia Pacific Ctr Theoret Phys, Gyeongbuk, South Korea;Coventry Univ, W Midlands, England;Hong Kong Baptist Univ, Hong Kong, Peoples R China;Korea Adv Inst Sci & Technol, Daejeon, South Korea;Ohio State Univ, Columbus, OH USA;Pohang Univ Sci & Technol, Gyeongbuk, South Korea | 1 | circadian;mechanisms;molecular;of;oscillations;reveal;timekeeping;waveforms | 6 | Foo, Mathias;Jo, Hang-Hyun;Kim, Jae Kyoung;Kim, Pan-Jun | NATURE PUBLISHING GROUP | Aalto Univ, Dept Comp Sci, FI-00076 Espoo, Finland;Abdus Salam Int Ctr Theoret Phys, I-34151 Trieste, Italy;Asia Pacific Ctr Theoret Phys, Pohang 37673, Gyeongbuk, South Korea;Coventry Univ, Sch Mech Aerosp & Automot Engn, Coventry CV1 5FB, W Midlands, England;Hong Kong Baptist Univ, Ctr Quantitat Syst Biol, Kowloon, Hong Kong, Peoples R China;Hong Kong Baptist Univ, Dept Biol, Kowloon, Hong Kong, Peoples R China;Hong Kong Baptist Univ, Dept Biol, Kowloon, Hong Kong, Peoples R China.; Kim, PJ (corresponding author), Hong Kong Baptist Univ, Ctr Quantitat Syst Biol, Kowloon, Hong Kong, Peoples R China.; Kim, PJ (corresponding author), Hong Kong Baptist Univ, Inst Computat & Theoret Studies, Kowloon, Hong Kong, Peoples R China.; Kim, PJ (corresponding author), Abdus Salam Int Ctr Theoret Phys, I-34151 Trieste, Italy;Hong Kong Baptist Univ, Inst Computat & Theoret Studies, Kowloon, Hong Kong, Peoples R China;Korea Adv Inst Sci & Technol, Dept Math Sci, Daejeon 34141, South Korea;Ohio State Univ, Dept Mol Genet, Columbus, OH 43210 USA;Pohang Univ Sci & Technol, Dept Phys, Pohang 37673, Gyeongbuk, South Korea | Article | Abdus Salam Int Ctr Theoret Phys;Hong Kong Baptist Univ | NEW YORK | null | null | Aalto Univ;Abdus Salam Int Ctr Theoret Phys;Asia Pacific Ctr Theoret Phys;Coventry Univ;Hong Kong Baptist Univ;Korea Adv Inst Sci & Technol;OHIO STATE UNIV;Pohang Univ Sci & Technol | Hong Kong Baptist University, Research Committee, Start-up Grant for New Academics;National Institutes of Health;National Research Foundation of Korea (NRF) - Ministry of Education;National Research Foundation of Korea (NRF) - Ministry of Science, ICT and Future Planning;Next-Generation BioGreen21 Program (Systems and Synthetic Agrobiotech Center), Rural Development Administration, Republic of Korea | Kim, PJ (corresponding author), Hong Kong Baptist Univ, Dept Biol, Kowloon, Hong Kong, Peoples R China.; Kim, PJ (corresponding author), Hong Kong Baptist Univ, Ctr Quantitat Syst Biol, Kowloon, Hong Kong, Peoples R China.; Kim, PJ (corresponding author), Hong Kong Baptist Univ, Inst Computat & Theoret Studies, Kowloon, Hong Kong, Peoples R China.; Kim, PJ (corresponding author), Abdus Salam Int Ctr Theoret Phys, I-34151 Trieste, Italy. | null | Foo, Mathias;Jo, Hang-Hyun;Kim, Jae Kyoung;Kim, Pan-Jun;Kim, Yeon Jeong;Somers, David E | 6 | 10 | 461,126,500,206 | Hong Kong Baptist University, Research Committee, Start-up Grant for New Academics;National Institutes of Health [R01GM093285];National Research Foundation of Korea (NRF) - Ministry of Education [2015R1D1A1A01058958];National Research Foundation of Korea (NRF) - Ministry of Science, ICT and Future Planning [N01160447];Next-Generation BioGreen21 Program (Systems and Synthetic Agrobiotech Center), Rural Development Administration, Republic of Korea [PJ01327305] | China;Finland;Italy;South Korea;UK;USA | COMMUNICATIONS BIOLOGY | China;Italy | null | null | Asia Pacific Ctr Theoret Phys, Pohang 37673, Gyeongbuk, South Korea | null | Foo, M;Jo, H H;Kim, J K;Kim, P J;Kim, Y J;Somers, D E | null | panjunkim@hkbu.edu.hk | circadian timekeeping mechanisms;molecular oscillations;waveforms | 6 | J | Life Sciences & Biomedicine - Other Topics;Science & Technology - Other Topics | biological oscillators;broad range;CELL-CYCLE;CIRCADIAN CLOCKS;circadian timekeeping;circadian timekeeping mechanisms;clock;cost;cyclic expression;developmental events;developmental stage-specific multicellular processes;GENE-EXPRESSION;hidden biochemical mechanisms;insect clocks;LESSONS;mammalian data;mathematical framework;MODELS;molecular oscillations;NEUROSPORA;numerous;OSCILLATIONS;particular waveforms;peak time differences;peak times;peak-time differences;PHOSPHORYLATION;pivotal role;positive arm components;previous plant;protein abundances;protein waveforms;proteins;quantification;rhythmic protein half-lives;RHYTHMS;seedling experiment;symmetries;Synthetic Genetic Oscillators;TARGETED DEGRADATION;time;tissue-specific;TRANSCRIPTION;underlying biochemical processes;waveform shapes;waveform-guided approach;waveforms | Jo, H H | CLOCK;GENE-EXPRESSION;LESSONS;MODELS;NEUROSPORA;PHOSPHORYLATION;QUANTIFICATION;RHYTHMS;TARGETED DEGRADATION;TRANSCRIPTION | null | [Jo, Hang-Hyun] Asia Pacific Ctr Theoret Phys, Pohang 37673, Gyeongbuk, South Korea. [Jo, Hang-Hyun] Pohang Univ Sci & Technol, Dept Phys, Pohang 37673, Gyeongbuk, South Korea. [Jo, Hang-Hyun] Aalto Univ, Dept Comp Sci, FI-00076 Espoo, Finland. [Kim, Yeon Jeong; Somers, David E.] Ohio State Univ, Dept Mol Genet, Columbus, OH 43210 USA. [Kim, Jae Kyoung] Korea Adv Inst Sci & Technol, Dept Math Sci, Daejeon 34141, South Korea. [Foo, Mathias] Coventry Univ, Sch Mech Aerosp & Automot Engn, Coventry CV1 5FB, W Midlands, England. [Kim, Pan-Jun] Hong Kong Baptist Univ, Dept Biol, Kowloon, Hong Kong, Peoples R China. [Kim, Pan-Jun] Hong Kong Baptist Univ, Ctr Quantitat Syst Biol, Kowloon, Hong Kong, Peoples R China. [Kim, Pan-Jun] Hong Kong Baptist Univ, Inst Computat & Theoret Studies, Kowloon, Hong Kong, Peoples R China. [Kim, Pan-Jun] Abdus Salam Int Ctr Theoret Phys, I-34151 Trieste, Italy. | This work was supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) Grant 2015R1D1A1A01058958 funded by the Ministry of Education (H.-H.J.) and by the National Research Foundation of Korea (NRF) Grants N01160447 funded by the Ministry of Science, ICT and Future Planning (J.K.K.). This work was also supported by National Institutes of Health grant R01GM093285 and by a grant from the Next-Generation BioGreen21 Program (Systems and Synthetic Agrobiotech Center, Project PJ01327305), Rural Development Administration, Republic of Korea (D.E.S). P.-J.K. acknowledges the support by Hong Kong Baptist University, Research Committee, Start-up Grant for New Academics. | biological oscillators;broad range;cell-cycle;circadian clocks;circadian timekeeping;cost;cyclic expression;developmental events;developmental stage-specific multicellular processes;hidden biochemical mechanisms;insect clocks;mammalian data;mathematical framework;numerous;oscillations;particular waveforms;peak time differences;peak times;peak-time differences;pivotal role;positive arm components;previous plant;protein abundances;protein waveforms;proteins;rhythmic protein half-lives;seedling experiment;symmetries;synthetic genetic oscillators;time;tissue-specific;underlying biochemical processes;waveform shapes;waveform-guided approach;waveforms | 10.1007/s00018-016-2378-8;10.1007/s00412-004-0296-2;10.1016/bs.mie.2014.10.009;10.1016/j.cell.2013.01.055;10.1016/j.celrep.2014.09.021;10.1016/j.celrep.2014.10.065;10.1016/j.cub.2011.03.060;10.1016/j.cub.2012.07.025;10.1016/j.molcel.2015.08.022;10.1016/j.neuron.2008.01.019;10.1016/j.tics.2016.12.008;10.1016/j.tplants.2013.11.007;10.1016/S0092-8674(01)00610-9;10.1016/S0092-8674(02)00825-5;10.1038/emboj.2010.76;10.1038/msb.2012.62;10.1038/nature02163;10.1038/nature10098;10.1038/s41467-017-01190-3;10.1038/s41467-018-03826-4;10.1038/srep05782;10.1073/pnas.0736949100;10.1073/pnas.0913256107;10.1073/pnas.1132112100;10.1073/pnas.1422242112;10.1073/pnas.1603799113;10.1074/jbc.M503526200;10.1074/jbc.M803471200;10.1093/emboj/20.3.307;10.1098/rsob.150042;10.1101/gad.397006;10.1103/PhysRevLett.115.218101;10.1105/tpc.107.053033;10.1105/tpc.109.072843;10.1105/tpc.109.072892;10.1111/j.1365-313X.2007.03258.x;10.1126/science.1121613;10.1126/science.1132430;10.1126/science.180.4085.498;10.1126/science.8128246;10.1126/science.aaa3794;10.1137/120867809;10.1177/0748730415573167;10.1186/s12915-015-0126-4;10.1186/s12915-015-0158-9;10.1371/journal.pcbi.1004748;10.1371/journal.pgen.1000023;10.1523/JNEUROSCI.0958-16.2016;10.7554/eLife.00669 | Asia Pacific Ctr Theoret Phys | Foo, M;Jo, H H;Kim, J K;Kim, P J;Kim, Y J;Somers, D E | Jo, H H: Asia Pacific Ctr Theoret Phys, Pohang 37673, Gyeongbuk, South Korea | Foo, Mathias;Jo, Hang-Hyun;Kim, Jae Kyoung | 2015R1D1A1A01058958;N01160447;PJ01327305;R01GM093285 | 49 | null | South Korea | Aalto Univ;Abdus Salam Int Ctr Theoret Phys;Asia Pacific Ctr Theoret Phys;Coventry Univ;Hong Kong Baptist Univ;Korea Adv Inst Sci & Technol;OHIO STATE UNIV;Pohang Univ Sci & Technol | Jo, Hang-Hyun | Green Submitted, Green Published, gold | CLOCK;GENE-EXPRESSION;LESSONS;MODELS;NEUROSPORA;PHOSPHORYLATION;QUANTIFICATION;RHYTHMS;TARGETED DEGRADATION;TRANSCRIPTION | Jo, Hang-Hyun; Kim, Yeon Jeong; Kim, Jae Kyoung; Foo, Mathias; Somers, David E.; Kim, Pan-Jun; | null | Aalto Univ, Dept Comp Sci, FI-00076 Espoo, Finland;Abdus Salam Int Ctr Theoret Phys, I-34151 Trieste, Italy;Asia Pacific Ctr Theoret Phys, Pohang 37673, Gyeongbuk, South Korea;Coventry Univ, Sch Mech Aerosp & Automot Engn, Coventry CV1 5FB, W Midlands, England;Hong Kong Baptist Univ, Ctr Quantitat Syst Biol, Kowloon, Hong Kong, Peoples R China;Hong Kong Baptist Univ, Dept Biol, Kowloon, Hong Kong, Peoples R China;Hong Kong Baptist Univ, Inst Computat & Theoret Studies, Kowloon, Hong Kong, Peoples R China;Korea Adv Inst Sci & Technol, Dept Math Sci, Daejeon 34141, South Korea;Ohio State Univ, Dept Mol Genet, Columbus, OH 43210 USA;Pohang Univ Sci & Technol, Dept Phys, Pohang 37673, Gyeongbuk, South Korea | Aalto Univ, Dept Comp Sci, FI-00076 Espoo, Finland;Abdus Salam Int Ctr Theoret Phys, I-34151 Trieste, Italy;Asia Pacific Ctr Theoret Phys, Pohang 37673, Gyeongbuk, South Korea;Coventry Univ, Sch Mech Aerosp & Automot Engn, Coventry CV1 5FB, W Midlands, England;Hong Kong Baptist Univ, Ctr Quantitat Syst Biol, Kowloon, Hong Kong, Peoples R China;Hong Kong Baptist Univ, Dept Biol, Kowloon, Hong Kong, Peoples R China;Hong Kong Baptist Univ, Inst Computat & Theoret Studies, Kowloon, Hong Kong, Peoples R China;Korea Adv Inst Sci & Technol, Dept Math Sci, Daejeon 34141, South Korea;Ohio State Univ, Dept Mol Genet, Columbus, OH 43210 USA;Pohang Univ Sci & Technol, Dept Phys, Pohang 37673, Gyeongbuk, South Korea | 2399-3642 | null | null | 1973;1994;2001;2002;2003;2004;2005;2006;2007;2008;2010;2011;2012;2013;2014;2015;2016;2017;2018 | 9 | Abdus Salam Int Ctr Theoret Phys, I-34151 Trieste, Italy;Hong Kong Baptist Univ, Ctr Quantitat Syst Biol, Kowloon, Hong Kong, Peoples R China;Hong Kong Baptist Univ, Dept Biol, Kowloon, Hong Kong, Peoples R China;Hong Kong Baptist Univ, Inst Computat & Theoret Studies, Kowloon, Hong Kong, Peoples R China | Commun. Biol. | Kim, Pan-Jun | NATURE PUBLISHING GROUP | ,;a;about;abundances;allows;also;and;approach;arm;as;be;between;biochemical;biological;both;broad;by;can;cell-cycle;circadian;clocks;components;cost;cyclic;data;derive;developmental;differences;do;enigmatic;events;experiment;expression;extended;facilitate;find;framework;genetic;half-lives;hidden;in;including;informative;insect;mammalian;mathematical;may;mechanisms;multicellular;numerous;of;or;orchestrating;oscillations;oscillators;our;over;own;particular;peak;peak-time;physiological;pivotal;plant;play;positive;previous;previously;processes;protein;proteins;range;reduced;reveal;rhythmic;role;seedling;shapes;stage-specific;substantially;such;supported;symmetries;synthesizing;synthetic;that;the;time;timekeeping;times;tissue-specific;to;underlying;various;waveform;waveform-guided;waveforms;we;well;where;with;within | Abdus Salam Int Ctr Theoret Phys;Hong Kong Baptist Univ | Circadian clocks play a pivotal role in orchestrating numerous physiological and developmental events. Waveform shapes of the oscillations of protein abundances can be informative about the underlying biochemical processes of circadian clocks. We derive a mathematical framework where waveforms do reveal hidden biochemical mechanisms of circadian timekeeping. We find that the cost of synthesizing proteins with particular waveforms can be substantially reduced by rhythmic protein half-lives over time, as supported by previous plant and mammalian data, as well as our own seedling experiment. We also find that previously enigmatic, cyclic expression of positive arm components within the mammalian and insect clocks allows both a broad range of peak time differences between protein waveforms and the symmetries of the waveforms about the peak times. Such various peak-time differences may facilitate tissue-specific or developmental stage-specific multicellular processes. Our waveform-guided approach can be extended to various biological oscillators, including cell-cycle and synthetic genetic oscillators. | AAR-9549-2021;F-1297-2015;F-4666-2012;GSO-3501-2022 | CLOCK;GENE-EXPRESSION;LESSONS;MODEL;NEUROSPORA;PHOSPHORYLATION;QUANTIFICATION;RHYTHMS;TARGETED DEGRADATION;TRANSCRIPTION | 1 | null | null | 11 | CLOCK;GENE-EXPRESSION;LESSONS;MODEL;NEUROSPORA;PHOSPHORYLATION;QUANTIFICATION;RHYTHMS;TARGETED DEGRADATION;TRANSCRIPTION | WOS:000461126500206 | Aalto Univ, Espoo, Finland;Abdus Salam Int Ctr Theoret Phys, Trieste, Italy;Asia Pacific Ctr Theoret Phys, Gyeongbuk, South Korea;Coventry Univ, W Midlands, England;Hong Kong Baptist Univ, Hong Kong, Peoples R China;Korea Adv Inst Sci & Technol, Daejeon, South Korea;OHIO STATE UNIV, COLUMBUS, OH USA;Pohang Univ Sci & Technol, Gyeongbuk, South Korea | China;Finland;Italy;South Korea;UK;USA | 2,018 | null | 0000-0001-7842-2172;0000-0002-4214-9204;0000-0002-9329-4997;0000-0003-1400-2659 | null | null | English | null | BMC BIOL;CELL;CELL MOL LIFE SCI;CELL REP;CHROMOSOMA;CURR BIOL;ELIFE;EMBO J;GENE DEV;J BIOL CHEM;J BIOL RHYTHM;J NEUROSCI;METHOD ENZYMOL;MOL CELL;MOL SYST BIOL;NAT COMMUN;NATURE;NEURON;OPEN BIOL;P NATL ACAD SCI USA;PHYS REV LETT;PLANT CELL;PLANT J;PLOS COMPUT BIOL;PLOS GENET;SCI REP-UK;SCIENCE;SIAM J APPL MATH;TRENDS COGN SCI;TRENDS PLANT SCI | Foo, Mathias;Jo, Hang-Hyun;Kim, Jae Kyoung;Kim, Pan-Jun;Kim, Yeon Jeong;Somers, David E | 2024-03-11
ER | Baudry, A;Besing, R C;Brody, S;Chen, Y;Christiano, R;Cole, S R;De Montaigu, A;Farré, E M;Fei, C Y;Flis, A;Foo, M;Fujiwara, S;Gachon, F;Hatakeyama, T S;Hsu, P Y;Hurley, J;Iitaka, C;Kiba, T;Kim, J K;Kim, W Y;Korencic, A;Lee, C;Leloup, J C;Liu, A C;Lück, S;Mcdearmon, E L;Mendoza-Viveros, L;Meng, Q J;Merrow, M;Más, P;Nagel, D H;Nakamichi, N;Narumi, R;O'Keeffe, K P;Patton, A P;Preitner, N;Sancar, C;Schwanhäusser, B;Scialdone, A;Sehgal, A;Tyson, J J;Van Ooijen, G;Vanselow, K;Wang, L;Yagita, K;Yin, L;Yoo, S H;Zhou, M | HO7LC | Hong Kong, Peoples R China.;Trieste, Italy | 11 | null | 8 | null | null | Foo, Mathias;Jo, Hang-Hyun;Kim, Jae Kyoung;Kim, Pan-Jun;Kim, Yeon Jeong;Somers, David E | COMMUN BIOL | COLUMBUS, OH USA;Daejeon, South Korea;Espoo, Finland;Gyeongbuk, South Korea;Hong Kong, Peoples R China;Trieste, Italy;W Midlands, England |
Chong, A;Cooper, K G;Finn, C E;Starr, T;Steele-Mortimer, O | 10.3389/fcimb.2017.00475 | 475 | PO BOX 110, EPFL INNOVATION PARK, BUILDING I, LAUSANNE, 1015, SWITZERLAND | 6v5q5d4r3s4s13563534ol1b425c2g2i2f592a | Predictable, Tunable Protein Production in <i>Salmonella</i> for Studying Host-Pathogen Interactions | NIAID | null | Steele-Mortimer, O (corresponding author), NIAID, Lab Bacteriol, Rocky Mt Labs, NIH, Hamilton, MT 59840 USA. | null | Chong, Audrey;Cooper, Kendal G;Finn, Ciaran E;Starr, Tregei;Steele-Mortimer, Olivia | Immunology;Microbiology | Intramural Research Program of the NIH, NIAID | WOS | Steele-Mortimer, O | NIAID, Hamilton, MT USA | 7 | ,;<i>Salmonella</i>;for;Host-Pathogen;in;interactions;predictable;production;protein;studying;tunable | 1 | null | FRONTIERS MEDIA SA | NIAID, Lab Bacteriol, Rocky Mt Labs, NIH, Hamilton, MT 59840 USA | Article | NIAID | LAUSANNE | null | null | Lab Bacteriol;NIAID | Intramural Research Program of the NIH, NIAID | Steele-Mortimer, O (corresponding author), NIAID, Lab Bacteriol, Rocky Mt Labs, NIH, Hamilton, MT 59840 USA. | null | Chong, Audrey;Cooper, Kendal G;Finn, Ciaran E;Starr, Tregei;Steele-Mortimer, Olivia | 4 | 1 | 415,297,300,001 | Intramural Research Program of the NIH, NIAID | USA | FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY | USA | null | null | NIAID, Lab Bacteriol, Rocky Mt Labs, NIH, Hamilton, MT 59840 USA | 2235-2988 | Chong, A;Cooper, K G;Finn, C E;Starr, T;Steele-Mortimer, O | NOV 16 | omortimer@niaid.nih.gov | <i>Salmonella</i>;Studying Host-Pathogen Interactions;Tunable Protein Production | 5 | J | Immunology;Microbiology | <i>Salmonella</i>;BACTERIAL;constitutive expression;COORDINATE REGULATION;efficient means;endogenous proteins;ENTERICA SEROVAR TYPHIMURIUM;episomal protein production;EPITHELIAL-CELLS;ESCHERICHIA-COLI;FLUORESCENT PROTEIN;GENE-EXPRESSION;GFP;green fluorescent protein;intracellular;INVASION GENES;multi-pronged approach;plasmid;plasmid copy number variation;plasmids;predictability;PROMOTER;promoters;Protein Production;Salmonella;several examples;Studying Host-Pathogen Interactions;synthetic biology;synthetic genetic elements;synthetic transcriptional terminator;SYSTEM;toxic effects;tunability;Tunable Protein Production;uniform production;use;variable-strength synthetic promoters;wide dynamic range | Cooper, K G | BACTERIAL;COORDINATE REGULATION;ENTERICA SEROVAR TYPHIMURIUM;EPITHELIAL-CELLS;ESCHERICHIA-COLI;FLUORESCENT PROTEIN;GENE-EXPRESSION;GFP;GREEN FLUORESCENT PROTEIN;intracellular;INVASION GENES;PLASMID;PROMOTER;PROMOTERS;Salmonella;Synthetic biology | null | [Cooper, Kendal G.; Chong, Audrey; Starr, Tregei; Finn, Ciaran E.; Steele-Mortimer, Olivia] NIAID, Lab Bacteriol, Rocky Mt Labs, NIH, Hamilton, MT 59840 USA. | This research was supported by the Intramural Research Program of the NIH, NIAID. We thank Robert Sauer (MIT) for the ProSeries promoters. pWSK29 Delta Plac was made by Leigh A. Knodler. We thank Paul Beare and members of the Steele-Mortimer lab for critical discussions on the manuscript. | constitutive expression;efficient means;endogenous proteins;episomal protein production;multi-pronged approach;plasmid copy number variation;plasmids;predictability;protein production;Salmonella;several examples;synthetic genetic elements;synthetic transcriptional terminator;system;toxic effects;tunability;uniform production;use;variable-strength synthetic promoters;wide dynamic range | 10.1016/0378-1119(91)90366-J;10.1016/0378-1119(95)00685-0;10.1016/j.ab.2011.03.036;10.1016/j.copbio.2005.04.003;10.1016/S0014-5793(02)02834-X;10.1016/S0167-7799(97)01155-4;10.1038/291238a0;10.1038/nbt1037;10.1038/nrg3094;10.1046/j.1365-2958.1996.00120.x;10.1046/j.1365-2958.1996.d01-1718.x;10.1046/j.1365-2958.2001.02230.x;10.1073/pnas.1000041107;10.1073/pnas.1006098107;10.1074/jbc.M008187200;10.1093/nar/gkq810;10.1099/mic.0.025700-0;10.1099/mic.0.032896-0;10.1111/j.1365-2958.1995.mmi_18040715.x;10.1111/j.1365-2958.1997.mmi525.x;10.1111/j.1365-2958.2006.05418.x;10.1111/j.1462-5822.2009.01356.x;10.1111/j.1600-0854.2008.00830.x;10.1111/mmi.12498;10.1128/IAI.01224-07;10.1128/IAI.01301-08;10.1128/IAI.73.10.7027-7031.2005;10.1139/w03-072;10.1186/1471-2180-13-258;10.1186/1754-1611-3-4;10.1186/gb-2006-7-10-r100;10.1371/journal.pone.0022260;10.1371/journal.pone.0038732;10.1371/journal.pone.0075991;10.1371/journal.ppat.1002143;10.1371/journal.ppat.1006354;10.2144/00281st02;10.3389/fmicb.2014.00172 | NIAID | Chong, A;Cooper, K G;Finn, C E;Starr, T;Steele-Mortimer, O | Cooper, K G: NIAID, Lab Bacteriol, Rocky Mt Labs, NIH, Hamilton, MT 59840 USA | Cooper, Kendal | null | 38 | null | USA | NIAID | Cooper, Kendal G | Green Published, gold | BACTERIAL;COORDINATE REGULATION;ENTERICA SEROVAR TYPHIMURIUM;EPITHELIAL-CELLS;ESCHERICHIA-COLI;GENE-EXPRESSION;GFP;GREEN FLUORESCENT PROTEIN;INVASION GENES;PROMOTERS | Cooper, Kendal G.; Chong, Audrey; Starr, Tregei; Finn, Ciaran E.; Steele-Mortimer, Olivia; | null | NIAID, Lab Bacteriol, Rocky Mt Labs, NIH, Hamilton, MT 59840 USA | NIAID, Lab Bacteriol, Rocky Mt Labs, NIH, Hamilton, MT 59840 USA | null | fluorescent protein;intracellular;plasmid;promoter;Salmonella;Synthetic biology | null | 1981;1991;1995;1996;1997;1998;2000;2001;2002;2003;2004;2005;2006;2008;2009;2010;2011;2012;2013;2014;2017 | 12 | NIAID, Lab Bacteriol, Rocky Mt Labs, NIH, Hamilton, MT 59840 USA | Front. Cell. Infect. Microbiol. | Steele-Mortimer, Olivia | FRONTIERS MEDIA SA | ,;a;an;and;approach;combined;constitutive;copy;describe;drive;dynamic;effects;efficient;elements;endogenous;episomal;examples;expression;fine-tune;fluorescent;genetic;here;improve;in;is;means;multi-pronged;number;of;out;over;plasmid;plasmids;predictability;production;promoters;protein;proteins;providing;range;Salmonella;series;several;synthetic;system;terminator;that;the;this;titrate;to;toxic;transcriptional;tunability;uniform;use;used;variable-strength;variation;we;were;where;which;wide;with;yielded | NIAID | Here we describe the use of synthetic genetic elements to improve the predictability and tunability of episomal protein production in Salmonella. We used a multi-pronged approach, in which a series of variable-strength synthetic promoters were combined with a synthetic transcriptional terminator, and plasmid copy number variation. This yielded a series of plasmids that drive uniform production of fluorescent and endogenous proteins, over a wide dynamic range. We describe several examples where this system is used to fine-tune constitutive expression in Salmonella, providing an efficient means to titrate out toxic effects of protein production. | IAS-1021-2023 | BACTERIAL;COORDINATE REGULATION;ENTERICA SEROVAR TYPHIMURIUM;EPITHELIAL-CELLS;ESCHERICHIA-COLI;GENE-EXPRESSION;GFP;GREEN FLUORESCENT PROTEIN;INVASION GENES;PROMOTER | 0 | null | fluorescent protein;intracellular;plasmid;promoter;Salmonella;Synthetic biology | 16 | ESCHERICHIA-COLI;BACTERIAL;COORDINATE REGULATION;ENTERICA SEROVAR TYPHIMURIUM;EPITHELIAL-CELLS;FLUORESCENT PROTEIN;GENE-EXPRESSION;GFP;GREEN FLUORESCENT PROTEIN;intracellular;INVASION GENES;PLASMID;PROMOTER;Salmonella;Synthetic biology | WOS:000415297300001 | NIAID, Hamilton, MT USA | USA | 2,017 | null | null | null | null | English | null | ANAL BIOCHEM;BIOTECHNIQUES;BMC MICROBIOL;CAN J MICROBIOL;CELL MICROBIOL;CURR OPIN BIOTECH;FEBS LETT;FRONT MICROBIOL;GENE;GENOME BIOL;INFECT IMMUN;J BIOL CHEM;J Biol Eng;MICROBIOL-SGM;MOL MICROBIOL;NAT BIOTECHNOL;NAT REV GENET;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PLOS ONE;PLOS PATHOG;TRAFFIC;TRENDS BIOTECHNOL | Chong, Audrey;Cooper, Kendal G;Finn, Ciaran E;Starr, Tregei;Steele-Mortimer, Olivia | 2024-03-11
ER | Bajaj, V;Carpenter, A E;Clark, L;Cooper, K G;Cormack, B P;Davis, J H;Drecktrah, D;Finn, C E;Galyov, E E;Hannig, G;Hebisch, E;Helaine, S;Henard, C A;Hoiseth, S K;Ibarra, J A;Iizuka, R;Kelly Jason, R;Knodler, L A;Lissemore, J L;Main-Hester, K L;Malik-Kale, P;Matic, J N;Mijakovic, I;Nikolic, N;Rang, C;Rosano, G L;Shaner, N C;Steele-Mortimer, O;Sturm, A;Valdivia, R H;Wang, R F;Weber, W;Wendland, M;Zhou, D G | FM7YG | Hamilton, MT USA | 12 | null | 1 | null | 29,201,859 | Chong, Audrey;Cooper, Kendal G;Finn, Ciaran E;Starr, Tregei;Steele-Mortimer, Olivia | FRONT CELL INFECT MI | Hamilton, MT USA |
Glasa, M;Gubisová, M;Havrlentová, M;Hudcovicová, M;Kraic, J;Matusíková, I;Mihálik, D;Moravcíková, J | 10.1016/j.ejbt.2017.08.002 | null | AV BRASIL 2950, PO BOX 4059, VALPARAISO, CHILE | 99vy5xu296o142sgl341h4e2g6067305f | Introduction of a synthetic <i>Thermococcus</i>-derived α-amlyase gene into barley genome for increased enzyme thermostability in grains | Univ Ss Cyril & Methodius Trnava | null | Matusíková, I (corresponding author), Univ Ss Cyril & Methodius, Fac Nat Sci, Dept Ecochem & Radioecol, SK-91701 Trnava, Slovakia. | null | Glasa, Miroslav;Gubisova, Marcela;Havrlentova, Michaela;Hudcovicova, Martina;Kraic, Jan;Matusikova, Ildik;Mihalik, Daniel;Moravcikova, Jana | Biotechnology & Applied Microbiology | Slovak Research and Development Agency [APVV-16-0051, APVV-380-12]; [VEGA 2/0035/17] | WOS | Matusíková, I | Natl Agr & Food Ctr, Piestany, Slovakia;Plant Sci & Biodivers Ctr SAS, Nitra, Slovakia;Slovak Acad Sci, Bratislava, Slovakia;Univ Ss Cyril & Methodius Trnava, Trnava, Slovakia;Univ Ss Cyril & Methodius, Trnava, Slovakia | 30 | <i>Thermococcus</i>-derived;a;barley;ENZYME;for;gene;genome;grains;in;increased;into;Introduction;of;synthetic;Thermostability;α-amlyase | 1 | Glasa, Miroslav;Gubisova, Marcela;Havrlentova, Michaela;Kraic, Jan;Matusikova, Ildiko;Mihalik, Daniel;Moravčíková, Jana | UNIV CATOLICA DE VALPARAISO | Natl Agr & Food Ctr, Res Inst Plant Prod, SK-92168 Piestany, Slovakia;Plant Sci & Biodivers Ctr SAS, Inst Plant Genet & Biotechnol, Akad 2,POB 39A, Nitra 95007, Slovakia;Slovak Acad Sci, Inst Virol, Biomed Res Ctr, Dubravska Cesta 9, Bratislava 84505, Slovakia;Univ Ss Cyril & Methodius Trnava, Fac Nat Sci, Dept Biotechnol, Nam J Herdu 2, SK-91701 Trnava, Slovakia;Univ Ss Cyril & Methodius, Fac Nat Sci, Dept Ecochem & Radioecol, SK-91701 Trnava, Slovakia | Article | Univ Ss Cyril & Methodius | VALPARAISO | null | null | Natl Agr & Food Ctr;Plant Sci & Biodivers Ctr SAS;Slovak Acad Sci;Univ Ss Cyril & Methodius;Univ Ss Cyril & Methodius Trnava | Slovak Research and Development Agency | Matusíková, I (corresponding author), Univ Ss Cyril & Methodius, Fac Nat Sci, Dept Ecochem & Radioecol, SK-91701 Trnava, Slovakia. | 5 | Glasa, Miroslav;Gubisova, Marcela;Havrlentova, Michaela;Hudcovicova, Martina;Kraic, Jan;Matusikova, Ildik;Mihalik, Daniel;Moravcikova, Jana | 12 | 5 | 416,721,500,002 | [VEGA 2/0035/17];Slovak Research and Development Agency [APVV-16-0051, APVV-380-12] | Slovakia | ELECTRONIC JOURNAL OF BIOTECHNOLOGY | Slovakia | null | null | Univ Ss Cyril & Methodius Trnava, Fac Nat Sci, Dept Biotechnol, Nam J Herdu 2, SK-91701 Trnava, Slovakia | 0717-3458 | Glasa, M;Gubisová, M;Havrlentová, M;Hudcovicová, M;Kraic, J;Matusíková, I;Mihálik, D;Moravcíková, J | NOV 15 | ildiko.matusikova@ucm.sk | barley genome;grains;increased enzyme thermostability;Introduction;synthetic <i>Thermococcus</i>-derived α-amlyase gene | 8 | J | Biotechnology & Applied Microbiology | 4 times;5.0;5.5;50 kDa active recombinant enzyme;60%;75 degrees C;75-85 degrees C;9%;9.39%;a-amylase;active;AMYLASE;Amylopectin;Amylose;background;barley;barley codon usage;barley genome;barley grains;Beer;beer production;biolistics;C 2017 Pontificia Universidad Catolica de Valparaiso;cloning;conclusions;control;corresponding sequence;cultivar;cvs;Effects;Elsevier B.V;endosperm-specific promoter 1Dx5;enzyme;enzyme activity;enzymes;expression;FERMENTATION;fermentation process;GENE;gene transfer;Glutenin;grain a-amylase activity;grains;heating;high temperatures;higher temperatures;Hordeum;hydrothermal Thermococcus;increased enzyme thermostability;Introduction;Levan;level;malt;model cv;Nitran;non-transgenic barley);non-transgenic controls;pH;pribina;process;production;promising tool;PROMOTER;promoters;pronounced (only 1.22 fold difference;residual a-amylase activity;results;rights reserved;Seed-directed expression;silico;stability;starting material;synthesis;synthetic <i>Thermococcus</i>-derived α-amlyase gene;synthetic gene;thermophilic bacteria;Thermotolerant bacteria;thermotolerant enzymes;transformed three Slovak barley cultivars Pribina;TRANSGENIC BARLEY;transgenic plants;utilization;WEB | Mihálik, D | AMYLASE;Amylopectin;Amylose;Beer;cloning;EXPRESSION;FERMENTATION;Gene transfer;Glutenin;Hordeum;LEVEL;PROMOTER;PROMOTERS;Seed-directed expression;STABILITY;Synthetic gene;Thermotolerant bacteria;TRANSGENIC BARLEY;WEB | 1 | [Mihalik, Daniel; Kraic, Jan; Havrlentova, Michaela] Univ Ss Cyril & Methodius Trnava, Fac Nat Sci, Dept Biotechnol, Nam J Herdu 2, SK-91701 Trnava, Slovakia. [Mihalik, Daniel; Gubisova, Marcela; Kraic, Jan; Hudcovicova, Martina; Havrlentova, Michaela] Natl Agr & Food Ctr, Res Inst Plant Prod, SK-92168 Piestany, Slovakia. [Moravcikova, Jana] Plant Sci & Biodivers Ctr SAS, Inst Plant Genet & Biotechnol, Akad 2,POB 39A, Nitra 95007, Slovakia. [Glasa, Miroslav] Slovak Acad Sci, Inst Virol, Biomed Res Ctr, Dubravska Cesta 9, Bratislava 84505, Slovakia. [Matusikova, Ildik] Univ Ss Cyril & Methodius, Fac Nat Sci, Dept Ecochem & Radioecol, SK-91701 Trnava, Slovakia. | This work was financed by the Slovak Research and Development Agency under contracts numbers APVV-16-0051 and APVV-380-12, and the grant VEGA 2/0035/17. | 4 times;5.0;5.5;50 kDa active recombinant enzyme;60%;75 degrees C;75-85 degrees C;9%;9.39%;a-amylase;active;background;barley;barley codon usage;barley grains;beer production;biolistics;conclusions;control;corresponding sequence;cultivar;cvs;effects;endosperm-specific promoter 1Dx5;enzyme;enzyme activity;enzymes;expression;fermentation process;gene;gene transfer;grain a-amylase activity;grains;heating;high temperatures;higher temperatures;hydrothermal Thermococcus;Levan;malt;model cv;Nitran;non-transgenic barley);non-transgenic controls;pH;pribina;process;promising tool;pronounced (only 1.22 fold difference;residual a-amylase activity;results;silico;starting material;synthesis;synthetic gene;thermophilic bacteria;thermotolerant enzymes;transformed three Slovak barley cultivars Pribina;transgenic plants;utilization | 10.1002/jobm.200310302;10.1007/978-1-59745-379-0_8;10.1007/BF00261246;10.1007/BF00272342;10.1007/BF01969712;10.1007/s00299-003-0630-9;10.1007/s10535-014-0406-9;10.1007/s11032-016-0554-z;10.1007/s11248-007-9144-5;10.1007/s11627-007-9068-z;10.1016/S0014-5793(02)02649-2;10.1016/S0141-0229(99)00142-8;10.1016/S0378-1097(00)00117-8;10.1023/A:1015509400123;10.1023/A:1022296017801;10.1023/A:1026535407570;10.1038/nprot.2009.2;10.1073/pnas.030527497;10.1093/nar/gkm219;10.1094/ASBCJ-63-0185;10.1111/j.1467-7652.2008.00394.x;10.1111/j.1550-7408.2006.00136.x;[10.1590/S1517-83822008000200027, 10.1590/S1517-838220080002000027] | Univ Ss Cyril & Methodius Trnava | Glasa, M;Gubisová, M;Havrlentová, M;Hudcovicová, M;Kraic, J;Matusíková, I;Mihálik, D;Moravcíková, J | Mihálik, D: Univ Ss Cyril & Methodius Trnava, Fac Nat Sci, Dept Biotechnol, Nam J Herdu 2, SK-91701 Trnava, Slovakia | Glasa, Miroslav;Hudcovicova, Martina;Kraic, Jan;Matusikova, Ildiko;Mihalik, Daniel;Moravčíková, Jana | APVV-16-0051;APVV-380-12;VEGA 2/0035/17 | 24 | null | Slovakia | Natl Agr & Food Ctr;Plant Sci & Biodivers Ctr SAS;Slovak Acad Sci;Univ Ss Cyril & Methodius;Univ Ss Cyril & Methodius Trnava | Mihalik, Daniel | gold | AMYLASE;CLONING;EXPRESSION;LEVEL;PROMOTERS;STABILITY;TRANSGENIC BARLEY;WEB | Mihalik, Daniel; Gubisova, Marcela; Kraic, Jan; Hudcovicova, Martina; Havrlentova, Michaela; Moravcikova, Jana; Glasa, Miroslav; Matusikova, Ildik; | null | Natl Agr & Food Ctr, Res Inst Plant Prod, SK-92168 Piestany, Slovakia;Plant Sci & Biodivers Ctr SAS, Inst Plant Genet & Biotechnol, Akad 2,POB 39A, Nitra 95007, Slovakia;Slovak Acad Sci, Inst Virol, Biomed Res Ctr, Dubravska Cesta 9, Bratislava 84505, Slovakia;Univ Ss Cyril & Methodius Trnava, Fac Nat Sci, Dept Biotechnol, Nam J Herdu 2, SK-91701 Trnava, Slovakia;Univ Ss Cyril & Methodius, Fac Nat Sci, Dept Ecochem & Radioecol, SK-91701 Trnava, Slovakia | Natl Agr & Food Ctr, Res Inst Plant Prod, SK-92168 Piestany, Slovakia;Plant Sci & Biodivers Ctr SAS, Inst Plant Genet & Biotechnol, Akad 2,POB 39A, Nitra 95007, Slovakia;Slovak Acad Sci, Inst Virol, Biomed Res Ctr, Dubravska Cesta 9, Bratislava 84505, Slovakia;Univ Ss Cyril & Methodius Trnava, Fac Nat Sci, Dept Biotechnol, Nam J Herdu 2, SK-91701 Trnava, Slovakia;Univ Ss Cyril & Methodius, Fac Nat Sci, Dept Ecochem & Radioecol, SK-91701 Trnava, Slovakia | null | Amylopectin;Amylose;Beer;fermentation;Gene transfer;Glutenin;Hordeum;promoter;Seed-directed expression;Synthetic gene;Thermotolerant bacteria | null | 1989;1992;1993;1996;2000;2002;2003;2004;2005;2007;2008;2009;2014;2016 | 1 | Univ Ss Cyril & Methodius, Fac Nat Sci, Dept Ecochem & Radioecol, SK-91701 Trnava, Slovakia | Electron. J. Biotechnol. | Matusikova, Ildik | UNIV CATOLICA DE VALPARAISO | (only;,;1.22;1Dx5;4;5.0;5.5;50;60%;75;75-85;9%;9.39%;:;a;a-amylase;about;above;active;activity;adapted;addition;after;and;are;at;background;bacteria;barley;barley);beer;between;biolistics;by;C;cloning;codon;compared;conclusions;control;controls;corresponding;cultivar;cultivars;cv;cvs;deactivated;degrees;difference;drying;effects;either;endosperm-specific;enhanced;enzyme;enzymes;expression;fermentation;fold;for;from;gene;generally;Golden;grain;grains;harboring;heating;high;higher;however;hydrothermal;in;into;introduced;is;kDa;less;Levan;limits;malt;material;model;more;Nitran;non-transgenic;obtained;of;optimally;pH;plants;Pribina;process;producing;production;promise;promising;promoter;pronounced;put;recombinant;residual;resulted;results;retaining;sensitive;sequence;silico;similar;Slovak;starting;synthesis;synthetic;temperatures;than;that;the;them;Thermococcus;thermophilic;thermotolerant;three;times;to;tool;transfer;transferred;transformed;transgenic;under;up;upon;usage;utilization;utilized;was;we;were;which;with | Univ Ss Cyril & Methodius | Background: The enzymes utilized in the process of beer production are generally sensitive to higher temperatures. About 60% of them are deactivated in drying the malt that limits the utilization of starting material in the fermentation process. Gene transfer from thermophilic bacteria is a promising tool for producing barley grains harboring thermotolerant enzymes. Results: Gene for a-amylase from hydrothermal Thermococcus, optimally active at 75-85 degrees C and pH between 5.0 and 5.5, was adapted in silico to barley codon usage. The corresponding sequence was put under control of the endosperm-specific promoter 1Dx5 and after synthesis and cloning transferred into barley by biolistics. In addition to model cultivar Golden Promise we transformed three Slovak barley cultivars Pribina, Levan and Nitran, and transgenic plants were obtained. Expression of the similar to 50 kDa active recombinant enzyme in grains of cvs. Pribina and Nitran resulted in retaining up to 9.39% of enzyme activity upon heating to 75 degrees C, which is more than 4 times higher compared to non-transgenic controls. In the model cv. Golden Promise the grain a-amylase activity upon heating was above 9% either, however, the effects of the introduced enzyme were less pronounced (only 1.22 fold difference compared with non-transgenic barley). Conclusions: Expression of the synthetic gene in barley enhanced the residual a-amylase activity in grains at high temperatures. | AAC-3814-2019;AAC-8950-2019;AAM-7111-2020;AAZ-3712-2020;JEO-7562-2023;W-4164-2018 | AMYLASE;CLONING;EXPRESSION;LEVEL;PROMOTER;STABILITY;TRANSGENIC BARLEY;WEB | 0 | null | Amylopectin;Amylose;Beer;fermentation;Gene transfer;Glutenin;Hordeum;promoter;Seed-directed expression;Synthetic gene;Thermotolerant bacteria | 5 | AMYLASE;Amylopectin;Amylose;Beer;cloning;EXPRESSION;FERMENTATION;GENE-TRANSFER;Glutenin;Hordeum;LEVEL;PROMOTER;Seed-directed expression;STABILITY;Synthetic gene;Thermotolerant bacteria;TRANSGENIC BARLEY;WEB | WOS:000416721500002 | Natl Agr & Food Ctr, Piestany, Slovakia;Plant Sci & Biodivers Ctr SAS, Nitra, Slovakia;Slovak Acad Sci, Bratislava, Slovakia;Univ Ss Cyril & Methodius Trnava, Trnava, Slovakia;Univ Ss Cyril & Methodius, Trnava, Slovakia | Slovakia | 2,017 | null | 0000-0001-5570-5065;0000-0001-6002-7107;0000-0002-3719-8634;0000-0002-8495-7971;0000-0003-1551-1295;0000-0003-2801-8870;0000-0003-3528-4114 | null | null | English | null | BIOL PLANTARUM;BRAZ J MICROBIOL;ENZYME MICROB TECH;EUPHYTICA;FEBS LETT;FEMS MICROBIOL LETT;IN VITRO CELL DEV-PL;J AM SOC BREW CHEM;J BASIC MICROB;J EUKARYOT MICROBIOL;MOL BREEDING;MOL GEN GENET;NAT PROTOC;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PLANT BIOTECHNOL J;PLANT CELL REP;PLANT MOL BIOL;THEOR APPL GENET;TRANSGENIC RES | Glasa, Miroslav;Gubisova, Marcela;Havrlentova, Michaela;Hudcovicova, Martina;Kraic, Jan;Matusikova, Ildik;Mihalik, Daniel;Moravcikova, Jana | 2024-03-11
ER | Anderson, O D;Choi, H W;Christensen, A H;Cu, S T;Dahleen, L S;Evans, D E;Ferreira-Nozawa, M S;Fincher G. B.;Furtado, A;Harwood Wendy A.;Horvath, H;Kandra, L;Kelley, L A;Kihara, M;Lévêque, E;Mihálik, D;Moreira, F G;Puigbò, P;Rooke, L;Skadsen, R W;Wang, D P;Wolf, N;Xu, X L | FO3IM | Trnava, Slovakia | 1 | null | 5 | null | null | Glasa, Miroslav;Gubisova, Marcela;Havrlentova, Michaela;Hudcovicova, Martina;Kraic, Jan;Matusikova, Ildik;Mihalik, Daniel;Moravcikova, Jana | ELECTRON J BIOTECHN | Bratislava, Slovakia;Nitra, Slovakia;Piestany, Slovakia;Trnava, Slovakia |
Arcak, M;Gomez, M M | 10.1021/acssynbio.7b00077 | null | 1155 16TH ST, NW, WASHINGTON, DC 20036 USA | 2n314m6r3y7130173p73f7603x725c6x3k4t1h | A Tug-of-War Mechanism for Pattern Formation in a Genetic Network | Univ Calif Berkeley | null | Gomez, MM (corresponding author), Univ Calif Berkeley, Elect Engn & Comp Sci, Berkeley, CA 94720 USA. | null | Arcak, Murat;Gomez, Marcella M | Biochemical Research Methods | Air Force Office of Scientific Research [FA9550-14-1-0089]; NIH National Institute of General Medical Sciences [1R01GM109460-01]; California Alliance Postdoctoral Fellowship; UC Presidents Postdoctoral Fellowship | WOS | Gomez, M M | Univ Calif Berkeley, Berkeley, CA USA | 6 | a;for;formation;genetic;in;Mechanism;network;Pattern;Tug-of-War | 1 | , Marcella;Arcak, Murat | AMER CHEMICAL SOC | Univ Calif Berkeley, Elect Engn & Comp Sci, Berkeley, CA 94720 USA | Article | Univ Calif Berkeley | WASHINGTON | null | null | Univ Calif Berkeley | Air Force Office of Scientific Research;California Alliance Postdoctoral Fellowship;NIH National Institute of General Medical Sciences;UC Presidents Postdoctoral Fellowship | Gomez, MM (corresponding author), Univ Calif Berkeley, Elect Engn & Comp Sci, Berkeley, CA 94720 USA. | 2066 | Arcak, Murat;Gomez, Marcella M | 14 | 1 | 416,204,100,010 | Air Force Office of Scientific Research [FA9550-14-1-0089];California Alliance Postdoctoral Fellowship;NIH National Institute of General Medical Sciences [1R01GM109460-01];UC Presidents Postdoctoral Fellowship | USA | ACS SYNTHETIC BIOLOGY | USA | null | null | Univ Calif Berkeley, Elect Engn & Comp Sci, Berkeley, CA 94720 USA | 2161-5063 | Arcak, M;Gomez, M M | NOV | mmgomez@berkeley.edu | Genetic Network;Pattern Formation;Tug-of-War Mechanism | 2 | J | Biochemistry & Molecular Biology | advance applications;analysis;BINDING;bistable system;cells;CONSTRUCTION;developmental systems;diffusible molecules;DIFFUSION;eigenvalues;EQUATIONS;expression;extended periods;genetic network;Genetic networks;inhibiting molecules;instability;instructions;long-term development;natural world;ongoing challenge;opposing bistable states;OSCILLATIONS;patches;pattern formation;patterns;PDEs;persistent modes;persistent patterns;PROPAGATION;quorum sensing;realizable synthetic gene network;relevant models;representative small scale model;results;ROBUST;simulation;spatial patterns;stability;STABILIZATION;successful demonstration;synthetic biology;systems;threshold;time;toggle switch;transient;tug-of-war;Tug-of-War Mechanism;Turing patterns;underlying mechanism;understanding;wavelength patterns | Gomez, M M | BINDING;CONSTRUCTION;EQUATIONS;EXPRESSION;INSTABILITY;OSCILLATIONS;pattern formation;PDEs;PROPAGATION;quorum sensing;ROBUST;STABILIZATION;SYSTEMS;toggle switch | 2056 | [Gomez, Marcella M.; Arcak, Murat] Univ Calif Berkeley, Elect Engn & Comp Sci, Berkeley, CA 94720 USA. | The authors thank Adam Arkin for discussions which led to examining the effects of leaky gene expression and crosstalk on patterning, Hernan Garcia for inspiring discussions on Drosophila embryogenesis, and Eduardo Sontag for bringing to our attention the references.<SUP>29-35</SUP> This work was funded by Air Force Office of Scientific Research FA9550-14-1-0089, NIH National Institute of General Medical Sciences 1R01GM109460-01, the California Alliance Postdoctoral Fellowship, and the UC Presidents Postdoctoral Fellowship. | advance applications;analysis;bistable system;cells;developmental systems;diffusible molecules;diffusion;eigenvalues;extended periods;genetic networks;inhibiting molecules;instructions;long-term development;natural world;ongoing challenge;opposing bistable states;patches;pattern formation;patterns;persistent modes;persistent patterns;realizable synthetic gene network;relevant models;representative small scale model;results;simulation;spatial patterns;stability;successful demonstration;synthetic biology;systems;threshold;time;toggle switch;transient;tug-of-war;Turing patterns;underlying mechanism;understanding;wavelength patterns | 10.1007/978-4-431-87704-2_4;10.1007/BF00289234;10.1007/BF01025992;10.1007/s00018-006-6296-z;10.1007/s00018-010-0536-y;10.1016/0022-0396(78)90033-5;10.1016/0022-0396(85)90020-8;10.1016/0022-5193(71)90154-8;10.1016/0167-2789(91)90204-M;10.1016/0378-1119(82)90042-7;10.1016/0959-437X(94)90068-E;10.1016/B978-0-12-385120-8.00002-4;10.1016/j.cell.2016.03.006;10.1016/j.molcel.2006.04.027;10.1016/j.physd.2008.12.005;10.1016/j.ydbio.2012.07.020;10.1016/S0304-4149(98)00080-5;10.1021/cr1000817;10.1029/2006JG000379;10.1038/225535b0;10.1038/35002131;10.1038/msb.2013.55;10.1038/nature03318;10.1038/nature03461;10.1073/pnas.0307571101;10.1073/pnas.0308265100;10.1073/pnas.0504604102;10.1073/pnas.0510398103;10.1073/pnas.1211902109;10.1073/pnas.1410022111;10.1073/pnas.89.9.3977;10.1074/jbc.M311194200;10.1088/0034-4885/61/4/002;10.1093/imamat/38.2.97;10.1098/rstb.1952.0012;10.1103/PhysRevLett.64.2953;10.1103/RevModPhys.65.851;10.1109/9.935065;10.1109/CDC.2013.6760286;10.1111/j.1365-2443.2005.00897.x;10.1111/j.1365-2958.2008.06221.x;10.1126/science.175.4022.634;10.1126/science.aaa3794;10.1137/0133023;10.1137/0142077;10.1137/0321027;10.1186/1741-7007-10-46;10.1186/1754-1611-3-10;10.1371/journal.pbio.1002042;10.1371/journal.pcbi.1000184;10.1371/journal.pcbi.1002331;10.1371/journal.pcbi.1004881;10.1371/journal.pone.0007086;10.1371/journal.pone.0021145;10.1529/biophysj.107.120827;10.2478/s11534-010-0076-y;10.2977/PRIMS/1195188180.MR555661;10.3934/mbe.2014.11.203 | Univ Calif Berkeley | Arcak, M;Gomez, M M | Gomez, M M: Univ Calif Berkeley, Elect Engn & Comp Sci, Berkeley, CA 94720 USA | null | 1R01GM109460-01;FA9550-14-1-0089 | 62 | null | USA | Univ Calif Berkeley | Gomez, Marcella M | Green Accepted, Green Submitted | BINDING;CONSTRUCTION;EQUATIONS;EXPRESSION;INSTABILITY;OSCILLATIONS;PROPAGATION;ROBUST;STABILIZATION;SYSTEMS | Gomez, Marcella M.; Arcak, Murat; | null | Univ Calif Berkeley, Elect Engn & Comp Sci, Berkeley, CA 94720 USA | Univ Calif Berkeley, Elect Engn & Comp Sci, Berkeley, CA 94720 USA | null | pattern formation;PDEs;quorum sensing;toggle switch | 11 | 1952;1970;1971;1972;1977;1978;1979;1982;1983;1985;1987;1990;1991;1992;1993;1994;1998;1999;2000;2001;2004;2005;2006;2007;2008;2009;2011;2012;2013;2014;2015;2016 | 5 | Univ Calif Berkeley, Elect Engn & Comp Sci, Berkeley, CA 94720 USA | ACS Synth. Biol. | Arcak, Murat | AMER CHEMICAL SOC | ";,;:;a;above;advance;an;analysis;and;applications;are;at;based;better;between;biologically;biology;bistable;but;can;cells;challenge;creates;demonstration;development;developmental;different;diffusible;diffusion;distinctly;eigenvalues;emerge;extended;for;formation;from;gene;generate;genetic;implies;imply;imprint;in;incorporating;inhibiting;instructions;is;just;long-term;longer;may;mechanism;model;models;modes;molecules;mutually;natural;network;networks;of;on;ongoing;opposing;order;paper;patches;pattern;patterning;patterns;periods;persist;persistent;prolonged;realizable;relevant;representative;resemble;results;scale;show;simulation;small;spatial;stability;states;successful;suffice;switch;synthesizing;synthetic;system;systems;that;the;this;threshold;through;time;to;toggle;transient;tug-of-war;Turing;underlying;understanding;verified;wavelength;we;with;world;would | Univ Calif Berkeley | Synthesizing spatial patterns with genetic networks is an ongoing challenge in synthetic biology. A successful demonstration of pattern formation would imply a better understanding of systems in the natural world and advance applications in synthetic biology. In developmental systems, transient patterning may suffice in order to imprint instructions for long-term development. In this paper we show that transient but persistent patterns can emerge from a realizable synthetic gene network based on a toggle switch. We show that a bistable system incorporating diffusible molecules can generate patterns that resemble Turing patterns but are distinctly different in the underlying mechanism: diffusion of mutually inhibiting molecules creates a prolonged "tug-of-war" between patches of cells at opposing bistable states. The patterns are transient but longer wavelength patterns persist for extended periods of time. Analysis of a representative small scale model implies the eigenvalues of the persistent modes are just above the threshold of stability. The results are verified through simulation of biologically relevant models. | null | BINDING;CONSTRUCTION;EQUATIONS;EXPRESSION;INSTABILITY;OSCILLATIONS;PROPAGATION;ROBUST;STABILITY;SYSTEM | 0 | null | pattern formation;PDEs;quorum sensing;toggle switch | 11 | BINDING;CONSTRUCTION;EQUATIONS;EXPRESSION;INSTABILITY;OSCILLATIONS;PATTERN-FORMATION;PDEs;PROPAGATION;quorum sensing;ROBUST;STABILITY;SYSTEM;toggle switch | WOS:000416204100010 | Univ Calif Berkeley, Berkeley, CA USA | USA | 2,017 | null | 0000-0001-9060-4032;0000-0001-9709-5015 | null | null | English | null | BIOPHYS J;BMC BIOL;CELL;CELL MOL LIFE SCI;CENT EUR J PHYS;CHEM REV;CURR OPIN GENET DEV;DEV BIOL;GENE;GENES CELLS;IEEE DECIS CONTR P;IEEE T AUTOMAT CONTR;IMA J APPL MATH;J BIOL CHEM;J Biol Eng;J DIFFER EQUATIONS;J GEOPHYS RES-BIOGEO;J STAT PHYS;J THEOR BIOL;KYBERNETIK;MATH BIOSCI ENG;METHOD ENZYMOL;MOL CELL;MOL MICROBIOL;MOL SYST BIOL;NATURE;P NATL ACAD SCI USA;Pattern formation by dynamic systems and pattern recognition;PATTERN FORMATION DY;PHILOS T ROY SOC B;PHYS REV E;PHYS REV LETT;PHYSICA D;PLOS BIOL;PLOS COMPUT BIOL;PLOS ONE;PUBLS RES I MATH SCI;REP PROG PHYS;REV MOD PHYS;SCIENCE;SIAM J APPL MATH;SIAM J CONTROL OPTIM;STOCH PROC APPL;TRANSLATIONS MATH MO | Arcak, Murat;Gomez, Marcella M | 2024-03-11
ER | Alper, H;Angeli, D;Arnold, L;Basak, G K;Basu, S;Bothma, J P;Cao, Y X L;Casten, R G;Castets, V;Cattani, A;Chen, Y;Churchill, M E A;Cohen, D J;Cross M.;Cross, M C;D'Odorico, P;Dekepper, P;Dinardo, S;Elliott, C M;Ermentrout, B;Futahashi, R;Gardner, T S;Gierer, A;Hsia, J;Igoshin, O A;Ishihara, S;Jaeger, J;Kharchenko, D;Kharchenko, D O;Kishimoto, K;Kondo, S;Kwiecinska, A A;Lengyel, I;Levin Sa.;Lopes, F J P;Mackey, M C;Matano, H;Mcginness, K E;Miyazako, H;Mori, Y;Nikolaev, E V;Othmer, H G;Papatsenko, D;Payne, S;Rinzel, J;Russell, D R;Salis, H M;Sanz-Anchelergue A.;Sohka Takayuki;Turing, A M;Umulis, D M;Venturelli, O S;Volpert A. I.;Wang, L H;Wang, Y C;Wilson, C J;Winfree, A T;Zaikin, A N | FN7ND | Berkeley, CA USA | 7 | null | 1 | null | 28,763,188 | Arcak, Murat;Gomez, Marcella M | ACS SYNTH BIOL | Berkeley, CA USA |
Kleinjan, D A;Rosser, S J;Sou, S N;Wardrope, C | 10.1038/s41467-017-01222-y | 1191 | MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND | 262r6pj6g14t402r606o521l3v6z4c14664h4u | Drug-tunable multidimensional synthetic gene control using inducible degron-tagged dCas9 effectors | Univ Edinburgh | null | Rosser, SJ (corresponding author), Univ Edinburgh, Inst Bioengn, Faraday Bldg,Kings Bldg, Edinburgh EH9 3DW 2, Midlothian, Scotland.;Rosser, SJ (corresponding author), Univ Edinburgh, Inst Quantitat Biol Biochem & Biotechnol, Sch Biol Sci, UK Ctr Mammalian Synthet Biol,SynthSys, Edinburgh EH9 3BF, Midlothian, Scotland. | null | Kleinjan, Dirk A;Rosser, Susan J;Sou, Si Nga;Wardrope, Caroline | Multidisciplinary Sciences | BBSRC [BB/M018040/1, BB/M018229/1]; Biotechnology and Biological Sciences Research Council [BB/M018229/1, BB/M018237/1, BB/M018040/1] Funding Source: researchfish; BBSRC [BB/M018229/1, BB/M018237/1, BB/M018040/1] Funding Source: UKRI | WOS | Rosser, S J | Univ Edinburgh, Midlothian, Scotland | 8 | control;dCas9;degron-tagged;drug-tunable;effectors;gene;inducible;multidimensional;synthetic;using | 1 | Rosser, Susan | NATURE PUBLISHING GROUP | Univ Edinburgh, Inst Bioengn, Faraday Bldg,Kings Bldg, Edinburgh EH9 3DW 2, Midlothian, Scotland;Univ Edinburgh, Inst Quantitat Biol Biochem & Biotechnol, Sch Biol Sci, UK Ctr Mammalian Synthet Biol,SynthSys, Edinburgh EH9 3BF, Midlothian, Scotland;Univ Edinburgh, Inst Quantitat Biol Biochem & Biotechnol, Sch Biol Sci, UK Ctr Mammalian Synthet Biol,SynthSys, Edinburgh EH9 3BF, Midlothian, Scotland.; Rosser, SJ (corresponding author), Univ Edinburgh, Inst Bioengn, Faraday Bldg,Kings Bldg, Edinburgh EH9 3DW 2, Midlothian, Scotland | Article | Univ Edinburgh | LONDON | null | null | Univ Edinburgh | BBSRC;Biotechnology and Biological Sciences Research Council | Rosser, SJ (corresponding author), Univ Edinburgh, Inst Quantitat Biol Biochem & Biotechnol, Sch Biol Sci, UK Ctr Mammalian Synthet Biol,SynthSys, Edinburgh EH9 3BF, Midlothian, Scotland.; Rosser, SJ (corresponding author), Univ Edinburgh, Inst Bioengn, Faraday Bldg,Kings Bldg, Edinburgh EH9 3DW 2, Midlothian, Scotland. | null | Kleinjan, Dirk A;Rosser, Susan J;Sou, Si Nga;Wardrope, Caroline | 22 | 2 | 413,894,100,013 | BBSRC [BB/M018040/1, BB/M018229/1];BBSRC [BB/M018229/1, BB/M018237/1, BB/M018040/1] Funding Source: UKRI;Biotechnology and Biological Sciences Research Council [BB/M018229/1, BB/M018237/1, BB/M018040/1] Funding Source: researchfish | UK | NATURE COMMUNICATIONS | UK | null | null | Univ Edinburgh, Inst Quantitat Biol Biochem & Biotechnol, Sch Biol Sci, UK Ctr Mammalian Synthet Biol,SynthSys, Edinburgh EH9 3BF, Midlothian, Scotland | 2041-1723 | Kleinjan, D A;Rosser, S J;Sou, S N;Wardrope, C | OCT 30 | Susan.Rosser@ed.ac.uk | drug-tunable multidimensional synthetic gene control;inducible degron-tagged dCas9 effectors | 4 | J | Science & Technology - Other Topics | ability;act;activated target gene expression states;activation;Cas9;cell;combinations;Cpf1 effector proteins;CRISPR-Cas9;CRISPR-Cas9 proteins (dCas9);degradable;DEGRADATION;DEPLETION;draw-back;drug-tunable artificial transcription factors;drug-tunable multidimensional synthetic gene control;functional activities;gene expression;heterologous transactivation domains;HUMAN-CELLS;inducible degron-tagged dCas9 effectors;issue;long-term presence;mammalian cells;multidimensional control;nuclease-deactivated variant;opening options;potent guide RNA sequence-directed inducer;proteins;REPRESSION;REPRESSOR;stabilisable orthologous dCas9;stable dCas9 effector;static environment;synthetic regulatory circuits;SYSTEM;toolkit;TRANSCRIPTION | Kleinjan, D A | ACTIVATION;CAS9;CRISPR-Cas9;DEGRADATION;DEPLETION;HUMAN-CELLS;Proteins;REPRESSION;SYSTEM;TRANSCRIPTION | null | [Kleinjan, Dirk A.; Wardrope, Caroline; Sou, Si Nga; Rosser, Susan J.] Univ Edinburgh, Inst Quantitat Biol Biochem & Biotechnol, Sch Biol Sci, UK Ctr Mammalian Synthet Biol,SynthSys, Edinburgh EH9 3BF, Midlothian, Scotland. [Rosser, Susan J.] Univ Edinburgh, Inst Bioengn, Faraday Bldg,Kings Bldg, Edinburgh EH9 3DW 2, Midlothian, Scotland. | This work was supported by grants from the BBSRC (BB/M018040/1 and BB/M018229/1) to S.J.R. | ability;act;activated target gene expression states;cell;combinations;Cpf1 effector proteins;CRISPR-Cas9 proteins (dCas9);degradable;draw-back;drug-tunable artificial transcription factors;functional activities;gene expression;heterologous transactivation domains;issue;long-term presence;mammalian cells;multidimensional control;nuclease-deactivated variant;opening options;potent guide RNA sequence-directed inducer;repressor;stabilisable orthologous dCas9;stable dCas9 effector;static environment;synthetic regulatory circuits;system;toolkit | 10.1016/j.biotechadv.2015.12.012;10.1016/j.cell.2014.09.029;10.1016/j.cell.2015.09.038;10.1016/j.celrep.2016.03.001;10.1016/j.chembiol.2010.07.009;10.1038/nature12466;10.1038/nature14136;10.1038/nbt.2623;10.1038/nbt.3528;10.1038/nchembio.2224;10.1038/nmeth.1401;10.1038/nmeth.3630;10.1038/nprot.2013.132;10.1038/nrm.2015.2;10.1038/nrm2468;10.1074/jbc.M114.583542;10.1126/science.1232033;10.7554/eLife.00471;[10.1038/NMETH.2681, 10.1038/nmeth.2681];[10.1038/NMETH.3580, 10.1038/nmeth.3580];[10.1038/NMETH.3733, 10.1038/nmeth.3733] | Univ Edinburgh | Kleinjan, D A;Rosser, S J;Sou, S N;Wardrope, C | Kleinjan, D A: Univ Edinburgh, Inst Quantitat Biol Biochem & Biotechnol, Sch Biol Sci, UK Ctr Mammalian Synthet Biol,SynthSys, Edinburgh EH9 3BF, Midlothian, Scotland | null | BB/M018040/1;BB/M018229/1;BB/M018237/1 | 21 | null | UK | Univ Edinburgh | Kleinjan, Dirk A | Green Published, gold | ACTIVATION;CAS9;CRISPR-CAS9;DEGRADATION;DEPLETION;HUMAN-CELLS;PROTEINS;REPRESSION;SYSTEM;TRANSCRIPTION | Kleinjan, Dirk A.; Wardrope, Caroline; Sou, Si Nga; Rosser, Susan J.; | null | Univ Edinburgh, Inst Bioengn, Faraday Bldg,Kings Bldg, Edinburgh EH9 3DW 2, Midlothian, Scotland;Univ Edinburgh, Inst Quantitat Biol Biochem & Biotechnol, Sch Biol Sci, UK Ctr Mammalian Synthet Biol,SynthSys, Edinburgh EH9 3BF, Midlothian, Scotland | Univ Edinburgh, Inst Bioengn, Faraday Bldg,Kings Bldg, Edinburgh EH9 3DW 2, Midlothian, Scotland;Univ Edinburgh, Inst Quantitat Biol Biochem & Biotechnol, Sch Biol Sci, UK Ctr Mammalian Synthet Biol,SynthSys, Edinburgh EH9 3BF, Midlothian, Scotland | null | null | null | 2008;2009;2010;2013;2014;2015;2016;2017 | 43 | Univ Edinburgh, Inst Bioengn, Faraday Bldg,Kings Bldg, Edinburgh EH9 3DW 2, Midlothian, Scotland;Univ Edinburgh, Inst Quantitat Biol Biochem & Biotechnol, Sch Biol Sci, UK Ctr Mammalian Synthet Biol,SynthSys, Edinburgh EH9 3BF, Midlothian, Scotland | Nat. Commun. | Rosser, Susan J | NATURE PUBLISHING GROUP | (dCas9);,;a;ability;act;activated;activities;address;and;artificial;as;be;between;can;cell;cells;circuits;combinations;conditionally;control;Cpf1;CRISPR-Cas9;dCas9;degradable;domains;draw-back;drug-tunable;effector;environment;expression;factors;for;functional;fused;gene;generated;guide;have;heterologous;imposing;in;inducer;issue;long-term;mammalian;multidimensional;nuclease-deactivated;of;on;opening;options;or;Orthogonal;orthologous;potent;precluding;presence;proteins;rapidly;regulatory;repressed;repressor;RNA;sequence-directed;stabilisable;stable;states;static;such;switch;synthetic;system;target;the;this;through;thus;to;toolkit;transactivation;transcription;variant;we | Univ Edinburgh | The nuclease-deactivated variant of CRISPR-Cas9 proteins (dCas9) fused to heterologous transactivation domains can act as a potent guide RNA sequence-directed inducer or repressor of gene expression in mammalian cells. In such a system the long-term presence of a stable dCas9 effector can be a draw-back precluding the ability to switch rapidly between repressed and activated target gene expression states, imposing a static environment on the synthetic regulatory circuits in the cell. To address this issue we have generated a toolkit of conditionally degradable or stabilisable orthologous dCas9 or Cpf1 effector proteins, thus opening options for multidimensional control of functional activities through combinations of orthogonal, drug-tunable artificial transcription factors. | null | ACTIVATION;CAS9;CRISPR-CAS9;DEGRADATION;DEPLETION;HUMAN-CELLS;PROTEIN;REPRESSION;SYSTEM;TRANSCRIPTION | 0 | null | null | 9 | ACTIVATION;CAS9;CRISPR-Cas9;DEGRADATION;DEPLETION;HUMAN-CELLS;PROTEIN;REPRESSION;SYSTEM;TRANSCRIPTION | WOS:000413894100013 | Univ Edinburgh, Midlothian, Scotland | UK | 2,017 | null | 0000-0002-2560-6485 | null | null | English | null | BIOTECHNOL ADV;CELL;CELL REP;CHEM BIOL;ELIFE;J BIOL CHEM;NAT BIOTECHNOL;NAT CHEM BIOL;NAT METHODS;NAT PROTOC;NAT REV MOL CELL BIO;NATURE;SCIENCE | Kleinjan, Dirk A;Rosser, Susan J;Sou, Si Nga;Wardrope, Caroline | 2024-03-11
ER | Brown, A J;Dominguez, A A;Esvelt, K M;Fu, Y F;Gilbert, L A;Iwamoto, M;Jinek, M;Kiani, S;Konermann, S;Larson, M H;Maji, B;Mali, P;Natsume, T;Nishimura, K;Oakes, B L;Ravid, T;Samejima, K;Thakore, P I;Zetsche, B | FL0ID | Midlothian, Scotland;Midlothian, Scotland. | 47 | null | 1 | null | 29,084,946 | Kleinjan, Dirk A;Rosser, Susan J;Sou, Si Nga;Wardrope, Caroline | NAT COMMUN | Midlothian, Scotland |
Du, L P;Duan, W L;Jia, Z L;Nie, L R;Wang, C J;Wang, T S;Xie, Q S;Zeng, C H;Zhang, C | 10.1016/j.physa.2017.04.052 | null | RADARWEG 29, 1043 NX AMSTERDAM, NETHERLANDS | 2o1n594yc1bb155p3c2k374j114nh5e2f7 | Emergent bimodality and switch induced by time delays and noises in a synthetic gene circuit | Kunming Univ Sci & Technol | null | Zeng, CH (corresponding author), Kunming Univ Sci & Technol, Fac Sci, Kunming 650500, Peoples R China. | null | Du, Liping;Duan, Weilong;Jia, Zhenglin;Nie, Linru;Wang, Canjun;Wang, Tonghuan;Xie, Qingshuang;Zeng, Chunhua;Zhang, Chun | Physics, Multidisciplinary | National Natural Science Foundation of China [11665014]; Natural Science Foundation of Yunnan Province [the study on gene switching behavior and related physical problems of miR-17-92 regulating cancer network with different delay]; Candidate Talents Training Fund of Yunnan Province [2015HB025, 2015HB064]; State Key Laboratory of Complex Nonferrous Metal Resources Clean Utilization [CNMRCUKF1506]; Science Research Fund of Yunnan Provincial Education Department [2016ZZX047, 2016YJS026] | WOS | Zeng, C H | Baoji Univ Arts & Sci, Baoji, Peoples R China;Kunming Univ Sci & Technol, Kunming, Peoples R China;Kunming Univ Sci & Technol, Yunnan, Peoples R China;Shaanxi Normal Univ, Xian, Peoples R China | 484 | a;and;bimodality;by;circuit;delays;emergent;gene;in;induced;noises;Switch;synthetic;time | 1 | Duan, Wei-Long | ELSEVIER | Baoji Univ Arts & Sci, Nonlinear Res Inst, Baoji 721016, Peoples R China;Kunming Univ Sci & Technol, Fac Sci, Kunming 650500, Peoples R China;Kunming Univ Sci & Technol, Kunhua Hosp, Peoples Hosp Yunnan Prov 1, Dept Anorectal Surgert, Kunming 650032, Yunnan, Peoples R China;Shaanxi Normal Univ, Sch Phys & Informat Technol, Xian 710062, Peoples R China | Article | Kunming Univ Sci & Technol | AMSTERDAM | null | null | Baoji Univ Arts & Sci;Kunming Univ Sci & Technol;Shaanxi Normal Univ | Candidate Talents Training Fund of Yunnan Province;National Natural Science Foundation of China;Natural Science Foundation of Yunnan Province;Science Research Fund of Yunnan Provincial Education Department;State Key Laboratory of Complex Nonferrous Metal Resources Clean Utilization | Zeng, CH (corresponding author), Kunming Univ Sci & Technol, Fac Sci, Kunming 650500, Peoples R China. | 266 | Du, Liping;Duan, Weilong;Jia, Zhenglin;Nie, Linru;Wang, Canjun;Wang, Tonghuan;Xie, Qingshuang;Zeng, Chunhua;Zhang, Chun | 29 | 4 | 404,823,200,024 | Candidate Talents Training Fund of Yunnan Province [2015HB025, 2015HB064];National Natural Science Foundation of China [11665014];Natural Science Foundation of Yunnan Province [the study on gene switching behavior and related physical problems of miR-17-92 regulating cancer network with different delay];Science Research Fund of Yunnan Provincial Education Department [2016ZZX047, 2016YJS026];State Key Laboratory of Complex Nonferrous Metal Resources Clean Utilization [CNMRCUKF1506] | China | PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS | China | null | null | Kunming Univ Sci & Technol, Fac Sci, Kunming 650500, Peoples R China | 0378-4371 | Du, L P;Duan, W L;Jia, Z L;Nie, L R;Wang, C J;Wang, T S;Xie, Q S;Zeng, C H;Zhang, C | OCT 15 | ynlxdj@163.com;zchh2009@126.com | emergent bimodality;noises;Switch;synthetic gene circuit;time delays | 9 | J | Physics | (i);(ii);2009;bistability;bistable system;C 2017 Elsevier B.V;COLORED NOISE;counterintuitive way;cross-correlation;deterministic case;effective potential;Effects;Emergent bimodality;emergent bistability;FEEDBACK LOOP;feedback loop(K);fluctuations;functions;high concentration state;INTRACELLULAR CALCIUM DYNAMICS;K;kinetic model;KINETIC-MODEL DRIVEN;maximum;maximum dilution rate;mean first passage time(MFPT);metastable state;metastable system;multistability;NDS phenomenon;noise;noise strengths;noise-delayed switching (NDS);Noises;NON-GAUSSIAN NOISES;numerical simulation;physical mechanisms;point;Probability distribution;probability distribution phenomenon;protein synthesis rate;results;rights reserved;stability;state;stochastic resonance;strength;SWITCH;Switch time;Synthetic gene circuit;SYSTEM;Tan;tau;theoretical analysis;time;time delay;time delay(tau);TIME DELAYS;Time-delayed feedback;transitions;two noises;two noises(lambda);view | Zhang, C | BISTABILITY;BISTABLE SYSTEM;COLORED NOISE;Emergent bimodality;FLUCTUATIONS;INTRACELLULAR CALCIUM DYNAMICS;KINETIC-MODEL DRIVEN;MULTISTABILITY;Noises;NON-GAUSSIAN NOISES;Probability distribution;stochastic resonance;Switch time;Time-delayed feedback;TRANSITIONS | 253 | [Zhang, Chun; Xie, Qingshuang; Wang, Tonghuan; Zeng, Chunhua; Nie, Linru; Duan, Weilong] Kunming Univ Sci & Technol, Fac Sci, Kunming 650500, Peoples R China. [Zhang, Chun] Shaanxi Normal Univ, Sch Phys & Informat Technol, Xian 710062, Peoples R China. [Du, Liping; Jia, Zhenglin] Kunming Univ Sci & Technol, Kunhua Hosp, Peoples Hosp Yunnan Prov 1, Dept Anorectal Surgert, Kunming 650032, Yunnan, Peoples R China. [Wang, Canjun] Baoji Univ Arts & Sci, Nonlinear Res Inst, Baoji 721016, Peoples R China. | This work was supported by the National Natural Science Foundation of China (Grant No. 11665014), the Natural Science Foundation of Yunnan Province [the study on gene switching behavior and related physical problems of miR-17-92 regulating cancer network with different delay (2018)], the Candidate Talents Training Fund of Yunnan Province (Project No. 2015HB025, 2015HB064), the State Key Laboratory of Complex Nonferrous Metal Resources Clean Utilization (under CNMRCUKF1506), and the Science Research Fund of Yunnan Provincial Education Department (Grant No. 2016ZZX047, 2016YJS026). | (i);(ii);2009;counterintuitive way;cross-correlation;deterministic case;effective potential;effects;emergent bimodality;emergent bistability;feedback loop;feedback loop(K);fluctuations;functions;high concentration state;K;kinetic model;maximum;maximum dilution rate;mean first passage time(MFPT);metastable state;metastable system;NDS phenomenon;noise;noise strengths;noise-delayed switching (NDS);numerical simulation;physical mechanisms;point;probability distribution phenomenon;protein synthesis rate;results;stability;state;strength;switch;synthetic gene circuit;system;Tan;tau;theoretical analysis;time;time delay;time delay(tau);two noises;two noises(lambda);view | 10.1007/BF01019737;10.1007/BF01306642;10.1016/0375-9601(85)90380-9;10.1016/0375-9601(94)90988-1;10.1016/0921-4534(96)00426-1;10.1016/j.amc.2016.07.041;10.1016/j.amc.2016.08.001;10.1016/j.chaos.2016.11.017;10.1016/j.physa.2008.07.018;10.1016/j.physa.2011.11.007;10.1016/j.physa.2014.08.042;10.1016/j.physleta.2006.11.006;10.1016/S0031-8914(40)90098-2;10.1016/S0375-9601(97)00599-9;10.1016/S0378-4371(03)00192-4;10.1016/S0378-4371(97)00630-4;10.1038/35066056;10.1038/35103078;10.1038/377209a0;10.1038/nature02298;10.1038/nchembio.218;10.1038/srep25067;10.1063/1.4745853;10.1063/1.532362;10.1073/pnas.1332628100;10.1088/1742-5468/2013/10/P10017;10.1103/PhysRevA.25.519;10.1103/PhysRevA.33.467;10.1103/PhysRevA.35.3086;10.1103/PhysRevA.38.2605;10.1103/PhysRevA.46.757;10.1103/PhysRevB.48.125;10.1103/PhysRevB.82.132405;10.1103/PhysRevE.50.2496;10.1103/PhysRevE.53.5786;10.1103/PhysRevE.59.3880;10.1103/PhysRevE.62.7478;10.1103/PhysRevE.64.035102;10.1103/PhysRevE.69.061103;10.1103/PhysRevE.70.031103;10.1103/PhysRevE.70.041907;10.1103/PhysRevE.71.031106;10.1103/PhysRevE.72.051907;10.1103/PhysRevE.72.061110;10.1103/PhysRevE.75.021107;10.1103/PhysRevE.75.041106;10.1103/PhysRevE.77.031107;10.1103/PhysRevE.79.041117;10.1103/PhysRevE.80.041110;10.1103/PhysRevE.82.041120;10.1103/PhysRevE.83.011903;10.1103/PhysRevLett.111.058104;10.1103/PhysRevLett.76.563;10.1103/PhysRevLett.78.994;10.1103/PhysRevLett.80.4815;10.1103/PhysRevLett.87.250602;10.1103/PhysRevLett.91.260601;10.1103/PhysRevLett.92.050601;10.1103/PhysRevLett.93.010601;10.1103/PhysRevLett.95.040601;10.1103/RevModPhys.62.251;10.1126/science.1109090;10.1140/epjb/e2003-00144-1;10.1140/epjb/e2012-30692-x;10.1140/epje/i2012-12011-4;10.1142/S0217979214502233;10.1142/S0218127495000417;10.1142/S0218127498000577;10.1152/ajpcell.1998.274.2.C531;10.1152/ajpcell.1999.277.4.C777;10.1209/0295-5075/81/10002;10.1371/journal.pone.0021104 | Kunming Univ Sci & Technol | Du, L P;Duan, W L;Jia, Z L;Nie, L R;Wang, C J;Wang, T S;Xie, Q S;Zeng, C H;Zhang, C | Zhang, C: Kunming Univ Sci & Technol, Fac Sci, Kunming 650500, Peoples R China | Duan, Wei-Long;WANG, CAN;Wang, Canjun | 11665014;2015HB025;2015HB064;2016YJS026;2016ZZX047;CNMRCUKF1506;the study on gene switching behavior and related physical problems of miR-17-92 regulating cancer network with different delay | 74 | null | China | Baoji Univ Arts & Sci;Kunming Univ Sci & Technol;Shaanxi Normal Univ | Zhang, Chun | null | BISTABILITY;BISTABLE SYSTEM;COLORED NOISE;FLUCTUATIONS;INTRACELLULAR CALCIUM DYNAMICS;KINETIC-MODEL DRIVEN;MULTISTABILITY;NON-GAUSSIAN NOISES;STOCHASTIC RESONANCE;TRANSITIONS | Zhang, Chun; Du, Liping; Xie, Qingshuang; Wang, Tonghuan; Zeng, Chunhua; Nie, Linru; Duan, Weilong; Jia, Zhenglin; Wang, Canjun; | null | Baoji Univ Arts & Sci, Nonlinear Res Inst, Baoji 721016, Peoples R China;Kunming Univ Sci & Technol, Fac Sci, Kunming 650500, Peoples R China;Kunming Univ Sci & Technol, Kunhua Hosp, Peoples Hosp Yunnan Prov 1, Dept Anorectal Surgert, Kunming 650032, Yunnan, Peoples R China;Shaanxi Normal Univ, Sch Phys & Informat Technol, Xian 710062, Peoples R China | Baoji Univ Arts & Sci, Nonlinear Res Inst, Baoji 721016, Peoples R China;Kunming Univ Sci & Technol, Fac Sci, Kunming 650500, Peoples R China;Kunming Univ Sci & Technol, Kunhua Hosp, Peoples Hosp Yunnan Prov 1, Dept Anorectal Surgert, Kunming 650032, Yunnan, Peoples R China;Shaanxi Normal Univ, Sch Phys & Informat Technol, Xian 710062, Peoples R China | 1873-2119 | Emergent bimodality;noise;Probability distribution;Switch time;Time-delayed feedback | null | 1940;1982;1984;1985;1986;1987;1988;1990;1992;1993;1994;1995;1996;1997;1998;1999;2000;2001;2003;2004;2005;2007;2008;2009;2010;2011;2012;2013;2014;2016;2017 | 15 | Kunming Univ Sci & Technol, Fac Sci, Kunming 650500, Peoples R China | Physica A | Wang, Canjun | ELSEVIER | (i);(ii);(NDS);,;2009;:;;;a;al;analysis;and;as;based;be;been;between;bimodality;bistability;by;called;can;case;cause;circuit;compared;concentration;counterintuitive;cross-correlation;delay;delay(tau);deterministic;dilution;disappear;distribution;effective;effects;emergent;enhance;enhances;et;exhibits;explained;feedback;first;fluctuations;for;from;functions;gene;have;high;in;investigated;is;it;K;kinetic;longer;loop;loop(K);maximum;mean;mechanisms;metastable;model;modify;NDS;noise;noise-delayed;noises;noises(lambda);numerical;obtaining;of;off;on;our;passage;phenomenon;physical;point;potential;probability;proposed;protein;rate;remains;results;show;shows;simulation;stability;state;states;strength;strengths;switch;switching;synthesis;synthetic;system;Tan;tau;that;the;theoretical;this;through;time;time(MFPT);to;two;view;way;while | Kunming Univ Sci & Technol | Based on the kinetic model for obtaining emergent bistability proposed by Tan et al. (2009), the effects of the fluctuations of protein synthesis rate and maximum dilution rate, the cross-correlation between two noises, and the time delay and the strength of the feedback loop in the synthetic gene circuit have been investigated through theoretical analysis and numerical simulation. Our results show that: (i) the fluctuations of protein synthesis rate and maximum dilution rate enhance the emergent bimodality of the probability distribution phenomenon, while the cross-correlation between two noises(lambda), the time delay(tau) and the strength of the feedback loop(K) cause it to disappear; and (ii) the mean first passage time(MFPT) as functions of the noise strengths exhibits a maximum, this maximum is called noise-delayed switching (NDS) of the high concentration state. The NDS phenomenon shows that the noise can modify the stability of a metastable system in a counterintuitive way, the system remains in the metastable state for a longer time compared to the deterministic case. And the tau and the K enhances the stability of the ON state. The physical mechanisms for the switch between the ON and OFF states can be explained from the point of view of the effective potential. | AAW-1868-2020;GWV-0969-2022;L-8946-2019 | BISTABILITY;BISTABLE SYSTEM;COLORED NOISE;FLUCTUATIONS;INTRACELLULAR CALCIUM DYNAMICS;KINETIC-MODEL DRIVEN;MULTISTABILITY;NON-GAUSSIAN NOISES;STOCHASTIC RESONANCE;TRANSITION | 0 | null | Emergent bimodality;Noises;Probability distribution;Switch time;Time-delayed feedback | 14 | BISTABILITY;BISTABLE SYSTEM;COLORED NOISE;Emergent bimodality;FLUCTUATIONS;INTRACELLULAR CALCIUM DYNAMICS;KINETIC-MODEL DRIVEN;MULTISTABILITY;NOISE;NON-GAUSSIAN NOISES;Probability distribution;stochastic resonance;Switch time;Time-delayed feedback;TRANSITION | WOS:000404823200024 | Baoji Univ Arts & Sci, Baoji, Peoples R China;Kunming Univ Sci & Technol, Kunming, Peoples R China;Kunming Univ Sci & Technol, Yunnan, Peoples R China;Shaanxi Normal Univ, Xian, Peoples R China | China | 2,017 | null | 0000-0001-8450-6217 | null | null | English | null | AM J PHYSIOL-CELL PH;APPL MATH COMPUT;CHAOS;CHAOS SOLITON FRACT;CHINESE J PHYS;EPL-EUROPHYS LETT;EUR PHYS J B;EUR PHYS J E;INT J BIFURCAT CHAOS;INT J MOD PHYS B;J MATH PHYS;J STAT MECH-THEORY E;J STAT PHYS;NAT CHEM BIOL;NAT REV GENET;NAT REV MOL CELL BIO;NATURE;P NATL ACAD SCI USA;PHYS LETT A;PHYS REV A;PHYS REV B;PHYS REV E;PHYS REV LETT;PHYSICA;PHYSICA A;PHYSICA C;PLOS ONE;REV MOD PHYS;SCI REP-UK;SCIENCE;Z PHYS B CON MAT | Du, Liping;Duan, Weilong;Jia, Zhenglin;Nie, Linru;Wang, Canjun;Wang, Tonghuan;Xie, Qingshuang;Zeng, Chunhua;Zhang, Chun | 2024-03-11
ER | Agoudov, N V;Agudov, N V;Borromeo, M;Bressloff, P C;Cao, L;Craig, E M;Curtin, D;Dayan, I;Duan, W L;Dubkov, A A;Fedchenia, I I;Fiasconaro, A;Fox, R F;Frank, T D;Gaudreault, M;Ghosh, S;Guardia, E;Guo, W;Gupta, C;Hanggi, P;Hasty, J;Hennig, D;Hirsch, J E;Hornos, J E M;Houlihan, J;Huber, D;Isaacs, F J;Janson, N B;Jia Z. L.;Jia, Y;Jia, Z L;Klosek, M M;Klosekdygas, M M;Kramers, H A;Lin, L;Liu, Q;Malakhov, A N;Mantegna, R N;Masoliver, J;Mei, D C;Nie, L R;Ozbudak, E M;Pankratov A. L.;Pankratov, A L;Pedraza, J M;Piwonski, T;Ramirezpiscina, L;Smirnov, A A;Smolen, P;Sun, G Z;Tan, C;Tsimring, L S;Tyson, J J;Wijgerde, M;Wu, D;Wu, D J;Xie, C W;Xu, Y;Zeng, C H;Zhang, Y | EZ6JC | Kunming, Peoples R China | 15 | null | 3 | null | null | Du, Liping;Duan, Weilong;Jia, Zhenglin;Nie, Linru;Wang, Canjun;Wang, Tonghuan;Xie, Qingshuang;Zeng, Chunhua;Zhang, Chun | PHYSICA A | Baoji, Peoples R China;Kunming, Peoples R China;Xian, Peoples R China;Yunnan, Peoples R China |
Karamasioti, E;Lormeau, C;Stelling, J | 10.1039/c7me00032d | null | THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND | 135b5u404m2b372g531y5p4w492m132n691773 | Computational design of biological circuits: putting parts into context | Swiss Fed Inst Technol | null | Stelling, J (corresponding author), Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, CH-4058 Basel, Switzerland.;Stelling, J (corresponding author), Swiss Fed Inst Technol, SIB Swiss Inst Bioinformat, CH-4058 Basel, Switzerland. | null | Karamasioti, Eleni;Lormeau, Claude;Stelling, Jorg | Chemistry, Physical;Engineering, Chemical;Materials Science, Multidisciplinary;Nanoscience & Nanotechnology | National Centre of Competence in Research (NCCR) Molecular Systems Engineering - Swiss National Science Foundation (SNSF) | WOS | Stelling, J | Life Sci Zurich Grad Sch, Zurich, Switzerland;Swiss Fed Inst Technol, Basel, Switzerland | 2 | :;biological;circuits;computational;Context;design;into;of;parts;putting | 1 | Magnard (Lormeau), Claude | ROYAL SOC CHEMISTRY | Life Sci Zurich Grad Sch, PhD Program Syst Biol, Zurich, Switzerland;Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, CH-4058 Basel, Switzerland;Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, CH-4058 Basel, Switzerland.; Stelling, J (corresponding author), Swiss Fed Inst Technol, SIB Swiss Inst Bioinformat, CH-4058 Basel, Switzerland;Swiss Fed Inst Technol, SIB Swiss Inst Bioinformat, CH-4058 Basel, Switzerland | Review | Swiss Fed Inst Technol | CAMBRIDGE | null | null | Life Sci Zurich Grad Sch;Swiss Fed Inst Technol | National Centre of Competence in Research (NCCR) Molecular Systems Engineering - Swiss National Science Foundation (SNSF) | Stelling, J (corresponding author), Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, CH-4058 Basel, Switzerland.; Stelling, J (corresponding author), Swiss Fed Inst Technol, SIB Swiss Inst Bioinformat, CH-4058 Basel, Switzerland. | 421 | Karamasioti, Eleni;Lormeau, Claude;Stelling, Jorg | 18 | 3 | 412,769,000,008 | National Centre of Competence in Research (NCCR) Molecular Systems Engineering - Swiss National Science Foundation (SNSF) | Switzerland | MOLECULAR SYSTEMS DESIGN & ENGINEERING | Switzerland | null | null | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, CH-4058 Basel, Switzerland | 2058-9689 | Karamasioti, E;Lormeau, C;Stelling, J | OCT 1 | joerg.stelling@bsse.ethz.ch | biological circuits;computational design;context;putting parts | 3 | J | Chemistry;Engineering;Materials Science;Science & Technology - Other Topics | 'plug-and-play' composition;analogies;AUTOMATED DESIGN;BAYESIAN DESIGN;biochemical systems;biological circuits;BIOLOGY;COMPUTATIONAL DESIGN;CONTEXT;context-aware computational design methods;context-dependent;desired tasks;electronics design;emerging methods;error cycles;ESCHERICHIA-COLI;experimental trial;GENE-EXPRESSION;limited use;main conceptual challenges;MESSENGER-RNA LEVELS;modularity;networks;number;overall;past decade;predictable;PROTEIN EXPRESSION;putting parts;rational design;recent progress;successful applications;synthetic;synthetic biology;synthetic circuit design;synthetic gene circuits;TRANSLATION INITIATION;well | Karamasioti, E | AUTOMATED DESIGN;BAYESIAN DESIGN;BIOCHEMICAL SYSTEMS;ESCHERICHIA-COLI;GENE-EXPRESSION;MESSENGER-RNA LEVELS;NETWORKS;PROTEIN EXPRESSION;Synthetic biology;TRANSLATION INITIATION | 410 | [Karamasioti, Eleni; Lormeau, Claude; Stelling, Jorg] Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, CH-4058 Basel, Switzerland. [Karamasioti, Eleni; Lormeau, Claude; Stelling, Jorg] Swiss Fed Inst Technol, SIB Swiss Inst Bioinformat, CH-4058 Basel, Switzerland. [Karamasioti, Eleni; Lormeau, Claude] Life Sci Zurich Grad Sch, PhD Program Syst Biol, Zurich, Switzerland. | We acknowledge financial support by the National Centre of Competence in Research (NCCR) Molecular Systems Engineering funded by the Swiss National Science Foundation (SNSF). | 'plug-and-play' composition;analogies;biology;context-aware computational design methods;context-dependent;desired tasks;electronics design;emerging methods;error cycles;experimental trial;limited use;main conceptual challenges;modularity;number;overall;past decade;predictable;rational design;recent progress;successful applications;synthetic;synthetic biology;synthetic circuit design;synthetic gene circuits;well | 10.1002/(SICI)1097-0061(20000115)16:1<11::AID-YEA502>3.0.CO;2-K;10.1002/biot.201200085;10.1006/jmbi.1993.1319;10.1007/978-1-4939-1878-2_1;10.1007/s40484-017-0096-3;10.1016/j.cbpa.2012.05.003;10.1016/j.cell.2008.09.050;10.1016/j.cell.2009.06.013;10.1016/j.cell.2009.12.001;10.1016/j.cell.2012.05.044;10.1016/j.cell.2012.08.040;10.1016/j.cell.2014.02.039;10.1016/j.cell.2014.10.002;10.1016/j.celrep.2013.06.023;10.1016/j.copbio.2009.08.007;10.1016/j.jmb.2015.10.004;10.1016/j.jmb.2015.10.025;10.1016/j.mib.2016.07.009;10.1016/j.molcel.2006.04.027;10.1016/j.molcel.2014.06.007;10.1016/j.molcel.2015.05.035;10.1016/j.tibtech.2016.02.010;10.1016/j.ymben.2011.09.002;10.1016/j.ymben.2012.10.006;10.1021/acssynbio.5b00205;10.1021/acssynbio.5b00232;10.1021/acssynbio.6b00075;10.1021/acssynbio.6b00361;10.1021/sb300084h;10.1021/sb400126a;10.1021/sb500236e;10.1021/sb500263b;10.1038/35002125;10.1038/msb.2011.94;10.1038/msb4100204;10.1038/nature02491;10.1038/nature07389;10.1038/nature16509;10.1038/nature19841;10.1038/nbt.1568;10.1038/nbt.3044;10.1038/nbt.3053;10.1038/nchembio.218;10.1038/nrm2698;10.1038/nrmicro2717;10.1038/nrmicro3239;10.1049/iet-syb.2011.0015;10.1063/1.4811182;10.1073/pnas.0501094102;10.1073/pnas.0809869106;10.1073/pnas.1017972108;10.1073/pnas.1119407109;10.1073/pnas.1312414110;10.1073/pnas.1316298111;10.1073/pnas.1416533112;10.1073/pnas.1517109113;10.1073/pnas.83.9.2850;10.1073/pnas.92.6.2184;10.1093/bioinformatics/btm362;10.1093/bioinformatics/btq479;10.1093/bioinformatics/btw415;10.1093/nar/gkn354;10.1093/nar/gkr1190;10.1093/nar/gkr616;10.1093/nar/gks1473;10.1093/nar/gku616;10.1093/nar/gkv1289;10.1098/rsfs.2011.0056;10.1098/rsif.2012.0671;10.1098/rsif.2016.0380;10.1101/cshperspect.a023978;10.1109/TAC.2010.2069631;10.1111/j.1365-2958.1990.tb00679.x;10.1126/science.1097064;10.1126/science.1109090;10.1126/science.1151153;10.1126/science.1207084;10.1126/science.aac7341;10.1126/science.aaf4006;10.1126/scisignal.2002152;10.1128/JB.184.18.5058-5066.2002;10.1186/1752-0509-2-24;10.1186/1752-0509-4-71;10.1186/s12918-016-0269-0;10.1371/journal.pcbi.1000534;10.1371/journal.pcbi.1001083;10.1371/journal.pcbi.1002811;10.1371/journal.pcbi.1002965;10.1371/journal.pcbi.1003486;10.1371/journal.pcbi.1003602;10.1371/journal.pone.0007002;10.1371/journal.pone.0016904;10.1371/journal.pone.0035529;10.1371/journal.pone.0091743;10.15252/msb.20134955;10.2144/000112011;10.3182/20080706-5-KR-1001.02683];10.3389/fbioe.2015.00093;10.3389/fgene.2016.00118;10.3389/fphys.2015.00281;[10.1016/j.cels.2016.01.004, 10.1016/j.cels.2016.02.010];[10.1038/NMETH.2926, 10.1038/nmeth.2926];[10.1038/NMETH.3339, 10.1038/nmeth.3339];[10.1038/NMETH.3727, 10.1038/nmeth.3727] | Swiss Fed Inst Technol | Karamasioti, E;Lormeau, C;Stelling, J | Karamasioti, E: Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, CH-4058 Basel, Switzerland | Stelling, Joerg | null | 109 | null | Switzerland | Life Sci Zurich Grad Sch;Swiss Fed Inst Technol | Karamasioti, Eleni | null | AUTOMATED DESIGN;BAYESIAN DESIGN;BIOCHEMICAL SYSTEMS;ESCHERICHIA-COLI;GENE-EXPRESSION;MESSENGER-RNA LEVELS;NETWORKS;PROTEIN EXPRESSION;SYNTHETIC BIOLOGY;TRANSLATION INITIATION | Karamasioti, Eleni; Lormeau, Claude; Stelling, Jorg; | null | Life Sci Zurich Grad Sch, PhD Program Syst Biol, Zurich, Switzerland;Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, CH-4058 Basel, Switzerland;Swiss Fed Inst Technol, SIB Swiss Inst Bioinformat, CH-4058 Basel, Switzerland | Life Sci Zurich Grad Sch, PhD Program Syst Biol, Zurich, Switzerland;Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, CH-4058 Basel, Switzerland;Swiss Fed Inst Technol, SIB Swiss Inst Bioinformat, CH-4058 Basel, Switzerland | null | null | 4 | 1986;1990;1993;1995;2000;2002;2004;2005;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016;2017 | 14 | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, CH-4058 Basel, Switzerland;Swiss Fed Inst Technol, SIB Swiss Inst Bioinformat, CH-4058 Basel, Switzerland | Mol. Syst. Des. Eng. | Stelling, Jorg | ROYAL SOC CHEMISTRY | 'plug-and-play';,;:;also;analogies;and;applications;are;as;biology;challenges;characterized;circuit;circuits;complex;composition;computational;conceptual;constructs;context-aware;context-dependent;cycles;decade;design;desired;electronics;emerging;error;experimental;for;gene;guide;has;here;highlight;however;increasingly;is;led;less;limited;main;many;methods;might;modularity;more;number;of;over;overall;past;perform;predictable;progress;rational;recent;reduce;revealed;robustly;successful;such;summarize;synthetic;tailored;tasks;that;the;to;towards;trial;use;we;well | Swiss Fed Inst Technol | The rational design of synthetic gene circuits has led to many successful applications over the past decade. However, increasingly complex constructs also revealed that analogies to electronics design such as modularity and 'plug-and-play' composition are of limited use: biology is less well characterized, more context-dependent, and overall less predictable. Here, we summarize the main conceptual challenges of synthetic circuit design to highlight recent progress towards more tailored, context-aware computational design methods for synthetic biology. Emerging methods to guide the rational design of synthetic circuits that robustly perform desired tasks might reduce the number of experimental trial and error cycles. | F-7499-2010 | AUTOMATED DESIGN;BAYESIAN DESIGN;BIOCHEMICAL SYSTEMS;ESCHERICHIA-COLI;GENE-EXPRESSION;MESSENGER-RNA LEVELS;NETWORKS;PROTEIN EXPRESSION;SYNTHETIC BIOLOGY;TRANSLATION INITIATION | 0 | null | null | 12 | ESCHERICHIA-COLI;AUTOMATED DESIGN;BAYESIAN DESIGN;BIOCHEMICAL SYSTEMS;GENE-EXPRESSION;MESSENGER-RNA LEVELS;NETWORKS;PROTEIN EXPRESSION;Synthetic biology;TRANSLATION INITIATION | WOS:000412769000008 | Life Sci Zurich Grad Sch, Zurich, Switzerland;Swiss Fed Inst Technol, Basel, Switzerland | Switzerland | 2,017 | null | 0000-0002-8141-0532 | null | null | English | null | 53 IEEE C DEC CONTR;ACS SYNTH BIOL;BIOINFORMATICS;BIOTECHNIQUES;BIOTECHNOL J;BMC SYST BIOL;CELL;CELL REP;CELL SYST;CHAOS;CSH PERSPECT BIOL;CURR OPIN BIOTECH;CURR OPIN CHEM BIOL;CURR OPIN MICROBIOL;FRONT BIOENG BIOTECH;FRONT GENET;FRONT PHYSIOL;IEEE T AUTOMAT CONTR;IET SYST BIOL;IFAC P;IFAC P VOLUMES;INTERFACE FOCUS;J BACTERIOL;J MOL BIOL;J R SOC INTERFACE;METAB ENG;METHODS MOL BIOL;MOL CELL;MOL MICROBIOL;MOL SYST BIOL;NAT BIOTECHNOL;NAT CHEM BIOL;NAT METHODS;NAT REV MICROBIOL;NAT REV MOL CELL BIO;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PLOS COMPUT BIOL;PLOS ONE;QUANT BIOL;SCI SIGNAL;SCIENCE;TRENDS BIOTECHNOL;YEAST | Karamasioti, Eleni;Lormeau, Claude;Stelling, Jorg | 2024-03-11
ER | Algar R. J. R.;Andrews B. W.;Appleton, E;Ausländer, D;Barnes, C P;Bashor, C J;Batt, G;Beal, J;Boada, Y;Bonde, M T;Borkowski, O;Borujeni, A E;Bowsher, C G;Boël, G;Bradley, R W;Brewster, R C;Briat, C;Brophy, J A N;Brown, A J;Cameron, D E;Carbonell Pablo;Cardinale, S;Ceroni, F;Chau, A H;Cheng, J K;Chubiz, L M;Cookson, N A;Dasika, M S;Davidsohn, N;Del Vecchio, D;Doyle F. J.;Elowitz, M B;Farasat, I;Fasani, R A;Gaspar, P;Giladi, H;Green, A A;Gunde, T;Gyorgy, A;Hafner, M;Hodgman, C E;Hussain, F;Huynh, L;Iadevaia, S;Jacques, N;Jayanthi, S;Jiang, P;Kalodimos, C G;Karr, J R;Klumpp, S;Kozak, M;Lomnitz, J G;Ma, W Z;Madrid, C;Marchisio, M A;Mcginness, K E;Medema, M H;Meng, H L;Mishra, D;Na, D;Nandagopal, N;Nielsen, A A K;Otero-Muras, I;Oteromuras, I;Ottoz, D S M;Oyarzún, D A;Pedraza, J M;Potvin-Trottier, L;Purcell, O;Purnick, P E M;Qian, Y L;Quax, T E F;Raj, A;Rhodius, V A;Rodrigo, G;Roehner, N;Rothschild, D;Rössger, K;Salis, H M;Sardanyés, J;Savageau, M A;Sen S.;Seo, S W;Skogestad S.;Stricker, J;Tan, C;Venturelli, O S;Vind, J;Wagner, A;Way, J C;Weisse, A Y;Welch, M;Wu, G;Wu, K;Xie, M;You, L C;Zechner, C;Zi, Z | FJ5EH | Basel, Switzerland;Basel, Switzerland. | 15 | null | 2 | null | null | Karamasioti, Eleni;Lormeau, Claude;Stelling, Jorg | MOL SYST DES ENG | Basel, Switzerland;Zurich, Switzerland |
Iannarelli, L;Matic, S;Morra, M;Noris, E;Pegoraro, M;Pergolizzi, B;Rossi, A M | 10.1007/s12033-017-0030-y | null | 999 RIVERVIEW DRIVE SUITE 208, TOTOWA, NJ 07512 USA | 30505d4t2a5i4u72m712g646p2a5g481b524d1z | Cloning and Expression Analysis of Human Amelogenin in <i>Nicotiana benthamiana</i> Plants by Means of a Transient Expression System | Natl Res Council Italy CNR | null | Noris, E (corresponding author), Natl Res Council Italy IPSP CNR, Inst Sustainable Plant Protect, Str Cacce 73, I-10135 Turin, Italy. | null | Iannarelli, Luca;Matic, Slavica;Morra, Marco;Noris, Emanuela;Pegoraro, Mattia;Pergolizzi, Barbara;Rossi, Andrea M | Biochemistry & Molecular Biology;Biotechnology & Applied Microbiology | grant for the Lagrange Project-CRT Foundation; European Community's Seventh Framework Program (FP7) EU PLAPROVA KBBE [227056] | WOS | Noris, E | Ist Nazl Ric Metrol, Turin, Italy;Natl Res Council Italy IPSP CNR, Turin, Italy;NobilBio Ric Srl, Portacomaro AT, Italy;Univ Torino, Grugliasco TO, Italy;Univ Torino, Orbassano TO, Italy | 59 | <i>Nicotiana;a;Amelogenin;Analysis;and;benthamiana</i>;by;cloning;expression;human;in;means;of;plants;system;Transient | 1 | Matić, Slavica;Noris, Emanuela;Pergolizzi, Barbara;ROSSI, Andrea Mario | HUMANA PRESS INC | Ist Nazl Ric Metrol, INRiM, Str Cacce 91, I-10135 Turin, Italy;Natl Res Council Italy IPSP CNR, Inst Sustainable Plant Protect, Str Cacce 73, I-10135 Turin, Italy;NobilBio Ric Srl, Via Valcastellana 28, I-14037 Portacomaro, AT, Italy;Univ Torino, AGROINNOVA, Grugliasco, TO, Italy;Univ Torino, Dept Clin & Biol Sci, AOU San Luigi, I-10043 Orbassano, TO, Italy;Univ Torino, Dipartimento Sci Agr Forestali & Alimentari, Entomol, Grugliasco, TO, Italy | Article | Natl Res Council Italy CNR | TOTOWA | null | null | Ist Nazl Ric Metrol;Natl Res Council Italy IPSP CNR;NobilBio Ric Srl;Univ Torino | European Community's Seventh Framework Program (FP7) EU PLAPROVA KBBE;grant for the Lagrange Project-CRT Foundation | Noris, E (corresponding author), Natl Res Council Italy IPSP CNR, Inst Sustainable Plant Protect, Str Cacce 73, I-10135 Turin, Italy. | 434 | Iannarelli, Luca;Matic, Slavica;Morra, Marco;Noris, Emanuela;Pegoraro, Mattia;Pergolizzi, Barbara;Rossi, Andrea M | 15 | 6 | 412,943,700,006 | European Community's Seventh Framework Program (FP7) EU PLAPROVA KBBE [227056];grant for the Lagrange Project-CRT Foundation | Italy | MOLECULAR BIOTECHNOLOGY | Italy | null | null | Natl Res Council Italy IPSP CNR, Inst Sustainable Plant Protect, Str Cacce 73, I-10135 Turin, Italy | 1073-6085 | Iannarelli, L;Matic, S;Morra, M;Noris, E;Pegoraro, M;Pergolizzi, B;Rossi, A M | OCT | a.rossi@inrim.it;barbara.pergolizzi@unito.it;emanuela.noris@ipsp.cnr.it;luca.iannarelli@unito.it;mattia.pegoraro@unito.it;mmorra@nobilbio.it;slavica.matic@unito.it | <i>Nicotiana benthamiana</i> Plants;expression Analysis;Human Amelogenin;Transient Expression System | 7 | J | Biochemistry & Molecular Biology;Biotechnology & Applied Microbiology | 12;150 mu g;22.8 +/- 3.8;389.5 +/- 86.6 nm;500 mu g;90% amelogenin;<i>Nicotiana benthamiana</i> Plants;acetic acid;affinity chromatography;Amelogenin;amelogenin per gram;arranged hydroxyapatite crystals;bimodal distribution;biomineralizing activity;BIOPHARMACEUTICALS;biotechnological products;BONE;chymotrypsin digestion;CODON USAGE;covering tissue;different purity;dynamic light scattering;enamel;enamel formation process;ENAMEL MATRIX PROTEINS;end;evolution;expression;expression Analysis;EXTRACTS;first report;fresh leaf tissue;genes;guide hydroxyapatite deposit;human;Human Amelogenin;hydrodynamic diameters;identity;IN-VITRO;intrinsic solubility properties;knowledge;MALDI-TOF-MS analysis;MOLECULES;NANOPARTICLES;nanoribbons;nanotechnological applications;nanotechnology;Nicotiana benthamiana;organic matrix;peptides;PERIODONTAL REGENERATION;PHOSPHATE;Plant biotechnology;plant codons;plant-made human amelogenin;plant-made protein;plants;processes;production;products;PROTEIN;RECOMBINANT HUMAN AMELOGENIN;RECOMBINANT PROTEINS;regenerative functions;SOLUBILITY;synthetic gene;synthetic genes;teeth;total amelogenin per gram;transient expression;Transient Expression System;transient transformation;two purification procedures;vascular tissue;wound healing;yielding | Pegoraro, M | Amelogenin;BIOPHARMACEUTICALS;CODON USAGE;ENAMEL MATRIX PROTEINS;EVOLUTION;IN-VITRO;MOLECULES;nanotechnology;PERIODONTAL REGENERATION;PHOSPHATE;Plant biotechnology;PRODUCTS;RECOMBINANT HUMAN AMELOGENIN;RECOMBINANT PROTEINS;SOLUBILITY;Synthetic gene;Transient expression | 425 | [Pegoraro, Mattia; Matic, Slavica; Noris, Emanuela] Natl Res Council Italy IPSP CNR, Inst Sustainable Plant Protect, Str Cacce 73, I-10135 Turin, Italy. [Pergolizzi, Barbara] Univ Torino, Dept Clin & Biol Sci, AOU San Luigi, I-10043 Orbassano, TO, Italy. [Iannarelli, Luca; Rossi, Andrea M.] Ist Nazl Ric Metrol, INRiM, Str Cacce 91, I-10135 Turin, Italy. [Morra, Marco] NobilBio Ric Srl, Via Valcastellana 28, I-14037 Portacomaro, AT, Italy. [Pegoraro, Mattia] Univ Torino, Dipartimento Sci Agr Forestali & Alimentari, Entomol, Grugliasco, TO, Italy. [Matic, Slavica] Univ Torino, AGROINNOVA, Grugliasco, TO, Italy. | The authors acknowledge a grant for the Lagrange Project-CRT Foundation awarded to M.P. S.M and M.P. were partially funded by the European Community's Seventh Framework Program (FP7/2007-2013) EU PLAPROVA KBBE-2008; Grant No. 227056. The authors thank Manuela Vecchiati and Daniele Marian for plant maintenance and Alberto Piastra for excellent assistance during the experiments. | 12;150 mu g;22.8 +/- 3.8;389.5 +/- 86.6 nm;500 mu g;90% amelogenin;acetic acid;affinity chromatography;amelogenin;amelogenin per gram;arranged hydroxyapatite crystals;bimodal distribution;biomineralizing activity;biotechnological products;bone;chymotrypsin digestion;covering tissue;different purity;dynamic light scattering;enamel;enamel formation process;end;expression;extracts;first report;fresh leaf tissue;genes;guide hydroxyapatite deposit;human;human amelogenin;hydrodynamic diameters;identity;intrinsic solubility properties;knowledge;MALDI-TOF-MS analysis;nanoparticles;nanoribbons;nanotechnological applications;Nicotiana benthamiana;organic matrix;peptides;plant codons;plant-made human amelogenin;plant-made protein;plants;processes;production;protein;regenerative functions;synthetic genes;teeth;total amelogenin per gram;transient transformation;two purification procedures;vascular tissue;wound healing;yielding | 10.1002/biot.201600381;10.1002/bit.26183;10.1002/jbm.a.10401;10.1007/s000180300003;10.1007/s00299-003-0710-x;10.1007/s11103-013-0036-1;10.1016/0003-2697(84)90394-4;10.1016/j.jchromb.2006.09.030;10.1016/j.jsb.2010.11.027;10.1016/j.pep.2005.05.010;10.1016/j.pep.2012.02.013;10.1016/j.tibtech.2004.04.006;10.1016/S0003-9861(02)00035-8;10.1021/bi802175a;10.1021/bm300942c;10.1021/bp040011m;10.1038/nrg1770;10.1046/j.1365-313X.2003.01676.x;10.1074/jbc.274.4.2464;10.1111/j.1365-2184.2012.00834.x;10.1111/j.1467-7652.2009.00434.x;10.1111/j.1467-7652.2010.00550.x;10.1111/j.1600-051X.1997.tb00247.x;10.1111/j.1600-051X.1997.tb00248.x;10.1111/j.1600-051X.2008.01264.x;10.1111/j.1600-0722.2006.00301.x;10.1111/j.1600-0722.2006.00325.x;10.1111/j.1600-0722.2011.00907.x;10.1111/j.1600-0765.2004.00733.x;10.1111/j.1601-6343.2009.01459.x;10.1111/j.1743-6109.2006.00117.x;10.1111/pbi.12076;10.1111/pbi.12299;10.1155/2014/256135;10.1177/0022034509354455;10.1177/0022034515577963;10.1177/00220345790580022701;10.1177/00220345980770060301;10.1177/154405910608500902;10.1186/1472-6750-11-106;10.1371/journal.pone.0033269;10.2174/187220810793611464;10.3109/03008209809017039;10.3390/agriculture5040901;[10.1586/erv.10.85, 10.1586/ERV.10.85] | Natl Res Council Italy IPSP CNR | Iannarelli, L;Matic, S;Morra, M;Noris, E;Pegoraro, M;Pergolizzi, B;Rossi, A M | Pegoraro, M: Natl Res Council Italy IPSP CNR, Inst Sustainable Plant Protect, Str Cacce 73, I-10135 Turin, Italy | Matić, Slavica;Noris, Emanuela;Pegoraro, Mattia;Pergolizzi, Barbara;Rossi, Andrea | 227056 | 50 | null | Italy | Ist Nazl Ric Metrol;Natl Res Council Italy IPSP CNR;NobilBio Ric Srl;Univ Torino | Pegoraro, Mattia | null | BIOPHARMACEUTICALS;ENAMEL MATRIX PROTEINS;EVOLUTION;IN-VITRO;MOLECULES;PERIODONTAL REGENERATION;PHOSPHATE;PRODUCTS;RECOMBINANT HUMAN AMELOGENIN;SOLUBILITY | Pegoraro, Mattia; Matic, Slavica; Pergolizzi, Barbara; Iannarelli, Luca; Rossi, Andrea M.; Morra, Marco; Noris, Emanuela; | null | Ist Nazl Ric Metrol, INRiM, Str Cacce 91, I-10135 Turin, Italy;Natl Res Council Italy IPSP CNR, Inst Sustainable Plant Protect, Str Cacce 73, I-10135 Turin, Italy;NobilBio Ric Srl, Via Valcastellana 28, I-14037 Portacomaro, AT, Italy;Univ Torino, AGROINNOVA, Grugliasco, TO, Italy;Univ Torino, Dept Clin & Biol Sci, AOU San Luigi, I-10043 Orbassano, TO, Italy;Univ Torino, Dipartimento Sci Agr Forestali & Alimentari, Entomol, Grugliasco, TO, Italy | Ist Nazl Ric Metrol, INRiM, Str Cacce 91, I-10135 Turin, Italy;Natl Res Council Italy IPSP CNR, Inst Sustainable Plant Protect, Str Cacce 73, I-10135 Turin, Italy;NobilBio Ric Srl, Via Valcastellana 28, I-14037 Portacomaro, AT, Italy;Univ Torino, AGROINNOVA, Grugliasco, TO, Italy;Univ Torino, Dept Clin & Biol Sci, AOU San Luigi, I-10043 Orbassano, TO, Italy;Univ Torino, Dipartimento Sci Agr Forestali & Alimentari, Entomol, Grugliasco, TO, Italy | 1559-0305 | Amelogenin;codon usage;nanotechnology;Plant biotechnology;recombinant protein;Synthetic gene;Transient expression | 9-10 | 1979;1984;1996;1997;1998;1999;2002;2003;2004;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016;2017 | 2 | Natl Res Council Italy IPSP CNR, Inst Sustainable Plant Protect, Str Cacce 73, I-10135 Turin, Italy | Mol. Biotechnol. | Noris, Emanuela | HUMANA PRESS INC | +/-;,;12;150;22.8;3.8;389.5;500;86.6;90%;a;acetic;acid;activity;affinity;agglomerates;amelogenin;an;analysis;and;applications;approximately;arranged;at;based;benthamiana;best;bimodal;biomineralizing;biotechnological;bone;both;by;carrying;chromatography;chymotrypsin;codons;completely;composed;confirmed;constructs;containing;covering;crystals;degraded;deposit;deposited;describe;diameters;different;digestion;distribution;dynamic;enamel;end;expression;extracts;facilitate;first;followed;following;for;formation;forming;fresh;from;functions;G;generated;genes;gram;guide;has;have;healing;here;human;hydrodynamic;hydroxyapatite;identity;in;intrinsic;is;knowledge;leaf;light;made;MALDI-TOF-MS;matrix;mu;nanoparticles;nanoribbons;nanotechnological;Nicotiana;nm;of;offering;on;optimized;or;organic;our;peptides;per;plant;plant-made;plants;possibility;procedures;process;processes;production;products;properties;protein;purification;purity;regenerative;regularly;report;respectively;scattering;seem;showed;solubility;synthetic;teeth;that;the;these;this;tissue;to;total;transformation;transient;two;use;using;vascular;was;we;were;with;wound;yielded;yielding | Natl Res Council Italy IPSP CNR | Enamel is the covering tissue of teeth, made of regularly arranged hydroxyapatite crystals deposited on an organic matrix composed of 90% amelogenin that is completely degraded at the end of the enamel formation process. Amelogenin has a biomineralizing activity, forming nanoparticles or nanoribbons that guide hydroxyapatite deposit, and regenerative functions in bone and vascular tissue and in wound healing. Biotechnological products containing amelogenin seem to facilitate these processes. Here, we describe the production of human amelogenin in plants by transient transformation of Nicotiana benthamiana with constructs carrying synthetic genes with optimized human or plant codons. Both genes yielded approximately 500 mu g of total amelogenin per gram of fresh leaf tissue. Two purification procedures based on affinity chromatography or on intrinsic solubility properties of the protein were followed, yielding from 12 to 150 mu g of amelogenin per gram of fresh leaf tissue, respectively, at different purity. The identity of the plant-made human amelogenin was confirmed by MALDI-TOF-MS analysis of peptides generated following chymotrypsin digestion. Using dynamic light scattering, we showed that plant extracts made in acetic acid containing human amelogenin have a bimodal distribution of agglomerates, with hydrodynamic diameters of 22.8 +/- 3.8 and 389.5 +/- 86.6 nm. To the best of our knowledge, this is the first report of expression of human amelogenin in plants, offering the possibility to use this plant-made protein for nanotechnological applications. | ABF-7030-2021;B-9419-2015;GMW-7522-2022;JFT-0766-2023;JNR-7612-2023;L-6810-2017 | BIOPHARMACEUTICALS;ENAMEL MATRIX PROTEINS;EVOLUTION;IN-VITRO;MOLECULES;PERIODONTAL REGENERATION;PHOSPHATE;PRODUCTS;RECOMBINANT HUMAN AMELOGENIN;SOLUBILITY | 0 | null | Amelogenin;codon usage;nanotechnology;Plant biotechnology;Recombinant proteins;Synthetic gene;Transient expression | 10 | Amelogenin;BIOPHARMACEUTICALS;CODON USAGE;ENAMEL MATRIX PROTEINS;EVOLUTION;IN-VITRO;MOLECULES;nanotechnology;PERIODONTAL REGENERATION;PHOSPHATE;Plant biotechnology;PRODUCTS;RECOMBINANT HUMAN AMELOGENIN;RECOMBINANT PROTEINS;SOLUBILITY;Synthetic gene;Transient expression | WOS:000412943700006 | Ist Nazl Ric Metrol, Turin, Italy;Natl Res Council Italy IPSP CNR, Turin, Italy;NobilBio Ric Srl, Portacomaro AT, Italy;Univ Torino, Grugliasco TO, Italy;Univ Torino, Orbassano TO, Italy | Italy | 2,017 | null | 0000-0001-5638-7978;0000-0001-8656-8841;0000-0002-0885-8744;0000-0003-4686-0068 | null | null | English | null | Adv Dent Res;AGRICULTURE-BASEL;ANAL BIOCHEM;ARCH BIOCHEM BIOPHYS;BIOCHEMISTRY-US;BIOMACROMOLECULES;BIOMED RES INT;BIOTECHNOL BIOENG;BIOTECHNOL J;BIOTECHNOL PROGR;BMC BIOTECHNOL;Br J Nurs;CELL MOL LIFE SCI;CELL PROLIFERAT;CONNECT TISSUE RES;CURR MED CHEM;EUR J ORAL SCI;EXPERT REV VACCINES;IRAN J PUBLIC HEALTH;J BIOL CHEM;J Biomed Eng Inform;J BIOMED MATER RES A;J CHROMATOGR B;J CLIN PERIODONTOL;J DENT RES;J PERIODONTAL RES;J STRUCT BIOL;NAT REV GENET;ORTHOD CRANIOFAC RES;PLANT BIOTECHNOL J;PLANT CELL REP;PLANT J;PLANT MOL BIOL;PLOS ONE;PROTEIN EXPRES PURIF;Recent Pat Biotechnol;TRENDS BIOTECHNOL;WOUND REPAIR REGEN | Iannarelli, Luca;Matic, Slavica;Morra, Marco;Noris, Emanuela;Pegoraro, Mattia;Pergolizzi, Barbara;Rossi, Andrea M | 2024-03-11
ER | Ahmad Adil;Barber, M J;Bond Emma;Bonde, J S;Bosshardt, D D;Butler, S J;Chamary, J V;Cheng, L;Davies, H M;Delak, K;Deutsch, D;Eastoe, J E;Gustafsson, C;Habelitz, S;Hahn, S;Hammarstrom, L;He, X D;Hober, S;Komarova, T V;Leelavathi, S;Lyngstadaas, S P;Margolis, H C;Martinez-Avila, O;Martinez-Avila, O M;Matic, S;Melnik, S;Menkhaus, T J;Nagano, T;Petta, V;Peyret, H;Powell, J D;Ravindranath, R M H;Ruan Qichao;Sainsbury, F;Tan, J;Taylor, A L;Thuenemann, E C;Tusé, D;Uskokovic, V;Veis, A;Voinnet, O;Vowden, P;Webster, G R;Wen, H B;Wu, F S;Yadegari, Z | FJ7MP | Turin, Italy | 2 | null | 4 | null | 28,801,830 | Iannarelli, Luca;Matic, Slavica;Morra, Marco;Noris, Emanuela;Pegoraro, Mattia;Pergolizzi, Barbara;Rossi, Andrea M | MOL BIOTECHNOL | Grugliasco TO, Italy;Orbassano TO, Italy;Portacomaro AT, Italy;Turin, Italy |
Ayra-Plasencia, J;Brown, G W;Lisby, M;Machín, F;Matos-Perdomo, E;Ramos-Pérez, C | 10.1534/g3.117.300104 | null | 9650 ROCKVILLE AVE, BETHESDA, MD 20814 USA | 6r23on1w2746v444053q4l2e2t1sp6w411j | Genome-Scale Genetic Interactions and Cell Imaging Confirm Cytokinesis as Deleterious to Transient Topoisomerase II Deficiency in <i>Saccharomyces cerevisiae</i> | Hosp Univ Nuestra Senora Candelaria | null | Machín, F (corresponding author), Hosp Univ Nuestra Senora Candelaria, Unidad Invest, Ctra Rosario 145, Santa Cruz De Tenerife 38010, Spain. | null | Ayra-Plasencia, Jessel;Brown, Grant W;Lisby, Michael;Machin, Felix;Matos-Perdomo, Emiliano;Ramos-Perez, Cristina | Genetics & Heredity | Spanish "Instituto de Salud Carlos III"; Spanish Ministry of Economy and Competitiveness; Agencia Canaria de Investigacion and Innovacion y Sociedad de la Informacion [TESIS20120109]; European Commission's European Regional Development Fund; Danish Agency for Science, Technology and Innovation; Villum Foundation; Canadian Cancer Society Research Institute [702310]; Canadian Institutes of Health Research [MOP-79368]; [PI12/00280]; [BFU2015-63902-R]; Villum Fonden [00011407] Funding Source: researchfish | WOS | Machín, F | Hosp Univ Nuestra Senora Candelaria, Santa Cruz De Tenerife, Spain;Univ Copenhagen, Copenhagen, Denmark;Univ La Laguna, Santa Cruz De T, Spain;Univ Toronto, ON M5S3E1, Canada | 7 | <i>Saccharomyces;and;as;cell;cerevisiae</i>;Confirm;Cytokinesis;Deficiency;Deleterious;genetic;genome-Scale;II;Imaging;in;interactions;to;Topoisomerase;Transient | 3 | Ayra Plasencia, Jessel;Brown, Grant;Lisby, Michael;Machín, Félix;Perdomo, Emiliano Matos | GENETICS SOCIETY AMERICA | Hosp Univ Nuestra Senora Candelaria, Unidad Invest, Ctra Rosario 145, Santa Cruz De Tenerife 38010, Spain;Univ Copenhagen, Dept Biol, DK-2200 Copenhagen, Denmark;Univ La Laguna, San Cristobal De Laguna 38200, Santa Cruz De T, Spain;Univ Toronto, Dept Biochem, Toronto, ON M5S3E1, Canada;Univ Toronto, Donnelly Ctr, Toronto, ON M5S3E1, Canada | Article | Hosp Univ Nuestra Senora Candelaria | BETHESDA | null | null | Hosp Univ Nuestra Senora Candelaria;Univ Copenhagen;Univ La Laguna;Univ Toronto | Agencia Canaria de Investigacion and Innovacion y Sociedad de la Informacion;Canadian Cancer Society Research Institute;Canadian Institutes of Health Research;Danish Agency for Science, Technology and Innovation;European Commission's European Regional Development Fund;Spanish "Instituto de Salud Carlos III";Spanish Ministry of Economy and Competitiveness;Villum Fonden;Villum Foundation | Machín, F (corresponding author), Hosp Univ Nuestra Senora Candelaria, Unidad Invest, Ctra Rosario 145, Santa Cruz De Tenerife 38010, Spain. | 3391 | Ayra-Plasencia, Jessel;Brown, Grant W;Lisby, Michael;Machin, Felix;Matos-Perdomo, Emiliano;Ramos-Perez, Cristina | 2 | 5 | 412,549,600,014 | [BFU2015-63902-R];[PI12/00280];Agencia Canaria de Investigacion and Innovacion y Sociedad de la Informacion [TESIS20120109];Canadian Cancer Society Research Institute [702310];Canadian Institutes of Health Research [MOP-79368];Danish Agency for Science, Technology and Innovation;European Commission's European Regional Development Fund;Spanish "Instituto de Salud Carlos III";Spanish Ministry of Economy and Competitiveness;Villum Fonden [00011407] Funding Source: researchfish;Villum Foundation | Canada;Denmark;Spain | G3-GENES GENOMES GENETICS | Spain | null | null | Hosp Univ Nuestra Senora Candelaria, Unidad Invest, Ctra Rosario 145, Santa Cruz De Tenerife 38010, Spain | 2160-1836 | Ayra-Plasencia, J;Brown, G W;Lisby, M;Machín, F;Matos-Perdomo, E;Ramos-Pérez, C | OCT | fmachin@funcanis.es | <i>Saccharomyces cerevisiae</i>;Cell Imaging;Cytokinesis;genome-Scale Genetic Interactions;Transient Topoisomerase II Deficiency | 6 | J | Genetics & Heredity | <i>Saccharomyces cerevisiae</i>;accelerated progression;acquiring hypomorphic mutations;acute;alleles;ANAPHASE;anaphase bridges;basis;broadly-used poison-sensitive top2-4;BUDDING YEAST;case;Cdc14;CDC14 PHOSPHATASE;cell biology experiments;cell cycle;Cell Imaging;chromatin;CHROMOSOME SEGREGATION;chromosomes;chronic sublethal Top2 downregulation;completion;conditions;critical MEN driver Cdc15;cytokinesis;destabilization;difference;DNA-REPLICATION;drugs;earlier steps;essential protein;execution;first-line anticancer drugs;genes encoding Top2;genetic protection;genome-Scale Genetic Interactions;genome-scale synthetic genetic array (SGA) analyses;hypersensitize cancer cells;hypomorphic mutations;massive entanglement;MEN;mitosis;mitotic catastrophe results;mitotic exit network;mitotic exit network (MEN);mutant;mutants;NOCUT CHECKPOINT;NUCLEAR DIVISION;nuclear segregation;permissive conditions;plasma membrane abscission;poison-resistant top2-5;resistance;resolves DNA catenations;slowing down mitotic progression;so-called Top2 poisons;suppressed top2-5 lethality;synthetic genetic array analysis;target;therapeutic strategy;time;Top2;Top2 deficiency;Top2 inactivation;Top2 poisons;top2 thermosensitive alleles;top2-4 and top2-5;top2-5;top2-5 cdc14-1;topoisomerase II;topoisomerase II (Top2);transient;transient inactivation;Transient Topoisomerase II Deficiency;tumors;two coisogenic Saccharomyces cerevisiae strains;ultrafine anaphase bridges | Ramos-Pérez, C | anaphase bridges;BUDDING YEAST;Cdc14;CDC14 PHOSPHATASE;CHROMOSOME SEGREGATION;COMPLETION;cytokinesis;DNA-REPLICATION;MITOSIS;mitotic exit network;MUTANTS;NOCUT CHECKPOINT;NUCLEAR DIVISION;plasma membrane abscission;synthetic genetic array analysis;top2-4 and top2-5;topoisomerase II | 3379 | [Ramos-Perez, Cristina; Ayra-Plasencia, Jessel; Matos-Perdomo, Emiliano; Machin, Felix] Hosp Univ Nuestra Senora Candelaria, Unidad Invest, Ctra Rosario 145, Santa Cruz De Tenerife 38010, Spain. [Ramos-Perez, Cristina; Ayra-Plasencia, Jessel; Matos-Perdomo, Emiliano] Univ La Laguna, San Cristobal De Laguna 38200, Santa Cruz De T, Spain. [Lisby, Michael] Univ Copenhagen, Dept Biol, DK-2200 Copenhagen, Denmark. [Ramos-Perez, Cristina; Brown, Grant W.] Univ Toronto, Dept Biochem, Toronto, ON M5S3E1, Canada. [Ramos-Perez, Cristina; Brown, Grant W.; Machin, Felix] Univ Toronto, Donnelly Ctr, Toronto, ON M5S3E1, Canada. | We thank other members of the labs for fruitful discussions and technical help. We also thank Manuel Mendoza for sending the plasmid to express the PM marker 2.PH-GFP. This work was supported by research grants PI12/00280 and BFU2015-63902-R to F.M. These grants were funded by the Spanish "Instituto de Salud Carlos III" and the Spanish Ministry of Economy and Competitiveness, respectively. Agencia Canaria de Investigacion and Innovacion y Sociedad de la Informacion supported C.R.-P. through a predoctoral fellowship (TESIS20120109). All these programs were cofinanced with the European Commission's European Regional Development Fund. The Danish Agency for Science, Technology and Innovation and the Villum Foundation supported the work performed by M.L. Funding to G.W.B. was provided by the Canadian Cancer Society Research Institute (Impact grant 702310) and the Canadian Institutes of Health Research (grant MOP-79368). The authors declare no conflicts of interest. | accelerated progression;acquiring hypomorphic mutations;acute;alleles;anaphase;basis;broadly-used poison-sensitive top2-4;case;cell biology experiments;cell cycle;chromatin;chromosomes;chronic sublethal Top2 downregulation;conditions;critical MEN driver Cdc15;cytokinesis;destabilization;difference;drugs;earlier steps;essential protein;execution;first-line anticancer drugs;genes encoding Top2;genetic protection;genome-scale synthetic genetic array (SGA) analyses;hypersensitize cancer cells;hypomorphic mutations;massive entanglement;MEN;mitosis;mitotic catastrophe results;mitotic exit network (MEN);mutant;nuclear segregation;permissive conditions;poison-resistant top2-5;resistance;resolves DNA catenations;slowing down mitotic progression;so-called Top2 poisons;suppressed top2-5 lethality;target;therapeutic strategy;time;Top2;Top2 deficiency;Top2 inactivation;Top2 poisons;top2 thermosensitive alleles;top2-5;top2-5 cdc14-1;topoisomerase II (Top2);transient;transient inactivation;tumors;two coisogenic Saccharomyces cerevisiae strains;ultrafine anaphase bridges | 10.1002/j.1460-2075.1984.tb02040.x;10.1002/j.1460-2075.1986.tb04315.x;10.1002/yea.1142;10.1007/978-1-61779-998-3_30;10.1007/s00294-015-0502-1;10.1007/s10577-017-9553-0;10.1016/0092-8674(89)90336-X;10.1016/j.cell.2006.01.045;10.1016/j.devcel.2013.10.018;10.1016/j.dnarep.2010.11.001;10.1016/j.molcel.2008.04.019;10.1016/j.molcel.2010.07.024;10.1016/S0076-6879(10)70007-0;10.1016/S0092-8674(04)00413-1;10.1016/S0092-8674(85)80028-3;10.1016/S0163-7258(03)00058-5;10.1016/S1534-5807(04)00128-5;10.1038/nature00935;10.1038/nbt.1832;10.1038/ncb1855;10.1038/ncb3343;10.1038/ncomms6652;10.1038/nmeth.1401;10.1038/nrc2607;10.1038/nrc2608;10.1038/nrc3599;10.1038/nrm.2016.111;10.1038/nrm3228;10.1038/sj.emboj.7601777;10.1046/j.1365-2443.2003.00643.x;10.1073/pnas.0900190106;10.1073/pnas.121006298;10.1073/pnas.81.9.2616;10.1074/jbc.270.27.16167;10.1083/jcb.200408087;10.1083/jcb.200511129;10.1083/jcb.201305157;10.1091/mbc.3.12.1443;10.1091/mbc.9.10.2803;10.1091/mbc.9.8.2173;10.1093/bioinformatics/bth456;10.1093/nar/gkn937;10.1093/nar/gkt400;10.1093/nar/gkt882;10.1101/gad.1367206;10.1101/gr.1239303;10.1126/science.1065810;10.1126/science.1201538;10.1128/MCB.9.1.159;10.1146/annurev.genet.38.072902.093051;10.1371/journal.pgen.1002509;10.1534/genetics.112.145516;10.4161/cc.11.2.18857;10.4161/cc.28370;10.4161/cc.4.7.1798 | Hosp Univ Nuestra Senora Candelaria | Ayra-Plasencia, J;Brown, G W;Lisby, M;Machín, F;Matos-Perdomo, E;Ramos-Pérez, C | Ramos-Pérez, C: Hosp Univ Nuestra Senora Candelaria, Unidad Invest, Ctra Rosario 145, Santa Cruz De Tenerife 38010, Spain | Lisby, Michael;Machín, Félix;Perdomo, Emiliano Matos | 00011407;702310;BFU2015-63902-R;MOP-79368;PI12/00280;TESIS20120109 | 59 | null | Spain | Hosp Univ Nuestra Senora Candelaria;Univ Copenhagen;Univ La Laguna;Univ Toronto | Ramos-Perez, Cristina | Green Submitted, gold, Green Published | ANAPHASE BRIDGES;BUDDING YEAST;CDC14 PHOSPHATASE;CHROMOSOME SEGREGATION;COMPLETION;DNA-REPLICATION;MITOSIS;MUTANTS;NOCUT CHECKPOINT;NUCLEAR DIVISION | Ramos-Perez, Cristina; Ayra-Plasencia, Jessel; Matos-Perdomo, Emiliano; Lisby, Michael; Brown, Grant W.; Machin, Felix; | null | Hosp Univ Nuestra Senora Candelaria, Unidad Invest, Ctra Rosario 145, Santa Cruz De Tenerife 38010, Spain;Univ Copenhagen, Dept Biol, DK-2200 Copenhagen, Denmark;Univ La Laguna, San Cristobal De Laguna 38200, Santa Cruz De T, Spain;Univ Toronto, Dept Biochem, Toronto, ON M5S3E1, Canada;Univ Toronto, Donnelly Ctr, Toronto, ON M5S3E1, Canada | Hosp Univ Nuestra Senora Candelaria, Unidad Invest, Ctra Rosario 145, Santa Cruz De Tenerife 38010, Spain;Univ Copenhagen, Dept Biol, DK-2200 Copenhagen, Denmark;Univ La Laguna, San Cristobal De Laguna 38200, Santa Cruz De T, Spain;Univ Toronto, Dept Biochem, Toronto, ON M5S3E1, Canada;Univ Toronto, Donnelly Ctr, Toronto, ON M5S3E1, Canada | null | anaphase bridges;Cdc14;cytokinesis;mitotic exit network;plasma membrane abscission;synthetic genetic array analysis;top2-4 and top2-5;topoisomerase II | 10 | 1984;1985;1986;1989;1991;1992;1993;1994;1995;1998;2000;2001;2002;2003;2004;2005;2006;2007;2008;2009;2010;2011;2012;2013;2014;2016;2017 | 5 | Hosp Univ Nuestra Senora Candelaria, Unidad Invest, Ctra Rosario 145, Santa Cruz De Tenerife 38010, Spain | G3-Genes Genomes Genet. | Machin, Felix | GENETICS SOCIETY AMERICA | (MEN);(SGA);(Top2);,;:;;;a;accelerated;acquiring;acute;against;all;alleles;also;an;analyses;anaphase;and;anticancer;array;at;basis;be;become;biology;both;bridges;broadly-used;by;cancer;carrying;case;catastrophe;catenations;cdc14-1;Cdc15;cell;cells;cerevisiae;chromatin;chromosomes;chronic;coisogenic;compared;conditions;correlated;critical;cycle;cytokinesis;deficiency;destabilization;differ;difference;discuss;disrupted;DNA;down;downregulation;driver;drugs;earlier;encoding;entanglement;especially;essential;execution;exit;experiments;find;first-line;for;from;furthermore;genes;genetic;genome-scale;have;here;hypersensitize;hypomorphic;i.e.;II;in;inactivated;inactivation;interestingly;is;lethality;many;massive;may;MEN;mitosis;mitotic;mutant;mutations;network;not;nuclear;observed;of;often;partly;performed;permissive;poison-resistant;poison-sensitive;poisons;progression;protection;protects;protein;resistance;resistant;resolves;results;Saccharomyces;segregation;slowing;so-called;steps;strains;strategy;stronger;sublethal;suggest;suppressed;synthetic;target;that;the;their;therapeutic;thermosensitive;these;this;through;time;to;Top2;top2-4;top2-5;topoisomerase;transient;tumors;two;ultrafine;under;was;we;were;when;whereas;whereby;with;within;yet | Hosp Univ Nuestra Senora Candelaria | Topoisomerase II (Top2) is an essential protein that resolves DNA catenations. When Top2 is inactivated, mitotic catastrophe results from massive entanglement of chromosomes. Top2 is also the target of many first-line anticancer drugs, the so-called Top2 poisons. Often, tumors become resistant to these drugs by acquiring hypomorphic mutations in the genes encoding Top2. Here, we have compared the cell cycle and nuclear segregation of two coisogenic Saccharomyces cerevisiae strains carrying top2 thermosensitive alleles that differ in their resistance to Top2 poisons: the broadly-used poison-sensitive top2-4 and the poison-resistant top2-5. Furthermore, we have performed genome-scale synthetic genetic array (SGA) analyses for both alleles under permissive conditions, chronic sublethal Top2 downregulation, and acute, yet transient, Top2 inactivation. We find that slowing down mitotic progression, especially at the time of execution of the mitotic exit network (MEN), protects against Top2 deficiency. In all conditions, genetic protection was stronger in top2-5; this correlated with cell biology experiments in this mutant, whereby we observed destabilization of both chromatin and ultrafine anaphase bridges by execution of MEN and cytokinesis. Interestingly, whereas transient inactivation of the critical MEN driver Cdc15 partly suppressed top2-5 lethality, this was not the case when earlier steps within anaphase were disrupted; i.e., top2-5 cdc14-1. We discuss the basis of this difference and suggest that accelerated progression through mitosis may be a therapeutic strategy to hypersensitize cancer cells carrying hypomorphic mutations in TOP2. | AAB-6796-2020;K-6569-2017;K-9814-2014 | ANAPHASE BRIDGES;BUDDING YEAST;CDC14 PHOSPHATASE;CHROMOSOME SEGREGATION;COMPLETION;DNA-REPLICATION;MITOSIS;MUTANTS;NOCUT CHECKPOINT;NUCLEAR DIVISION | 0 | null | anaphase bridges;Cdc14;cytokinesis;mitotic exit network;plasma membrane abscission;synthetic genetic array analysis;top2-4 and top2-5;topoisomerase II | 13 | anaphase bridges;BUDDING YEAST;Cdc14;CDC14 PHOSPHATASE;CHROMOSOME SEGREGATION;COMPLETION;cytokinesis;DNA-REPLICATION;MITOSIS;mitotic exit network;MUTANTS;NOCUT CHECKPOINT;NUCLEAR DIVISION;plasma membrane abscission;synthetic genetic array analysis;top2-4 and top2-5;topoisomerase II | WOS:000412549600014 | Hosp Univ Nuestra Senora Candelaria, Santa Cruz De Tenerife, Spain;Univ Copenhagen, Copenhagen, Denmark;Univ La Laguna, Santa Cruz De T, Spain;Univ Toronto, ON M5S3E1, Canada | Canada;Denmark;Spain | 2,017 | null | 0000-0001-9783-3591;0000-0002-4830-5247;0000-0002-9002-5003;0000-0003-1052-4214;0000-0003-4559-7798 | null | null | English | null | ANNU REV GENET;BIOINFORMATICS;CANCER RES;CELL;CELL CYCLE;CHROMOSOME RES;CURR GENET;DEV CELL;DNA REPAIR;EMBO J;GENE DEV;GENES CELLS;GENETICS;GENOME RES;J BIOL CHEM;J CELL BIOL;METHOD ENZYMOL;METHODS MOL BIOL;MOL BIOL CELL;MOL CELL;MOL CELL BIOL;NAT BIOTECHNOL;NAT CELL BIOL;NAT COMMUN;NAT METHODS;NAT REV CANCER;NAT REV MOL CELL BIO;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;P NATL ACAD SCI-BIOL;PHARMACOL REV;PHARMACOL THERAPEUT;PLOS GENET;SCIENCE;YEAST | Ayra-Plasencia, Jessel;Brown, Grant W;Lisby, Michael;Machin, Felix;Matos-Perdomo, Emiliano;Ramos-Perez, Cristina | 2024-03-11
ER | Akimitsu, N;Amaral, N;Andrews, C A;Baryshnikova, A;Baxter, J;Bembenek, J;Boyle, E I;Chan, K L;Charbin, A;Cuyien, S;D'Amours, D;Deweese, J E;Dinardo, S;Dulev, S;Fachinetti, D;García-Luis, J;Germann, S M;Giaever, G;Gorbsky, G J;Holm, C;Holohan, C;Janke, C;Jannatipour, M;Jaspersen, S L;Kalitsis, P;Kim, R A;Larsen, A K;Li, Z J;Lisby, M;Machín, F;Mcgrew, J T;Meitinger, F;Mendoza, M;Nishimura, K;Nitiss, J L;Norden, C;Perego, P;Pommier, Y;Quevedo, O;Ross, K E;Shannon, P;Shapiro, A B;Silva Sonia;Stegmeier, F;Thomas, W;Tong, A H Y;Uemura, T;Vos, S M;Wagih, O;Weiss, E L;Wheatley, S P | FJ2IQ | Santa Cruz De Tenerife, Spain | 5 | null | 4 | null | 28,839,115 | Ayra-Plasencia, Jessel;Brown, Grant W;Lisby, Michael;Machin, Felix;Matos-Perdomo, Emiliano;Ramos-Perez, Cristina | G3-GENES GENOM GENET | Copenhagen, Denmark;ON M5S3E1, Canada;Santa Cruz De T, Spain;Santa Cruz De Tenerife, Spain |
Fussenegger, M;Teixeira, A P | 10.1016/j.copbio.2017.06.004 | null | THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, OXON, ENGLAND | 6s1r3q3u5x2660245h2y2v6v6x4242295q4f3v4t | Synthetic biology-inspired therapies for metabolic diseases | Swiss Fed Inst Technol | null | Fussenegger, M (corresponding author), Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Mattenstr 26, CH-4058 Basel, Switzerland.;Fussenegger, M (corresponding author), Univ Basel, Fac Sci, Mattenstr 26, CH-4058 Basel, Switzerland. | null | Fussenegger, Martin;Teixeira, Ana Palma | Biochemical Research Methods;Biotechnology & Applied Microbiology | European Research Council (ERC) advanced grant (ProNet) [321381]; National Centre of Competence in Research (NCCR) for Molecular Systems Engineering | WOS | Fussenegger, M | IBET, Oeiras, Portugal;ITQB NOVA, Oeiras, Portugal;Swiss Fed Inst Technol, Basel, Switzerland;Univ Basel, Basel, Switzerland | 47 | biology-inspired;Diseases;for;Metabolic;synthetic;therapies | 2 | Palma Teixeira, Ana | ELSEVIER SCI LTD | IBET, Ave Republ, P-2781157 Oeiras, Portugal;ITQB NOVA, Inst Tecnol Quim & Biol Antonio Xavier, Ave Republ, P-2780157 Oeiras, Portugal;Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Mattenstr 26, CH-4058 Basel, Switzerland;Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Mattenstr 26, CH-4058 Basel, Switzerland.; Fussenegger, M (corresponding author), Univ Basel, Fac Sci, Mattenstr 26, CH-4058 Basel, Switzerland;Univ Basel, Fac Sci, Mattenstr 26, CH-4058 Basel, Switzerland | Review | Swiss Fed Inst Technol;Univ Basel | OXFORD | null | null | IBET;ITQB NOVA;Swiss Fed Inst Technol;Univ Basel | European Research Council (ERC) advanced grant (ProNet);National Centre of Competence in Research (NCCR) for Molecular Systems Engineering | Fussenegger, M (corresponding author), Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Mattenstr 26, CH-4058 Basel, Switzerland.; Fussenegger, M (corresponding author), Univ Basel, Fac Sci, Mattenstr 26, CH-4058 Basel, Switzerland. | 66 | Fussenegger, Martin;Teixeira, Ana Palma | 29 | 4 | 413,381,100,010 | European Research Council (ERC) advanced grant (ProNet) [321381];National Centre of Competence in Research (NCCR) for Molecular Systems Engineering | Portugal;Switzerland | CURRENT OPINION IN BIOTECHNOLOGY | Switzerland | null | null | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Mattenstr 26, CH-4058 Basel, Switzerland | 0958-1669 | Fussenegger, M;Teixeira, A P | OCT | fussenegger@bsse.ethz.ch | Metabolic Diseases;synthetic biology-inspired therapies | 2 | J | Biochemistry & Molecular Biology;Biotechnology & Applied Microbiology | ability;addressable;adjusted dose;animal models;autonomous therapeutic programs;basis;clinical application;conventional therapies;devices;diseased states;dysfunctions;effective therapeutic behaviors;expression;future developments;GLUCOSE-HOMEOSTASIS;HEPATOCYTE GROWTH-FACTOR;host metabolism;interface;mammalian cells;MAMMALIAN-CELLS;Metabolic Diseases;Mice;native signaling pathways;network topologies;new hope;possibilities;potential;range;repurposing;synthetic biology-inspired therapies;synthetic gene networks;tackle metabolic disorders;therapeutic molecule;TRANSGENE-CONTROL | Teixeira, A P | EXPRESSION;GLUCOSE-HOMEOSTASIS;HEPATOCYTE GROWTH-FACTOR;MAMMALIAN-CELLS;MICE;TRANSGENE-CONTROL | 59 | [Teixeira, Ana Palma; Fussenegger, Martin] Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Mattenstr 26, CH-4058 Basel, Switzerland. [Teixeira, Ana Palma] ITQB NOVA, Inst Tecnol Quim & Biol Antonio Xavier, Ave Republ, P-2780157 Oeiras, Portugal. [Teixeira, Ana Palma] IBET, Ave Republ, P-2781157 Oeiras, Portugal. [Fussenegger, Martin] Univ Basel, Fac Sci, Mattenstr 26, CH-4058 Basel, Switzerland. | Work in the laboratory of MF was financially supported in part through a European Research Council (ERC) advanced grant (ProNet, no. 321381) and in part by the National Centre of Competence in Research (NCCR) for Molecular Systems Engineering. | ability;addressable;adjusted dose;animal models;autonomous therapeutic programs;basis;clinical application;conventional therapies;devices;diseased states;dysfunctions;effective therapeutic behaviors;future developments;host metabolism;interface;mammalian cells;metabolic diseases;native signaling pathways;network topologies;new hope;possibilities;potential;range;repurposing;synthetic gene networks;tackle metabolic disorders;therapeutic molecule | 10.1002/wsbm.1345;10.1016/j.cell.2013.02.022;10.1016/j.cell.2016.01.011;10.1016/j.copbio.2015.01.010;10.1016/j.jhep.2010.12.004;10.1016/j.jhep.2016.03.020;10.1016/j.molcel.2014.06.007;10.1016/j.pharmthera.2013.12.014;10.1016/j.ymben.2008.12.001;10.1016/S0140-6736(94)90067-1;10.1038/gt.2010.51;10.1038/nbt.1617;10.1038/nbt.1775;10.1038/nbt.2351;10.1038/nbt731;10.1038/ncomms11247;10.1038/ncomms3825;10.1038/nm.3730;10.1038/nm0103-104;10.1038/nrc3179;10.1038/nrd2005;10.1038/nrg3563;10.1038/nrm2904;10.1038/s41551-016-0005;10.1073/pnas.040552697;10.1073/pnas.0901501106;10.1073/pnas.1216801110;10.1073/pnas.1312414110;10.1073/pnas.89.12.5547;10.1093/nar/gkm652;10.1093/nar/gku545;10.1098/rstb.2005.1762;10.1111/j.1399-3089.2007.00384.x;10.1111/j.1440-1746.2010.06549.x;10.1126/science.1203535;10.1126/science.1216753;10.1126/science.aaf4006;10.1126/scitranslmed.aac4964;10.1136/jcp.28.6.506;10.1146/annurev-pharmtox-011613-135921;10.1161/ATVBAHA.107.151092;10.2337/db12-0935;[10.1038/NCHEMBIO.2281, 10.1038/nchembio.2281] | Swiss Fed Inst Technol | Fussenegger, M;Teixeira, A P | Teixeira, A P: Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Mattenstr 26, CH-4058 Basel, Switzerland | Palma Teixeira, Ana;Teixeira, Ana P | 321381 | 43 | null | Switzerland | IBET;ITQB NOVA;Swiss Fed Inst Technol;Univ Basel | Teixeira, Ana Palma | null | EXPRESSION;GLUCOSE-HOMEOSTASIS;HEPATOCYTE GROWTH-FACTOR;MAMMALIAN-CELLS;MICE;TRANSGENE-CONTROL | Teixeira, Ana Palma; Fussenegger, Martin; | null | IBET, Ave Republ, P-2781157 Oeiras, Portugal;ITQB NOVA, Inst Tecnol Quim & Biol Antonio Xavier, Ave Republ, P-2780157 Oeiras, Portugal;Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Mattenstr 26, CH-4058 Basel, Switzerland;Univ Basel, Fac Sci, Mattenstr 26, CH-4058 Basel, Switzerland | IBET, Ave Republ, P-2781157 Oeiras, Portugal;ITQB NOVA, Inst Tecnol Quim & Biol Antonio Xavier, Ave Republ, P-2780157 Oeiras, Portugal;Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Mattenstr 26, CH-4058 Basel, Switzerland;Univ Basel, Fac Sci, Mattenstr 26, CH-4058 Basel, Switzerland | 1879-0429 | null | null | 1975;1992;1994;2000;2002;2003;2005;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016;2017 | 20 | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Mattenstr 26, CH-4058 Basel, Switzerland;Univ Basel, Fac Sci, Mattenstr 26, CH-4058 Basel, Switzerland | Curr. Opin. Biotechnol. | Fussenegger, Martin | ELSEVIER SCI LTD | ,;a;ability;addressable;adjusted;an;and;animal;application;are;autonomous;basis;be;been;behaviors;between;bringing;brought;by;cells;clinical;closer;conventional;customized;developments;devices;discriminate;discuss;diseased;diseases;disorders;dose;dysfunctions;effective;effectively;engineer;expanded;for;formed;future;gene;genetically;greatly;has;have;healthy;here;hope;host;important;in;installed;interface;mammalian;metabolic;metabolism;models;molecule;native;network;networks;new;not;of;our;outline;pathways;possibilities;potential;producing;programs;range;recently;repurposing;respond;signaling;simply;states;successfully;such;synthetic;tackle;technology;that;the;therapeutic;therapies;this;to;topologies;treat;treating;using;validated;we;will;with | Swiss Fed Inst Technol;Univ Basel | Our ability to engineer mammalian cells with effective therapeutic behaviors has brought new hope for treating metabolic diseases. Synthetic gene networks have been customized to interface with the host metabolism, discriminate between healthy and diseased states, and respond by producing an adjusted dose of the therapeutic molecule. Such devices have the potential to treat a range of dysfunctions that are simply not addressable using conventional therapies. Recently, the repurposing of native signaling pathways has formed the basis of autonomous therapeutic programs genetically installed in mammalian cells and has greatly expanded the possibilities to effectively tackle metabolic disorders. Here, we outline network topologies that have been successfully validated in animal models of metabolic diseases and discuss future developments that will be important for bringing this technology closer to clinical application. | F-5594-2011;JND-7641-2023 | EXPRESSION;GLUCOSE-HOMEOSTASIS;HEPATOCYTE GROWTH-FACTOR;MAMMALIAN-CELLS;MICE;TRANSGENE CONTROL | 1 | null | null | 8 | EXPRESSION;GLUCOSE-HOMEOSTASIS;HEPATOCYTE GROWTH-FACTOR;MAMMALIAN-CELLS;MICE;TRANSGENE CONTROL | WOS:000413381100010 | IBET, Oeiras, Portugal;ITQB NOVA, Oeiras, Portugal;Swiss Fed Inst Technol, Basel, Switzerland;Univ Basel, Basel, Switzerland | Portugal;Switzerland | 2,017 | null | 0000-0002-9208-8737 | null | null | English | null | ANNU REV PHARMACOL;ARTERIOSCL THROM VAS;CELL;CURR OPIN BIOTECH;DIABETES;GENE THER;J CLIN PATHOL;J GASTROEN HEPATOL;J HEPATOL;LANCET;METAB ENG;MOL CELL;NAT BIOMED ENG;NAT BIOTECHNOL;NAT CHEM BIOL;NAT COMMUN;NAT MED;NAT REV CANCER;NAT REV DRUG DISCOV;NAT REV GENET;NAT REV MOL CELL BIO;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PHARMACOL THERAPEUT;PHILOS T R SOC B;SCI TRANSL MED;SCIENCE;WIRES SYST BIOL MED;XENOTRANSPLANTATION | Fussenegger, Martin;Teixeira, Ana Palma | 2024-03-11
ER | Ausländer, D;Bacchus, W;Bai, P;Barnes, S;Beerli, R R;Elliott, R B;Gao, H;Gitzinger, M;Gossen, M;Grundy, S M;Hartenbach, S;Heng, B C;Kemmer, C;Lim, W A;Macdonald, P E;Maroun, C R;Müller, M;Nakamura, T;Orive, G;Pols, T W H;Qi, L S;Roybal, K T;Rössger, K;Sadelain, M;Saxena, P;Schukur, L;Shigematsu, H;Soonshiong, P;Stanley, S A;Tabar, V;Weber, W;Xie, M;Xie, M Q;Ye, H F;Zhang, F | FK3JJ | Basel, Switzerland;Basel, Switzerland. | 24 | null | 4 | null | 28,662,442 | Fussenegger, Martin;Teixeira, Ana Palma | CURR OPIN BIOTECH | Basel, Switzerland;Oeiras, Portugal |
Cai, Y J;Deng, H X;Gao, R J;Liao, X R | 10.1016/j.gene.2017.06.019 | null | RADARWEG 29, 1043 NX AMSTERDAM, NETHERLANDS | 2b6x73v31245i203d424l2c684a4n6e554x2wz | CRISPR system in filamentous fungi: Current achievements and future directions | JiangNan Univ | null | Liao, XR; Cai, YJ (corresponding author), Jiangnan Univ, Sch Biotechnol, Minist Educ, Key Lab Ind Biotechnol, 1800 Lihu Rd, Wuxi 214122, Jiangsu, Peoples R China. | null | Cai, Yujie;Deng, Huaxiang;Gao, Ruijie;Liao, Xiangru | Genetics & Heredity | National Science Foundation of China [21275066]; Six-talent peak program [SWYY-126]; Fundamental Research of Doctor of Philosophy [2050205, 205020502] | WOS | Cai, Y J;Liao, X R | JiangNan Univ, Jiangsu, Peoples R China | 627 | :;achievements;and;CRISPR;Current;directions;filamentous;fungi;future;in;system | 1 | null | ELSEVIER | Jiangnan Univ, Sch Biotechnol, Minist Educ, Key Lab Ind Biotechnol, 1800 Lihu Rd, Wuxi 214122, Jiangsu, Peoples R China;YJ (corresponding author), Jiangnan Univ, Sch Biotechnol, Minist Educ, Key Lab Ind Biotechnol, 1800 Lihu Rd, Wuxi 214122, Jiangsu, Peoples R China | Review | JiangNan Univ | AMSTERDAM | null | null | JiangNan Univ | Fundamental Research of Doctor of Philosophy;National Science Foundation of China;Six-talent peak program | Liao, XR; Cai, YJ (corresponding author), Jiangnan Univ, Sch Biotechnol, Minist Educ, Key Lab Ind Biotechnol, 1800 Lihu Rd, Wuxi 214122, Jiangsu, Peoples R China. | 221 | Cai, Yujie;Deng, Huaxiang;Gao, Ruijie;Liao, Xiangru | 137 | 1 | 407,658,000,028 | Fundamental Research of Doctor of Philosophy [2050205, 205020502];National Science Foundation of China [21275066];Six-talent peak program [SWYY-126] | China | GENE | China | null | null | Jiangnan Univ, Sch Biotechnol, Minist Educ, Key Lab Ind Biotechnol, 1800 Lihu Rd, Wuxi 214122, Jiangsu, Peoples R China | 0378-1119 | Cai, Y J;Deng, H X;Gao, R J;Liao, X R | SEP 5 | xrliao@jiangnan.edu.cn;yjcai@jiangnan.edu.cn | CRISPR system;Current achievements;filamentous fungi;future directions | 4 | J | Genetics & Heredity | ASPERGILLUS-NIDULANS;BACTERIA;basic research;bioenergy process;biosynthetic gene clusters;Cas9;CAS9 NUCLEASES;chromatin dynamics;complex environmental signals;confirmation;continuous metabolite biosynthesis;CRISPR complex;CRISPR system;CRISPR/Cas9 system;CRISPR/Cas9 systems;current;Current achievements;current knowledge;different approaches;different ways;DNA;drug discovery;EFFECTOR GENE;efficiency;eukaryotes;fast;features;filamentous fungi;filamentous fungi share;future directions;GENE;genome;genome editing;highlight several methods;HUMAN-CELLS;humans;interspaced short palindromic repeats (CRISPR)/Cas9 system;mammals;metabolite flux;nuclease specificity;numerous active metabolites;OFF-TARGET CLEAVAGE;off-target mutations;pathogenesis decoding;PATHWAY;plants;POLYKETIDE SYNTHASES;positive clones;potential applications;response;review;selective markers;simple;specificity;Synthetic gene circuit;systemic research;toxic;traditional genetic approaches;transcriptional regulation;VARIANTS;versatile technology | Deng, H X | ASPERGILLUS-NIDULANS;BIOSYNTHETIC GENE CLUSTERS;CAS9 NUCLEASES;CRISPR/Cas9 system;DNA;DRUG DISCOVERY;EFFECTOR GENE;FILAMENTOUS FUNGI;GENOME;genome editing;HUMAN-CELLS;OFF-TARGET CLEAVAGE;POLYKETIDE SYNTHASES;SPECIFICITY;Synthetic gene circuit;Transcriptional regulation | 212 | [Deng, Huaxiang; Gao, Ruijie; Liao, Xiangru; Cai, Yujie] Jiangnan Univ, Sch Biotechnol, Minist Educ, Key Lab Ind Biotechnol, 1800 Lihu Rd, Wuxi 214122, Jiangsu, Peoples R China. | This study was financially supported by the National Science Foundation of China (Grant No. 21275066), Six-talent peak program at 2016 (Grant No. SWYY-126), the Fundamental Research of Doctor of Philosophy at 2014 (Grant No. 2050205), the Fundamental Research of Doctor of Philosophy at 2015 (Grant No. 205020502). | bacteria;basic research;bioenergy process;Cas9;chromatin dynamics;complex environmental signals;confirmation;continuous metabolite biosynthesis;CRISPR complex;CRISPR/Cas9 system;CRISPR/Cas9 systems;current;current knowledge;different approaches;different ways;drug discovery;efficiency;eukaryotes;fast;features;filamentous fungi;filamentous fungi share;gene;highlight several methods;humans;interspaced short palindromic repeats (CRISPR)/Cas9 system;mammals;metabolite flux;nuclease specificity;numerous active metabolites;off-target mutations;pathogenesis decoding;pathway;plants;positive clones;potential applications;response;review;selective markers;simple;synthetic gene circuit;systemic research;toxic;traditional genetic approaches;variants;versatile technology | 10.1002/(SICI)1099-0518(20000201)38:3<594::AID-POLA24>3.0.CO;2-#;10.1002/bit.25662;10.1007/s00253-009-2239-6;10.1007/s10529-015-2015-x;10.1016/j.biotechadv.2016.12.003;10.1016/j.cell.2013.02.022;10.1016/j.cell.2013.08.021;10.1016/j.cell.2014.09.029;10.1016/j.cell.2014.11.017;10.1016/j.cell.2014.11.052;10.1016/j.cell.2016.10.044;10.1016/j.cell.2016.11.017;10.1016/j.cell.2016.12.009;10.1016/j.celrep.2014.09.044;10.1016/j.chom.2012.09.003;10.1016/j.fgb.2015.09.001;10.1016/j.fgb.2015.12.007;10.1016/j.fgb.2017.03.001;10.1016/j.mimet.2017.01.015;10.1016/j.procbio.2017.02.012;10.1016/j.stem.2014.06.011;10.1016/j.ymben.2015.12.003;10.1021/acschembio.6b00213;10.1021/acssynbio.6b00080;10.1021/acssynbio.6b00082;10.1021/acssynbio.6b00203;10.1021/ja3016395;10.1021/ja401945a;10.1021/ja8088185;10.1038/celldisc.2015.7;10.1038/nature14136;10.1038/nature16526;10.1038/nature17042;10.1038/nbt.2623;10.1038/nbt.2647;10.1038/nbt.2808;10.1038/nbt.2842;10.1038/nbt.3101;10.1038/nbt.3117;10.1038/nbt.3127;10.1038/nbt.3155;10.1038/nbt.3245;10.1038/nbt.3481;10.1038/nbt.3609;10.1038/nbt.3737;10.1038/nbt0502-497;10.1038/nchembio.2007.7;10.1038/nmeth.2812;10.1038/nprot.2013.143;10.1038/nprot.2016.104;10.1038/nrcardio.2015.208;10.1038/nrd3267;10.1038/nrg.2016.28;10.1038/nrg2641;10.1038/nrmicro.2015.24;10.1038/nrmicro2790;10.1038/nrmicro3496;10.1038/s41598-017-00883-5;10.1038/srep45763;10.1073/pnas.1420024112;10.1084/jem.20092449;10.1093/bioinformatics/btu048;10.1093/nar/gkt135;10.1093/nar/gku402;10.1093/nar/gkv1533;10.1093/nar/gkw398;10.1093/nar/gkw407;10.1093/nar/gnj011;10.1111/1574-6976.12009;10.1111/j.1469-8137.2010.03413.x;10.1111/mpp.12318;10.1126/science.1154711;10.1126/science.1225829;10.1126/science.1231143;10.1126/science.aad5227;10.1128/EC.00107-15;10.1146/annurev.biophys.093008.131348;10.1186/s12934-016-0613-5;10.1186/s13068-016-0693-9;10.1186/s40694-015-0015-1;10.1371/journal.pone.0003647;10.1371/journal.pone.0133085;10.1371/journal.pone.0169712;10.1534/genetics.115.175166;10.3109/07388551.2015.1060189;10.3389/fmicb.2017.00225;10.5498/wjp.v6.i1.1;[10.1038/NCHEMBIO.1897, 10.1038/nchembio.1897];[10.1038/NMETH.2926, 10.1038/nmeth.2926];[10.1038/NMETH.3284, 10.1038/nmeth.3284];[10.1038/NMETH.4042, 10.1038/nmeth.4042] | JiangNan Univ | Cai, Y J;Deng, H X;Gao, R J;Liao, X R | Deng, H X: Jiangnan Univ, Sch Biotechnol, Minist Educ, Key Lab Ind Biotechnol, 1800 Lihu Rd, Wuxi 214122, Jiangsu, Peoples R China | null | 2050205;205020502;21275066;SWYY-126 | 95 | null | China | JiangNan Univ | Deng, Huaxiang | hybrid | ASPERGILLUS-NIDULANS;BIOSYNTHETIC GENE CLUSTERS;CAS9 NUCLEASES;DNA;EFFECTOR GENE;GENOME;HUMAN-CELLS;OFF-TARGET CLEAVAGE;POLYKETIDE SYNTHASES;SPECIFICITY | Deng, Huaxiang; Gao, Ruijie; Liao, Xiangru; Cai, Yujie; | null | Jiangnan Univ, Sch Biotechnol, Minist Educ, Key Lab Ind Biotechnol, 1800 Lihu Rd, Wuxi 214122, Jiangsu, Peoples R China | Jiangnan Univ, Sch Biotechnol, Minist Educ, Key Lab Ind Biotechnol, 1800 Lihu Rd, Wuxi 214122, Jiangsu, Peoples R China | 1879-0038 | CRISPR-Cas9 system;drug discovery;Filamentous fungi;genome editing;Synthetic gene circuit;Transcriptional regulation | null | 2000;2002;2006;2007;2008;2009;2010;2012;2013;2014;2015;2016;2017 | 46 | Jiangnan Univ, Sch Biotechnol, Minist Educ, Key Lab Ind Biotechnol, 1800 Lihu Rd, Wuxi 214122, Jiangsu, Peoples R China | Gene | Cai, Yujie | ELSEVIER | (CRISPR)/Cas9;,;a;active;also;and;applications;approaches;are;as;bacteria;basic;been;bioenergy;biosynthesis;but;Cas9;chromatin;circuit;clones;clustered;complex;confirmation;continuous;CRISPR;CRISPR/Cas9;current;decoding;describe;detect;different;discovery;discuss;drug;dynamics;efficiency;ensure;environmental;eukaryotes;express;fast;features;filamentous;flux;for;fungi;gene;generally;genetic;has;highlight;how;humans;improve;in;inefficient;interspaced;its;knowledge;mammals;many;Markers;metabolite;metabolites;methods;mutations;nuclease;numerous;of;off-target;offers;on;palindromic;pathogenesis;pathway;plants;positive;potential;process;produce;redirect;regularly;repeats;research;response;review;screen;selective;several;share;short;signals;simple;some;specificity;summarized;synthetic;system;systemic;systems;technology;that;the;they;this;to;toxic;traditional;transform;used;variants;various;versatile;ways;we;which;widely;with | JiangNan Univ | As eukaryotes, filamentous fungi share many features with humans, and they produce numerous active metabolites, some of which are toxic. Traditional genetic approaches are generally inefficient, but the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system that has been widely used for basic research on bacteria, mammals and plants offers a simple, fast, versatile technology for systemic research on filamentous fungi. In this review, we summarized the current knowledge on Cas9 and its variants, various selective markers used to screen positive clones, different ways used to detect off-target mutations, and different approaches used to express and transform the CRISPR complex. We also highlight several methods that improve the nuclease specificity and efficiency, and discuss current and potential applications of CRISPR/Cas9 system in filamentous fungi for pathogenesis decoding, confirmation of the gene and pathway, bioenergy process, drug discovery, and chromatin dynamics. We also describe how the synthetic gene circuit of CRISPR/Cas9 systems has been used in the response to various complex environmental signals to redirect metabolite flux and ensure continuous metabolite biosynthesis. | null | ASPERGILLUS-NIDULANS;BIOSYNTHETIC GENE-CLUSTER;CAS9 NUCLEASES;DNA;EFFECTOR GENE;GENOME;HUMAN-CELLS;OFF-TARGET CLEAVAGE;POLYKETIDE SYNTHASE;SPECIFICITY | 2 | null | CRISPR/Cas9 system;drug discovery;Filamentous fungi;genome editing;Synthetic gene circuit;Transcriptional regulation | 10 | ASPERGILLUS-NIDULANS;BIOSYNTHETIC GENE-CLUSTER;CAS9 NUCLEASES;CRISPR/Cas9 system;DNA;DRUG DISCOVERY;EFFECTOR GENE;FILAMENTOUS FUNGI;GENOME;genome editing;HUMAN-CELLS;OFF-TARGET CLEAVAGE;Polyketide synthase;Transcriptional regulation;SPECIFICITY;synthetic gene circuits | WOS:000407658000028 | JiangNan Univ, Jiangsu, Peoples R China | China | 2,017 | null | null | null | null | English | null | ACS CHEM BIOL;ACS SYNTH BIOL;ANNU REV BIOPHYS;APPL MICROBIOL BIOT;BIOINFORMATICS;BIORESOUR TECHNOL;BIOTECHNOL ADV;BIOTECHNOL BIOENG;BIOTECHNOL BIOFUELS;BIOTECHNOL LETT;CELL;CELL DISCOV;CELL HOST MICROBE;CELL REP;CELL STEM CELL;CRIT REV BIOTECHNOL;EUKARYOT CELL;FEMS MICROBIOL REV;FRONT MICROBIOL;Fungal Biol Biotechnol;FUNGAL GENET BIOL;GENETICS;J AM CHEM SOC;J EXP MED;J MICROBIOL METH;J POLYM SCI POL CHEM;METAB ENG;MICROB CELL FACT;MOL PLANT PATHOL;NAT BIOTECHNOL;NAT CHEM BIOL;NAT METHODS;NAT PROTOC;NAT REV CARDIOL;NAT REV DRUG DISCOV;NAT REV GENET;NAT REV MICROBIOL;NATURE;NEW PHYTOL;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PLOS ONE;PROCESS BIOCHEM;RES MICROBIOL;SCI REP-UK;SCIENCE;WORLD J PSYCHIATR | Cai, Yujie;Deng, Huaxiang;Gao, Ruijie;Liao, Xiangru | 2024-03-11
ER | Ahuja, M;Arazoe, T;Bae, S;Barrios-González, J;Boboila, C;Brophy, J A N;Brown, E D;Chen, B;Chen, J J;Chiang, Y M;Cho, H;Cong, L;Crawford, J M;Deng H.;Dicarlo, J E;Dou, D L;Dow, L E;Engler, C;Fang, Y F;Farboud, B;Frock, R L;Fu, Y F;Fuller, K K;Gao, Y C;Gilbert, L A;Grundy, S M;Hamad, B;Heigwer, F;Hirashima, K;Hsu, P D;Hübner, M R;Jakociunas, T;Jinek, M;Kang, H S;Katayama, T;Keller, N P;Khrunyk, Y;Kiely, D E;Kim, D;Kim, J S;Kleinstiver, B P;Komor, A C;Konermann, S;Kuivanen, J;Labun, K;Lin, Y N;Liu, Q;Liu, R;Ma H.;Ma, H H;Matsu-Ura Toru;Mehtiö, T;Miyagishi, M;Nielsen, M L;Nihongaki, Y;Nodvig, C S;Oliveros, J C;Park, P J;Pawluk, A;Pohl, C;Qi, L S;Qin, H;Raffaele, S;Ran, F A;Rauch, B J;Ren, X J;Richardson, C D;Rutledge, P J;Sander, J D;Sarkari P.;Schuster M.;Schuster, M;Slaymaker, I M;Smanski, M J;Smith, C;Sugano, S S;Tsai, S Q;Wang, X L;Weber, J;Wenderoth, M;Weyda, I;Wilkinson, B;Woloshuk, C P;Yeh, H H;Zalatan, J G;Zetsche, B;Zhang, C;Zhang, L;Zischewski, J | FD6SK | Jiangsu, Peoples R China | 51 | null | 1 | null | 28,625,564 | Cai, Yujie;Deng, Huaxiang;Gao, Ruijie;Liao, Xiangru | GENE | Jiangsu, Peoples R China |
Alam, S;Hasan, S M R | 10.1109/TCSII.2016.2618366 | null | 445 HOES LANE, PISCATAWAY, NJ 08855-4141 USA | 4n2y1a4e402x6f2e111g1d5p95303o54635d17 | A Gene-Protein-miRNA Electronic Oscillator | Massey Univ | null | Hasan, SMR (corresponding author), Massey Univ, Sch Engn & Adv Technol, Ctr Res Analog & VLSI Microsyst Design, Auckland 0632, New Zealand. | null | Alam, Sadia;Hasan, S M Rezaul | Engineering, Electrical & Electronic | null | WOS | Hasan, S M R | Massey Univ, Auckland, New Zealand | 64 | a;electronic;Gene-Protein-miRNA;Oscillator | 1 | Hasan, Rezaul | IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC | Massey Univ, Sch Engn & Adv Technol, Ctr Res Analog & VLSI Microsyst Design, Auckland 0632, New Zealand | Article | Massey Univ | PISCATAWAY | null | null | Massey Univ | null | Hasan, SMR (corresponding author), Massey Univ, Sch Engn & Adv Technol, Ctr Res Analog & VLSI Microsyst Design, Auckland 0632, New Zealand. | 1011 | Alam, Sadia;Hasan, S M Rezaul | 7 | 1 | 408,771,000,003 | null | New Zealand | IEEE TRANSACTIONS ON CIRCUITS AND SYSTEMS II-EXPRESS BRIEFS | New Zealand | null | null | Massey Univ, Sch Engn & Adv Technol, Ctr Res Analog & VLSI Microsyst Design, Auckland 0632, New Zealand | 1549-7747 | Alam, S;Hasan, S M R | SEP | hasanmic@massey.ac.nz | Gene-Protein-miRNA Electronic Oscillator | 2 | J | Engineering | another gene;biological behavior;biological domain;brief;cells;circuit runs;CIRCUITS;complementary micro-ribonucleic acid (miRNA) genes;designing complex synthetic gene regulatory networks;electronic oscillator circuit model;expression;external stimulus;feasibility procedure;GENE;gene expression;Gene-Protein-miRNA Electronic Oscillator;messenger-RNA (mRNA) degradation;messenger-RNA transcripts;micro-ribonucleic acid (miRNA);MICRORNA;MYC;OSCILLATOR;oscillatory network;proposed gene-protein-miRNA electronic oscillator;PROTEIN;proteins;remaining three;REPRESSION;research;six genes;three;TRANSCRIPTION;translational level;unique relationship;valuable | Alam, S | CELLS;CIRCUITS;EXPRESSION;GENE;messenger-RNA (mRNA) degradation;micro-ribonucleic acid (miRNA);MICRORNA;MYC;OSCILLATOR;PROTEIN;REPRESSION;TRANSCRIPTION | 1007 | [Alam, Sadia; Hasan, S. M. Rezaul] Massey Univ, Sch Engn & Adv Technol, Ctr Res Analog & VLSI Microsyst Design, Auckland 0632, New Zealand. | null | another gene;biological behavior;biological domain;brief;circuit runs;complementary micro-ribonucleic acid (miRNA) genes;designing complex synthetic gene regulatory networks;electronic oscillator circuit model;external stimulus;feasibility procedure;gene;gene expression;messenger-RNA transcripts;oscillatory network;proposed gene-protein-miRNA electronic oscillator;proteins;remaining three;research;six genes;three;transcription;translational level;unique relationship;valuable | 10.1002/j.1460-2075.1990.tb07612.x;10.1016/j.celrep.2012.05.017;10.1038/nature01257;10.1038/nature07389;10.1038/ncomms4399;10.1049/el.2014.2144;10.1073/pnas.1220176110;10.1109/JPROC.2004.826600;10.1109/TCSI.2008.925632;10.1109/TCSI.2013.2245451;10.1111/gtc.12009;10.1158/0008-5472.CAN-07-2462;10.1371/journal.pone.0014668;10.3390/ijms140714346 | Massey Univ | Alam, S;Hasan, S M R | Alam, S: Massey Univ, Sch Engn & Adv Technol, Ctr Res Analog & VLSI Microsyst Design, Auckland 0632, New Zealand | Hasan, S. M. Rezaul | null | 14 | null | New Zealand | Massey Univ | Alam, Sadia | null | CELLS;CIRCUITS;EXPRESSION;MICRORNA;MYC | Alam, Sadia; Hasan, S. M. Rezaul; | null | Massey Univ, Sch Engn & Adv Technol, Ctr Res Analog & VLSI Microsyst Design, Auckland 0632, New Zealand | Massey Univ, Sch Engn & Adv Technol, Ctr Res Analog & VLSI Microsyst Design, Auckland 0632, New Zealand | 1558-3791 | genes;messenger-RNA (mRNA) degradation;micro-ribonucleic acid (miRNA);oscillations;Proteins;repression;transcription | 9 | 1990;2002;2004;2007;2008;2011;2012;2013;2014 | 1 | Massey Univ, Sch Engn & Adv Technol, Ctr Res Analog & VLSI Microsyst Design, Auckland 0632, New Zealand | IEEE Trans. Circuits Syst. II-Express Briefs | Hasan, S M Rezaul | IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC | (miRNA);,;a;acid;also;among;an;analyzing;and;another;any;are;at;be;because;behavior;biological;brief;by;can;circuit;complementary;complex;controlled;degrading;designing;domain;each;electronic;employed;expression;external;fabricate;feasibility;forming;gene;gene-protein-miRNA;genes;in;is;level;messenger-RNA;micro-ribonucleic;mimicking;model;network;networks;of;oscillator;oscillatory;out;presented;presents;procedure;proposed;proteins;regulatory;relationship;remaining;research;runs;six;stimulus;synthesize;synthetic;the;their;this;three;to;transcription;transcripts;translational;unique;used;valuable;which;while;without | Massey Univ | This brief presents an electronic oscillator circuit model mimicking a unique relationship among six genes. Three out of the six genes are employed to synthesize proteins, while the remaining three are their complementary micro-ribonucleic acid (miRNA) genes degrading the messenger-RNA transcripts at the translational level of gene expression. The circuit runs without any external stimulus because the transcription of each gene is controlled by another gene in forming the oscillatory network. A feasibility procedure is also presented, which can be used to fabricate the proposed gene-protein-miRNA electronic oscillator in the biological domain. This research is valuable in designing complex synthetic gene regulatory networks and analyzing their biological behavior. | AAE-6733-2020 | CELLS;CIRCUITS;EXPRESSION;MICRORNAS;MYC | 2 | null | gene;messenger-RNA (mRNA) degradation;micro-ribonucleic acid (miRNA);oscillator;protein;repression;transcription | 5 | CELLS;CIRCUITS;EXPRESSION;GENE;messenger-RNA (mRNA) degradation;micro-ribonucleic acid (miRNA);MICRORNA;MYC;OSCILLATIONS;PROTEIN;REPRESSION;TRANSCRIPTION | WOS:000408771000003 | Massey Univ, Auckland, New Zealand | New Zealand | 2,017 | null | 0000-0003-0428-3311 | null | null | English | null | CANCER RES;CELL REPORTS;ELECTRON LETT;EMBO J;GENES CELLS;IEEE T CIRCUITS-I;INT J MOL SCI;NAT COMMUN;NATURE;P IEEE;P NATL ACAD SCI USA;PLOS ONE | Alam, Sadia;Hasan, S M Rezaul | 2024-03-11
ER | Alam, S;Bonev, B;Cimadamore, F;Goodfellow, M;Grignani, F;Hasan, S M R;Hasty, J;Kiparissides, A;Rosa, A;Sampson, V B;Simpson, M L;Stricker, J;Tan, S L | FF3BR | Auckland, New Zealand | 1 | null | 1 | null | null | Alam, Sadia;Hasan, S M Rezaul | IEEE T CIRCUITS-II | Auckland, New Zealand |
Baumgart, L;Hasty, J;Mather, W | 10.1038/ng.3915 | null | 75 VARICK ST, 9TH FLR, NEW YORK, NY 10013-1917 USA | 7w56r2644mq2j5m373s1n1c2a696m6a4t1x | Synchronized DNA cycling across a bacterial population | Univ Calif San Diego | null | Hasty, J (corresponding author), Univ Calif San Diego, BioCircuits Inst, La Jolla, CA 92093 USA.;Hasty, J (corresponding author), Univ Calif San Diego, Dept Bioengn, La Jolla, CA 92093 USA.;Hasty, J (corresponding author), Univ Calif San Diego, Div Biol Sci, Mol Biol Sect, La Jolla, CA 92093 USA. | null | Baumgart, Leo;Hasty, Jeff;Mather, William | Genetics & Heredity | NSF [MCB-1616997, MCB-1330180]; Div Of Molecular and Cellular Bioscience; Direct For Biological Sciences [1330180] Funding Source: National Science Foundation | WOS | Hasty, J | Univ Calif San Diego, La Jolla, CA USA;Virginia Polytech Inst & State Univ, Blacksburg, VA USA | 49 | a;across;Bacterial;cycling;DNA;population;synchronized | 1 | Baumgart, Leo | NATURE PUBLISHING GROUP | Univ Calif San Diego, BioCircuits Inst, La Jolla, CA 92093 USA;Univ Calif San Diego, Dept Bioengn, La Jolla, CA 92093 USA;Univ Calif San Diego, Div Biol Sci, Mol Biol Sect, La Jolla, CA 92093 USA;Univ Calif San Diego, Div Biol Sci, Mol Biol Sect, La Jolla, CA 92093 USA.; Hasty, J (corresponding author), Univ Calif San Diego, BioCircuits Inst, La Jolla, CA 92093 USA.; Hasty, J (corresponding author), Univ Calif San Diego, Dept Bioengn, La Jolla, CA 92093 USA;Virginia Polytech Inst & State Univ, Dept Biol, Blacksburg, VA 24061 USA;Virginia Polytech Inst & State Univ, Dept Phys, Blacksburg, VA 24061 USA | Article | Univ Calif San Diego | NEW YORK | null | null | Univ Calif San Diego;Virginia Polytech Inst & State Univ | Direct For Biological Sciences;Div Of Molecular and Cellular Bioscience;NSF | Hasty, J (corresponding author), Univ Calif San Diego, Div Biol Sci, Mol Biol Sect, La Jolla, CA 92093 USA.; Hasty, J (corresponding author), Univ Calif San Diego, BioCircuits Inst, La Jolla, CA 92093 USA.; Hasty, J (corresponding author), Univ Calif San Diego, Dept Bioengn, La Jolla, CA 92093 USA. | + | Baumgart, Leo;Hasty, Jeff;Mather, William | 38 | 5 | 406,397,900,020 | Direct For Biological Sciences [1330180] Funding Source: National Science Foundation;Div Of Molecular and Cellular Bioscience;NSF [MCB-1616997, MCB-1330180] | USA | NATURE GENETICS | USA;USA.; | null | null | Univ Calif San Diego, Div Biol Sci, Mol Biol Sect, La Jolla, CA 92093 USA | 1061-4036 | Baumgart, L;Hasty, J;Mather, W | AUG | hasty@bioeng.ucsd.edu | bacterial population;synchronized DNA cycling | 3 | J | Genetics & Heredity | alternative approach;bacterial population;cells;central challenge;circuit control element;circuit elements;CIRCUITS;colony-wide DNA cycling;computation;control;copy number modulation;defining goal;DNA copy number;dynamic regulation;Escherichia coli;ESCHERICHIA-COLI;form;gene circuitry;gene expression;gene networks;generalizable principle;lack;larger networks;living cells;logic gates;logical combination;modular design;origin;orthogonal elements;plasmid copy number oscillations via;plasmids;precise temporal modulation;predictable dynamic control;promoter-level regulation;promoters;QUORUM;replication;small gene circuits;synchronized DNA cycling;synthetic biology;synthetic gene circuits;use;variety | Baumgart, L | CIRCUITS;COMPUTATION;ESCHERICHIA-COLI;gene networks;LIVING CELLS;logic gates;ORIGIN;plasmids;QUORUM;REPLICATION | 1282 | [Baumgart, Leo; Hasty, Jeff] Univ Calif San Diego, Div Biol Sci, Mol Biol Sect, La Jolla, CA 92093 USA. [Baumgart, Leo; Hasty, Jeff] Univ Calif San Diego, BioCircuits Inst, La Jolla, CA 92093 USA. [Mather, William] Virginia Polytech Inst & State Univ, Dept Phys, Blacksburg, VA 24061 USA. [Mather, William] Virginia Polytech Inst & State Univ, Dept Biol, Blacksburg, VA 24061 USA. [Hasty, Jeff] Univ Calif San Diego, Dept Bioengn, La Jolla, CA 92093 USA. | We thank R. Johnson for assistance with microfluidic device design and fabrication, and P.J. Steiner and J. Humphries for helpful input and discussions. We are also grateful to the laboratory of B. Palsson for generously providing access to real-time PCR equipment. This work was supported by the NSF (award MCB-1616997 to J.H. and L.B.; award MCB-1330180 to W.M.). | alternative approach;cells;central challenge;circuit control element;circuit elements;colony-wide DNA cycling;control;copy number modulation;defining goal;DNA copy number;dynamic regulation;Escherichia coli;form;gene circuitry;gene expression;generalizable principle;lack;larger networks;logical combination;modular design;orthogonal elements;plasmid copy number oscillations via;precise temporal modulation;predictable dynamic control;promoter-level regulation;promoters;small gene circuits;synthetic biology;synthetic gene circuits;use;variety | 10.1002/biot.201300258;10.1006/plas.1997.1319;10.1016/0092-8674(83)90502-0;10.1016/0092-8674(86)90369-7;10.1016/j.cell.2009.04.048;10.1016/j.cell.2014.01.068;10.1016/j.cell.2015.06.012;10.1016/j.copbio.2014.04.009;10.1038/35002125;10.1038/35002131;10.1038/msb.2011.94;10.1038/nature02491;10.1038/nature03461;10.1038/nature07389;10.1038/nature08753;10.1038/nature09565;10.1038/nature10722;10.1038/nature11516;10.1038/nbt.2510;10.1038/ncomms11658;10.1073/pnas.0402940101;10.1073/pnas.1202344109;10.1093/bioinformatics/btl485;10.1093/nar/12.6.2641;10.1101/gad.12.9.1338;10.1103/PhysRevLett.102.068105;10.1126/science.1172005;10.1126/science.1205527;10.1126/science.1232758;10.1128/jb.179.2.557-562.1997;10.1186/1475-2859-7-6;10.1371/journal.pone.0011909;[10.1038/NMETH.2019, 10.1038/nmeth.2019];[10.1038/NMETH.2926, 10.1038/nmeth.2926] | Univ Calif San Diego | Baumgart, L;Hasty, J;Mather, W | Baumgart, L: Univ Calif San Diego, Div Biol Sci, Mol Biol Sect, La Jolla, CA 92093 USA | null | 1330180;MCB-1330180;MCB-1616997 | 34 | null | USA | Univ Calif San Diego;Virginia Polytech Inst & State Univ | Baumgart, Leo | null | CIRCUITS;COMPUTATION;ESCHERICHIA-COLI;GENE NETWORKS;LIVING CELLS;LOGIC GATES;ORIGIN;PLASMIDS;QUORUM;REPLICATION | Baumgart, Leo; Mather, William; Hasty, Jeff; | null | Univ Calif San Diego, BioCircuits Inst, La Jolla, CA 92093 USA;Univ Calif San Diego, Dept Bioengn, La Jolla, CA 92093 USA;Univ Calif San Diego, Div Biol Sci, Mol Biol Sect, La Jolla, CA 92093 USA;Virginia Polytech Inst & State Univ, Dept Biol, Blacksburg, VA 24061 USA;Virginia Polytech Inst & State Univ, Dept Phys, Blacksburg, VA 24061 USA | Univ Calif San Diego, BioCircuits Inst, La Jolla, CA 92093 USA;Univ Calif San Diego, Dept Bioengn, La Jolla, CA 92093 USA;Univ Calif San Diego, Div Biol Sci, Mol Biol Sect, La Jolla, CA 92093 USA;Virginia Polytech Inst & State Univ, Dept Biol, Blacksburg, VA 24061 USA;Virginia Polytech Inst & State Univ, Dept Phys, Blacksburg, VA 24061 USA | 1546-1718 | null | 8 | 1983;1984;1986;1997;1998;2000;2004;2005;2006;2008;2009;2010;2011;2012;2013;2014;2015;2016 | 25 | Univ Calif San Diego, BioCircuits Inst, La Jolla, CA 92093 USA;Univ Calif San Diego, Dept Bioengn, La Jolla, CA 92093 USA;Univ Calif San Diego, Div Biol Sci, Mol Biol Sect, La Jolla, CA 92093 USA | Nature Genet. | Hasty, Jeff | NATURE PUBLISHING GROUP | ,;a;adapted;adds;allowing;alternative;although;an;and;approach;as;be;been;biology;can;cells;central;challenge;characterized;circuit;circuitry;circuits;coli;colony-wide;combination;compatible;constructed;control;coordinate;copy;cycling;defining;design;DNA;due;dynamic;element;elements;engineer;engineered;Escherichia;explored;expression;for;form;gene;generalizable;goal;have;in;into;is;lack;larger;layer;logical;modular;modulation;networks;number;of;often;Orthogonal;oscillations;other;plasmid;precise;predictable;primarily;principle;promoter-level;promoters;readily;regulation;relatively;remains;require;requiring;small;specially;synthetic;tasks;temporal;that;the;their;this;to;use;variety;via;we;with;without | Univ Calif San Diego | A defining goal of synthetic biology is to engineer cells to coordinate tasks that often require precise temporal modulation of gene expression. Although a variety of relatively small gene circuits have been constructed and characterized, their logical combination into larger networks remains a central challenge. This is due primarily to the lack of compatible and orthogonal elements for predictable dynamic control of gene expression. As an alternative approach to promoter-level regulation, we explored the use of DNA copy number as a circuit control element. We engineered colony-wide DNA cycling in Escherichia coli in the form of plasmid copy number oscillations via a modular design that can be readily adapted for use with other gene circuitry. Copy number modulation is a generalizable principle that adds a layer of control to synthetic gene circuits, allowing dynamic regulation of circuit elements without requiring specially engineered promoters. | null | CIRCUITS;COMPUTATION;ESCHERICHIA-COLI;GENE NETWORKS;LIVING CELLS;LOGIC GATES;ORIGIN;PLASMID;QUORUM;REPLICATION | 4 | null | null | 5 | ESCHERICHIA-COLI;CIRCUITS;COMPUTATION;gene networks;LIVING CELLS;logic gates;ORIGIN;PLASMID;QUORUM;REPLICATION | WOS:000406397900020 | Univ Calif San Diego, La Jolla, CA USA;Virginia Polytech Inst & State Univ, Blacksburg, VA USA | USA | 2,017 | null | 0000-0002-2773-5897 | null | null | English | null | BIOINFORMATICS;BIOTECHNOL J;CELL;CURR OPIN BIOTECH;GENE DEV;J BACTERIOL;MICROB CELL FACT;MOL SYST BIOL;NAT BIOTECHNOL;NAT COMMUN;NAT METHODS;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PHYS REV LETT;PLASMID;PLOS ONE;SCIENCE | Baumgart, Leo;Hasty, Jeff;Mather, William | 2024-03-11
ER | Basu, S;Bonnet, J;Brophy, J A N;Cookson, N A;Danino, T;Elowitz, M B;Friedland, A E;Gardner, T S;Gottesman, S;Hoops, S;Kobayashi, H;Marguet, P;Mather, W;Moon, T S;Narula, J;Panayotatos, N;Prindle, A;Purcell, O;Roquet, N;Rubens, J R;Schindelin, J;Selzer, G;Siuti, P;Skulj, M;Slager, J;Stevens, A M;Stricker, J;Tabor, J J;Tamsir, A;Tomizawa, J;Wróbel, B;Xie, Z;You, L C | FB8OI | La Jolla, CA USA;La Jolla, CA USA. | 31 | null | 2 | null | 28,692,067 | Baumgart, Leo;Hasty, Jeff;Mather, William | NAT GENET | Blacksburg, VA USA;La Jolla, CA USA |
Calarco, J A;Gracida, X;Norris, A D | 10.7554/eLife.28129 | e28129 | SHERATON HOUSE, CASTLE PARK, CAMBRIDGE, CB3 0AX, ENGLAND | 1b39576g4w3qi1vk4q3n65246m2r3a1d6o5g2c | CRISPR-mediated genetic interaction profiling identifies RNA binding proteins controlling metazoan fitness | Harvard Univ | null | Calarco, JA (corresponding author), Harvard Univ, FAS Ctr Syst Biol, Cambridge, MA 02138 USA.;Calarco, JA (corresponding author), Univ Toronto, Dept Cell & Syst Biol, Toronto, ON, Canada. | null | Calarco, John A;Gracida, Xicotencatl;Norris, Adam D | Biology | NIH Office of the Director NIH Early Independence Award [DP5OD009153]; Harvard University Bauer Fellows Program; University of Toronto; Charles King postdoctoral fellowship; Natural Sciences and Engineering Research Council of Canada [RGPIN-2017-06573] | WOS | Calarco, J A | Harvard Univ, Cambridge, MA USA;Southern Methodist Univ, Dallas, TX USA;Univ Toronto, Toronto ON, Canada | 6 | binding;controlling;CRISPR-mediated;fitness;genetic;Identifies;Interaction;metazoan;profiling;Proteins;RNA | 2 | Norris, Adam | eLIFE SCIENCES PUBL LTD | Harvard Univ, FAS Ctr Syst Biol, Cambridge, MA 02138 USA;Harvard Univ, FAS Ctr Syst Biol, Cambridge, MA 02138 USA.; Calarco, JA (corresponding author), Univ Toronto, Dept Cell & Syst Biol, Toronto, ON, Canada;Southern Methodist Univ, Dept Biol Sci, Dallas, TX 75275 USA;Univ Toronto, Dept Cell & Syst Biol, Toronto, ON, Canada | Article | Harvard Univ;Univ Toronto | CAMBRIDGE | null | null | Canada;Harvard Univ;Southern Methodist Univ;Univ Toronto | Charles King postdoctoral fellowship;Harvard University Bauer Fellows Program;Natural Sciences and Engineering Research Council of Canada;NIH Office of the Director NIH Early Independence Award;University of Toronto | Calarco, JA (corresponding author), Harvard Univ, FAS Ctr Syst Biol, Cambridge, MA 02138 USA.; Calarco, JA (corresponding author), Univ Toronto, Dept Cell & Syst Biol, Toronto, ON, Canada. | null | Calarco, John A;Gracida, Xicotencatl;Norris, Adam D | 3 | 3 | 406,918,100,001 | Charles King postdoctoral fellowship;Harvard University Bauer Fellows Program;Natural Sciences and Engineering Research Council of Canada [RGPIN-2017-06573];NIH Office of the Director NIH Early Independence Award [DP5OD009153];University of Toronto | Canada;USA | ELIFE | Canada;USA.; | null | null | Harvard Univ, FAS Ctr Syst Biol, Cambridge, MA 02138 USA | 2050-084X | Calarco, J A;Gracida, X;Norris, A D | JUL 18 | calarco@utoronto.ca | CRISPR-mediated genetic interaction;RNA binding proteins controlling metazoan fitness | 3 | J | Life Sciences & Biomedicine - Other Topics | 14 conserved RNA binding protein genes;approaches;biological pathways;biological questions;Caenorhabditis elegans;CAENORHABDITIS-ELEGANS;complex genetic traits;CRISPR-mediated genetic interaction;CRISPR-SGI;CRISPR/Cas9-based Synthetic Genetic Interaction (CRISPR-SGI) approach enabling systematic double-mutant generation;critical role;diseases;double mutants;double mutants displayed fitness defects;ELAVL ortholog exc-7;expression;feasible;genes;genetic interaction screens;insulin signaling;isoforms;lifespan extension;LONGEVITY;MBNL1/2 ortholog mbl-1;mechanisms;metazoans;MUTATIONS;NEURONS;null-alleles;one interaction;organismal health;paradigm;PATHWAY;possible single;PRE-MESSENGER-RNA;regulating hundreds;RESTRICTION;revealing synthetic interactions;rich genetic interaction landscape;RNA binding proteins;RNA binding proteins controlling metazoan fitness;screened interactions;SELECTION;serve;shortened lifespan;synthetic genetic analysis;technique;transcripts;understanding | Norris, A D | CAENORHABDITIS-ELEGANS;EXPRESSION;LONGEVITY;MECHANISMS;MUTATIONS;NEURONS;PATHWAY;PRE-MESSENGER-RNA;RESTRICTION;SELECTION | null | [Norris, Adam D.; Gracida, Xicotencatl; Calarco, John A.] Harvard Univ, FAS Ctr Syst Biol, Cambridge, MA 02138 USA. [Norris, Adam D.] Southern Methodist Univ, Dept Biol Sci, Dallas, TX 75275 USA. [Calarco, John A.] Univ Toronto, Dept Cell & Syst Biol, Toronto, ON, Canada. | NIH Office of the Director NIH Early Independence Award DP5OD009153 John A Calarco; Harvard University Bauer Fellows Program John A Calarco; University of Toronto John A Calarco; Charles King postdoctoral fellowship Adam D Norris; Natural Sciences and Engineering Research Council of Canada Discovery Grant RGPIN-2017-06573 John A Calarco | 14 conserved RNA binding protein genes;approaches;biological pathways;biological questions;Caenorhabditis elegans;complex genetic traits;CRISPR-SGI;CRISPR/Cas9-based Synthetic Genetic Interaction (CRISPR-SGI) approach enabling systematic double-mutant generation;critical role;diseases;double mutants;double mutants displayed fitness defects;ELAVL ortholog exc-7;feasible;genes;genetic interaction screens;insulin signaling;isoforms;lifespan extension;MBNL1/2 ortholog mbl-1;metazoans;null-alleles;one interaction;organismal health;paradigm;possible single;regulating hundreds;revealing synthetic interactions;rich genetic interaction landscape;RNA binding proteins;screened interactions;serve;shortened lifespan;synthetic genetic analysis;technique;transcripts;understanding | 10.1007/978-1-4939-1221-6_1;10.1016/0012-1606(81)90459-0;10.1016/j.cell.2005.08.031;10.1016/j.cell.2012.06.041;10.1016/j.gde.2012.12.006;10.1016/j.molcel.2014.05.004;10.1016/j.tig.2008.05.004;10.1016/j.tig.2013.01.004;10.1016/j.tins.2015.02.003;10.1016/S0012-1606(03)00040-X;10.1016/S1046-2023(03)00050-1;10.1038/40194;10.1038/nature03809;10.1038/nature05304;10.1038/nature12311;10.1038/nature20789;10.1038/ng1844;10.1038/NMETH.1534;10.1038/nrg3160;10.1038/nrg3482;10.1038/nrg3813;10.1038/nrm2777;10.1073/pnas.0712255105;10.1073/pnas.95.22.13091;10.1083/jcb.200407085;10.1093/bioinformatics/btn615;10.1093/bioinformatics/bts635;10.1093/nar/gkq767;10.1097/00001756-200512190-00005;10.1101/gad.182477.111;10.1101/gr.114645.110;10.1101/gr.184390.114;10.1101/gr.192518.115;10.1126/science.1154584;10.1126/science.1165942;10.1126/science.1180823;10.1126/science.277.5328.942;10.1126/science.278.5341.1319;10.1146/annurev.genet.39.073003.114751;10.1186/1471-2164-9-488;10.1186/1749-8104-7-7;10.1186/gb-2005-6-5-r45;10.1186/gb-2006-7-7-r63;10.1186/gb-2010-11-10-r106;10.1186/jbiol58;10.1371/journal.pgen.1003325;10.1371/journal.pgen.1003921;10.1534/genetics.115.180679;10.1534/genetics.115.182162;[10.1038/nmeth.1239, 10.1038/NMETH.1239];[10.1038/NMETH.1463, 10.1038/nmeth.1463] | Harvard Univ | Calarco, J A;Gracida, X;Norris, A D | Norris, A D: Harvard Univ, FAS Ctr Syst Biol, Cambridge, MA 02138 USA | null | DP5OD009153;RGPIN-2017-06573 | 54 | null | USA | Harvard Univ;Southern Methodist Univ;Univ Toronto | Norris, Adam D | Green Published, gold | CAENORHABDITIS-ELEGANS;EXPRESSION;LONGEVITY;MECHANISMS;MUTATIONS;NEURONS;PATHWAY;PRE-MESSENGER-RNA;RESTRICTION;SELECTION | Norris, Adam D.; Gracida, Xicotencatl; Calarco, John A.; | null | Harvard Univ, FAS Ctr Syst Biol, Cambridge, MA 02138 USA;Southern Methodist Univ, Dept Biol Sci, Dallas, TX 75275 USA;Univ Toronto, Dept Cell & Syst Biol, Toronto, ON, Canada | Harvard Univ, FAS Ctr Syst Biol, Cambridge, MA 02138 USA;Southern Methodist Univ, Dept Biol Sci, Dallas, TX 75275 USA;Univ Toronto, Dept Cell & Syst Biol, Toronto, ON, Canada | null | null | null | 1974;1981;1994;1997;1998;2003;2004;2005;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016;2017 | 22 | Harvard Univ, FAS Ctr Syst Biol, Cambridge, MA 02138 USA;Univ Toronto, Dept Cell & Syst Biol, Toronto, ON, Canada | eLife | Calarco, John A | eLIFE SCIENCES PUBL LTD | (CRISPR-SGI);,;14;a;aided;all;analysis;and;applicable;applying;approach;approaches;are;as;been;between;binding;biological;both;Caenorhabditis;complex;comprehensively;conserved;CRISPR-SGI;CRISPR/Cas9-based;critical;defects;diseases;displayed;double;double-mutant;ELAVL;elegans;enabling;exc-7;extension;feasible;fitness;for;generating;generation;genes;genetic;have;health;here;however;hundreds;in;insulin;interaction;interactions;isoforms;landscape;lifespan;maintaining;many;may;mbl-1;MBNL1/2;metazoans;mutants;not;null-alleles;of;one;organismal;ortholog;other;our;paradigm;pathways;play;possible;present;protein;proteins;questions;regulating;required;revealing;reveals;rich;RNA;role;screened;screens;serve;set;severely;shortened;signaling;single;synthetic;systematic;technique;the;this;through;thus;to;traits;transcripts;understanding;we;will;with;within | Harvard Univ;Univ Toronto | Genetic interaction screens have aided our understanding of complex genetic traits, diseases, and biological pathways. However, approaches for synthetic genetic analysis with null-alleles in metazoans have not been feasible. Here, we present a CRISPR/Cas9-based Synthetic Genetic Interaction (CRISPR-SGI) approach enabling systematic double-mutant generation. Applying this technique in Caenorhabditis elegans, we comprehensively screened interactions within a set of 14 conserved RNA binding protein genes, generating all possible single and double mutants. Many double mutants displayed fitness defects, revealing synthetic interactions. For one interaction between the MBNL1/2 ortholog mbl-1 and the ELAVL ortholog exc-7, double mutants displayed a severely shortened lifespan. Both genes are required for regulating hundreds of transcripts and isoforms, and both may play a critical role in lifespan extension through insulin signaling. Thus, CRISPR-SGI reveals a rich genetic interaction landscape between RNA binding proteins in maintaining organismal health, and will serve as a paradigm applicable to other biological questions. | null | CAENORHABDITIS-ELEGANS;EXPRESSION;LONGEVITY;MECHANISM;MUTATIONS;NEURONS;PATHWAY;PRE-MESSENGER-RNA;RESTRICTION;SELECTION | 0 | null | null | 18 | CAENORHABDITIS-ELEGANS;EXPRESSION;LONGEVITY;MECHANISM;MUTATIONS;NEURONS;PATHWAY;PRE-MESSENGER-RNA;RESTRICTION;SELECTION | WOS:000406918100001 | Harvard Univ, Cambridge, MA USA;Southern Methodist Univ, Dallas, TX USA;Univ Toronto, Toronto ON, Canada | Canada;USA | 2,017 | null | 0000-0002-0570-7414 | null | null | English | null | ADV EXP MED BIOL;ANNU REV GENET;BIOINFORMATICS;BMC GENOMICS;CELL;CURR OPIN GENET DEV;DEV BIOL;GENE DEV;GENETICS;GENOME BIOL;GENOME RES;J Biol;J CELL BIOL;METHODS;MOL CELL;NAT GENET;NAT METHODS;NAT REV GENET;NAT REV MOL CELL BIO;NATURE;NEURAL DEV;NEUROREPORT;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PLOS GENET;SCIENCE;TRENDS GENET;TRENDS NEUROSCI | Calarco, John A;Gracida, Xicotencatl;Norris, Adam D | 2024-03-11
ER | Anders, S;Anyanful, A;Asikainen, S;Barberan-Soler, S;Baryshnikova, A;Baugh, L R;Brenner, S;Brooks, A N;Butland, G;Byrne Alexandra, B;Calixto, A;Carbon, S;Castello, A;Chalfie, M;Chen, M;Collins, S R;Costanzo, M;Dickinson, D J;Dixon, S J;Dobin, A;Elkon, R;Firnhaber, C;Fujita, M;Gehman, L T;Gerstberger, S;Heintz, C;Hulsen, T;Kamath, R S;Kimura, K D;Lakowski, B;Lehner, B;Lin, K;Lukong, K E;Lundquist, E A;Mani, R;Muñoz, M J;Norris, A D;Nussbacher, J K;Ogg, S;Ramani, A K;Ray, D;Schoenberg, D R;Schuldiner, M;Sieburth, D;Simone, L E;Spilker, K A;Sreedharan, J;Ule, J;Van Nostrand, E L;Vance, C;Wang, E T | FC5YR | Cambridge, MA USA.;Toronto ON, Canada | 23 | null | 3 | null | 28,718,764 | Calarco, John A;Gracida, Xicotencatl;Norris, Adam D | ELIFE | Cambridge, MA USA;Dallas, TX USA;Toronto ON, Canada |
Busch, A;Castagnini, M;Forest, K T;Georgiadou, M;Goosens, V J;Pelicic, V;Waksman, G | 10.1073/pnas.1618539114 | null | 2101 CONSTITUTION AVE NW, WASHINGTON, DC 20418 USA | 3w1y4vl5z1i6x4id4or5e652z3c3b3w1f3h5h | Reconstitution of a minimal machinery capable of assembling periplasmic type IV pili | Imperial Coll London | null | Pelicic, V (corresponding author), Imperial Coll London, Med Res Council, Ctr Mol Bacteriol & Infect, London SW7 2AZ, England. | null | Busch, Andreas;Castagnini, Marta;Forest, Katrina T;Georgiadou, Michaella;Goosens, Vivianne J;Pelicic, Vladimir;Waksman, Gabriel | Multidisciplinary Sciences | MRC [MR/L008408/1, MR/K018434/1]; NIH [R01GM59721]; long-term fellowship from the European Molecular Biology Organization; Marie Curie IEF; Medical Research Council [MR/L008408/1, MR/J006874/1, MR/K018434/1] Funding Source: researchfish; MRC [MR/L008408/1, MR/K018434/1, MR/J006874/1] Funding Source: UKRI | WOS | Pelicic, V | Birkbeck Coll, London, England;Imperial Coll London, London, England;UCL, London, England;Univ Wisconsin Madison, Madison, WI USA | 114 | a;ASSEMBLING;capable;IV;machinery;Minimal;of;PERIPLASMIC;pili;reconstitution;type | 2 | Goosens, Vivianne;Pelicic, Vladimir | NATL ACAD SCIENCES | Birkbeck Coll, London WC1E 7HX, England;Imperial Coll London, Med Res Council, Ctr Mol Bacteriol & Infect, London SW7 2AZ, England;UCL, Inst Struct & Mol Biol, London WC1E 7HX, England;Univ Wisconsin Madison, Dept Bacteriol, Madison, WI 53706 USA | Article | Imperial Coll London | WASHINGTON | null | null | Birkbeck Coll;Imperial Coll London;UCL;Univ Wisconsin Madison | long-term fellowship from the European Molecular Biology Organization;Marie Curie IEF;Medical Research Council;MRC;NIH | Pelicic, V (corresponding author), Imperial Coll London, Med Res Council, Ctr Mol Bacteriol & Infect, London SW7 2AZ, England. | E4986 | Busch, Andreas;Castagnini, Marta;Forest, Katrina T;Georgiadou, Michaella;Goosens, Vivianne J;Pelicic, Vladimir;Waksman, Gabriel | 14 | 4 | 403,687,300,013 | long-term fellowship from the European Molecular Biology Organization;Marie Curie IEF;Medical Research Council [MR/L008408/1, MR/J006874/1, MR/K018434/1] Funding Source: researchfish;MRC [MR/L008408/1, MR/K018434/1, MR/J006874/1] Funding Source: UKRI;MRC [MR/L008408/1, MR/K018434/1];NIH [R01GM59721] | UK;USA | PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA | UK | null | null | Imperial Coll London, Med Res Council, Ctr Mol Bacteriol & Infect, London SW7 2AZ, England | 0027-8424 | Busch, A;Castagnini, M;Forest, K T;Georgiadou, M;Goosens, V J;Pelicic, V;Waksman, G | JUN 20 | v.pelicic@imperial.ac.uk | assembling periplasmic type IV pili;minimal machinery;reconstitution | 7 | J | Science & Technology - Other Topics | 15 conserved proteins;Archaea;ASPARTIC-ACID PROTEASES;assembling periplasmic type IV pili;assembly;BACTERIA;bacterial pathogens;building Tfp;complex multistep process;corresponding proteins;CRYSTAL-STRUCTURE;cytoplasmic membrane;eight synthetic genes;filament assembly;II SECRETION SYSTEM;INNER MEMBRANE PLATFORM;key virulence factors;large group;limited understanding;macromolecular assemblies;macromolecular complex;mechanistic understanding;minimal machinery;model gram-negative species;molecular mechanisms;multipurpose filamentous nanomachines;MYXOCOCCUS-XANTHUS;NEISSERIA-MENINGITIDIS;nonnative heterologous host;PREPILIN PEPTIDASES;prokaryotes;PROTEIN PILM;reconstitute;RECONSTITUTION;remarkable dynamic filaments;results;synthetic biology;synthetic biology approach;tfp biogenesis;THERMUS-THERMOPHILUS;TWITCHING MOTILITY;type IV filamentous nanomachines;type IV pili;type IV pili (Tfp) | Goosens, V J | ASPARTIC-ACID PROTEASES;CRYSTAL-STRUCTURE;filament assembly;II SECRETION SYSTEM;INNER MEMBRANE PLATFORM;MYXOCOCCUS-XANTHUS;NEISSERIA-MENINGITIDIS;PREPILIN PEPTIDASES;PROTEIN PILM;Synthetic biology;THERMUS-THERMOPHILUS;TWITCHING MOTILITY;type IV filamentous nanomachines;type IV pili | E4978 | [Goosens, Vivianne J.; Georgiadou, Michaella; Castagnini, Marta; Pelicic, Vladimir] Imperial Coll London, Med Res Council, Ctr Mol Bacteriol & Infect, London SW7 2AZ, England. [Busch, Andreas; Waksman, Gabriel] UCL, Inst Struct & Mol Biol, London WC1E 7HX, England. [Busch, Andreas; Waksman, Gabriel] Birkbeck Coll, London WC1E 7HX, England. [Forest, Katrina T.] Univ Wisconsin Madison, Dept Bacteriol, Madison, WI 53706 USA. | We acknowledge the support of employees and the use of experimental resources of Instruct, a landmark ESFRI project. We are grateful to Sophie Helaine (Imperial College London), Christoph Tang (University of Oxford), and Rome Voulhoux (CNRS, Marseille) for critical reading of this manuscript. This work was funded by MRC grants (to V.P., MR/L008408/1; to G.W., MR/K018434/1) and an NIH grant (to K.T.F., R01GM59721). A.B. was supported by a long-term fellowship from the European Molecular Biology Organization and a Marie Curie IEF. | 15 conserved proteins;Archaea;assembly;bacteria;bacterial pathogens;building Tfp;complex multistep process;corresponding proteins;cytoplasmic membrane;eight synthetic genes;filament assembly;key virulence factors;large group;limited understanding;macromolecular assemblies;macromolecular complex;mechanistic understanding;minimal machinery;model gram-negative species;molecular mechanisms;multipurpose filamentous nanomachines;nonnative heterologous host;prokaryotes;reconstitute;remarkable dynamic filaments;results;synthetic biology approach;tfp biogenesis;type IV pili (Tfp) | 10.1002/j.1460-2075.1995.tb07155.x;10.1002/mbo3.51;10.1016/j.jmb.2009.09.034;10.1016/j.jmb.2009.09.037;10.1016/j.jmb.2010.03.028;10.1016/j.jsb.2014.07.006;10.1016/j.molcel.2013.01.014;10.1016/j.str.2016.08.010;10.1016/j.tibs.2011.04.002;10.1038/35024105;10.1038/nature10218;10.1038/ncomms13015;10.1038/sj.emboj.7601544;10.1046/j.1365-2958.1998.00723.x;10.1073/pnas.1312313110;10.1073/pnas.95.25.14973;10.1074/jbc.275.2.1502;10.1074/jbc.M111.243535;10.1074/jbc.M113.453506;10.1074/jbc.M115.701284;10.1074/jbc.M116.718353;10.1093/emboj/19.23.6408;10.1093/femsre/fuu001;10.1111/j.1365-2958.2004.04364.x;10.1111/j.1365-2958.2004.04372.x;10.1111/j.1365-2958.2005.04591.x;10.1111/j.1365-2958.2006.05341.x;10.1111/j.1365-2958.2011.07903.x;10.1111/j.1365-2958.2012.08062.x;10.1111/mmi.13237;10.1126/science.aad2001;10.1128/IAI.65.11.4836-4842.1997;10.1128/JB.00032-13;10.1128/JB.00060-07;10.1128/JB.00996-08;10.1128/JB.01094-13;10.1128/JB.01230-06;10.1128/JB.01236-06;10.1128/JB.01547-06;10.1128/jb.177.14.4121-4130.1995;10.1128/MMBR.00035-12;10.1186/gb-2009-10-10-r110;10.1371/journal.pone.0070144 | Imperial Coll London | Busch, A;Castagnini, M;Forest, K T;Georgiadou, M;Goosens, V J;Pelicic, V;Waksman, G | Goosens, V J: Imperial Coll London, Med Res Council, Ctr Mol Bacteriol & Infect, London SW7 2AZ, England | Busch, Andreas;Pelicic, Vladimir | MR/J006874/1;MR/K018434/1;MR/L008408/1;R01GM59721 | 44 | null | UK | Birkbeck Coll;Imperial Coll London;UCL;Univ Wisconsin Madison | Goosens, Vivianne J | Bronze, Green Published, Green Accepted, Green Submitted | ASPARTIC-ACID PROTEASES;CRYSTAL-STRUCTURE;II SECRETION SYSTEM;INNER MEMBRANE PLATFORM;MYXOCOCCUS-XANTHUS;NEISSERIA-MENINGITIDIS;PREPILIN PEPTIDASES;PROTEIN PILM;THERMUS-THERMOPHILUS;TWITCHING MOTILITY | Goosens, Vivianne J.; Busch, Andreas; Georgiadou, Michaella; Castagnini, Marta; Forest, Katrina T.; Waksman, Gabriel; Pelicic, Vladimir; | null | Birkbeck Coll, London WC1E 7HX, England;Imperial Coll London, Med Res Council, Ctr Mol Bacteriol & Infect, London SW7 2AZ, England;UCL, Inst Struct & Mol Biol, London WC1E 7HX, England;Univ Wisconsin Madison, Dept Bacteriol, Madison, WI 53706 USA | Birkbeck Coll, London WC1E 7HX, England;Imperial Coll London, Med Res Council, Ctr Mol Bacteriol & Infect, London SW7 2AZ, England;UCL, Inst Struct & Mol Biol, London WC1E 7HX, England;Univ Wisconsin Madison, Dept Bacteriol, Madison, WI 53706 USA | null | filament assembly;Synthetic biology;type IV filamentous nanomachines;type IV pili | 25 | 1995;1997;1998;2000;2005;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016 | 19 | Imperial Coll London, Med Res Council, Ctr Mol Bacteriol & Infect, London SW7 2AZ, England | Proc. Natl. Acad. Sci. U. S. A. | Pelicic, Vladimir | NATL ACAD SCIENCES | (Tfp);,;15;a;and;approach;Archaea;are;assemblies;assembly;at;bacteria;bacterial;better;biochemically;biogenesis;biology;building;capable;characterized;complex;composed;conserved;contribute;corresponding;cytoplasmic;define;dynamic;eight;factors;filament;filamentous;filaments;form;genes;Gram-negative;group;have;here;heterologous;host;improve;in;is;IV;key;large;limited;machinery;macromolecular;many;mechanisms;mechanistic;Membrane;minimal;model;molecular;multipurpose;multistep;nanomachines;nearly;nonnative;of;on;our;pathogens;pili;process;prokaryotes;promote;proteins;purified;reconstitute;relies;remarkable;results;show;species;sufficient;synthetic;tfp;that;the;to;type;ubiquitous;understanding;used;virulence;we;which;widespread | Imperial Coll London | Type IV pili (Tfp), which are key virulence factors in many bacterial pathogens, define a large group of multipurpose filamentous nanomachines widespread in Bacteria and Archaea. Tfp biogenesis is a complex multistep process, which relies on macromolecular assemblies composed of 15 conserved proteins in model gram-negative species. To improve our limited understanding of the molecular mechanisms of filament assembly, we have used a synthetic biology approach to reconstitute, in a nonnative heterologous host, a minimal machinery capable of building Tfp. Here we show that eight synthetic genes are sufficient to promote filament assembly and that the corresponding proteins form a macromolecular complex at the cytoplasmic membrane, which we have purified and characterized biochemically. Our results contribute to a better mechanistic understanding of the assembly of remarkable dynamic filaments nearly ubiquitous in prokaryotes. | ABD-3102-2021;N-3755-2017;O-1911-2015 | ASPARTIC-ACID PROTEASES;CRYSTAL-STRUCTURE;II SECRETION SYSTEM;INNER MEMBRANE PLATFORM;MYXOCOCCUS-XANTHUS;NEISSERIA-MENINGITIDIS;PREPILIN PEPTIDASES;PROTEIN PILM;THERMUS-THERMOPHILUS;TWITCHING MOTILITIES | 0 | null | filament assembly;Synthetic biology;type IV filamentous nanomachines;type IV pili | 9 | ASPARTIC-ACID PROTEASES;CRYSTAL-STRUCTURE;filament assembly;II SECRETION SYSTEM;INNER MEMBRANE PLATFORM;MYXOCOCCUS-XANTHUS;NEISSERIA-MENINGITIDIS;PREPILIN PEPTIDASES;PROTEIN PILM;Synthetic biology;THERMUS-THERMOPHILUS;TWITCHING MOTILITIES;type IV filamentous nanomachines;type IV pili | WOS:000403687300013 | Birkbeck Coll, London, England;Imperial Coll London, London, England;UCL, London, England;Univ Wisconsin Madison, Madison, WI USA | UK;USA | 2,017 | null | 0000-0002-7808-5185;0000-0002-9456-4995 | null | null | English | null | EMBO J;FEMS MICROBIOL REV;GENOME BIOL;INFECT IMMUN;J BACTERIOL;J BIOL CHEM;J MOL BIOL;J STRUCT BIOL;MICROBIOL MOL BIOL R;MICROBIOLOGYOPEN;MOL CELL;MOL MICROBIOL;NAT COMMUN;NATURE;P NATL ACAD SCI USA;PLOS ONE;SCIENCE;STRUCTURE;THESIS;TRENDS BIOCHEM SCI | Busch, Andreas;Castagnini, Marta;Forest, Katrina T;Georgiadou, Michaella;Goosens, Vivianne J;Pelicic, Vladimir;Waksman, Gabriel | 2024-03-11
ER | Aly, K A;Arts, J;Ayers, M;Balasingham, S V;Berry, J L;Bischof, L F;Carbonnelle, E;Chang, Y W;Francetic, O;Friedrich, C;Georgiadou, M;Giltner, C L;Gurung, I;Guzman, L M;Hu, J;Hélaine, S;Karuppiah, V;Kolappan, S;Koo, J;Korotkov, K V;Lapointe, C F;Li, C Y;Lu, C;Mancl, J M;Mccallum, M;Mclaughlin, L S;Merz, A J;Pujol, C;Reindl, S;Rusniok, C;Sampaleanu, L M;Sandkvist, M;Szabó, Z;Takhar, H K;Tammam, S;Winther-Larsen, H C;Wolfgang, M;Yamagata, A | EY0YL | London, England | 21 | null | 4 | null | 28,588,140 | Busch, Andreas;Castagnini, Marta;Forest, Katrina T;Georgiadou, Michaella;Goosens, Vivianne J;Pelicic, Vladimir;Waksman, Gabriel | P NATL ACAD SCI USA | London, England;Madison, WI USA |
Freemont, P S;MacDonald, J T;Moore, S J | 10.1042/BST20170011 | null | 1ST FLR, 10 QUEEN STREET PLACE, LONDON, ENGLAND | 536j1n3n2i3h1i3s5k5u60z3y2q62635g1v344f | Cell-free synthetic biology for <i>in vitro</i> prototype engineering | Ctr Synthet Biol & Innovat | null | Freemont, PS (corresponding author), Ctr Synthet Biol & Innovat, Dept Med, South Kensington Campus, London, England. | null | Freemont, Paul S;MacDonald, James T;Moore, Simon J | Biochemistry & Molecular Biology | Biotechnology and Biological Sciences Research Council [BB/L027852/1] Funding Source: researchfish; Engineering and Physical Sciences Research Council [EP/J02175X/1] Funding Source: researchfish; BBSRC [BB/L027852/1] Funding Source: UKRI; EPSRC [EP/J02175X/1] Funding Source: UKRI | WOS | Freemont, P S | Ctr Synthet Biol & Innovat, London, England | 45 | <i>in;biology;Cell-Free;engineering;for;prototype;synthetic;Vitro</i> | 1 | MacDonald, James;Moore, Simon | PORTLAND PRESS LTD | Ctr Synthet Biol & Innovat, Dept Med, South Kensington Campus, London, England | Review | Intelligent Synthet Biol Ctr | LONDON | null | null | Ctr Synthet Biol & Innovat | BBSRC;Biotechnology and Biological Sciences Research Council;Engineering and Physical Sciences Research Council;EPSRC | Freemont, PS (corresponding author), Ctr Synthet Biol & Innovat, Dept Med, South Kensington Campus, London, England. | 791 | Freemont, Paul S;MacDonald, James T;Moore, Simon J | 30 | 1 | 403,882,400,018 | BBSRC [BB/L027852/1] Funding Source: UKRI;Biotechnology and Biological Sciences Research Council [BB/L027852/1] Funding Source: researchfish;Engineering and Physical Sciences Research Council [EP/J02175X/1] Funding Source: researchfish;EPSRC [EP/J02175X/1] Funding Source: UKRI | UK | BIOCHEMICAL SOCIETY TRANSACTIONS | UK | null | null | Ctr Synthet Biol & Innovat, Dept Med, South Kensington Campus, London, England | 0300-5127 | Freemont, P S;MacDonald, J T;Moore, S J | JUN 15 | p.freemont@imperial.ac.uk | <i>in vitro</i> prototype engineering;cell-free synthetic biology | 3 | J | Biochemistry & Molecular Biology | <i>in vitro</i> prototype engineering;cell-free look set;cell-free prototype designs;Cell-free synthetic biology;cell-free transcription-translation;development;discipline;E-COLI;Ebola);efficient;exemplar efforts;expanding field;expression;FREE PROTEIN-SYNTHESIS;functioning synthetic genetic circuits;gene circuit cascades;IMPLEMENTATION;interface;living cells;mathematical modelling;medical test kits;natural product pathways;networks;new;new synthetic life;new tools;next stages;on-site identification;precision engineering;prototype designs;rapid iterative design cycles;rapid prototyping platform;rapid turnover times;re-designed;regeneration;RNA-POLYMERASE;synthetic biological devices;synthetic biology;systems will;TRANSCRIPTION-TRANSLATION SYSTEM;transition;translation;viruses (Zika | Moore, S J | E-COLI;EFFICIENT;EXPRESSION;FREE PROTEIN-SYNTHESIS;IMPLEMENTATION;INTERFACE;NETWORKS;REGENERATION;RNA-POLYMERASE;TRANSCRIPTION-TRANSLATION SYSTEM | 785 | [Moore, Simon J.; MacDonald, James T.; Freemont, Paul S.] Ctr Synthet Biol & Innovat, Dept Med, South Kensington Campus, London, England. | null | cell-free look set;cell-free prototype designs;cell-free transcription-translation;development;discipline;Ebola);exemplar efforts;expanding field;functioning synthetic genetic circuits;gene circuit cascades;living cells;mathematical modelling;medical test kits;natural product pathways;new;new synthetic life;new tools;next stages;on-site identification;precision engineering;prototype designs;rapid iterative design cycles;rapid prototyping platform;rapid turnover times;re-designed;synthetic biological devices;synthetic biology;systems will;transition;translation;viruses (Zika | 10.1002/anie.200700390;10.1002/biot.201300545;10.1002/biot.201400330;10.1002/biot.201600678;10.1002/bit.1121;10.1002/bit.20026;10.1002/bit.20528;10.1002/bit.22666;10.1002/bit.23103;10.1002/bit.26253;10.1002/btpr.1509;10.1002/btpr.2082;10.1007/BF00332721;10.1016/j.biochi.2013.11.025;10.1016/j.cbpa.2010.11.020;10.1016/j.cbpa.2012.05.179;10.1016/j.cbpa.2014.09.028;10.1016/j.cell.2014.06.034;10.1016/j.cell.2014.10.004;10.1016/j.cell.2016.04.059;10.1016/j.copbio.2012.02.002;10.1016/j.ymben.2011.09.002;10.1016/j.ymben.2016.03.002;10.1016/j.ymben.2016.09.008;10.1016/S0959-440X(00)00172-X;10.1021/acssynbio.5b00296;10.1021/acssynbio.6b00017;10.1021/acssynbio.6b00031;10.1021/acssynbio.6b00250;10.1021/bp049789y;10.1021/sb300049p;10.1021/sb300104f;10.1021/sb4000993;10.1021/sb400131a;10.1021/sb400203p;10.1021/sb400206c;10.1023/B:JSFG.0000029204.57846.7d;10.1038/228227a0;10.1038/531401a;10.1038/90802;10.1038/msb.2008.57;10.1038/msb4100090;10.1038/nature08187;10.1038/ncomms2620;10.1038/ncomms6305;10.1038/nprot.2007.426;10.1038/nprot.2015.082;10.1038/nrmicro1991;10.1038/srep08663;10.1038/srep39349;10.1073/pnas.1206011109;10.1073/pnas.1311166110;10.1073/pnas.47.10.1580;10.1073/pnas.47.10.1588;10.1073/pnas.48.4.666;10.1073/pnas.74.1.54;10.1093/nar/gkr1191;10.1093/nar/gkt052;10.1093/nar/gkt226;10.1093/nar/gku233;10.1101/071100];10.1103/PhysRevLett.106.048104;10.1109/CDC.2013.6760079;10.1111/j.1432-1033.1996.0881u.x;10.1111/j.1574-6976.2010.00254.x;10.1126/science.aac7341;10.1128/JB.124.1.364-372.1975;10.1155/2012/931943;10.3791/50762;10.7554/eLife.09771;[10.1038/NNANO.2012.65, 10.1038/nnano.2012.65];[10.1371/journal.pone.0096185, 10.1371/journal.pone.0090225] | Ctr Synthet Biol & Innovat | Freemont, P S;MacDonald, J T;Moore, S J | Moore, S J: Ctr Synthet Biol & Innovat, Dept Med, South Kensington Campus, London, England | Moore, Simon | BB/L027852/1;EP/J02175X/1 | 74 | null | UK | Ctr Synthet Biol & Innovat | Moore, Simon J | hybrid, Green Published, Green Submitted, Green Accepted | E-COLI;EFFICIENT;EXPRESSION;FREE PROTEIN-SYNTHESIS;IMPLEMENTATION;INTERFACE;NETWORKS;REGENERATION;RNA-POLYMERASE;TRANSCRIPTION-TRANSLATION SYSTEM | Moore, Simon J.; MacDonald, James T.; Freemont, Paul S.; | null | Ctr Synthet Biol & Innovat, Dept Med, South Kensington Campus, London, England | Ctr Synthet Biol & Innovat, Dept Med, South Kensington Campus, London, England | 1470-8752 | null | null | 1961;1962;1970;1975;1977;1984;1996;2001;2004;2005;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016;2017 | 31 | Ctr Synthet Biol & Innovat, Dept Med, South Kensington Campus, London, England | Biochem. Soc. Trans. | Freemont, Paul S | PORTLAND PRESS LTD | (Zika;,;a;aid;an;and;as;be;biological;biology;blueprinting;can;cascades;cell-free;cells;circuit;circuits;coupled;cycles;debugged;design;designs;development;devices;discipline;Ebola);efforts;engineer;engineered;engineering;exemplar;expanding;field;for;from;functioning;gene;genetic;hoped;hosts;identification;in;include;into;is;it;iterative;itself;kits;lends;life;living;look;mathematical;medical;microbial;modelling;natural;new;next;of;on-site;pathways;platform;precision;product;prototype;prototyping;provide;rapid;re-designed;remain;set;slow;stages;such;synthetic;systems;test;tested;that;the;this;times;to;tools;towards;transcription-translation;transition;translation;turnover;unlock;unsuited;viruses;while;will;with;within | Ctr Synthet Biol & Innovat | Cell-free transcription-translation is an expanding field in synthetic biology as a rapid prototyping platform for blueprinting the design of synthetic biological devices. Exemplar efforts include translation of prototype designs into medical test kits for on-site identification of viruses (Zika and Ebola), while gene circuit cascades can be tested, debugged and re-designed within rapid turnover times. Coupled with mathematical modelling, this discipline lends itself towards the precision engineering of new synthetic life. The next stages of cell-free look set to unlock new microbial hosts that remain slow to engineer and unsuited to rapid iterative design cycles. It is hoped that the development of such systems will provide new tools to aid the transition from cell-free prototype designs to functioning synthetic genetic circuits and engineered natural product pathways in living cells. | HLP-4614-2023 | E. COLI;EFFICIENT;EXPRESSION;FREE PROTEIN-SYNTHESIS;IMPLEMENTATION;INTERFACE;NETWORKS;REGENERATION;RNA-POLYMERASE;TRANSCRIPTION-TRANSLATION SYSTEM | 2 | null | null | 7 | E. coli;EFFICIENT;EXPRESSION;FREE PROTEIN-SYNTHESIS;IMPLEMENTATION;INTERFACE;NETWORKS;REGENERATION;RNA-POLYMERASE;TRANSCRIPTION-TRANSLATION SYSTEM | WOS:000403882400018 | Ctr Synthet Biol & Innovat, London, England | UK | 2,017 | null | 0000-0001-9675-4429;0000-0002-1968-206X | null | null | English | null | ACS SYNTH BIOL;ANGEW CHEM INT EDIT;BIOCHIMIE;BioRxiv;BIOTECHNOL BIOENG;BIOTECHNOL J;BIOTECHNOL PROGR;CELL;CURR OPIN BIOTECH;CURR OPIN CHEM BIOL;CURR OPIN STRUC BIOL;ELIFE;EUR J BIOCHEM;FEMS MICROBIOL REV;IEEE DECIS CONTR P;J BACTERIOL;Journal of Structural and Functional Genomics;JOVE-J VIS EXP;METAB ENG;METHODS MOL BIOL;MOD SIMUL ENG;MOL GEN GENET;MOL SYST BIOL;NAT BIOTECHNOL;NAT COMMUN;NAT NANOTECHNOL;NAT PROTOC;NAT REV MICROBIOL;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PHYS REV LETT;PLOS ONE;SCI REP-UK;SCIENCE | Freemont, Paul S;MacDonald, James T;Moore, Simon J | 2024-03-11
ER | Akabayov, B;Albayrak, C;Brustad, E M;Bujara, M;Cai, Q;Calhoun Kara A.;Caschera, F;Chamberl.M;Chappell, J;Chizzolini, F;Cimermancic, P;De Maddalena, L L;Dudley, Q M;Eisenstein, M;Elani, Y;Ellis, R J;Etlinger, J D;Findlay, H E;Forster, A C;Gan, R;Garamella, J;Geertz, M;Harris, D C;Hartley A, D;Heyman, Y;Hockenberry, A J;Hodgman, C E;Jaenicke, L;Jewett, M C;Jones, G H;Karig, D K;Karim, A S;Karzbrun, E;Kelwick, R;Kigawa Takanori;Kim, D M;Kim, J;Kuruma, Y;Kwon, Y C;Li, J;Liu, D V;Martin, W;Matthaei, J H;Moore S.J.;Moore, S J;Niederholtmeyer, H;Nielsen, A A K;Nirenberg, M;Pardee, K;Schwarz, D;Shimizu, Y;Shin, J;Siegal-Gaskins, D;Sun, Z Z;Takahashi, M K;Thompson, J;Tuza, Z A;Vendeville, A;Voloshin, A M;Wang, H H;Wang, H M;Yang, W C;You, C;Zawada, J F | EY3OR | London, England | 35 | null | 1 | 3 | 28,620,040 | Freemont, Paul S;MacDonald, James T;Moore, Simon J | BIOCHEM SOC T | London, England |
Blumenthal, A;Fernandez, B | 10.1007/s10884-015-9449-7 | null | 233 SPRING ST, NEW YORK, NY 10013 USA | 142k1g2wt212v6u2v6tm5d46j24d5b55o3t | Population Dynamics of Globally Coupled Degrade-and-Fire Oscillators | NYU | null | Fernandez, B (corresponding author), Univ Paris 07, CNRS, Lab Probabilites & Modeles Aleatoires, F-75205 Paris 13, France.;Fernandez, B (corresponding author), Univ Toulon & Var, Aix Marseille Univ, CNRS, Ctr Phys Theor, Campus Luminy, F-13288 Marseille 09, France. | null | Blumenthal, Alex;Fernandez, Bastien | Mathematics;Mathematics, Applied | null | WOS | Fernandez, B | NYU, New York, NY USA;Univ Paris, Paris, France;Univ Toulon & Var, Marseille, France | 29 | coupled;Degrade-and-Fire;dynamics;Globally;of;Oscillators;population | 2 | Blumenthal, Alex | SPRINGER | NYU, Courant Inst Math Sci, 251 Mercer St, New York, NY 10012 USA;Univ Paris 07, CNRS, Lab Probabilites & Modeles Aleatoires, F-75205 Paris 13, France;Univ Paris 07, CNRS, Lab Probabilites & Modeles Aleatoires, F-75205 Paris 13, France.; Fernandez, B (corresponding author), Univ Toulon & Var, Aix Marseille Univ, CNRS, Ctr Phys Theor, Campus Luminy, F-13288 Marseille 09, France;Univ Toulon & Var, Aix Marseille Univ, CNRS, Ctr Phys Theor, Campus Luminy, F-13288 Marseille 09, France | Article | Univ Paris 07;Univ Toulon & Var | NEW YORK | null | null | Lab Probabilites & Modeles Aleatoires;NYU;Univ Paris 07;Univ Toulon & Var | null | Fernandez, B (corresponding author), Univ Paris 07, CNRS, Lab Probabilites & Modeles Aleatoires, F-75205 Paris 13, France.; Fernandez, B (corresponding author), Univ Toulon & Var, Aix Marseille Univ, CNRS, Ctr Phys Theor, Campus Luminy, F-13288 Marseille 09, France. | 547 | Blumenthal, Alex;Fernandez, Bastien | 4 | 3 | 401,663,600,009 | null | France;USA | JOURNAL OF DYNAMICS AND DIFFERENTIAL EQUATIONS | France | null | null | NYU, Courant Inst Math Sci, 251 Mercer St, New York, NY 10012 USA | 1040-7294 | Blumenthal, A;Fernandez, B | JUN | alex@cims.nyu.edu;fernandez@cpt.univ-mrs.fr | Coupled Degrade-and-Fire Oscillators;population Dynamics | 2 | J | Mathematics | analysis;Asymptotic dynamics;asymptotic features;bacteria-embedded synthetic genetic circuits;cluster distribution;colonies;Coupled Degrade-and-Fire Oscillators;coupling parameter;criterion;dynamics' main features;existence;Genetic circuits;global inhibitory coupling;increased;initial value problem;KURAMOTO;large groups;large times;limit;MODEL;model parameters;one-dimensional profiles;periodic orbits;population cluster distribution;population dynamics;POPULATIONS;Pulse-coupled oscillators;regime;sharp transition;Singular differential equation;situation;SYNCHRONIZATION;synchronized oscillators perdure;time evolution;trajectories;trajectory behaviors;transition | Blumenthal, A | Asymptotic dynamics;Genetic circuits;KURAMOTO;MODEL;Pulse-coupled oscillators;Singular differential equation;SYNCHRONIZATION | 523 | [Blumenthal, Alex] NYU, Courant Inst Math Sci, 251 Mercer St, New York, NY 10012 USA. [Fernandez, Bastien] Univ Paris 07, CNRS, Lab Probabilites & Modeles Aleatoires, F-75205 Paris 13, France. [Fernandez, Bastien] Univ Toulon & Var, Aix Marseille Univ, CNRS, Ctr Phys Theor, Campus Luminy, F-13288 Marseille 09, France. | null | analysis;asymptotic features;bacteria-embedded synthetic genetic circuits;cluster distribution;colonies;coupling parameter;criterion;dynamics' main features;existence;global inhibitory coupling;increased;initial value problem;large groups;large times;limit;model parameters;one-dimensional profiles;periodic orbits;population cluster distribution;populations;pulse-coupled oscillators;regime;sharp transition;singular differential equation;situation;synchronized oscillators perdure;time evolution;trajectories;trajectory behaviors;transition | 10.1007/s00285-013-0680-8;10.1016/0024-3795(92)90267-E;10.1016/0167-2789(91)90075-K;10.1016/S0167-2789(00)00094-4;10.1038/35103078;10.1038/nature08753;10.1103/PhysRevE.48.1483;10.1103/PhysRevE.60.2160;10.1103/PhysRevE.84.051916;10.1103/PhysRevLett.102.068105;10.1103/PhysRevLett.74.1570;10.1103/RevModPhys.77.137;10.1109/TAC.2012.2229811;10.1137/0150098 | NYU | Blumenthal, A;Fernandez, B | Blumenthal, A: NYU, Courant Inst Math Sci, 251 Mercer St, New York, NY 10012 USA | null | null | 22 | null | USA | NYU;Univ Paris 07;Univ Toulon & Var | Blumenthal, Alex | Green Submitted | KURAMOTO;MODEL;SYNCHRONIZATION | Blumenthal, Alex; Fernandez, Bastien; | null | NYU, Courant Inst Math Sci, 251 Mercer St, New York, NY 10012 USA;Univ Paris 07, CNRS, Lab Probabilites & Modeles Aleatoires, F-75205 Paris 13, France;Univ Toulon & Var, Aix Marseille Univ, CNRS, Ctr Phys Theor, Campus Luminy, F-13288 Marseille 09, France | NYU, Courant Inst Math Sci, 251 Mercer St, New York, NY 10012 USA;Univ Paris 07, CNRS, Lab Probabilites & Modeles Aleatoires, F-75205 Paris 13, France;Univ Toulon & Var, Aix Marseille Univ, CNRS, Ctr Phys Theor, Campus Luminy, F-13288 Marseille 09, France | 1572-9222 | Asymptotic dynamics;Genetic circuits;Pulse-coupled oscillators;Singular differential equation | 2 | 1960;1964;1975;1984;1990;1991;1992;1993;1995;1999;2000;2001;2003;2005;2009;2010;2011;2013;2014 | 1 | Univ Paris 07, CNRS, Lab Probabilites & Modeles Aleatoires, F-75205 Paris 13, France;Univ Toulon & Var, Aix Marseille Univ, CNRS, Ctr Phys Theor, Campus Luminy, F-13288 Marseille 09, France | J. Dyn. Differ. Equ. | Fernandez, Bastien | SPRINGER | ,;a;address;all;analysis;and;any;are;as;asymptotic;asymptotically;attracting;bacteria-embedded;be;behaviors;by;can;characterize;circuits;cluster;colonies;coupling;criterion;depending;differential;distribution;dynamics';equation;evolution;existence;experiments;features;for;genetic;global;governed;groups;in;increased;inhibitory;initial;inspired;is;large;limit;main;model;obtained;of;on;one-dimensional;only;orbits;oscillators;paper;parameter;parameters;particular;perdure;periodic;population;populations;problem;profiles;prove;pulse-coupled;regime;reports;represented;reveals;separates;sharp;singular;situation;sufficiently;synchronized;synthetic;that;the;their;this;time;times;to;trajectories;trajectory;transition;value;we;where;which;with | Univ Paris 07;Univ Toulon & Var | This paper reports the analysis of a model of pulse-coupled oscillators with global inhibitory coupling, inspired by experiments on colonies of bacteria-embedded synthetic genetic circuits. Populations are represented by one-dimensional profiles and their time evolution is governed by a singular differential equation. We address the initial value problem and characterize the dynamics' main features. In particular, we prove that all trajectory behaviors are asymptotically periodic, with asymptotic features only depending on the population cluster distribution and on the model parameters. A criterion is obtained for the existence of attracting periodic orbits, which reveals the existence of a sharp transition as the coupling parameter is increased. The transition separates a regime where any cluster distribution can be obtained in the limit of large times, to a situation where only trajectories with sufficiently large groups of synchronized oscillators perdure. | null | KURAMOTO;MODEL;SYNCHRONIZATION | 0 | null | Asymptotic dynamics;Genetic circuits;Pulse-coupled oscillators;Singular differential equation | 25 | Asymptotic dynamics;Genetic circuits;KURAMOTO;MODEL;Pulse-coupled oscillators;Singular differential equation;SYNCHRONIZATION | WOS:000401663600009 | NYU, New York, NY USA;Univ Paris, Paris, France;Univ Toulon & Var, Marseille, France | France;USA | 2,017 | null | 0000-0002-6777-7848 | null | null | English | null | BIOL FEEDBACKS;CHEM OSCILLATIONS WA;COMMUNICATION;IEEE T AUTOMAT CONTR;J MATH BIOL;LINEAR ALGEBRA APPL;MATH ASPECTS HEART P;NAT REV MOL CELL BIO;NATURE;P NETHERLANDS ACAD;PHYS REV E;PHYS REV LETT;PHYSICA D;REV MOD PHYS;SIAM J APPL MATH;Theory and Application of the Z-Transform Method | Blumenthal, Alex;Fernandez, Bastien | 2024-03-11
ER | Abbott, L F;Acebrón, J A;Berger, M A;Bressloff, P C;Danino, T;Ernst, U;Fernandez, B;Jury E. I.;Key Ellen;Kuramoto Y.;Kuramoto, Y;Mather, W;Mauroy, A;Mirollo, R E;Peskin, C S;Pikovsky A.;Rota G.;Senn, W;Strogatz, S H;Thomas, R;Tyson, J J | EV3MO | Marseille, France;Paris, France. | 1 | null | 3 | null | null | Blumenthal, Alex;Fernandez, Bastien | J DYN DIFFER EQU | Marseille, France;New York, NY USA;Paris, France |
Kanodia, H;Loake, G J;Mehrotra, R;Mehrotra, S;Renganaath, K | 10.1016/j.biotechadv.2017.03.006 | null | THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND | 53665m3mc1r4j3g302t56r1k5b9242e652o5y | Towards combinatorial transcriptional engineering | Birla Inst Technol & Sci BITS Pilani | null | Mehrotra, R (corresponding author), Birla Inst Technol & Sci BITS Pilani, Dept Biol Sci, Pilani 333031, Rajasthan, India. | null | Kanodia, Harsh;Loake, Gary J;Mehrotra, Rajesh;Mehrotra, Sandhya;Renganaath, Kaushik | Biotechnology & Applied Microbiology | BBSRC; Biotechnology and Biological Sciences Research Council [1068674] Funding Source: researchfish | WOS | Mehrotra, R | Birla Inst Technol & Sci BITS Pilani, Rajasthan, India;Univ Edinburgh, Midlothian, Scotland | 35 | Combinatorial;engineering;towards;Transcriptional | 2 | Kanodia, Harsh | PERGAMON-ELSEVIER SCIENCE LTD | Birla Inst Technol & Sci BITS Pilani, Dept Biol Sci, Pilani 333031, Rajasthan, India;Univ Edinburgh, Inst Mol Plant Sci, Sch Biol Sci, Kings Bldg, Edinburgh EH9 3BF, Midlothian, Scotland | Review | Birla Inst Technol & Sci BITS Pilani | OXFORD | null | null | Birla Inst Technol & Sci BITS Pilani;Univ Edinburgh | BBSRC;Biotechnology and Biological Sciences Research Council | Mehrotra, R (corresponding author), Birla Inst Technol & Sci BITS Pilani, Dept Biol Sci, Pilani 333031, Rajasthan, India. | 405 | Kanodia, Harsh;Loake, Gary J;Mehrotra, Rajesh;Mehrotra, Sandhya;Renganaath, Kaushik | 74 | 2 | 399,431,200,005 | BBSRC;Biotechnology and Biological Sciences Research Council [1068674] Funding Source: researchfish | India;UK | BIOTECHNOLOGY ADVANCES | India | null | null | Birla Inst Technol & Sci BITS Pilani, Dept Biol Sci, Pilani 333031, Rajasthan, India | 0734-9750 | Kanodia, H;Loake, G J;Mehrotra, R;Mehrotra, S;Renganaath, K | MAY-JUN | rmehrotra@pilani.bits-pilani.ac.in | combinatorial transcriptional engineering | 5 | J | Biotechnology & Applied Microbiology | 'parts-off;application indiverse fields;applied research;approach holds;basic;C 2017 Elsevier Inc;combinatorial transcriptional engineering;CRISPR;discussion;DNA-BINDING PROTEINS;ends;field;future development;gene expression;genetic cascades;GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE;HYBRID PROMOTERS;immense scope;limitations;modular nature;multiple;predictable input-output characteristics;programming inducibilty;promise;PROMOTER;promoters;rational combinatorial engineering principles;recent technologies;regulatory circuits;requirement;rights reserved;robust modules;SACCHAROMYCES-CEREVISIAE;scope;shelf' approach;synthetic biology;synthetic gene networks;synthetic modules;synthetic transcriptional engineering;TAL EFFECTORS;Tale;three principle strands;transcription factors;Transcriptional engineering;transcriptional factor engineering;transcriptional unit;transcriptional units;UPSTREAM ACTIVATION SITES;YARROWIA-LIPOLYTICA;YEAST PROMOTERS;ZINC-FINGER | Mehrotra, R | CRISPR;DNA-BINDING PROTEINS;gene expression;GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE;HYBRID PROMOTERS;PROMOTERS;SACCHAROMYCES-CEREVISIAE;Synthetic biology;synthetic gene networks;TAL EFFECTORS;Tale;TRANSCRIPTION FACTORS;Transcriptional engineering;UPSTREAM ACTIVATION SITES;YARROWIA-LIPOLYTICA;YEAST PROMOTERS;ZINC-FINGER | 390 | [Mehrotra, Rajesh; Renganaath, Kaushik; Kanodia, Harsh; Mehrotra, Sandhya] Birla Inst Technol & Sci BITS Pilani, Dept Biol Sci, Pilani 333031, Rajasthan, India. [Loake, Gary J.] Univ Edinburgh, Inst Mol Plant Sci, Sch Biol Sci, Kings Bldg, Edinburgh EH9 3BF, Midlothian, Scotland. | We would like to thank Prof. PK Gupta (CCS University, Meerut, India) for proofreading the manuscript and providing valuable suggestions. Research in the Loake lab is supported by the BBSRC. RM is thankful to Indian National Science academy and Royal Society of Edinburgh for support as bilateral exchange fellow to visit Loake lab. RM and SM are thankful to Department of Biological Sciences, BITS, Pilani for infrastructure support. | 'parts-off;application indiverse fields;applied research;approach holds;basic;discussion;ends;field;future development;genetic cascades;immense scope;limitations;modular nature;multiple;predictable input-output characteristics;programming inducibilty;promise;promoter;rational combinatorial engineering principles;recent technologies;regulatory circuits;requirement;robust modules;scope;shelf' approach;synthetic modules;synthetic transcriptional engineering;three principle strands;transcriptional engineering;transcriptional factor engineering;transcriptional unit;transcriptional units | 10.1002/(SICI)1097-0290(19980420)58:2/3<191::AID-BIT11>3.0.CO;2-G;10.1002/biot.201200120;10.1002/biot.201600029;10.1002/bit.21129;10.1002/bit.24552;10.1002/yea.1043;10.1007/s00253-012-4421-5;10.1007/s11103-011-9755-3;10.1007/s11103-015-0281-6;10.1016/0092-8674(84)90243-5;10.1016/0378-1119(84)90002-7;10.1016/0378-1119(88)90399-X;10.1016/0378-1119(90)90159-O;10.1016/j.bpj.2012.12.015;10.1016/j.cell.2004.06.013;10.1016/j.cell.2011.02.020;10.1016/j.cell.2012.05.045;10.1016/j.cell.2013.02.022;10.1016/j.cell.2013.06.044;10.1016/j.cell.2014.04.047;10.1016/j.cell.2014.09.039;10.1016/j.cell.2014.10.002;10.1016/j.cell.2014.11.052;10.1016/j.chembiol.2009.02.005;10.1016/j.copbio.2011.12.015;10.1016/j.copbio.2015.10.001;10.1016/j.jtbi.2010.07.034;10.1016/j.molcel.2008.06.016;10.1016/j.molcel.2014.04.022;10.1016/j.tibtech.2005.12.003;10.1016/j.tibtech.2015.12.014;10.1016/j.tplants.2007.01.002;10.1016/j.ymben.2013.07.006;10.1016/j.ymeth.2014.06.014;10.1016/S0959-440X(00)00107-X;10.1016/S0969-2126(00)00161-1;10.1021/acssynbio.5b00147;10.1021/bi00616a007;10.1021/ja3065667;10.1021/nn501589f;10.1021/sb400081r;10.1021/sb400091p;10.1021/sb400114p;10.1021/sb400134k;10.1021/sb400137b;10.1021/sb500372z;10.1038/293717a0;10.1038/89617;10.1038/cr.2012.127;10.1038/msb4100058;10.1038/msb4100073;10.1038/mt.2013.56;10.1038/nature04473;10.1038/nature06867;10.1038/nature14136;10.1038/nbt.1536;10.1038/nbt.1589;10.1038/nbt.1591;10.1038/nbt.1767;10.1038/nbt.2170;10.1038/nbt.2205;10.1038/nbt.3245;10.1038/nbt.3528;10.1038/nchembio.1736;10.1038/nchembio.1753;10.1038/ncomms5002;10.1038/ncomms8810;10.1038/NMETH.1542;10.1038/NMETH937;10.1038/nprot.2011.431;10.1038/scientificamerican0606-44;10.1038/sj.gt.3302724;10.1073/pnas.0504604102;10.1073/pnas.0608451104;10.1073/pnas.0811011106;10.1073/pnas.0914803107;10.1073/pnas.1004290107;10.1073/pnas.78.4.2199;10.1073/pnas.81.24.7860;10.1073/pnas.94.15.8168;10.1074/jbc.C112.408864;10.1089/hum.2006.17.949;10.1091/mbc.E11-05-0466;10.1093/bioinformatics/btv664;10.1093/nar/14.22.8963;10.1093/nar/gks1313;10.1093/nar/gks1446;10.1093/nar/gks199;10.1093/nar/gks404;10.1093/nar/gkt1326;10.1093/nar/gku329;10.1093/nar/gku651;10.1093/nar/gkv036;10.1093/nar/gkv1053;10.1093/nar/gkv1343;10.1093/nar/gkv1497;10.1093/nar/gkv466;10.1093/nar/gkv616;10.1093/nar/gkw553;10.1101/gr.106732.110;10.1107/S2053230X13033037;10.1111/j.1567-1364.2011.00769.x;10.1111/j.1582-4934.2008.00371.x;10.1111/pbi.12005;10.1111/tpj.12843;10.1126/science.1106914;10.1126/science.1109090;10.1126/science.1204094;10.1126/science.1207084;10.1126/science.1231143;10.1128/AEM.05763-11;10.1128/AEM.68.5.2397-2403.2002;10.1128/JB.108.1.179-183.1971;10.1128/MCB.14.6.3834;10.1128/MCB.6.12.4335;10.1128/MCB.9.2.442;10.1146/annurev.arplant.47.1.23;10.1146/annurev.biochem.70.1.313;10.1146/annurev.genet.34.1.77;10.1155/2013/407263;10.1186/1471-2105-11-346;10.1186/1471-2164-14-203;10.1186/1471-2164-6-25;10.1186/1472-6750-11-108;10.1186/1756-8935-7-20;10.1371/journal.pcbi.1002811;10.1371/journal.pone.0007526;10.1371/journal.pone.0033279;10.1534/g3.113.008847;10.1534/genetics.111.127019;10.3748/wjg.v11.i34.5295;[10.1038/NMETH.2030, 10.1038/nmeth.2030];[10.1038/nmeth.2598, 10.1038/NMETH.2598];[10.1038/nmeth.2600, 10.1038/NMETH.2600];[10.1038/NMETH.2681, 10.1038/nmeth.2681];[10.1038/NMETH.2969, 10.1038/nmeth.2969];[10.1038/NMETH.3433, 10.1038/nmeth.3433];[10.1038/NMETH.3696, 10.1038/nmeth.3696];[10.1371/journal.pone.0085755, 10.1371/journal.pone.0091606, 10.1371/journal.pone.0098300, 10.1371/journal.pone.0089315] | Birla Inst Technol & Sci BITS Pilani | Kanodia, H;Loake, G J;Mehrotra, R;Mehrotra, S;Renganaath, K | Mehrotra, R: Birla Inst Technol & Sci BITS Pilani, Dept Biol Sci, Pilani 333031, Rajasthan, India | Mehrotra, Rajesh | 1068674 | 147 | null | India | Birla Inst Technol & Sci BITS Pilani;Univ Edinburgh | Mehrotra, Rajesh | Green Accepted | DNA-BINDING PROTEINS;GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE;HYBRID PROMOTERS;SACCHAROMYCES-CEREVISIAE;SYNTHETIC GENE NETWORKS;TAL EFFECTORS;UPSTREAM ACTIVATION SITES;YARROWIA-LIPOLYTICA;YEAST PROMOTERS;ZINC-FINGER | Mehrotra, Rajesh; Renganaath, Kaushik; Kanodia, Harsh; Loake, Gary J.; Mehrotra, Sandhya; | null | Birla Inst Technol & Sci BITS Pilani, Dept Biol Sci, Pilani 333031, Rajasthan, India;Univ Edinburgh, Inst Mol Plant Sci, Sch Biol Sci, Kings Bldg, Edinburgh EH9 3BF, Midlothian, Scotland | Birla Inst Technol & Sci BITS Pilani, Dept Biol Sci, Pilani 333031, Rajasthan, India;Univ Edinburgh, Inst Mol Plant Sci, Sch Biol Sci, Kings Bldg, Edinburgh EH9 3BF, Midlothian, Scotland | 1873-1899 | CRISPR;gene expression;promoter;Synthetic biology;Tale;transcription factor;Transcriptional engineering | 3 | 1964;1971;1978;1981;1982;1983;1984;1985;1986;1988;1989;1990;1992;1994;1996;1997;1998;2000;2001;2002;2003;2004;2005;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016 | 14 | Birla Inst Technol & Sci BITS Pilani, Dept Biol Sci, Pilani 333031, Rajasthan, India | Biotechnol. Adv. | Mehrotra, Sandhya | PERGAMON-ELSEVIER SCIENCE LTD | 'parts-off;,;:;a;achieve;and;application;applied;approach;basic;cascades;characteristics;circuits;combinatorial;composed;construct;context;customized;design;development;discuss;discussion;emphasizes;ends;engineering;factor;field;fields;for;future;genetic;have;here;holds;immense;in;indiverse;inducibilty;input-output;into;it;limitations;makes;modular;modules;multiple;nature;of;our;possible;predictable;principle;principles;programming;promise;promoter;rational;recent;regulatory;requirement;research;review;robust;scope;seek;seeks;shelf';some;strands;such;synthetic;technologies;that;the;these;this;three;to;transcriptional;unit;units;using;we;with | Birla Inst Technol & Sci BITS Pilani | The modular nature of the transcriptional unit makes it possible to design robust modules with predictable input-output characteristics using a 'parts-off a shelf' approach. Customized regulatory circuits composed of multiple such transcriptional units have immense scope for application indiverse fields of basic and applied research. Synthetic transcriptional engineering seeks to construct such genetic cascades. Here, we discuss the three principle strands of transcriptional engineering: promoter and transcriptional factor engineering, and programming inducibilty into synthetic modules. In this context, we review the scope and limitations of some recent technologies that seek to achieve these ends. Our discussion emphasizes a requirement for rational combinatorial engineering principles and the promise this approach holds for the future development of this field. | AAO-6490-2021;AAT-9860-2021 | DNA-BINDING PROTEINS;GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE;HYBRID PROMOTER;SACCHAROMYCES-CEREVISIAE;SYNTHETIC GENE NETWORKS;TAL EFFECTORS;UPSTREAM ACTIVATION SITES;YARROWIA-LIPOLYTICA;YEAST PROMOTERS;ZINC FINGERS | 2 | null | CRISPR;gene expression;Promoters;Synthetic biology;Tale;Transcription factors;Transcriptional engineering | 16 | SACCHAROMYCES-CEREVISIAE;CRISPR;DNA-BINDING PROTEINS;GENE-EXPRESSION;GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE;hybrid promoter;PROMOTER;Synthetic biology;synthetic gene networks;TAL EFFECTORS;Tale;transcription factor;Transcriptional engineering;UPSTREAM ACTIVATION SITES;YARROWIA-LIPOLYTICA;YEAST PROMOTERS;ZINC FINGERS | WOS:000399431200005 | Birla Inst Technol & Sci BITS Pilani, Rajasthan, India;Univ Edinburgh, Midlothian, Scotland | India;UK | 2,017 | null | 0009-0005-6102-3112 | null | null | English | null | ACS NANO;ACS SYNTH BIOL;ACTA CRYSTALLOGR F;ANNU REV BIOCHEM;ANNU REV GENET;ANNU REV PLANT PHYS;APPL ENVIRON MICROB;APPL MICROBIOL BIOT;BIOCHEMISTRY-US;BIOINFORMATICS;BIOMED RES INT;BIOPHYS J;BIOTECHNOL BIOENG;BIOTECHNOL J;BMC BIOINFORMATICS;BMC BIOTECHNOL;BMC GENOMICS;CELL;CELL RES;CHEM BIOL;CURR OPIN BIOTECH;CURR OPIN STRUC BIOL;ENHANCED YEAST TRANS;EPIGENET CHROMATIN;FEMS YEAST RES;GENE;GENE THER;GENETICS;GENOME RES;HUM GENE THER;J AM CHEM SOC;J BACTERIOL;J BIOL CHEM;J CELL MOL MED;J MOL MICROB BIOTECH;J THEOR BIOL;Journal of Molecular and Applied Genetics;METAB ENG;METHODS;MOL BIOL CELL;MOL CELL;MOL CELL BIOL;MOL SYST BIOL;MOL THER;NAT BIOTECHNOL;NAT CHEM BIOL;NAT COMMUN;NAT METHODS;NAT PROTOC;NAT STRUCT BIOL;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;P NATL ACAD SCI-BIOL;PLANT BIOTECHNOL J;PLANT J;PLANT MOL BIOL;PLOS COMPUT BIOL;PLOS ONE;SCI AM;SCIENCE;STRUCT FOLD DES;TRENDS BIOTECHNOL;TRENDS PLANT SCI;WORLD J GASTROENTERO;YEAST | Kanodia, Harsh;Loake, Gary J;Mehrotra, Rajesh;Mehrotra, Sandhya;Renganaath, Kaushik | 2024-03-11
ER | Agmon, N;Alber, T;Alper, H;Andrianantoandro, E;Ang, J;Baker, D;Bassel, J;Bhattacharjee, S;Bitter, G A;Blackburn, M C;Blazeck, J;Blount, B A;Boch, J;Bogdanove, A J;Brewster, R C;Brückner, K;Bultmann, S;Chen, X J;Choo, Y;Cong, L;Curran, K A;Da Silva, N A;De Lange, O;Deboer, H A;Deng, D;Denis, C L;Didovyk, A;Douglas, H C;Ellis, T;Esvelt, K M;Farzadfard, F;Fine, E J;Gaj, T;Garg, A;Gatignol, A;Gibson, D G;Gilbert, L A;Green, A A;Guarente, L;Guido, N J;Hahn, S;Hammer, K;He, W J;Hitzeman, R A;Holkers, M;Holland, M J;Jensen, P R;Jeppsson, M;Johnston, M;Jusiak, B;Juven-Gershon, T;Kabadi, A M;Kellermann, E;Keung, A J;Khalil, A S;Kiani, S;Kinney, J B;Konermann, S;Kumar, S;Lam, F H;Le Bec, C;Leavitt, J M;Lee, T I;Lemken, M L;Li, Y Q;Liu, J;Liu, W S;Lu, T K;Lundqvist, M;Ma, A N;Madzak, C;Maeder, M L;Mazumder, M;Mcalister, L;Mcisaac, R S;Mehrotra, R;Mendoza-Vargas, A;Mercer, A C;Meyer, P;Mitchell, L A;Mnaimneh, S;Mogno, I;Molina, C;Moore, R;Murphy, K F;Nandagopal, N;Nevoigt, E;Nihongaki, Y;Nishizawa, M;Nissim, L;Oakes, B L;Ogden, J E;Osborn, M J;Pabo, C O;Patel, S;Patwardhan, R P;Pedraza, J M;Perez-Pinera, P;Polstein, L R;Purcell, O;Qi, L S;Rajkumar, A S;Rao, C V;Redden, H;Reyon, D;Rogers, J K;Rosenberg S.;Rosenfeld, N;Sander, J D;Sanjana, N E;Schlabach, M R;Sengstag, C;Sharon, E;Shechner, D M;Siegele, D A;Siegl, T;Smolke, C D;Solem, C;Stella, S;Tanenbaum, M E;Taylor, N D;Upadhyay, S K;Valton, J;Venter, M;Vilar, J M G;Vogl, T;Wang, B S;Weber, W;Wolfe, S A;Xi, L Q;Yang, K;Zalatan, J G | ES3LN | Rajasthan, India | 15 | null | 2 | null | 28,300,614 | Kanodia, Harsh;Loake, Gary J;Mehrotra, Rajesh;Mehrotra, Sandhya;Renganaath, Kaushik | BIOTECHNOL ADV | Midlothian, Scotland;Rajasthan, India |
Bentley, W E;Chang, M W;Hwang, I Y;Koh, E;Lee, Y S;March, J C;Wong, A | 10.1038/ncomms15028 | 15028 | MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND | 65k5a2nv6s3w5w6q2a3d4h1b1gkh2k136s47 | Engineered probiotic <i>Escherichia coli</i> can eliminate and prevent <i>Pseudomonas aeruginosa</i> gut infection in animal models | Natl Univ Singapore | null | Chang, MW (corresponding author), Natl Univ Singapore, Dept Biochem, Yong Loo Lin Sch Med, Singapore 117596, Singapore.;Chang, MW (corresponding author), Natl Univ Singapore, NUS Synthet Biol Clin & Technol Innovat SynCTI, Inst Life Sci, Singapore 117456, Singapore. | null | Bentley, William E;Chang, Matthew Wook;Hwang, In Young;Koh, Elvin;Lee, Yung Seng;March, John C;Wong, Adison | Multidisciplinary Sciences | National Medical Research Council of Singapore [CBRG11nov109]; Synthetic Biology Initiative of the National University of Singapore [DPRT/943/09/14]; Summit Research Program of the National University Health System [NUHSRO/2,016/053/SRP/05]; U.S. Air Force [FA/2,386/12/1/4,055]; U.S. Defense Threat Reduction Agency [HDTRA1-13-0037] | WOS | Chang, M W | Cornell Univ, Ithaca, NY USA;Natl Univ Singapore, Singapore, Singapore;Univ Maryland, College Pk, MD USA | 8 | <i>Escherichia;<i>Pseudomonas;aeruginosa</i>;and;animal;can;coli</i>;eliminate;engineered;gut;in;infection;MODELS;Prevent;Probiotic | 2 | Hwang, In Young;Koh, Elvin;Lee, Yung Seng;Wong, Adison | NATURE PUBLISHING GROUP | Cornell Univ, Dept Biol & Environm Engn, Ithaca, NY 14853 USA;Natl Univ Singapore, Dept Biochem, Yong Loo Lin Sch Med, Singapore 117596, Singapore;Natl Univ Singapore, Dept Biochem, Yong Loo Lin Sch Med, Singapore 117596, Singapore.; Chang, MW (corresponding author), Natl Univ Singapore, NUS Synthet Biol Clin & Technol Innovat SynCTI, Inst Life Sci, Singapore 117456, Singapore;Natl Univ Singapore, NUS Synthet Biol Clin & Technol Innovat SynCTI, Inst Life Sci, Singapore 117456, Singapore;Natl Univ Singapore, Yong Loo Lin Sch Med, Dept Paediat, S-119074 Singapore, Singapore;Univ Maryland, Fischell Dept Bioengn, College Pk, MD 20742 USA | Article | Natl Univ Singapore | LONDON | null | null | Cornell Univ;Natl Univ Singapore;Univ Maryland | National Medical Research Council of Singapore;Summit Research Program of the National University Health System;Synthetic Biology Initiative of the National University of Singapore;U.S. Air Force;U.S. Defense Threat Reduction Agency | Chang, MW (corresponding author), Natl Univ Singapore, Dept Biochem, Yong Loo Lin Sch Med, Singapore 117596, Singapore.; Chang, MW (corresponding author), Natl Univ Singapore, NUS Synthet Biol Clin & Technol Innovat SynCTI, Inst Life Sci, Singapore 117456, Singapore. | null | Bentley, William E;Chang, Matthew Wook;Hwang, In Young;Koh, Elvin;Lee, Yung Seng;March, John C;Wong, Adison | 203 | 5 | 398,828,300,001 | National Medical Research Council of Singapore [CBRG11nov109];Summit Research Program of the National University Health System [NUHSRO/2,016/053/SRP/05];Synthetic Biology Initiative of the National University of Singapore [DPRT/943/09/14];U.S. Air Force [FA/2,386/12/1/4,055];U.S. Defense Threat Reduction Agency [HDTRA1-13-0037] | Singapore;USA | NATURE COMMUNICATIONS | Singapore;Singapore.; | null | null | Natl Univ Singapore, Dept Biochem, Yong Loo Lin Sch Med, Singapore 117596, Singapore | 2041-1723 | Bentley, W E;Chang, M W;Hwang, I Y;Koh, E;Lee, Y S;March, J C;Wong, A | APR 11 | matthew_chang@nuhs.edu.sg | <i>Pseudomonas aeruginosa</i> gut infection;animal models;probiotic <i>Escherichia coli</i> | 7 | J | Science & Technology - Other Topics | <i>Pseudomonas aeruginosa</i> gut infection;animal models;anti-biofilm enzyme;BACTERIA;CAENORHABDITIS-ELEGANS;COMMENSAL BACTERIA;development;Escherichia coli;expression;findings;GENE;gut infection;gut infections;host;IMMUNITY;kill Pseudomonas aeruginosa;laboratory strain;mice);microorganisms;modified version;networks;NISSLE 1917;P. aeruginosa;PATHOGENS;potential prophylactic;probiotic;probiotic <i>Escherichia coli</i>;probiotic strain Escherichia coli Nissle 1917;PROTEIN;specific pathogens;synthetic genetic system;SYSTEM;therapeutic activities;therapeutic activity;TRACT;two animal models (Caenorhabditis elegans;VIRULENCE;vitro;vivo prophylactic | Hwang, I Y | CAENORHABDITIS-ELEGANS;COMMENSAL BACTERIA;EXPRESSION;IMMUNITY;NETWORKS;NISSLE 1917;PATHOGENS;PROTEIN;TRACT;VIRULENCE | null | [Hwang, In Young; Koh, Elvin; Wong, Adison; Chang, Matthew Wook] Natl Univ Singapore, Dept Biochem, Yong Loo Lin Sch Med, Singapore 117596, Singapore. [Hwang, In Young; Koh, Elvin; Wong, Adison; Lee, Yung Seng; Chang, Matthew Wook] Natl Univ Singapore, NUS Synthet Biol Clin & Technol Innovat SynCTI, Inst Life Sci, Singapore 117456, Singapore. [March, John C.] Cornell Univ, Dept Biol & Environm Engn, Ithaca, NY 14853 USA. [Bentley, William E.] Univ Maryland, Fischell Dept Bioengn, College Pk, MD 20742 USA. [Lee, Yung Seng] Natl Univ Singapore, Yong Loo Lin Sch Med, Dept Paediat, S-119074 Singapore, Singapore. | We thank Dr Kai Yang for his assistance during the animal experiments in this study and Shen Liang (Senior Biostatistian, Yong Loo Lin School of Medicine, NUS) for his advice on data and statistical analysis. This work was supported by the National Medical Research Council of Singapore (CBRG11nov109), the Synthetic Biology Initiative of the National University of Singapore (DPRT/943/09/14), the Summit Research Program of the National University Health System (NUHSRO/2,016/053/SRP/05), the U.S. Air Force (FA/2,386/12/1/4,055) and the U.S. Defense Threat Reduction Agency (HDTRA1-13-0037). This work used the resources of the NUS Bio-Foundry, a bio-manufacturing research facility located at the National University of Singapore. | anti-biofilm enzyme;bacteria;development;Escherichia coli;findings;gene;gut infection;gut infections;host;kill Pseudomonas aeruginosa;laboratory strain;mice);microorganisms;modified version;P. aeruginosa;potential prophylactic;probiotic;probiotic strain Escherichia coli Nissle 1917;specific pathogens;synthetic genetic system;system;therapeutic activities;therapeutic activity;two animal models (Caenorhabditis elegans;virulence;vitro;vivo prophylactic | 10.1002/bit.260350704;10.1002/cbic.201300410;10.1002/ibd.20377;10.1007/978-1-59745-570-1_24;10.1007/BF00383013;10.1016/0022-3468(94)90264-X;10.1016/j.copbio.2012.03.004;10.1016/j.febslet.2010.06.021;10.1016/j.femsim.2004.10.023;10.1016/S0140-6736(03)14409-1;10.1021/sb4000367;10.1021/sb4000417;10.1038/ja.2015.98;10.1038/msb.2011.46;10.1038/msb.2011.55;10.1038/mt.2014.36;10.1038/nature18930;10.1038/nbt1413;10.1038/ncomms9500;10.1046/j.1365-2958.2000.01716.x;10.1073/pnas.0602138103;10.1073/pnas.0800442106;10.1073/pnas.1001294107;10.1073/pnas.120163297;10.1073/pnas.96.2.715;10.1097/00000658-199308000-00001;10.1097/00000658-200010000-00003;10.1099/jmm.0.008672-0;10.1126/science.1192588;10.1126/science.280.5361.295;10.1128/AAC.00509-11;10.1128/AAC.00635-06;10.1128/IAI.00059-09;10.1128/IAI.00428-10;10.1128/IAI.73.4.2262-2272.2005;10.1128/JB.187.1.382-387.2005;10.1128/JCM.37.6.1771-1776.1999;10.1128/JCM.42.5.1915-1922.2004;10.1136/gutjnl-2013-304786;10.1186/1476-0711-5-14;10.1186/1754-1611-5-12;10.1371/journal.pone.0001308;10.1371/journal.pone.0053957;10.1371/journal.pone.0065965;10.2337/db14-0635;10.3109/07357909209032787;10.3389/fcimb.2013.00115 | Natl Univ Singapore | Bentley, W E;Chang, M W;Hwang, I Y;Koh, E;Lee, Y S;March, J C;Wong, A | Hwang, I Y: Natl Univ Singapore, Dept Biochem, Yong Loo Lin Sch Med, Singapore 117596, Singapore | Chang, Matthew Wook;Hwang, In Young;LEE, YS;Lee, Yung Seng | 016/053/SRP/05;055;386/12/1/4;CBRG11nov109;DPRT/943/09/14;FA/2;HDTRA1-13-0037;NUHSRO/2 | 48 | null | Singapore | Cornell Univ;Natl Univ Singapore;Univ Maryland | Hwang, In Young | Green Published, gold | CAENORHABDITIS-ELEGANS;COMMENSAL BACTERIA;EXPRESSION;IMMUNITY;NETWORKS;NISSLE 1917;PATHOGENS;PROTEIN;TRACT;VIRULENCE | Hwang, In Young; Koh, Elvin; Wong, Adison; March, John C.; Bentley, William E.; Lee, Yung Seng; Chang, Matthew Wook; | null | Cornell Univ, Dept Biol & Environm Engn, Ithaca, NY 14853 USA;Natl Univ Singapore, Dept Biochem, Yong Loo Lin Sch Med, Singapore 117596, Singapore;Natl Univ Singapore, NUS Synthet Biol Clin & Technol Innovat SynCTI, Inst Life Sci, Singapore 117456, Singapore;Natl Univ Singapore, Yong Loo Lin Sch Med, Dept Paediat, S-119074 Singapore, Singapore;Univ Maryland, Fischell Dept Bioengn, College Pk, MD 20742 USA | Cornell Univ, Dept Biol & Environm Engn, Ithaca, NY 14853 USA;Natl Univ Singapore, Dept Biochem, Yong Loo Lin Sch Med, Singapore 117596, Singapore;Natl Univ Singapore, NUS Synthet Biol Clin & Technol Innovat SynCTI, Inst Life Sci, Singapore 117456, Singapore;Natl Univ Singapore, Yong Loo Lin Sch Med, Dept Paediat, S-119074 Singapore, Singapore;Univ Maryland, Fischell Dept Bioengn, College Pk, MD 20742 USA | null | null | null | 1985;1989;1990;1992;1993;1994;1998;1999;2000;2003;2004;2005;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016 | 253 | Natl Univ Singapore, Dept Biochem, Yong Loo Lin Sch Med, Singapore 117596, Singapore;Natl Univ Singapore, NUS Synthet Biol Clin & Technol Innovat SynCTI, Inst Life Sci, Singapore 117456, Singapore | Nat. Commun. | Chang, Matthew Wook | NATURE PUBLISHING GROUP | (Caenorhabditis;,;1917;a;activities;activity;aeruginosa;against;allows;an;and;animal;anti-biofilm;as;bacteria;be;can;coli;developed;development;during;elegans;encoding;engineered;enzyme;Escherichia;findings;further;gene;generate;genetic;genetically;gut;here;host;in;including;infection;infections;inhibit;kill;laboratory;mice);microorganisms;models;modified;Nissle;of;or;P.;pathogens;potential;previously;probiotic;prophylactic;Pseudomonas;sense;shows;specific;strain;support;synthetic;system;that;the;their;therapeutic;these;to;two;use;version;virulence;vitro;vivo;we;with | Natl Univ Singapore | Bacteria can be genetically engineered to kill specific pathogens or inhibit their virulence. We previously developed a synthetic genetic system that allows a laboratory strain of Escherichia coli to sense and kill Pseudomonas aeruginosa in vitro. Here, we generate a modified version of the system, including a gene encoding an anti-biofilm enzyme, and use the probiotic strain Escherichia coli Nissle 1917 as host. The engineered probiotic shows in vivo prophylactic and therapeutic activity against P. aeruginosa during gut infection in two animal models (Caenorhabditis elegans and mice). These findings support the further development of engineered microorganisms with potential prophylactic and therapeutic activities against gut infections. | F-2169-2014;G-6220-2010;JTU-4754-2023;S-1284-2019 | CAENORHABDITIS-ELEGANS;COMMENSAL BACTERIA;EXPRESSION;IMMUNIZATION;NETWORKS;NISSLE 1917;PATHOGENS;PROTEIN;TRACT;VIRULENCE | 35 | null | null | 11 | CAENORHABDITIS-ELEGANS;COMMENSAL BACTERIA;EXPRESSION;IMMUNIZATION;NETWORKS;NISSLE 1917;PATHOGENS;PROTEIN;TRACT;VIRULENCE | WOS:000398828300001 | CORNELL UNIV, ITHACA, NY USA;Natl Univ Singapore, Singapore, Singapore;Univ Maryland, College Pk, MD USA | Singapore;USA | 2,017 | null | 0000-0002-1253-0557;0000-0002-1953-2002;0000-0002-5803-0857;0000-0003-0470-6177 | null | null | English | null | ACS SYNTH BIOL;Ann Clin Microbiol Antimicrob;ANN SURG;ANTIMICROB AGENTS CH;BIOTECHNOL BIOENG;CANCER INVEST;CHEMBIOCHEM;CURR OPIN BIOTECH;DIABETES;FEBS LETT;FEMS IMMUNOL MED MIC;FRONT CELL INFECT MI;GUT;INFECT IMMUN;INFLAMM BOWEL DIS;J ANTIBIOT;J BACTERIOL;J BIOL CHEM;J Biol Eng;J CLIN MICROBIOL;J MED MICROBIOL;J PEDIATR SURG;LANCET;MOL GEN GENET;MOL MICROBIOL;MOL SYST BIOL;MOL THER;NAT BIOTECHNOL;NAT COMMUN;NATURE;P NATL ACAD SCI USA;PLOS ONE;SCIENCE | Bentley, William E;Chang, Matthew Wook;Hwang, In Young;Koh, Elvin;Lee, Yung Seng;March, John C;Wong, Adison | 2024-03-11
ER | Alverdy, J;Bentley, W E;Canton, B;Ceri, H;Chuang, C H;Datsenko, K A;Davies, D G;De Jonge, E;Din, M O;Duan, F F;Duan, F P;Duval, M;Farr, C;Goh, Y L;Gupta, S;Hancock, V;Itoh, Y;Koh, A Y;Leatham, M P;Lee, T S;Ling, H;Lu, T K;Maltby, R;Markou, P;Marshall, J C;Moskowitz, S M;Okuda, J;Parret, A;Powell Jennifer R.;Rasouliha, B H;Renwick, M J;Rolston, K V I;Rowe, M I;Saeidi, N;Schultz, M;Scott, M;Smith, E E;St Jean, A T;Tan, M W;Terrell, J L;Ukena, S N;Volzing, K;Walsh, C T;Watanabe, R;Wessely, F;Westendorf, A M;Wild, J;Zaborina Olga | ER5FY | Singapore, Singapore;Singapore, Singapore. | 299 | null | 3 | null | 28,398,304 | Bentley, William E;Chang, Matthew Wook;Hwang, In Young;Koh, Elvin;Lee, Yung Seng;March, John C;Wong, Adison | NAT COMMUN | College Pk, MD USA;Ithaca, NY USA;Singapore, Singapore |
Appleton, E;Densmore, D;Madsen, C;Roehner, N | 10.1101/cshperspect.a023978 | a023978 | 1 BUNGTOWN RD, COLD SPRING HARBOR, NY 11724 USA | 266u1s3i3r6d6y425h5p471j2n51462t191n6z16 | Design Automation in Synthetic Biology | Harvard Univ | null | Densmore, D (corresponding author), Boston Univ, Biol Design Ctr, Boston, MA 02215 USA.;Densmore, D (corresponding author), Boston Univ, Dept Elect & Comp Engn, Boston, MA 02215 USA. | null | Appleton, Evan;Densmore, Douglas;Madsen, Curtis;Roehner, Nicholas | Cell Biology | null | WOS | Densmore, D | Boston Univ, Boston, MA USA;Harvard Univ, Boston, MA USA | 9 | Automation;biology;design;in;synthetic | 1 | null | COLD SPRING HARBOR LAB PRESS | Boston Univ, Biol Design Ctr, Boston, MA 02215 USA;Boston Univ, Biol Design Ctr, Boston, MA 02215 USA.; Densmore, D (corresponding author), Boston Univ, Dept Elect & Comp Engn, Boston, MA 02215 USA;Boston Univ, Dept Elect & Comp Engn, Boston, MA 02215 USA;Harvard Univ, Harvard Med Sch, Dept Genet, Boston, MA 02115 USA | Article | Boston Univ | COLD SPRING HARBOR | null | null | Boston Univ;Harvard Univ | null | Densmore, D (corresponding author), Boston Univ, Biol Design Ctr, Boston, MA 02215 USA.; Densmore, D (corresponding author), Boston Univ, Dept Elect & Comp Engn, Boston, MA 02215 USA. | null | Appleton, Evan;Densmore, Douglas;Madsen, Curtis;Roehner, Nicholas | 22 | 3 | 398,037,400,005 | null | USA | COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY | USA;USA.; | null | null | Harvard Univ, Harvard Med Sch, Dept Genet, Boston, MA 02115 USA | 1943-0264 | Appleton, E;Densmore, D;Madsen, C;Roehner, N | APR | dougd@bu.edu | design Automation;synthetic biology | 4 | J | Cell Biology | areas;BDA tools areas-specify;bio-design automation (BDA) tools;build;building;category;combinatorial design;design Automation;designing;designing systems;desired behavior;DNA;existing software tools;functionality;learn-and;MARKUP LANGUAGE;modern synthetic genetic regulatory networks;optimization;platform;problems;review;SELECTION;simulation;software tools;STANDARD;synthetic biology;systems;target behavior;testing;tool;tools;two types;work;workflow | Appleton, E | COMBINATORIAL DESIGN;DNA;MARKUP LANGUAGE;OPTIMIZATION;PLATFORM;SELECTION;SIMULATION;STANDARD;SYSTEMS;TOOL | null | [Appleton, Evan] Harvard Univ, Harvard Med Sch, Dept Genet, Boston, MA 02115 USA. [Madsen, Curtis; Roehner, Nicholas; Densmore, Douglas] Boston Univ, Biol Design Ctr, Boston, MA 02215 USA. [Madsen, Curtis; Roehner, Nicholas; Densmore, Douglas] Boston Univ, Dept Elect & Comp Engn, Boston, MA 02215 USA. | null | areas;BDA tools areas-specify;bio-design automation (BDA) tools;build;building;category;design automation;designing;designing systems;desired behavior;existing software tools;functionality;learn-and;modern synthetic genetic regulatory networks;problems;review;software tools;synthetic biology;systems;target behavior;testing;tools;two types;work;workflow | 10.1007/978-1-62703-450-0_10;10.1007/978-3-319-23401-4_16;10.1007/s10009-005-0187-8;10.1007/s11693-008-9013-4;10.1016/0021-9991(76)90041-3;10.1016/j.pep.2005.10.020;10.1016/j.tibtech.2011.09.001;10.1016/j.tibtech.2013.10.005;10.1016/j.ymben.2014.11.012;10.1016/S0168-9525(98)01659-X;10.1021/acssynbio.5b00124;10.1021/acssynbio.5b00194;10.1021/acssynbio.5b00210;10.1021/acssynbio.5b00215;10.1021/acssynbio.5b00219;10.1021/acssynbio.5b00232;10.1021/acssynbio.5b00284;10.1021/acssynbio.6b00146;10.1021/j100540a008;10.1021/jacs.6b01453;10.1021/sb2000116;10.1021/sb300030d;10.1021/sb300032y;10.1021/sb300034m;10.1021/sb300062c;10.1021/sb300084h;10.1021/sb300095m;10.1021/sb400024s;10.1021/sb400066m;10.1021/sb400139h;10.1021/sb400161v;10.1021/sb4001728;10.1021/sb500053j;10.1021/sb500352b;10.1023/A:1020926525495;10.1038/520141a;10.1038/msb4100073;10.1038/nature04342;10.1038/nature07389;10.1038/nature08187;10.1038/nbt.1568;10.1038/nbt.2891;10.1038/nbt.2899;10.1038/nbt.3063;10.1038/nbt0708-771;10.1038/nbt1209-1099;10.1038/nbt1413;10.1038/NINDIA.2010.145];10.1038/NMETH1010;10.1038/nprot.2011.308;10.1063/1.1613254;10.1063/1.1824902;10.1073/pnas.85.8.2444;10.1089/10665270252833208;10.1093/bib/bbp011;10.1093/bioinformatics/btg015;10.1093/bioinformatics/bti046;10.1093/bioinformatics/btl485;10.1093/bioinformatics/btm091;10.1093/bioinformatics/btn468;10.1093/bioinformatics/btp029;10.1093/bioinformatics/btp401;10.1093/bioinformatics/btp457;10.1093/bioinformatics/btr048;10.1093/bioinformatics/btt772;10.1093/nar/16.5.1861;10.1093/nar/gkg595;10.1093/nar/gkl274;10.1093/nar/gkp361;10.1093/nar/gkq165;10.1093/nar/gkr433;10.1093/nar/gks531;10.1093/nar/gks596;10.1093/nar/gkt1139;10.1098/rsif.2008.0516.focus;10.1098/rstb.2005.1676;10.1109/JPROC.2008.925458;10.1126/science.1231143;10.1126/science.aac7341;10.1145/2641571;10.1145/2660773;10.1186/1752-0509-2-24;10.1186/1752-0509-4-45;10.1186/1754-1611-2-5;10.1186/1754-1611-3-19;10.1186/1754-1611-3-4;10.1186/1754-1611-7-13;10.1371/journal.pbio.1002310;10.1371/journal.pone.0003647;10.1371/journal.pone.0006441;10.1371/journal.pone.0016765;10.1371/journal.pone.0018882;10.1371/journal.pone.0021622;10.1371/journal.pone.0022490;10.3389/fbioe.2014.00042;10.3389/fbioe.2015.00093;1721.1/66172;[10.1016/S0076-6879(11)87019-9, 10.1016/B978-0-12-381270-4.00019-6];[10.1038/NMETH.1318, 10.1038/nmeth.1318];[10.1038/NMETH.2939, 10.1038/nmeth.2939];[10.1038/NMETH.3252, 10.1038/nmeth.3252] | Harvard Univ | Appleton, E;Densmore, D;Madsen, C;Roehner, N | Appleton, E: Harvard Univ, Harvard Med Sch, Dept Genet, Boston, MA 02115 USA | Densmore, Douglas | null | 115 | null | USA | Boston Univ;Harvard Univ | Appleton, Evan | Green Published, Bronze | COMBINATORIAL DESIGN;DNA;MARKUP LANGUAGE;OPTIMIZATION;PLATFORM;SELECTION;SIMULATION;STANDARD;SYSTEMS;TOOL | Appleton, Evan; Madsen, Curtis; Roehner, Nicholas; Densmore, Douglas; | null | Boston Univ, Biol Design Ctr, Boston, MA 02215 USA;Boston Univ, Dept Elect & Comp Engn, Boston, MA 02215 USA;Harvard Univ, Harvard Med Sch, Dept Genet, Boston, MA 02115 USA | Boston Univ, Biol Design Ctr, Boston, MA 02215 USA;Boston Univ, Dept Elect & Comp Engn, Boston, MA 02215 USA;Harvard Univ, Harvard Med Sch, Dept Genet, Boston, MA 02115 USA | null | null | 4 | 1864;1966;1976;1977;1988;1992;1995;1999;2000;2002;2003;2004;2005;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016 | 44 | Boston Univ, Biol Design Ctr, Boston, MA 02215 USA;Boston Univ, Dept Elect & Comp Engn, Boston, MA 02215 USA | Cold Spring Harbor Perspect. Biol. | Densmore, Douglas | COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT | (BDA);,;a;analyzing;and;are;areas;areas-specify;automation;BDA;be;behavior;bio-design;biology;build;building;called;can;category;create;design;designed;designing;desired;detail;discuss;existing;for;functionality;genetic;how;in;introduce;learn-and;modern;networks;of;problems;refers;regulatory;review;show;software;solve;some;synthetic;systems;target;test;testing;that;the;then;these;they;this;to;together;tools;two;types;used;we;with;work;workflow | Boston Univ | Design automation refers to a category of software tools for designing systems that work together in a workflow for designing, building, testing, and analyzing systems with a target behavior. In synthetic biology, these tools are called bio-design automation (BDA) tools. In this review, we discuss the BDA tools areas-specify, design, build, test, and learn-and introduce the existing software tools designed to solve problems in these areas. We then detail the functionality of some of these tools and show how they can be used together to create the desired behavior of two types of modern synthetic genetic regulatory networks. | AAC-7059-2020 | COMBINATORIAL DESIGN;DNA;MARKUP LANGUAGE;OPTIMIZATION;PLATFORM;SELECTION;SIMULATION;STANDARD;SYSTEM;TOOL | 0 | null | null | 27 | COMBINATORIAL DESIGN;DNA;MARKUP LANGUAGE;OPTIMIZATION;PLATFORM;SELECTION;SIMULATION;STANDARD;SYSTEM;TOOL | WOS:000398037400005 | Boston Univ, Boston, MA USA;Harvard Univ, Boston, MA USA | USA | 2,017 | null | null | null | null | English | null | 3 INT WORKSH BIOD AU;5 RICHARD TAPIA CELE;85 RFC;ACM J EMERG TECH COM;ACM Journal on Emerging Technologies in Computing Systems;ACS SYNTH BIOL;BIOINFORMATICS;BMC SYST BIOL;BRIEF BIOINFORM;COMMUNICATION;Deterministic versus stochastic modelling in biochemistry and systems biology;FRONT BIOENG BIOTECH;Front Bioeng Biotechnol;International Journal on Software Tools for Technology Transfer;J AM CHEM SOC;J Biol Eng;J CHEM PHYS;J COMPUT BIOL;J COMPUT PHYS;J PHARMACOKINET BIOP;J PHYS CHEM-US;J R SOC INTERFACE;LECT N BIOINFORMAT;LECT NOTES COMPUT SC;METAB ENG;METHOD ENZYMOL;METHODS MOL BIOL;MOL SYST BIOL;NAT BIOTECHNOL;NAT INDIA;NAT METHODS;NAT PROTOC;NATURE;NUCLEIC ACIDS RES;P EPSRC EM COMP PAR;P IEEE;P NATL ACAD SCI USA;PHILOS T R SOC B;PLOS BIOL;PLOS ONE;PROTEIN EXPRES PURIF;SCIENCE;Syst Synth Biol;The Verilog hardware description language;THESIS;TRENDS BIOTECHNOL;TRENDS GENET | Appleton, Evan;Densmore, Douglas;Madsen, Curtis;Roehner, Nicholas | 2024-03-11
ER | [Anonymous];Andrianantoandro, E;Appleton, E;Arkin, A;Bates, J T;Beal, J;Bhatia, S;Bilitchenko, L;Bilofsky, H S;Blakes, J;Borujeni, A E;Canton, B;Cao, Y;Castillo-Hair, S M;Chakrabarti, S;Chandran Deepak;Chelliah Vijayalakshmi;Cong, L;Czar, M J;Dasika, M S;De Jong, H;Densmore D.;Densmore, D;Densmore, D M;Dhar Pk.;Drummond, A J;Endy, D;Engler, C;Funahashi, A;Galdzicki M.;Galdzicki, M;Gibson, D G;Gillespie, D T;Goler J.A.;Haiyao Huang;Ham, T S;Hayden, E C;Hill, A D;Hillson, N J;Hinton, A;Hoops, S;Huber, W;Hucka, M;Huynh, L;Iverson, S V;Jang, S S;Kahl, L J;Kelly Jason, R;Kim, T Y;Koressaar, T;Kwiatkowska, M;Leaver-Fay, A;Lecca Paola.;Li, M Z;Linshiz, G;Lux, M W;Lynch Michael;Madsen, C;Marchisio Mario Andrea;Mcadams, H H;Mirschel, S;Misirli, G;Myers, C J;Nestorov, I A;Nielsen, A A K;Oberortner, E;Olivier, B G;Pearson, W R;Pedersen, M;Petri Carl Adam;Quan, J Y;Quinn, J Y;Quintin, M;Raman, K;Rocha, I;Rodrigo Guillermo;Rodrigo, G;Roehner, N;Salis, H M;Sarrion-Perdigones, A;Sauro H.;Schellenberger, J;Shetty Reshma, P;Smanski, M J;Smith, L P;Smolke, C D;Starruy, J;Stricker, J;Thomas Donald E.;Thompson, R;Untergasser, A;Vasilev, V;Vilanova, C;Waage P.;Wang, H H;Weber, E;Wilson, E H;Wu, G;Yaman, F;Younes H. L. S.;Zuker, M | EQ4HR | Boston, MA USA;Boston, MA USA. | 50 | null | 2 | null | 28,246,188 | Appleton, Evan;Densmore, Douglas;Madsen, Curtis;Roehner, Nicholas | CSH PERSPECT BIOL | Boston, MA USA |
Chan, H F;Leong, K W;Ma, S;Tian, J | 10.1039/c6nr08224f | null | THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND | o76o276l2g3a6f1t4g674w5c6o6s1b1n141c5f | High-throughput screening of microchip-synthesized genes in programmable double-emulsion droplets | Duke Univ | null | Leong, KW (corresponding author), Columbia Univ, Dept Biomed Engn, New York, NY 10027 USA.;Leong, KW (corresponding author), Columbia Univ, Dept Syst Biol, New York, NY 10027 USA.;Leong, KW (corresponding author), Duke Univ, Dept Biomed Engn, Durham, NC 27705 USA. | null | Chan, H F;Leong, K W;Ma, S;Tian, J | Chemistry, Multidisciplinary;Materials Science, Multidisciplinary;Nanoscience & Nanotechnology;Physics, Applied | NIH [HL109442, AI096305, GM110494]; Guangdong Innovative and Entrepreneurial Research Team Program [2013S086]; Global Research Laboratory Program (Korean NSF GRL) [2015032163]; Sir Edward Youde Memorial Fund Council (Hong Kong) | WOS | Leong, K W | Chinese Acad Sci, Tianjin, Peoples R China;Columbia Univ, New York, NY USA;Duke Univ, Durham, NC USA;Gen Biosyst Inc, Morrisville, NY USA;MIT, Cambridge, MA USA | 9 | double-emulsion;droplets;genes;high-throughput;in;microchip-synthesized;of;programmable;screening | 2 | Chan, Fai;Leong, Kam W | ROYAL SOC CHEMISTRY | Chinese Acad Sci, Tianjin Inst Ind Biotechnol, Tianjin 300308, Peoples R China;Columbia Univ, Dept Biomed Engn, New York, NY 10027 USA;Columbia Univ, Dept Syst Biol, New York, NY 10027 USA;Duke Univ, Dept Biomed Engn, Durham, NC 27705 USA;Duke Univ, Dept Biomed Engn, Durham, NC 27705 USA.; Leong, KW (corresponding author), Columbia Univ, Dept Biomed Engn, New York, NY 10027 USA.; Leong, KW (corresponding author), Columbia Univ, Dept Syst Biol, New York, NY 10027 USA;Gen Biosyst Inc, Morrisville, NY 27560 USA;MIT, Dept Mech Engn, Cambridge, MA 02139 USA | Article | Columbia Univ;Duke Univ | CAMBRIDGE | null | null | Chinese Acad Sci;Columbia Univ;Duke Univ;Gen Biosyst Inc;MIT | Global Research Laboratory Program (Korean NSF GRL);Guangdong Innovative and Entrepreneurial Research Team Program;NIH;Sir Edward Youde Memorial Fund Council (Hong Kong) | Leong, KW (corresponding author), Duke Univ, Dept Biomed Engn, Durham, NC 27705 USA.; Leong, KW (corresponding author), Columbia Univ, Dept Biomed Engn, New York, NY 10027 USA.; Leong, KW (corresponding author), Columbia Univ, Dept Syst Biol, New York, NY 10027 USA. | 3495 | Chan, H F;Leong, K W;Ma, S;Tian, J | 92 | 6 | 397,125,500,017 | Global Research Laboratory Program (Korean NSF GRL) [2015032163];Guangdong Innovative and Entrepreneurial Research Team Program [2013S086];NIH [HL109442, AI096305, GM110494];Sir Edward Youde Memorial Fund Council (Hong Kong) | China;USA | NANOSCALE | USA;USA.; | null | null | Duke Univ, Dept Biomed Engn, Durham, NC 27705 USA | 2040-3364 | Chan, H F;Leong, K W;Ma, S;Tian, J | MAR 14 | kam.leong@columbia.edu | high-throughput screening;microchip-synthesized genes;programmable double-emulsion droplets | 4 | J | Chemistry;Materials Science;Physics;Science & Technology - Other Topics | 100 bacteria per droplet;100 times;24 h;amplification;aqueous phase analysis;automated microfluidic devices;BACTERIA;bacteria bearing individual fluorescent gene variants;biotechnology;coli) cells;COMPARTMENTALIZATION;conventional bulk experiment;custom-built microarray inkjet synthesizer;DE droplets;demanding high-throughput screening technology;detectable fluorescence signals;DNA;droplet technology;ENCAPSULATION;ENRICHMENT;error correction method;Escherichia coli (E;evolution;expression;external phase;external solution initiates target gene expression;fluorescence signals;fluorescence-activated cell sorting (FACS);fluorescent clones;fluorescent proteins;functionalities;functionally-correct genes;high-throughput screening;highthroughput;individualized assays;induced expression;inner droplet environment;intact droplets;isopropyl beta-D-1-thiogalactopyranoside (IPTG);least;LIBRARIES;limitations;microchip-synthesized genes;MICROENVIRONMENT;MICROFLUIDICS;microfluidics-generated water-in-oil-in-water (W/O/W) double emulsion (DE) droplets;optimization;permeation;POLYMERASE EXTENSION CLONING;potential;programmable double-emulsion droplets;proliferation;PROTEIN EXPRESSION;rapid advances;recent advances;red fluorescent protein (rfp) gene;screening;screening DE droplets;screening platform;single cells;SINGLE-CELLS;single-emulsion droplets;synthetic biology;synthetic fluorescent proteins;synthetic gene variants;synthetic genes;thin oil;time-and labor-intensive cell culture;vast number;water-in-oil (W/O) emulsion droplets | Chan, H F | AMPLIFICATION;DNA;ENCAPSULATION;EVOLUTION;LIBRARIES;MICROENVIRONMENT;MICROFLUIDICS;POLYMERASE EXTENSION CLONING;PROTEIN EXPRESSION;SINGLE-CELLS | 3485 | [Chan, H. F.; Ma, S.; Tian, J.; Leong, K. W.] Duke Univ, Dept Biomed Engn, Durham, NC 27705 USA. [Chan, H. F.; Leong, K. W.] Columbia Univ, Dept Biomed Engn, New York, NY 10027 USA. [Ma, S.; Tian, J.] Gen Biosyst Inc, Morrisville, NY 27560 USA. [Tian, J.] Chinese Acad Sci, Tianjin Inst Ind Biotechnol, Tianjin 300308, Peoples R China. [Leong, K. W.] Columbia Univ, Dept Syst Biol, New York, NY 10027 USA. [Chan, H. F.] MIT, Dept Mech Engn, Cambridge, MA 02139 USA. | Funding support from NIH (HL109442, AI096305, GM110494), the Guangdong Innovative and Entrepreneurial Research Team Program No. 2013S086, and the Global Research Laboratory Program (Korean NSF GRL; 2015032163) is acknowledged. HFC acknowledges fellowship support from the Sir Edward Youde Memorial Fund Council (Hong Kong). | 100 bacteria per droplet;100 times;24 h;aqueous phase analysis;automated microfluidic devices;bacteria;bacteria bearing individual fluorescent gene variants;biotechnology;coli) cells;compartmentalization;conventional bulk experiment;custom-built microarray inkjet synthesizer;DE droplets;demanding high-throughput screening technology;detectable fluorescence signals;droplet technology;enrichment;error correction method;Escherichia coli (E;expression;external phase;external solution initiates target gene expression;fluorescence signals;fluorescence-activated cell sorting (FACS);fluorescent clones;fluorescent proteins;functionalities;functionally-correct genes;high-throughput screening;highthroughput;individualized assays;induced expression;inner droplet environment;intact droplets;isopropyl beta-D-1-thiogalactopyranoside (IPTG);least;limitations;microchip-synthesized genes;microfluidics-generated water-in-oil-in-water (W/O/W) double emulsion (DE) droplets;optimization;permeation;potential;proliferation;protein expression;rapid advances;recent advances;red fluorescent protein (rfp) gene;screening;screening DE droplets;screening platform;single cells;single-emulsion droplets;synthetic biology;synthetic fluorescent proteins;synthetic gene variants;synthetic genes;thin oil;time-and labor-intensive cell culture;vast number;water-in-oil (W/O) emulsion droplets | 10.1002/bit.20289;10.1002/cbic.200900384;10.1002/smll.201502932;10.1007/s00253-011-3642-3;10.1016/j.addr.2012.10.003;10.1016/j.biomaterials.2013.03.002;10.1016/j.cbpa.2008.01.027;10.1016/j.tibtech.2011.10.002;10.1016/S0958-1669(99)00003-8;10.1021/ac2022794;10.1021/nn203012q;10.1021/nn500810n;10.1038/nature03151;10.1038/nbt.1716;10.1038/nbt.1847;10.1038/nbt.2421;10.1038/nbt0798-652;10.1038/nmeth.2137;10.1038/nprot.2010.181;10.1038/srep03462;10.1039/b805456h;10.1039/c1lc20317g;10.1039/c2lc90046g;10.1063/1.3528299;10.1073/pnas.0809851105;10.1073/pnas.0910781107;10.1093/nar/gkh793;10.1093/nar/gkh879;10.1093/nar/gkq677;10.1093/nar/gks546;10.1093/rb/rbw009;10.1186/2047-217X-1-4;10.1371/journal.pone.0006441;[10.1039/c2lc00013j, 10.1039/C2LC00013J] | Duke Univ | Chan, H F;Leong, K W;Ma, S;Tian, J | Chan, H F: Duke Univ, Dept Biomed Engn, Durham, NC 27705 USA | Chan, Fai;Leong, Kam W | 2013S086;2015032163;AI096305;GM110494;HL109442 | 35 | null | USA | Chinese Acad Sci;Columbia Univ;Duke Univ;Gen Biosyst Inc;MIT | Chan, H F | Green Accepted | AMPLIFICATION;DNA;ENCAPSULATION;EVOLUTION;LIBRARIES;MICROENVIRONMENT;MICROFLUIDICS;POLYMERASE EXTENSION CLONING;PROTEIN EXPRESSION;SINGLE-CELLS | Chan, H. F.; Ma, S.; Tian, J.; Leong, K. W.; | null | Chinese Acad Sci, Tianjin Inst Ind Biotechnol, Tianjin 300308, Peoples R China;Columbia Univ, Dept Biomed Engn, New York, NY 10027 USA;Columbia Univ, Dept Syst Biol, New York, NY 10027 USA;Duke Univ, Dept Biomed Engn, Durham, NC 27705 USA;Gen Biosyst Inc, Morrisville, NY 27560 USA;MIT, Dept Mech Engn, Cambridge, MA 02139 USA | Chinese Acad Sci, Tianjin Inst Ind Biotechnol, Tianjin 300308, Peoples R China;Columbia Univ, Dept Biomed Engn, New York, NY 10027 USA;Columbia Univ, Dept Syst Biol, New York, NY 10027 USA;Duke Univ, Dept Biomed Engn, Durham, NC 27705 USA;Gen Biosyst Inc, Morrisville, NY 27560 USA;MIT, Dept Mech Engn, Cambridge, MA 02139 USA | 2040-3372 | null | 10 | 1998;1999;2004;2005;2008;2009;2010;2011;2012;2013;2014;2016 | 24 | Columbia Univ, Dept Biomed Engn, New York, NY 10027 USA;Columbia Univ, Dept Syst Biol, New York, NY 10027 USA;Duke Univ, Dept Biomed Engn, Durham, NC 27705 USA | Nanoscale | Leong, K W | ROYAL SOC CHEMISTRY | (DE);(E;(FACS);(IPTG);(rfp);(W/O);(W/O/W);,;100;24;a;advances;allows;an;analysis;and;aqueous;are;as;assays;at;automated;bacteria;bearing;beta-d-1-thiogalactopyranoside;biology;biotechnology;bulk;by;cannot;cell;cells;clones;coli;coli);communicate;compartmentalization;containing;conventional;correction;culture;custom-built;de;demanding;demonstrated;detectable;devices;double;droplet;droplets;easily;employing;emulsion;enable;encapsulated;enhanced;enrichment;environment;error;Escherichia;experiment;expression;external;fluorescence;fluorescence-activated;fluorescent;for;from;functionalities;functionally-correct;further;gene;generates;genes;h;help;high-throughput;highthroughput;however;in;incompatible;increasingly;individual;individualized;induced;initiates;inkjet;inner;intact;into;is;isopropyl;labor-intensive;layer;least;limitations;method;microarray;microchip-synthesized;microfluidic;microfluidics-generated;miniaturized;number;obviates;of;oil;optimization;overcome;per;permeation;phase;platform;potential;present;proliferation;protein;proteins;rapid;realize;recent;red;required;screened;screening;signals;similar;single;single-emulsion;solution;sorting;such;synthesized;synthesizer;synthetic;target;technology;that;the;then;these;thin;this;through;time-and;times;to;typically;using;variants;vast;water-in-oil;water-in-oil-in-water;we;where;which;with;within | Columbia Univ;Duke Univ | The rapid advances in synthetic biology and biotechnology are increasingly demanding high-throughput screening technology, such as screening of the functionalities of synthetic genes for optimization of protein expression. Compartmentalization of single cells in water-in-oil (W/O) emulsion droplets allows screening of a vast number of individualized assays, and recent advances in automated microfluidic devices further help realize the potential of droplet technology for high-throughput screening. However these single-emulsion droplets are incompatible with aqueous phase analysis and the inner droplet environment cannot easily communicate with the external phase. We present a highthroughput, miniaturized screening platform for microchip-synthesized genes using microfluidics-generated water-in-oil-in-water (W/O/W) double emulsion (DE) droplets that overcome these limitations. Synthetic gene variants of fluorescent proteins are synthesized with a custom-built microarray inkjet synthesizer, which are then screened for expression in Escherichia coli (E. coli) cells. Bacteria bearing individual fluorescent gene variants are encapsulated as single cells into DE droplets where fluorescence signals are enhanced by 100 times within 24 h of proliferation. Enrichment of functionally-correct genes by employing an error correction method is demonstrated by screening DE droplets containing fluorescent clones of bacteria with the red fluorescent protein (rfp) gene. Permeation of isopropyl beta-D-1-thiogalactopyranoside (IPTG) through the thin oil layer from the external solution initiates target gene expression. The induced expression of the synthetic fluorescent proteins from at least similar to 100 bacteria per droplet generates detectable fluorescence signals to enable fluorescence-activated cell sorting (FACS) of the intact droplets. This technology obviates time-and labor-intensive cell culture typically required in conventional bulk experiment. | O-9302-2019;P-5970-2014 | AMPLIFICATION;DNA;ENCAPSULATION;EVOLUTION;LIBRARIES;MICROENVIRONMENT;MICROFLUIDICS;POLYMERASE EXTENSION CLONING;PROTEIN EXPRESSION;SINGLE-CELL | 3 | null | null | 11 | AMPLIFICATION;DNA;ENCAPSULATION;EVOLUTION;LIBRARIES;MICROENVIRONMENT;MICROFLUIDICS;POLYMERASE EXTENSION CLONING;PROTEIN EXPRESSION;SINGLE-CELL | WOS:000397125500017 | Chinese Acad Sci, Tianjin, Peoples R China;Columbia Univ, New York, NY USA;Duke Univ, Durham, NC USA;Gen Biosyst Inc, Morrisville, NY USA;MIT, Cambridge, MA USA | China;USA | 2,017 | null | 0000-0002-8133-4955;0000-0003-0573-1251 | null | null | English | null | ACS NANO;ADV DRUG DELIVER REV;ANAL CHEM;APPL MICROBIOL BIOT;BIOMATERIALS;BIOMICROFLUIDICS;BIOTECHNOL BIOENG;CHEMBIOCHEM;CURR OPIN BIOTECH;CURR OPIN CHEM BIOL;GIGASCIENCE;IEEE ENG MED BIOL SO;LAB CHIP;NAT BIOTECHNOL;NAT METHODS;NAT PROTOC;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PLOS ONE;REGEN BIOMATER;SCI REP-UK;SMALL;TRENDS BIOTECHNOL | Chan, H F;Leong, K W;Ma, S;Tian, J | 2024-03-11
ER | Agresti, J J;Antipov, E;Baneyx, F;Bershtein, S;Borovkov, A Y;Chan, H F;Chang, C M;Chen, F Y;Chiu, Y L;Edd, J F;Hung, P J;Juul, S;Kemna, E W M;Kim, H;Kosuri, S;Ma, S Y;Malakar, P;Myers F. B.;Quan, J Y;Richmond, K E;Schatz, M C;Schwartz, J J;Shendure, J;Tawfik, D S;Tian, J D;Wu, H W;Yang, G Y;Yang, S K;Zhang, Y;Zhou, X C | EP1DL | Durham, NC USA.;New York, NY USA;New York, NY USA. | 27 | null | 5 | null | 28,239,692 | Chan, H F;Leong, K W;Ma, S;Tian, J | NANOSCALE | Cambridge, MA USA;Durham, NC USA;Morrisville, NY USA;New York, NY USA;Tianjin, Peoples R China |
Ausländer, D;Ausländer, S;Folcher, M;Fussenegger, M;Müller, M;Sikorski, J;Spinnler, A | 10.1038/NCHEMBIO.2281 | null | 75 VARICK ST, 9TH FLR, NEW YORK, NY 10013-1917 USA | 2o2u6u1yl3l6ja2d3q472r241a562s4z145q3y | Designed cell consortia as fragrance-programmable analog-to-digital converters | Swiss Fed Inst Technol | null | Fussenegger, M (corresponding author), Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland.;Fussenegger, M (corresponding author), Univ Basel, Fac Sci, Basel, Switzerland. | null | Auslander, David;Auslander, Simon;Folcher, Marc;Fussenegger, Martin;Muller, Marius;Sikorski, Julian;Spinnler, Andrea | Biochemistry & Molecular Biology | European Research Council (ERC) [321381]; National Centre of Competence in Research (NCCR) for Molecular Systems Engineering | WOS | Fussenegger, M | Swiss Fed Inst Technol, Basel, Switzerland;Univ Basel, Basel, Switzerland | 13 | analog-to-digital;as;cell;consortia;converters;designed;fragrance-programmable | 1 | Folcher, marc | NATURE PUBLISHING GROUP | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland;Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland.; Fussenegger, M (corresponding author), Univ Basel, Fac Sci, Basel, Switzerland;Univ Basel, Fac Sci, Basel, Switzerland | Article | Swiss Fed Inst Technol;Univ Basel | NEW YORK | null | null | Swiss Fed Inst Technol;Univ Basel | European Research Council (ERC);National Centre of Competence in Research (NCCR) for Molecular Systems Engineering | Fussenegger, M (corresponding author), Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland.; Fussenegger, M (corresponding author), Univ Basel, Fac Sci, Basel, Switzerland. | + | Auslander, David;Auslander, Simon;Folcher, Marc;Fussenegger, Martin;Muller, Marius;Sikorski, Julian;Spinnler, Andrea | 59 | 2 | 394,431,500,015 | European Research Council (ERC) [321381];National Centre of Competence in Research (NCCR) for Molecular Systems Engineering | Switzerland | NATURE CHEMICAL BIOLOGY | Switzerland | null | null | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland | 1552-4450 | Ausländer, D;Ausländer, S;Folcher, M;Fussenegger, M;Müller, M;Sikorski, J;Spinnler, A | MAR | fussenegger@bsse.ethz.ch | designed cell consortia;fragrance-programmable analog-to-digital converters | 7 | J | Biochemistry & Molecular Biology | 2-bit AND-;ADC;bioelectronic interfaces synchronizing analog metabolic pathways;CANCER-CELLS;cell-based therapy goals;control cellular activities;CONTROLLED TRANSGENE EXPRESSION;designed cell consortia;development;diffusible cell-to-cell signaling compounds;digital electronic circuits;digital electronics;digital gene expression;digital precision;digitization unit;dynamic remote control;electromagnetic waves;fragrance-programmable analog-to-digital converters;gas-to-liquid transducer converting fragrance intensity;genetic amplifier circuit;homeostasis;living cells;logic gates;mammalian cells;MAMMALIAN-CELLS;Mice;multiple sampling-and-quantization modules sensing analog gaseous fragrance inputs;NOR-gate logic;novel biosensors;OR-;principles;programmable arithmetic calculations;rational engineering;recombinase-based digital expression switches enabling 2-bit processing;remote control;signal-to-noise ratio;single cells;synchronized cell consortia;synthetic ADCs;synthetic biology;synthetic circuits;synthetic gene networks;synthetic multilayered gaseous-fragrance-programmable analog-to-digital converter (ADC);SYSTEM;TRANSGENES | Müller, M | CANCER-CELLS;CONTROLLED TRANSGENE EXPRESSION;HOMEOSTASIS;LIVING CELLS;logic gates;MAMMALIAN-CELLS;MICE;PRINCIPLES;SYNTHETIC CIRCUITS;SYSTEM | 309 | [Muller, Marius; Auslander, Simon; Spinnler, Andrea; Auslander, David; Sikorski, Julian; Folcher, Marc; Fussenegger, Martin] Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland. [Fussenegger, Martin] Univ Basel, Fac Sci, Basel, Switzerland. | We thank T. Horn, E. Montani, T. Lopes and V. Jaeggin for their support with microscopy and flow cytometry. We thank F. Sedlmayer, V. Viswam, S. Burgel and P. Buchmann for their generous advice and O. Chepurny and G. Holz (Department of Physiology and Neuroscience, New York University School of Medicine, New York, USA), H. Matsunami (Department of Molecular Genetics and Microbiology, Duke University Medical Center, North Carolina, USA), H. Ye (Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China) and W. Bacchus (Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland) for providing plasmids and genetic components. This work was supported by a European Research Council (ERC) advanced grant (ProNet, no. 321381) and in part by funding from the National Centre of Competence in Research (NCCR) for Molecular Systems Engineering awarded to M.F. | 2-bit AND-;ADC;bioelectronic interfaces synchronizing analog metabolic pathways;cell-based therapy goals;control cellular activities;development;diffusible cell-to-cell signaling compounds;digital electronic circuits;digital electronics;digital gene expression;digital precision;digitization unit;dynamic remote control;electromagnetic waves;gas-to-liquid transducer converting fragrance intensity;genetic amplifier circuit;logic gates;mammalian cells;multiple sampling-and-quantization modules sensing analog gaseous fragrance inputs;NOR-gate logic;novel biosensors;OR-;programmable arithmetic calculations;rational engineering;recombinase-based digital expression switches enabling 2-bit processing;remote control;signal-to-noise ratio;single cells;synchronized cell consortia;synthetic ADCs;synthetic biology;synthetic gene networks;synthetic multilayered gaseous-fragrance-programmable analog-to-digital converter (ADC);transgenes | 10.1016/j.cell.2004.11.021;10.1016/j.cell.2016.01.011;10.1016/j.cell.2016.01.012;10.1016/j.copbio.2007.09.002;10.1016/j.cub.2006.07.007;10.1016/j.jconrel.2010.11.016;10.1016/j.molcel.2014.06.007;10.1016/j.ymben.2011.06.003;10.1016/j.ymben.2013.11.003;10.1021/sb300044r;10.1038/35011540;10.1038/35016072;10.1038/35093026;10.1038/74493;10.1038/msb.2010.99;10.1038/nature07616;10.1038/nature08959;10.1038/nature09565;10.1038/nature09679;10.1038/nature11149;10.1038/nature11516;10.1038/nbt.1617;10.1038/nbt.2510;10.1038/nchembio.1680;10.1038/ncomms11658;10.1038/ncomms6392;10.1038/nm.3646;10.1038/nn.2841;10.1038/nrg3094;10.1038/nrg3197;10.1073/pnas.0901501106;10.1073/pnas.1001721107;10.1073/pnas.1111704108;10.1073/pnas.1514383113;10.1073/pnas.1604391113;10.1074/jbc.M109.099689;10.1093/nar/13.12.4267;10.1093/nar/gkm466;10.1093/nar/gkr1251;10.1093/nar/gng069;10.1126/science.1172005;10.1126/science.1203535;10.1126/science.1205527;10.1126/science.1216753;10.1126/science.1232758;10.1126/science.1249168;10.1126/science.aad8559;10.1126/scitranslmed.aac4964;[10.1038/NMETH.2926, 10.1038/nmeth.2926];[10.1038/NMETH.2996, 10.1038/nmeth.2996];[10.1038/NMETH.3147, 10.1038/nmeth.3147] | Swiss Fed Inst Technol | Ausländer, D;Ausländer, S;Folcher, M;Fussenegger, M;Müller, M;Sikorski, J;Spinnler, A | Müller, M: Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland | Folcher, marc | 321381 | 51 | null | Switzerland | Swiss Fed Inst Technol;Univ Basel | Muller, Marius | null | CANCER-CELLS;CONTROLLED TRANSGENE EXPRESSION;HOMEOSTASIS;LIVING CELLS;LOGIC GATES;MAMMALIAN-CELLS;MICE;PRINCIPLES;SYNTHETIC CIRCUITS;SYSTEM | Muller, Marius; Auslander, Simon; Spinnler, Andrea; Auslander, David; Sikorski, Julian; Folcher, Marc; Fussenegger, Martin; | null | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland;Univ Basel, Fac Sci, Basel, Switzerland | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland;Univ Basel, Fac Sci, Basel, Switzerland | 1552-4469 | null | 3 | 1985;1999;2000;2001;2003;2004;2006;2007;2009;2010;2011;2012;2013;2014;2015;2016 | 36 | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland;Univ Basel, Fac Sci, Basel, Switzerland | Nat. Chem. Biol. | Fussenegger, Martin | NATURE PUBLISHING GROUP | (ADC);,;2-bit;;;a;achieve;activities;ADC;ADCs;advances;allowing;amplifier;analog;analog-to-digital;and;AND-;arithmetic;bioelectronic;biology;biosensors;calculations;can;cell;cell-based;cell-to-cell;cells;cellular;circuit;circuits;complexity;compounds;consists;consortia;control;converter;converting;designed;development;diffusible;digital;digitization;dynamic;electromagnetic;electronic;electronics;enable;enabling;engineering;expression;for;fragrance;gas-to-liquid;gaseous;gaseous-fragrance-programmable;gates;gene;genetic;goals;have;improve;in;inputs;intensity;interfaces;into;logic;mammalian;may;metabolic;modules;multilayered;multiple;nearly;networks;NOR-gate;novel;of;or;OR-;pathways;perform;precision;processing;programmable;provide;ratio;rational;reached;recombinase-based;remote;remotely;sampling-and-quantization;sensing;signal-to-noise;signaling;single;switches;synchronized;synchronizing;synthetic;that;the;therapy;through;to;transducer;transgenes;unit;waves;we;with | Swiss Fed Inst Technol;Univ Basel | Synthetic biology advances the rational engineering of mammalian cells to achieve cell-based therapy goals. Synthetic gene networks have nearly reached the complexity of digital electronic circuits and enable single cells to perform programmable arithmetic calculations or to provide dynamic remote control of transgenes through electromagnetic waves. We designed a synthetic multilayered gaseous-fragrance-programmable analog-to-digital converter (ADC) allowing for remote control of digital gene expression with 2-bit AND-, OR- and NOR-gate logic in synchronized cell consortia. The ADC consists of multiple sampling-and-quantization modules sensing analog gaseous fragrance inputs; a gas-to-liquid transducer converting fragrance intensity into diffusible cell-to-cell signaling compounds; a digitization unit with a genetic amplifier circuit to improve the signal-to-noise ratio; and recombinase-based digital expression switches enabling 2-bit processing of logic gates. Synthetic ADCs that can remotely control cellular activities with digital precision may enable the development of novel biosensors and may provide bioelectronic interfaces synchronizing analog metabolic pathways with digital electronics. | HGD-3318-2022 | CANCER-CELLS;CONTROLLING TRANSGENE EXPRESSION;HOMEOSTASIS;LIVING CELLS;LOGIC GATES;MAMMALIAN-CELLS;MICE;PRINCIPLES;SYNTHETIC CIRCUITS;SYSTEM | 0 | null | null | 9 | CANCER-CELLS;CONTROLLING TRANSGENE EXPRESSION;HOMEOSTASIS;LIVING CELLS;logic gates;MAMMALIAN-CELLS;MICE;PRINCIPLES;SYNTHETIC CIRCUITS;SYSTEM | WOS:000394431500015 | Swiss Fed Inst Technol, Basel, Switzerland;Univ Basel, Basel, Switzerland | Switzerland | 2,017 | null | 0000-0002-3544-0554 | null | null | English | null | ACS SYNTH BIOL;CELL;CURR BIOL;CURR OPIN BIOTECH;J BIOL CHEM;J CONTROL RELEASE;METAB ENG;MOL CELL;MOL SYST BIOL;NAT BIOTECHNOL;NAT CHEM BIOL;NAT COMMUN;NAT MED;NAT METHODS;NAT NEUROSCI;NAT REV GENET;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;SCI TRANSL MED;SCIENCE | Auslander, David;Auslander, Simon;Folcher, Marc;Fussenegger, Martin;Muller, Marius;Sikorski, Julian;Spinnler, Andrea | 2024-03-11
ER | Ausländer, D;Ausländer, S;Benenson, Y;Bonnet, J;Boorsma, M;Brophy, J A N;Bushdid, C;Chen, Y Y;Clark, B;Dreosti, E;Fenno, L E;Firestein, S;Folcher, M;Friedland, A E;Gitzinger, M;Hahnloser, R H R;Hartwell, L H;Kemmer, C;Lapique, N;Moon, T S;Morel, M;Morsut, L;Nern, A;Nissim, L;Regot, S;Riccione, K A;Roquet, N;Roybal, K T;Rubens, J R;Rössger, K;Saito, H;Saxena, P;Schukur, L;Schönhuber, N;Siuti, P;Sprinzak, D;Stanley, S A;Tamsir, A;Tigges, M;Tohe, A;Tubio, M R;Weber, W;Xie, Z;Yang, L;Ye, H F | EL2DY | Basel, Switzerland;Basel, Switzerland. | 46 | null | 2 | null | 28,092,361 | Auslander, David;Auslander, Simon;Folcher, Marc;Fussenegger, Martin;Muller, Marius;Sikorski, Julian;Spinnler, Andrea | NAT CHEM BIOL | Basel, Switzerland |
Standage-Beier, K;Wang, X | 10.1007/s11705-017-1618-2 | null | 233 SPRING ST, NEW YORK, NY 10013 USA | l34u29584p2r3h3b4j5s5s6j6c2r37384w67j | Genome reprogramming for synthetic biology | Arizona State Univ | null | Wang, X (corresponding author), Arizona State Univ, Sch Biol & Hlth Syst Engn, Tempe, AZ 85287 USA. | null | Standage-Beier, Kylie;Wang, Xiao | Engineering, Chemical | National Institutes of Health [GM106081] | WOS | Wang, X | Arizona State Univ, Tempe, AZ USA | 11 | biology;for;genome;reprogramming;synthetic | 1 | Wang, Xiao | SPRINGER | Arizona State Univ, Sch Biol & Hlth Syst Engn, Tempe, AZ 85287 USA;Arizona State Univ, Sch Life Sci, Tempe, AZ 85287 USA | Review | Arizona State Univ | NEW YORK | null | null | Arizona State Univ | National Institutes of Health | Wang, X (corresponding author), Arizona State Univ, Sch Biol & Hlth Syst Engn, Tempe, AZ 85287 USA. | 45 | Standage-Beier, Kylie;Wang, Xiao | 48 | 2 | 398,723,700,005 | National Institutes of Health [GM106081] | USA | FRONTIERS OF CHEMICAL SCIENCE AND ENGINEERING | USA | null | null | Arizona State Univ, Sch Life Sci, Tempe, AZ 85287 USA | 2095-0179 | Standage-Beier, K;Wang, X | MAR | xiaowang@asu.edu | genome reprogramming;synthetic biology | 2 | J | Engineering | ability;advanced DNA synthesis;assembly methods;BACTERIA;bacteriophage resistance;biotechnology;cells;central;CHROMOSOMAL INTEGRATION;CRISPR;CRISPR-Cas;deletion;digitized DNA sequence;directed evolution;DNA;DNA sequences;Genome Engineering;genome engineering tools;genome reprogramming;genomes;increased genetic stability;interspace short palindromic repeats;J. Craig Venter Institute (JCVI)-syn 3.0;myriad advances;new directed evolution methods;new programmable tools;NUCLEASES;ORGANISMS;predictable biological function;programmable genome engineering tools;rational design;recent advances;recent development;RECOMBINASE;reengineer genomes;rewriting;RNA-guided;synthetic biology;synthetic gene systems;synthetic organisms;systems;tools;useful new phenotypes | Standage-Beier, K | BACTERIA;CELLS;CHROMOSOMAL INTEGRATION;CRISPR;CRISPR-CAS;DELETION;directed evolution;DNA;genome engineering;NUCLEASES;RATIONAL DESIGN;RECOMBINASE;Synthetic biology;SYSTEMS | 37 | [Standage-Beier, Kylie] Arizona State Univ, Sch Life Sci, Tempe, AZ 85287 USA. [Wang, Xiao] Arizona State Univ, Sch Biol & Hlth Syst Engn, Tempe, AZ 85287 USA. | Work by the Xiao Wang laboratory has been supported by National Institutes of Health Grant GM106081. | ability;advanced DNA synthesis;assembly methods;bacteriophage resistance;biotechnology;central;digitized DNA sequence;DNA sequences;genome engineering tools;genomes;increased genetic stability;interspace short palindromic repeats;J. Craig Venter Institute (JCVI)-syn 3.0;myriad advances;new directed evolution methods;new programmable tools;organisms;predictable biological function;programmable genome engineering tools;recent advances;recent development;reengineer genomes;rewriting;RNA-guided;synthetic biology;synthetic gene systems;synthetic organisms;tools;useful new phenotypes | 10.1002/biot.201600053;10.1016/j.ab.2016.07.008;10.1016/j.biotechadv.2016.08.002;10.1016/j.cell.2013.09.040;10.1016/j.chembiol.2014.10.008;10.1016/j.jbiotec.2015.02.005;10.1016/j.mib.2016.07.005;10.1016/j.tibtech.2016.02.004;10.1021/acssynbio.5b00007;10.1021/acssynbio.5b00132;10.1021/acssynbio.5b00187;10.1021/acssynbio.5b00196;10.1021/acssynbio.6b00080;10.1021/sb400021j;10.1021/sb500255k;10.1038/35002131;10.1038/msb.2013.41;10.1038/nature08187;10.1038/nature08480;10.1038/nature10403;10.1038/nature14592;10.1038/nature15386;10.1038/nature16526;10.1038/nbt.1536;10.1038/nbt.2508;10.1038/nbt.2623;10.1038/nbt.2808;10.1038/nbt.2842;10.1038/nbt.2908;10.1038/nbt.2909;10.1038/nbt.3063;10.1038/nbt.3404;10.1038/nbt.3467;10.1038/nbt1409;10.1038/ncomms3503;10.1038/nprot.2014.045;10.1038/nprot.2014.084;10.1038/nrg1088;10.1038/nrg3746;10.1038/nrmicro2577;10.1038/srep30714;10.1039/c5ib00252d;10.1073/pnas.1120788109;10.1073/pnas.1423143112;10.1073/pnas.252535999;10.1093/nar/gkp1193;10.1093/nar/gks751;10.1093/nar/gkt135;10.1093/nar/gku509;10.1093/nar/gkw064;10.1099/mic.0.023960-0;10.1101/gr.217202;10.1126/science.1126439;10.1126/science.1144622;10.1126/science.1159689;10.1126/science.1165771;10.1126/science.1173759;10.1126/science.1190719;10.1126/science.1205822;10.1126/science.1225829;10.1126/science.1231143;10.1126/science.1232033;10.1126/science.1241459;10.1126/science.1256272;10.1126/science.aad5227;10.1126/science.aad6253;10.1126/science.aag0511;10.1128/JB.183.9.2834-2841.2001;10.1146/annurev-micro-091014-104441;10.1371/journal.pone.0102873;10.1534/genetics.110.120782;[10.1038/NMETH.1318, 10.1038/nmeth.1318];[10.1038/NMETH.2205, 10.1038/nmeth.2205];[10.1038/NMETH.2926, 10.1038/nmeth.2926];[10.1038/NMETH.2969, 10.1038/nmeth.2969];[10.1038/NMETH.3580, 10.1038/nmeth.3580] | Arizona State Univ | Standage-Beier, K;Wang, X | Standage-Beier, K: Arizona State Univ, Sch Life Sci, Tempe, AZ 85287 USA | Wang, Xiao | GM106081 | 77 | null | USA | Arizona State Univ | Standage-Beier, Kylie | null | BACTERIA;CELLS;CHROMOSOMAL INTEGRATION;CRISPR-CAS;DELETION;DIRECTED EVOLUTION;DNA;NUCLEASES;RECOMBINASE;SYSTEMS | Standage-Beier, Kylie; Wang, Xiao; | null | Arizona State Univ, Sch Biol & Hlth Syst Engn, Tempe, AZ 85287 USA;Arizona State Univ, Sch Life Sci, Tempe, AZ 85287 USA | Arizona State Univ, Sch Biol & Hlth Syst Engn, Tempe, AZ 85287 USA;Arizona State Univ, Sch Life Sci, Tempe, AZ 85287 USA | 2095-0187 | CRISPR;genome engineering;rational design;Synthetic biology | 1 | 2000;2001;2002;2003;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016 | 4 | Arizona State Univ, Sch Biol & Hlth Syst Engn, Tempe, AZ 85287 USA | Front. Chem. Sci. Eng. | Wang, Xiao | SPRINGER | (JCVI)-syn;,;3.0;a;ability;advanced;advances;also;and;as;assembly;bacteriophage;biological;biology;biotechnology;central;clustered;construction;Craig;development;digitized;directed;DNA;enable;enabled;engineered;engineering;evolution;facilitate;for;from;fully;function;gene;generate;genetic;genome;genomes;go;has;have;here;implementation;in;increased;Institute;interspace;is;J.;methods;myriad;new;of;organisms;palindromic;phenotypes;predictable;programmable;radically;rational;recent;redesign;reengineer;regularly;repeats;resistance;restructured;rewriting;RNA-guided;sequence;sequences;short;spurred;stability;such;summarize;synthesis;synthetic;systems;the;these;to;tools;useful;Venter;we;with | Arizona State Univ | The ability to go from a digitized DNA sequence to a predictable biological function is central to synthetic biology. Genome engineering tools facilitate rewriting and implementation of engineered DNA sequences. Recent development of new programmable tools to reengineer genomes has spurred myriad advances in synthetic biology. Tools such as clustered regularly interspace short palindromic repeats enable RNA-guided rational redesign of organisms and implementation of synthetic gene systems. New directed evolution methods generate organisms with radically restructured genomes. These restructured organisms have useful new phenotypes for biotechnology, such as bacteriophage resistance and increased genetic stability. Advanced DNA synthesis and assembly methods have also enabled the construction of fully synthetic organisms, such as J. Craig Venter Institute (JCVI)-syn 3.0. Here we summarize the recent advances in programmable genome engineering tools. | A-8414-2008 | BACTERIA;CELLS;CHROMOSOMAL INTEGRATION;CRISPR-CAS;DELETION;DIRECTED EVOLUTION;DNA;NUCLEASES;RECOMBINASE;SYSTEM | 2 | null | CRISPR;genome engineering;rational design;Synthetic biology | 9 | BACTERIA;CELLS;CHROMOSOMAL INTEGRATION;CRISPR;CRISPR-CAS;DELETION;directed evolution;DNA;genome engineering;NUCLEASES;RATIONAL DESIGN;RECOMBINASE;Synthetic biology;SYSTEM | WOS:000398723700005 | Arizona State Univ, Tempe, AZ USA | USA | 2,017 | null | 0000-0002-4056-0155 | null | null | English | null | ACS SYNTH BIOL;ANAL BIOCHEM;ANNU REV MICROBIOL;BIOTECHNOL ADV;BIOTECHNOL J;CELL;CHEM BIOL;CURR OPIN MICROBIOL;GENETICS;GENOME RES;INTEGR BIOL-UK;J BACTERIOL;J BIOTECHNOL;MICROBIOL-SGM;MOL SYST BIOL;NAT BIOTECHNOL;NAT COMMUN;NAT METHODS;NAT PROTOC;NAT REV GENET;NAT REV MICROBIOL;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PLOS ONE;SCI REP-UK;SCIENCE;TRENDS BIOTECHNOL | Standage-Beier, Kylie;Wang, Xiao | 2024-03-11
ER | Bao, Z H;Barrick, J E;Bassalo, M C;Brophy, J A N;Brouns, S J J;Choi, K R;Cong, L;Cooper, V S;Csörgo, B;Dicarlo, J E;Doyon, Y;Dymond, J S;Elena, S F;Ellis, T;Enyeart, P J;Farzadfard, F;Faucon, P C;Fu, Y F;Gardner, T S;Gibson, D G;Guilinger, J P;Hao, H H;He, X J;Hutchison, C A;Isaacs, F J;Jakociunas, T;Jiang, W Y;Jinek, M;Kang, H S;Kannan, K;Karas, B J;Karpinski, J;Kiani, S;Kleinstiver, B P;Kolisnychenko, V;Krishnakumar, R;Kuhlman, T E;Lajoie, M J;Lartigue, C;Li, Q;Liao, C;Litcofsky, K D;Makarova, K S;Mali, P;Marraffini, L A;Mojica, F J M;Mosberg, J A;Mougiakos, I;Perli, S D;Pál, C;Pósfai, G;Ran, F A;Sander, J D;Santos, C N S;Slaymaker, I M;Smanski, M J;St-Pierre, F;Standage-Beier, K;Temme, K;Tsai, S Q;Tsarmpopoulos, I;Wang, H H;Wang, L Z;Wang, Y;Wu, F Q;Wu, M;Yokobayashi, Y | ER3UD | Tempe, AZ USA | 6 | null | 1 | null | null | Standage-Beier, Kylie;Wang, Xiao | FRONT CHEM SCI ENG | Tempe, AZ USA |
Ma, J K C;Teh, A Y H;Webster, G R | 10.1002/bit.26183 | null | 111 RIVER ST, HOBOKEN 07030-5774, NJ USA | 3l5h3k3we5y6t2m12483f6f3b2w6q664u662w3a | Synthetic gene designThe rationale for codon optimization and implications for molecular pharming in plants | St Georges Univ London | null | Teh, AYH (corresponding author), St Georges Univ London, Mol Immunol Unit, Inst Infect & Immun, London SW17 0RE, England. | null | Ma, Julian K -C;Teh, Audrey Y -H;Webster, Gina R | Biotechnology & Applied Microbiology | European Research Council; Hotung Foundation; Wellcome Trust | WOS | Teh, A Y H | St Georges Univ London, London, England | 114 | and;codon;designThe;for;gene;Implications;in;molecular;optimization;pharming;plants;rationale;synthetic | 1 | Ma, Julian;Teh, Audrey;Webster, Gina | WILEY | St Georges Univ London, Mol Immunol Unit, Inst Infect & Immun, London SW17 0RE, England | Review | St Georges Univ London | HOBOKEN | null | null | St Georges Univ London | European Research Council;Hotung Foundation;Wellcome Trust | Teh, AYH (corresponding author), St Georges Univ London, Mol Immunol Unit, Inst Infect & Immun, London SW17 0RE, England. | 502 | Ma, Julian K -C;Teh, Audrey Y -H;Webster, Gina R | 46 | 1 | 394,606,000,002 | European Research Council;Hotung Foundation;Wellcome Trust | UK | BIOTECHNOLOGY AND BIOENGINEERING | UK | null | null | St Georges Univ London, Mol Immunol Unit, Inst Infect & Immun, London SW17 0RE, England | 0006-3592 | Ma, J K C;Teh, A Y H;Webster, G R | MAR | ateh@sgul.ac.uk | codon optimization;Implications;molecular pharming;plants;synthetic gene designThe rationale | 3 | J | Biotechnology & Applied Microbiology | 114;2017;492-502;altering codon usage;altering codons;area;BACILLUS-SUBTILIS;BETA-GLUCANASE;bioeng;biotechnol;c 2016 Wiley Periodicals;case study;CELL-LINE;Codon optimization;codon optimization impact;codon usage bias;computer programmes;consideration;degeneracy;developments;difficulties;ESCHERICHIA-COLI;evidence;evidence based rational approach;factors affecting codon selection;gene sequence;gene sequence optimization process;genes;Genetic Code;heterologous protein expression;HETEROLOGOUS PROTEINS;implications;inc;low levels;molecular pharming;multiple codon sequences;multiple inter-linked factors affecting protein expression need;optimal gene sequence;particular synonymous codons;plants;practised;preferred use;primary structure;process;PROTEIN;PROTEIN EXPRESSION;recombinant expression systems;recombinant protein expression;review;rulebook;same protein;secondary structure;significant effect;strategy;synonymous codon substitutions;synonymous codons;synonymous substitutions;Synthetic gene design;synthetic gene designThe rationale;TARGET GENE;term;TRANSFER-RNA-SYNTHETASE;USAGE FREQUENCIES;will;years | Webster, G R | BACILLUS-SUBTILIS;BETA-GLUCANASE;CELL-LINE;ESCHERICHIA-COLI;Genetic code;HETEROLOGOUS PROTEIN EXPRESSION;HETEROLOGOUS PROTEINS;PROTEIN EXPRESSION;SECONDARY STRUCTURE;synonymous codons;TARGET GENE;TRANSFER-RNA-SYNTHETASE;USAGE FREQUENCIES | 492 | [Webster, Gina R.; 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Teh, Audrey Y. -H.; Ma, Julian K. -C.; | null | St Georges Univ London, Mol Immunol Unit, Inst Infect & Immun, London SW17 0RE, England | St Georges Univ London, Mol Immunol Unit, Inst Infect & Immun, London SW17 0RE, England | 1097-0290 | Genetic code;heterologous protein expression;synonymous codon | 3 | 1961;1975;1981;1982;1984;1985;1986;1989;1990;1991;1994;1995;1996;1997;1998;1999;2000;2001;2002;2003;2004;2005;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016 | 43 | St Georges Univ London, Mol Immunol Unit, Inst Infect & Immun, London SW17 0RE, England | Biotechnol. Bioeng. | Ma, Julian K C | WILEY | ,;114;2017;492-502;:;;;a;accepted;affect;affected;affecting;aid;all;allows;altering;an;and;any;approach;area;as;based;be;become;been;benefit;bias;bioeng;biotechnol;can;case;code;codon;codons;completely;computer;consideration;consistently;degeneracy;design;developed;developments;difficult;difficulties;discussed;effect;encode;encountered;evidence;expression;factors;for;from;gene;genes;genetic;given;had;has;have;heterologous;however;if;impact;improve;in;inter-linked;into;is;it;levels;low;molecular;multiple;need;not;now;of;on;optimal;optimization;optimizing;over;particular;pharming;plants;practised;predict;preferred;primary;process;programmes;protein;rational;recombinant;regarded;relevant;review;reviewed;rulebook;same;selection;sequence;sequences;should;significant;silent;still;strategy;structure;study;substitutions;synonymous;synthetic;systems;taken;term;that;the;these;this;to;understood;usage;use;using;various;was;when;which;widely;will;with;within;years | St Georges Univ London | Degeneracy in the genetic code allows multiple codon sequences to encode the same protein. Codon usage bias in genes is the term given to the preferred use of particular synonymous codons. Synonymous codon substitutions had been regarded as silent as the primary structure of the protein was not affected; however, it is now accepted that synonymous substitutions can have a significant effect on heterologous protein expression. Codon optimization, the process of altering codons within the gene sequence to improve recombinant protein expression, has become widely practised. Multiple inter-linked factors affecting protein expression need to be taken into consideration when optimizing a gene sequence. Over the years, various computer programmes have been developed to aid in the gene sequence optimization process. However, as the rulebook for altering codon usage to affect protein expression is still not completely understood, it is difficult to predict which strategy, if any, will design the optimal gene sequence. In this review, codon usage bias and factors affecting codon selection will be discussed and the evidence for codon optimization impact will be reviewed for recombinant protein expression using plants as a case study. These developments will be relevant to all recombinant expression systems; however, molecular pharming in plants is an area which has consistently encountered difficulties with low levels of recombinant protein expression, and should benefit from an evidence based rational approach to synthetic gene design. Biotechnol. Bioeng. 2017;114: 492-502. | AAK-1126-2021 | BACILLUS-SUBTILIS;BETA-GLUCANASE;CELL-LINES;ESCHERICHIA-COLI;HETEROLOGOUS PROTEINS;PROTEIN EXPRESSION;SECONDARY STRUCTURE;TARGET GENE;TRANSFER-RNA SYNTHETASE;USAGE FREQUENCIES | 0 | null | Genetic code;heterologous protein expression;synonymous codons | 11 | ESCHERICHIA-COLI;BACILLUS-SUBTILIS;BETA-GLUCANASE;CELL-LINES;Gene targeting;GENETIC-CODE;HETEROLOGOUS PROTEINS;HETEROLOGOUS PROTEIN EXPRESSION;PROTEIN EXPRESSION;SECONDARY STRUCTURE;synonymous codon;TRANSFER-RNA SYNTHETASE;USAGE FREQUENCIES | WOS:000394606000002 | St Georges Univ London, London, England | UK | 2,017 | null | 0000-0001-9899-0855;0000-0003-0767-0042;0000-0003-1827-4328 | null | null | English | null | ANIM FEED SCI TECH;ANNU REV GENET;ANNU REV PLANT BIOL;APPL ENVIRON MICROB;APPL MICROBIOL BIOT;ARCH BIOCHEM BIOPHYS;BIOINFORMATICS;BIOTECHNOL ADV;BIOTECHNOL APPL BIOC;BIOTECHNOL BIOENG;BIOTECHNOL BIOFUELS;BIOTECHNOL J;BMC BIOINFORMATICS;BMC BIOTECHNOL;BMC GENOMICS;BMC SYST BIOL;CANCER RES;CELL;CLIN EXP VACCINE RES;CURR OPIN BIOTECH;CURR PHARM DESIGN;EMBO REP;EUR J BIOCHEM;FEBS LETT;FEMS YEAST RES;FRONT BIOENG BIOTECH;GENE;GENES GENET SYST;GENETICS;GENOME BIOL;HUM VACCINES;INT J MOL SCI;ISME J;J ANIM SCI;J BACTERIOL;J BIOL CHEM;J BIOTECHNOL;J CELL BIOL;J GEN VIROL;J I BREWING;J MOL BIOL;J MOL EVOL;J R SOC INTERFACE;J THEOR BIOL;J VIROL;MBIO;METHODS MOL BIOL;MICROB CELL FACT;MICROBIOL REV;MOL BIOL EVOL;MOL CELL;NAT BIOTECHNOL;NAT REV GENET;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PHILOS T R SOC B;PLANT BIOTECHNOL J;PLANT CELL REP;PLANT J;PLANT PHYSIOL;PLOS GENET;PLOS ONE;PROTEIN EXPRES PURIF;PROTEIN SCI;Q REV BIOPHYS;SCI REP-UK;SCIENCE;TRENDS BIOCHEM SCI;TRENDS BIOTECHNOL;TRENDS GENET;TRENDS PLANT SCI;VACCINE;ZBL BAKT II NATUR | Ma, Julian K -C;Teh, Audrey Y -H;Webster, Gina R | 2024-03-11
ER | Akashi, H;Andersson, S G E;Angov, E;Arévalo-Herrera, M;Ask, M;Askelson, T E;Bamforth C. W.;Ban, N;Batard, Y;Binder, A;Bonomo, J;Borriss, R;Cannarrozzi, G;Carlini, D B;Carton, J M;Chamary, J V;Chen, Y;Chevance, F F V;Chin, J X;Coleman, J R;Crick, F H;Dammeyer, T;Daniel, E;Daniell, H;Desai, P N;Deutscher, M P;Dittmar, K A;Dong, H J;Drummond, D A;Dubeau, M P;Duret, L;Ehrenberg, M;Elf, J;Erpel, F;Fahimi, H;Fath, S;Fincher, G B;Fredrick, K;Fu, W Q;Fuglsang, A;Gaspar, P;Geisler, C;Goodenbour, J M;Gould, N;Gouy, M;Graham, H;Green, R T;Grote, A;Guadalupe-Medina, V;Guimaraes, J C;Guo, L;Gustafsson, C;Gutman, G A;Harcum, S W;Hershberg, R;Hesselman, K;Ikemura, T;Ingolia, N T;Irwin, B;Jensen, L G;Kaminska, M;Kanaya, S;Kane, J F;Karkhah, A;Kirchner, S;Ko, J H;Komar, A A;Kudla, G;Kyriacou, S V;Lanza, A M;Li, H X;Li, X Q;Liu, X W;Ma, J K C;Maclean, J;Maghodia, A B;Manuel, E R;Mason, H S;Matthäus, F;Meng, J;Mihálik, D;Milne, N;Mirande, M;Moura, G R;Mueller, S;Occhialini, A;Overkamp, W;Paul, M;Paul, M J;Percudani, R;Perlak, F J;Pierlé, S A;Plotkin, J B;Puigbò, P;Reilman, E;Rybicki, E P;Shabalina, S A;Shah, K;Sharp, P M;Singer, M;Solis-Escalante, D;Sorensen, M A;Stoger, E;Stoletzki, N;Suo, G L;Tegel, H;Thanaraj, T A;Thomas, D R;Tuller, T;Van Der Woude, A D;Welch, M;Wu, G;Zhao, H J;Zhou, J;Zhou, T;Zull, J E | EL4QN | London, England | 48 | null | 1 | null | 27,618,314 | Ma, Julian K C;Teh, Audrey Y H;Webster, Gina R | BIOTECHNOL BIOENG | London, England |
Ding, Y Q;Liu, G S;Niu, H X;Wang, S G;Wang, W J;Yin, G Y;Zhang, D Y;Zhang, H B;Zhang, J | 10.3389/fpls.2017.00157 | 157 | AVENUE DU TRIBUNAL FEDERAL 34, LAUSANNE, CH-1015, SWITZERLAND | 4y596jn386lz4y49201h3815ye3j5c64h3i | Jasmonate-sensitivity-assisted screening and characterization of nicotine synthetic mutants from activation-tagged population of tobacco (<i>Nicotiana tabacum</i> L.) | Southwest Univ | null | Zhang, HB (corresponding author), Chinese Acad Agr Sci, Tobacco Res Inst, Qingdao, Peoples R China. | null | Ding, Yongqiang;Liu, Guanshan;Niu, Haixia;Wang, Sangen;Wang, Wenjing;Yin, Guoying;Zhang, Dingyu;Zhang, Hongbo;Zhang, Jie | Plant Sciences | null | WOS | Zhang, H B | Chinese Acad Agr Sci, Qingdao, Peoples R China;Southwest Univ, Chongqing, Peoples R China | 8 | (<i>Nicotiana;activation-tagged;and;characterization;From;jasmonate-sensitivity-assisted;L;mutants;nicotine;of;population;screening;synthetic;tabacum</i>;Tobacco | 1 | Wang, Bingwu;Wang, Wenjing | FRONTIERS MEDIA SA | Chinese Acad Agr Sci, Tobacco Res Inst, Qingdao, Peoples R China;Southwest Univ, Coll Agron & Biotechnol, Chongqing, Peoples R China | Article | Chinese Acad Agr Sci | LAUSANNE | null | null | Chinese Acad Agr Sci;Southwest Univ | null | Zhang, HB (corresponding author), Chinese Acad Agr Sci, Tobacco Res Inst, Qingdao, Peoples R China. | null | Ding, Yongqiang;Liu, Guanshan;Niu, Haixia;Wang, Sangen;Wang, Wenjing;Yin, Guoying;Zhang, Dingyu;Zhang, Hongbo;Zhang, Jie | 19 | 2 | 393,820,100,001 | null | China | FRONTIERS IN PLANT SCIENCE | China | null | null | Southwest Univ, Coll Agron & Biotechnol, Chongqing, Peoples R China | 1664-462X | Ding, Y Q;Liu, G S;Niu, H X;Wang, S G;Wang, W J;Yin, G Y;Zhang, D Y;Zhang, H B;Zhang, J | FEB 13 | zhanghongbo@caas.cn | activation-tagged population;characterization;jasmonate-sensitivity-assisted screening;nicotine synthetic mutants;Tobacco (<i>Nicotiana tabacum</i> L | 9 | J | Plant Sciences | abnormal JA responses;activation-tagged population;ALKALOID BIOSYNTHESIS;altered JA-response;amphitetraploid origin;approach;ARABIDOPSIS;characterization;commercial quality;defense system;derivatives (JAs);ENZYME-ACTIVITIES;expression;finding;first;five mutants thatmaintained stable nicotine contents;functional genomics;genes;germination;IDENTIFICATION;identifying novel regulators;insertional mutagenesis;JA responses;JA-regulated nicotine biosynthesis;JA-sensitivity;jasmonate;jasmonate-sensitivity;jasmonate-sensitivity-assisted screening;method;METHYL JASMONATE;mutant;mutants;N. tabacum;nicotine;nicotine formation;nicotine synthesis;nicotine synthetic genes;nicotine synthetic mutants;nicotine-synthetic mutants;nictine;phytohormone regulators;potentials;process;root elongation;scarce;screening;screening nicotine mutants;Secondary metabolite;simple;SYLVESTRIS;themutants;three generations;tobacco;Tobacco (<i>Nicotiana tabacum</i> L;tobacco (Nicotiana tabacum L;transcription factors;transcriptional changes;unclear;underlying molecular mechanism | Yin, G Y | activation-tagged population;ALKALOID BIOSYNTHESIS;ARABIDOPSIS;ENZYME-ACTIVITIES;EXPRESSION;FUNCTIONAL GENOMICS;GENES;INSERTIONAL MUTAGENESIS;jasmonate-sensitivity;METHYL JASMONATE;MUTANT;nictine;SYLVESTRIS;tobacco;TRANSCRIPTION FACTORS | null | [Yin, Guoying; Niu, Haixia; Ding, Yongqiang; Zhang, Dingyu; Zhang, Jie; Wang, Sangen] Southwest Univ, Coll Agron & Biotechnol, Chongqing, Peoples R China. [Wang, Wenjing; Liu, Guanshan; Zhang, Hongbo] Chinese Acad Agr Sci, Tobacco Res Inst, Qingdao, Peoples R China. | null | abnormal JA responses;activation-tagged population;altered JA-response;amphitetraploid origin;approach;commercial quality;defense system;derivatives (JAs);expression;finding;first;five mutants thatmaintained stable nicotine contents;germination;identification;identifying novel regulators;JA responses;JA-regulated nicotine biosynthesis;JA-sensitivity;jasmonate;method;mutants;N. tabacum;nicotine;nicotine formation;nicotine synthesis;nicotine synthetic genes;nicotine-synthetic mutants;phytohormone regulators;potentials;process;root elongation;scarce;screening;screening nicotine mutants;secondary metabolite;simple;themutants;three generations;tobacco;tobacco (Nicotiana tabacum L;transcriptional changes;unclear;underlying molecular mechanism | 10.1007/978-1-61779-809-2_9;10.1007/BF00194760;10.1007/BF00347813;10.1007/BF00391419;10.1007/BF02041987;10.1007/PL00001841;10.1007/s00425-014-2186-z;10.1007/s00438-015-0989-7;10.1007/s10265-005-0231-5;10.1007/s11103-008-9425-2;10.1007/s11103-013-0116-2;10.1007/s11240-008-9461-2;10.1016/0304-4211(84)90141-X];10.1016/j.phytochem.2009.09.004;10.1016/j.phytochem.2013.06.002;10.1016/j.phytochem.2014.05.017;10.1016/S0031-9422(00)80751-7;10.1016/S0031-9422(00)94511-4;10.1016/S0958-1669(00)00075-6;10.1016/S1369-5266(03)00045-1;10.1021/ac60039a013;10.1038/nature05960;10.1038/nature09430;10.1046/j.1365-313X.1998.00220.x;10.1071/AR06154;10.1073/pnas.0812512106;10.1073/pnas.1108620108;10.1073/pnas.89.15.6837;10.1073/pnas.95.14.8113;10.1080/15592324.2015.1035852;10.1093/jxb/erl051;10.1093/mp/ssr056;10.1093/mp/sss128;10.1093/pcp/pcd001;10.1093/pcp/pcm018;10.1093/pcp/pcn077;10.1093/pcp/pcr063;10.1094/PD-72-0892;10.1101/PDB.PROT5177.];10.1104/pp.003327;10.1104/pp.014357;10.1104/pp.101.3.839;10.1104/pp.107.115691;10.1104/pp.108.132811;10.1104/pp.110.170878;10.1104/pp.114.251645;10.1104/pp.122.4.1003;10.1104/pp.32.2.86;10.1104/pp.64.2.236;10.1105/tpc.012963;10.1105/tpc.6.5.723;10.1105/tpc.6.5.751;10.1111/j.1365-313X.2010.04186.x;10.1126/science.94.2443.396;10.1146/annurev.arplant.59.032607.092825;10.1186/gb-2013-14-6-r60;10.1271/BBB.62.1448.];10.1371/journal.pbio.0020217;10.1371/journal.pone.0108789;10.1371/journal.pone.0117273;10.4161/psb.2.4.4008;10.5511/plantbiotechnology.13.0221a | Southwest Univ | Ding, Y Q;Liu, G S;Niu, H X;Wang, S G;Wang, W J;Yin, G Y;Zhang, D Y;Zhang, H B;Zhang, J | Yin, G Y: Southwest Univ, Coll Agron & Biotechnol, Chongqing, Peoples R China | li, xiao;Wang, Bingwu;Wang, Wenjing;zhang, hongbo | null | 64 | null | China | Chinese Acad Agr Sci;Southwest Univ | Yin, Guoying | Green Published, gold | ALKALOID BIOSYNTHESIS;ARABIDOPSIS;ENZYME-ACTIVITIES;EXPRESSION;FUNCTIONAL GENOMICS;GENES;INSERTIONAL MUTAGENESIS;METHYL JASMONATE;SYLVESTRIS;TRANSCRIPTION FACTORS | Yin, Guoying; Wang, Wenjing; Niu, Haixia; Ding, Yongqiang; Zhang, Dingyu; Zhang, Jie; Liu, Guanshan; Wang, Sangen; Zhang, Hongbo; | null | Chinese Acad Agr Sci, Tobacco Res Inst, Qingdao, Peoples R China;Southwest Univ, Coll Agron & Biotechnol, Chongqing, Peoples R China | Chinese Acad Agr Sci, Tobacco Res Inst, Qingdao, Peoples R China;Southwest Univ, Coll Agron & Biotechnol, Chongqing, Peoples R China | null | activation-tagged population;jasmonate-sensitivity;mutant;nictine;tobacco | null | 1941;1950;1957;1966;1979;1984;1985;1986;1988;1989;1992;1993;1994;1996;1998;2000;2001;2002;2003;2004;2005;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015 | 2 | Chinese Acad Agr Sci, Tobacco Res Inst, Qingdao, Peoples R China | Front. Plant Sci. | Zhang, Hongbo | FRONTIERS MEDIA SA | (JAs);(Nicotiana;,;;;a;abnormal;activation-tagged;altered;amphitetraploid;an;and;approach;are;based;biosynthesis;changes;commercial;contents;defense;derivatives;describe;determine;effective;elongation;expression;finding;first;five;for;formation;from;generations;genes;germination;here;however;identification;identifying;important;in;involved;is;its;JA;JA-regulated;JA-response;JA-sensitivity;jasmonate;L;largely;levels;low-cost;measured;mechanism;metabolite;method;molecular;mutants;N.;nicotine;nicotine-synthetic;novel;obtained;of;on;origin;owing;phytohormone;population;potentials;process;quality;regulators;relatively;remains;research;responses;root;scarce;screened;screening;secondary;seed;shows;simple;stable;successfully;synthesis;synthetic;system;tabacum;that;thatmaintained;the;themutants;then;this;three;to;tobacco;transcriptional;unclear;underlying;we;were;with | Chinese Acad Agr Sci | Nicotine is a secondary metabolite that is important to the defense system and commercial quality of tobacco (Nicotiana tabacum L.). Jasmonate and its derivatives (JAs) are phytohormone regulators of nicotine formation; however, the underlying molecular mechanism of this process remains largely unclear. Owing to the amphitetraploid origin of N. tabacum, research on screening and identification of nicotine-synthetic mutants is relatively scarce. Here, we describe a method based on JA-sensitivity for screening nicotine mutants from an activation-tagged population of tobacco. In this approach, the mutants were first screened for abnormal JA responses in seed germination and root elongation, and then the levels of nicotine synthesis and expression of nicotine synthetic genes in the mutants with altered JA-response were measured to determine the nicotine-synthetic mutants. We successfully obtained five mutants thatmaintained stable nicotine contents and JA responses for three generations. This method is simple, effective and low-cost, and the finding of transcriptional changes of nicotine synthetic genes in themutants shows potentials for identifying novel regulators involved in JA-regulated nicotine biosynthesis. | AAR-5498-2021;AAU-8450-2021;GZK-9398-2022;HJP-5134-2023 | ENZYME-ACTIVITIES;ALKALOID BIOSYNTHESIS;ARABIDOPSIS;EXPRESSION;FUNCTIONAL GENOMICS;GENE;INSERTIONAL MUTAGENESIS;METHYL JASMONATE;SYLVESTRIS;TRANSCRIPTION FACTORS | 0 | null | activation-tagged population;jasmonate-sensitivity;mutant;nictine;tobacco | 11 | ENZYME-ACTIVITIES;activation-tagged population;ALKALOID BIOSYNTHESIS;ARABIDOPSIS;EXPRESSION;FUNCTIONAL GENOMICS;GENE;INSERTIONAL MUTAGENESIS;jasmonate-sensitivity;METHYL JASMONATE;MUTANTS;nictine;SYLVESTRIS;tobacco;transcription factor | WOS:000393820100001 | Chinese Acad Agr Sci, Qingdao, Peoples R China;Southwest Univ, Chongqing, Peoples R China | China | 2,017 | null | 0000-0002-2234-503X;0000-0003-4035-8552 | null | null | English | null | Acta Agronomica Sinica;ANAL CHEM;ANNU REV PLANT BIOL;AUST J AGR RES;BENTH BIOSCI BIOTECH;CHEMOECOLOGY;COLD SPRING HARB PRO;CURR OPIN BIOTECH;CURR OPIN PLANT BIOL;ENTOMOL EXP APPL;GENOME BIOL;J EXP BOT;J PLANT GROWTH REGUL;J PLANT RES;METHODS MOL BIOL;MOL GENET GENOMICS;MOL PLANT;NATURE;P NATL ACAD SCI USA;PHYTOCHEMISTRY;PLANT BIOTECHNOL-NAR;PLANT CELL;PLANT CELL PHYSIOL;PLANT CELL TISS ORG;PLANT DIS;PLANT J;PLANT MOL BIOL;PLANT PHYSIOL;PLANT SCI LETT;PLANT SIGNAL BEHAV;PLANTA;PLOS BIOL;PLOS ONE;PRIMARY SECONDARY ME;SCIENCE | Ding, Yongqiang;Liu, Guanshan;Niu, Haixia;Wang, Sangen;Wang, Wenjing;Yin, Guoying;Zhang, Dingyu;Zhang, Hongbo;Zhang, Jie | 2024-03-11
ER | Ayliffe, M A;Baldwin, I T;Chou, W M;Chung, H S;Clarke J. D.;Dawson, R F;Deboer, K D;Dewey, R E;Farmer, E E;Feys, B J F;Gou Xiaoping;Harlman C. L.;He, S Z;Hibi, N;Hildreth, S B;Howe, G A;Imaizumi, R;Ishida, Y;Jeong, D H;Kajikawa, M;Kato, K;Katoh, A;Kazan, K;Lewis, R S;Li, C J;Liu, F;Marsch-Martinez, N;Mathews, H;Memelink, J;Meyer, A;Morita, M;Parinov, S;Rhodes M. J. C.;Saitoh, F;Saleki, R;Saunders, J W;Sears, M T;Sheard, L B;Shi, Q M;Shitan Nobukazu;Shitan, N;Shoji, T;Sierro, N;Staswick, P E;Steppuhn, A;Thines, B;Thurston, R;Tiburcio, A F;Todd, A T;Tso, T C;Voelckel, C;Wagner, R;Wang, X W;Weigel, D;Willits, C O;Yoneyama K.;Zha Xiangmin;Zhang, H B | EK3IO | Qingdao, Peoples R China | 2 | null | 2 | null | 28,243,248 | Ding, Yongqiang;Liu, Guanshan;Niu, Haixia;Wang, Sangen;Wang, Wenjing;Yin, Guoying;Zhang, Dingyu;Zhang, Hongbo;Zhang, Jie | FRONT PLANT SCI | Chongqing, Peoples R China;Qingdao, Peoples R China |
Bittihn, P;Hasty, J;Tsimring, L S | 10.1103/PhysRevLett.118.028102 | 028102 | ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA | 3q5v6u145v13146j4d5kk3x263is2c3i3q4k3u | Suppression of Beneficial Mutations in Dynamic Microbial Populations | Univ Calif San Diego | null | Bittihn, P (corresponding author), Univ Calif San Diego, BioCircuits Inst, La Jolla, CA 92093 USA.;Bittihn, P (corresponding author), Univ Calif San Diego, San Diego Ctr Syst Biol, La Jolla, CA 92093 USA. | null | Bittihn, Philip;Hasty, Jeff;Tsimring, Lev S | Physics, Multidisciplinary | NIH [R01-GM069811, P50-GM085764]; NSF [MCB-1121748]; San Diego Center for Systems Biology; HFSP fellowship [LT000840/2014-C] | WOS | Bittihn, P | Univ Calif San Diego, La Jolla, CA USA | 118 | Beneficial;dynamic;in;microbial;Mutations;of;populations;suppression | 1 | Bittihn, Philip;Tsimring, Lev | AMER PHYSICAL SOC | Univ Calif San Diego, BioCircuits Inst, La Jolla, CA 92093 USA;Univ Calif San Diego, BioCircuits Inst, La Jolla, CA 92093 USA.; Bittihn, P (corresponding author), Univ Calif San Diego, San Diego Ctr Syst Biol, La Jolla, CA 92093 USA;Univ Calif San Diego, Dept Bioengn, La Jolla, CA 92093 USA;Univ Calif San Diego, Div Biol Sci, Mol Biol Sect, La Jolla, CA 92093 USA;Univ Calif San Diego, San Diego Ctr Syst Biol, La Jolla, CA 92093 USA | Article | Univ Calif San Diego | COLLEGE PK | null | null | Univ Calif San Diego | HFSP fellowship;NIH;NSF;San Diego Center for Systems Biology | Bittihn, P (corresponding author), Univ Calif San Diego, BioCircuits Inst, La Jolla, CA 92093 USA.; Bittihn, P (corresponding author), Univ Calif San Diego, San Diego Ctr Syst Biol, La Jolla, CA 92093 USA. | null | Bittihn, Philip;Hasty, Jeff;Tsimring, Lev S | 16 | 4 | 391,927,700,012 | HFSP fellowship [LT000840/2014-C];NIH [R01-GM069811, P50-GM085764];NSF [MCB-1121748];San Diego Center for Systems Biology | USA | PHYSICAL REVIEW LETTERS | USA;USA.; | null | null | Univ Calif San Diego, BioCircuits Inst, La Jolla, CA 92093 USA | 0031-9007 | Bittihn, P;Hasty, J;Tsimring, L S | JAN 12 | pbittihn@ucsd.edu | Beneficial Mutations;Dynamic Microbial Populations;suppression | 3 | J | Physics | analytical expressions;bacterial populations;Beneficial Mutations;BOTTLENECKS;certain growth advantages;covering arbitrary population sizes;dilution factor;dilution factors;Dynamic Microbial Populations;evolution;evolution experiments;extensive numerical simulations;FIXATION;growth advantage;growth advantages;MUTATIONS;nontrivially;periodic dilutions;POPULATIONS;preferential elimination;probability;quantitative predictions;results;single stochastic model;spread;stability;suppression;suppression factor;synthetic gene circuits | Bittihn, P | BOTTLENECKS;EVOLUTION;FIXATION;PROBABILITY | null | [Bittihn, Philip; Hasty, Jeff; Tsimring, Lev S.] Univ Calif San Diego, BioCircuits Inst, La Jolla, CA 92093 USA. [Bittihn, Philip; Hasty, Jeff; Tsimring, Lev S.] Univ Calif San Diego, San Diego Ctr Syst Biol, La Jolla, CA 92093 USA. [Hasty, Jeff] Univ Calif San Diego, Dept Bioengn, La Jolla, CA 92093 USA. [Hasty, Jeff] Univ Calif San Diego, Div Biol Sci, Mol Biol Sect, La Jolla, CA 92093 USA. | All authors acknowledge funding from NIH Grant No. R01-GM069811, from NSF Grant No. MCB-1121748 and partial support from the San Diego Center for Systems Biology, NIH Grant No. P50-GM085764. P. B. also acknowledges support from HFSP fellowship LT000840/2014-C. | analytical expressions;bacterial populations;beneficial mutations;certain growth advantages;covering arbitrary population sizes;dilution factor;dilution factors;evolution experiments;extensive numerical simulations;growth advantage;growth advantages;mutations;nontrivially;periodic dilutions;populations;preferential elimination;quantitative predictions;results;single stochastic model;spread;stability;suppression factor;synthetic gene circuits | 10.1002/jctb.5020220206;10.1006/tpbi.1999.1436;10.1016/j.mbs.2008.03.006;10.1016/S0040-5809(02)00002-3;10.1017/S0305004100015644;10.1017/S0370164600023993];10.1038/nature10722;10.1063/1.1824902;10.1073/pnas.0912451107;10.1073/pnas.1403232111;10.1093/bioinformatics/bts130;10.1111/j.1558-5646.2008.00595.x;10.1126/science.1243357;10.1186/1754-1611-4-12;10.1534/g3.111.000406;10.1534/genetics.108.093013;10.1534/genetics.110.124297;10.2307/2332354 | Univ Calif San Diego | Bittihn, P;Hasty, J;Tsimring, L S | Bittihn, P: Univ Calif San Diego, BioCircuits Inst, La Jolla, CA 92093 USA | Bittihn, Philip | LT000840/2014-C;MCB-1121748;P50-GM085764;R01-GM069811 | 23 | null | USA | Univ Calif San Diego | Bittihn, Philip | Green Accepted, hybrid | BOTTLENECKS;EVOLUTION;FIXATION;PROBABILITY | Bittihn, Philip; Hasty, Jeff; Tsimring, Lev S.; | null | Univ Calif San Diego, BioCircuits Inst, La Jolla, CA 92093 USA;Univ Calif San Diego, Dept Bioengn, La Jolla, CA 92093 USA;Univ Calif San Diego, Div Biol Sci, Mol Biol Sect, La Jolla, CA 92093 USA;Univ Calif San Diego, San Diego Ctr Syst Biol, La Jolla, CA 92093 USA | Univ Calif San Diego, BioCircuits Inst, La Jolla, CA 92093 USA;Univ Calif San Diego, Dept Bioengn, La Jolla, CA 92093 USA;Univ Calif San Diego, Div Biol Sci, Mol Biol Sect, La Jolla, CA 92093 USA;Univ Calif San Diego, San Diego Ctr Syst Biol, La Jolla, CA 92093 USA | 1079-7114 | null | 2 | 1922;1927;1930;1948;1962;1972;1997;2000;2001;2002;2005;2008;2009;2010;2011;2012;2013;2014 | 9 | Univ Calif San Diego, BioCircuits Inst, La Jolla, CA 92093 USA;Univ Calif San Diego, San Diego Ctr Syst Biol, La Jolla, CA 92093 USA | Phys. Rev. Lett. | Tsimring, Lev S | AMER PHYSICAL SOC | ,;a;advantage;advantages;analytical;and;arbitrary;are;bacterial;beneficial;by;certain;circuits;confirm;covering;depends;derive;dilution;dilutions;elimination;essential;evolution;experiments;expressions;extensive;factor;factors;find;for;gene;grows;growth;improve;in;interpret;model;mutations;nontrivially;numerical;of;on;our;periodic;population;populations;predictions;preferential;quantitative;resulting;results;simulations;single;sizes;spread;stability;stochastic;suppression;synthetic;that;the;to;undergo;we;with | Univ Calif San Diego | Quantitative predictions for the spread of mutations in bacterial populations are essential to interpret evolution experiments and to improve the stability of synthetic gene circuits. We derive analytical expressions for the suppression factor for beneficial mutations in populations that undergo periodic dilutions, covering arbitrary population sizes, dilution factors, and growth advantages in a single stochastic model. We find that the suppression factor grows with the dilution factor and depends nontrivially on the growth advantage, resulting in the preferential elimination of mutations with certain growth advantages. We confirm our results by extensive numerical simulations. | E-2078-2011 | BOTTLENECKS;EVOLUTION;FIXATION;PROBABILITIES | 0 | null | null | 5 | bottleneck;EVOLUTION;FIXATION;PROBABILITY | WOS:000391927700012 | Univ Calif San Diego, La Jolla, CA USA | USA | 2,017 | null | 0000-0002-1276-9381;0000-0003-0709-3548 | null | null | English | null | BIOINFORMATICS;BIOMETRIKA;EVOLUTION;GENETICS;J APPL CHEM BIOTECHN;J Biol Eng;J CHEM PHYS;MATH BIOSCI;NATURE;P CAMB PHILOS SOC;P NATL ACAD SCI USA;P R SOC EDINB;P ROY SOC EDINB B;SCIENCE;THEOR POPUL BIOL | Bittihn, Philip;Hasty, Jeff;Tsimring, Lev S | 2024-03-11
ER | Campos, P R A;Cao, Y;Fisher R.;Fisher R. A.;Haldane, J B S;Handel, A;Heffernan, J M;Hubbarde, J E;Iyer-Biswas, S;Kendall, D G;Kimura, M;Loh, E;Mather, W H;Otto, S P;Pollak, E;Prindle, A;Sleight Sean, C;Uecker, H;Wahl, L M;Watson, T G;Wielgoss, S;Wiser, M J | EH7BL | La Jolla, CA USA;La Jolla, CA USA. | 11 | null | 1 | null | 28,128,631 | Bittihn, Philip;Hasty, Jeff;Tsimring, Lev S | PHYS REV LETT | La Jolla, CA USA |
Li, J;Liang, Q;Marchisio, M A;Song, W J | 10.1186/s13036-016-0040-5 | 19 | 236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND | 5z2vm544e5p582c4ax5n6u1667176a1f96c47 | Can terminators be used as insulators into yeast synthetic gene circuits? | Harbin Inst Technol | null | Marchisio, MA (corresponding author), Harbin Inst Technol, Sch Life Sci & Technol, 2 Yikuang St, Harbin 150080, Peoples R China. | null | Li, Jing;Liang, Qiang;Marchisio, Mario Andrea;Song, Wenjiang | Biochemical Research Methods;Biotechnology & Applied Microbiology | National Natural Science Foundation of China [3157080528] | WOS | Marchisio, M A | Harbin Inst Technol, Harbin, Peoples R China | 10 | ?;as;be;can;circuits;gene;insulators;into;synthetic;Terminators;used;yeast | 1 | Marchisio, Mario Andrea | BIOMED CENTRAL LTD | Harbin Inst Technol, Sch Life Sci & Technol, 2 Yikuang St, Harbin 150080, Peoples R China | Article | Harbin Inst Technol | LONDON | null | null | Harbin Inst Technol | National Natural Science Foundation of China | Marchisio, MA (corresponding author), Harbin Inst Technol, Sch Life Sci & Technol, 2 Yikuang St, Harbin 150080, Peoples R China. | null | Li, Jing;Liang, Qiang;Marchisio, Mario Andrea;Song, Wenjiang | 11 | 1 | 390,315,300,001 | National Natural Science Foundation of China [3157080528] | China | JOURNAL OF BIOLOGICAL ENGINEERING | China | null | null | Harbin Inst Technol, Sch Life Sci & Technol, 2 Yikuang St, Harbin 150080, Peoples R China | 1754-1611 | Li, J;Liang, Q;Marchisio, M A;Song, W J | DEC 16 | marchisio@hit.edu.cn | insulators;terminators;yeast synthetic gene circuits | 4 | J | Biochemistry & Molecular Biology;Biotechnology & Applied Microbiology | ACTIVATOR PROTEINS;background;BACTERIA;bacterial terminators;bound;building synthetic gene circuit;conclusions;CYC1 yeast constitutive promoter;data;different yeast terminators (natural;DNA;Efficiency element;eukaryotic TATA box i.e;every upstream activating sequences;expression;FACTOR TUF;front;hexamer sequence;Insulation;insulator efficiency element;insulators;medium-strength constitutive yeast promoters;MESSENGER-RNA;non-negligible decrease;non-weak promoters;principle;PROMOTER;promoter enhancers;promoter sequence;promoter transcriptional activity;PROTEIN;PROTEIN EXPRESSION;read-through;removed;results;RNA polymerase II;RNA polymerase II molecules;RNA polymerase unspecific binding;S. Cerevisiae;SACCHAROMYCES-CEREVISIAE;sequence;synthetic);TATA box;TATA boxes;TATA ELEMENTS;terminator;TERMINATORS;TRANSCRIPTION;transcription units;upstream gene;way promoter leakage;working;yeast S. cerevisiae;yeast S. cerevisiae terminators;yeast synthetic gene circuits | Song, W J | DNA;Efficiency element;EXPRESSION;FACTOR TUF;Insulation;MESSENGER-RNA;PROMOTER;PROTEIN;S. cerevisiae;SACCHAROMYCES-CEREVISIAE;SEQUENCE;TATA box;TATA ELEMENTS;Terminator;TRANSCRIPTION | null | [Song, Wenjiang; Li, Jing; Liang, Qiang; Marchisio, Mario Andrea] Harbin Inst Technol, Sch Life Sci & Technol, 2 Yikuang St, Harbin 150080, Peoples R China. | We acknowledge financial support by the National Natural Science Foundation of China grant number 3157080528. | activator proteins;background;bacteria;bacterial terminators;bound;building synthetic gene circuit;conclusions;CYC1 yeast constitutive promoter;data;different yeast terminators (natural;DNA;efficiency element;eukaryotic TATA box i.e;every upstream activating sequences;front;hexamer sequence;insulation;insulator efficiency element;medium-strength constitutive yeast promoters;non-negligible decrease;non-weak promoters;principle;promoter;promoter enhancers;promoter sequence;promoter transcriptional activity;protein expression;read-through;removed;results;RNA polymerase II;RNA polymerase II molecules;RNA polymerase unspecific binding;synthetic);TATA box;TATA boxes;terminator;terminators;transcription units;upstream gene;way promoter leakage;working;yeast S. cerevisiae;yeast S. cerevisiae terminators | 10.1002/bit.24552;10.1002/yea.1130;10.1007/BF00293817;10.1007/BF02705117;10.1007/s004380050466;10.1016/0092-8674(84)90243-5;10.1016/0378-1119(93)90681-R;10.1016/0378-1119(95)00037-7;10.1016/0378-1119(96)00337-X;10.1016/j.ymben.2013.07.001;10.1016/S0968-0004(96)10057-8;10.1021/ACSSYNBIO.6B00165.];10.1021/sb4001504;10.1021/sb5003357;10.1038/msb4100168;10.1038/nbt.2891;10.1038/nbt1413;10.1073/pnas.82.24.8562;10.1093/nar/gkp687;10.1093/nar/gkt256;10.1101/gad.4.4.503;10.1101/gad.5.4.616;10.1128/MCB.10.8.3859;10.1128/MCB.12.6.2690;10.1128/MCB.9.12.5298;10.1186/1471-2105-10-106;10.1186/1754-1611-8-6;10.1371/journal.pone.0016765;10.1371/journal.pone.0067902;10.1534/g3.111.001917;10.2144/000113672;10.3389/fbioe.2014.00042 | Harbin Inst Technol | Li, J;Liang, Q;Marchisio, M A;Song, W J | Song, W J: Harbin Inst Technol, Sch Life Sci & Technol, 2 Yikuang St, Harbin 150080, Peoples R China | Marchisio, Mario Andrea | 3157080528 | 39 | null | China | Harbin Inst Technol | Song, Wenjiang | gold, Green Published | DNA;EXPRESSION;FACTOR TUF;MESSENGER-RNA;PROMOTER;PROTEIN;SACCHAROMYCES-CEREVISIAE;SEQUENCE;TATA ELEMENTS;TRANSCRIPTION | Song, Wenjiang; Li, Jing; Liang, Qiang; Marchisio, Mario Andrea; | null | Harbin Inst Technol, Sch Life Sci & Technol, 2 Yikuang St, Harbin 150080, Peoples R China | Harbin Inst Technol, Sch Life Sci & Technol, 2 Yikuang St, Harbin 150080, Peoples R China | null | Efficiency element;Insulation;S. cerevisiae;TATA box;Terminator | null | 1984;1985;1989;1990;1991;1992;1993;1995;1996;1997;2000;2002;2003;2004;2006;2007;2008;2009;2011;2012;2013;2014;2015;2016 | 22 | Harbin Inst Technol, Sch Life Sci & Technol, 2 Yikuang St, Harbin 150080, Peoples R China | J. Biol. Eng. | Marchisio, Mario Andrea | BIOMED CENTRAL LTD | (natural;,;:;a;able;activating;activator;activity;an;and;as;at;avoid;background;bacteria;bacterial;be;bind;binding;bound;box;boxes;building;by;can;cause;cerevisiae;circuit;competing;conclusions;constitutive;contain;CYC1;data;decrease;different;differently;DNA;due;efficiency;either;element;enhancers;eukaryotic;every;expression;from;front;gene;hence;hexamer;i.e;II;in;insulated;insulation;insulator;interfere;is;it;leakage;medium-strength;molecules;moreover;non-negligible;non-weak;of;or;other;our;placing;polymerase;preferable;principle;promoter;promoters;protein;proteins;put;read-through;recognized;removed;resembles;results;RNA;S.;seems;sequence;sequences;stripped;strong;strongly;suggests;synthetic;synthetic);targeting;TATA;terminator;terminators;that;the;this;to;transcription;transcriptional;units;unspecific;upon;upstream;verified;way;we;when;with;working;yeast | Harbin Inst Technol | Background: In bacteria, transcription units can be insulated by placing a terminator in front of a promoter. In this way promoter leakage due to the read-through from an upstream gene or RNA polymerase unspecific binding to the DNA is, in principle, removed. Differently from bacterial terminators, yeast S. cerevisiae terminators contain a hexamer sequence, the efficiency element, that strongly resembles the eukaryotic TATA box i.e. the promoter sequence recognized and bound by RNA polymerase II. Results: By placing different yeast terminators (natural and synthetic) in front of the CYC1 yeast constitutive promoter stripped of every upstream activating sequences and TATA boxes, we verified that the efficiency element is able to bind RNA polymerase II, hence working as a TATA box. Moreover, terminators put in front of strong and medium-strength constitutive yeast promoters cause a non-negligible decrease in the promoter transcriptional activity. Conclusions: Our data suggests that RNA polymerase II molecules upon binding the insulator efficiency element interfere with protein expression by competing either with activator proteins at the promoter enhancers or other RNA polymerase II molecules targeting the TATA box. Hence, it seems preferable to avoid the insulation of non-weak promoters when building synthetic gene circuit in yeast S. cerevisiae. | ABE-8451-2020 | DNA;EXPRESSION;FACTOR TUF;MESSENGER-RNA;PROMOTER;PROTEIN;SACCHAROMYCES-CEREVISIAE;SEQUENCE;TATA ELEMENT;TRANSCRIPTION | 3 | null | Efficiency element;Insulation;S. cerevisiae;TATA box;Terminator | 13 | SACCHAROMYCES-CEREVISIAE;DNA;Efficiency element;EXPRESSION;FACTOR TUF;INSULATOR;MESSENGER-RNA;PROMOTER;PROTEIN;S. cerevisiae;SEQUENCE;TATA box;TATA ELEMENT;TERMINATION;TRANSCRIPTION | WOS:000390315300001 | Harbin Inst Technol, Harbin, Peoples R China | China | 2,016 | null | 0000-0002-5102-1069 | null | null | English | null | ACS SYNTH BIOL;BIOTECHNIQUES;BIOTECHNOL BIOENG;BMC BIOINFORMATICS;CELL;Front Bioeng Biotechnol;GENE;GENE DEV;GENES-BASEL;INTRO SYSTEMS BIOL;J BIOL CHEM;J Biol Eng;J BIOSCIENCES;METAB ENG;METHOD ENZYMOL;MOL CELL BIOL;MOL CLONING;MOL GEN GENET;MOL SYST BIOL;NAT BIOTECHNOL;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PLOS ONE;TRENDS BIOCHEM SCI;YEAST | Li, Jing;Liang, Qiang;Marchisio, Mario Andrea;Song, Wenjiang | 2024-03-11
ER | Alon, U;Bitter, G A;Blazeck, J;Brambilla, A;Canton, B;Chasman, D I;Chee, M K;Curran, K A;Engler, C;Galdzicki, M;Gibson, D G;Gietz, R D;Grilly, C;Guarente, L;Guo, Z J;Hahn, S;Hahne, F;Harbury, P A B;Huie, M A;Krebber, A;Kurtz, S;Lee, S;Lewin B.;Looke, M;Louvion, J F;Lubliner, S;Macpherson, M I;Marchisio Mario Andrea;Marchisio, M A;Mishra, A K;Mumberg, D;Sambrook J.;Sheff, M A;Vignais, M L;Weber, E;Wobbe, C R | EF4PU | Harbin, Peoples R China | 23 | null | 1 | null | 28,018,483 | Li, Jing;Liang, Qiang;Marchisio, Mario Andrea;Song, Wenjiang | J BIOL ENG | Harbin, Peoples R China |
Angelidou, G;Boone, C;Demosthenous, P;Kirmizis, A;Kyriakou, D;Luis, B J S;Promponas, V J;Stavrou, E | 10.1186/s12915-016-0325-7 | 106 | CAMPUS, 4 CRINAN ST, LONDON N1 9XW, ENGLAND | 1fw1r5cvjl1i3k2b71q4h2m6d686j667253 | Functional characterisation of long intergenic non-coding RNAs through genetic interaction profiling in <i>Saccharomyces cerevisiae</i> | Univ Cyprus | null | Kirmizis, A (corresponding author), Univ Cyprus, Dept Biol Sci, CY-1678 Nicosia, Cyprus. | null | Angelidou, Georgia;Boone, Charles;Demosthenous, Panayiota;Kirmizis, Antonis;Kyriakou, Dimitris;Luis, Bryan-Joseph San;Promponas, Vasilis J;Stavrou, Emmanouil | Biology | European Research Council (ERC-Stg) [N.260797] | WOS | Kirmizis, A | Univ Cyprus, Nicosia, Cyprus;Univ Toronto, Toronto ON, Canada | 14 | <i>Saccharomyces;cerevisiae</i>;characterisation;functional;genetic;in;Interaction;intergenic;long;non-coding;of;profiling;RNAs;through | 2 | Kirmizis, Antonis;Promponas, Vasilis J | BMC | Univ Cyprus, Dept Biol Sci, CY-1678 Nicosia, Cyprus;Univ Toronto, Donnelly Ctr, 160 Coll St, Toronto, ON M5S 3E1, Canada | Article | Univ Cyprus | LONDON | null | null | Univ Cyprus;Univ Toronto | European Research Council (ERC-Stg) | Kirmizis, A (corresponding author), Univ Cyprus, Dept Biol Sci, CY-1678 Nicosia, Cyprus. | null | Angelidou, Georgia;Boone, Charles;Demosthenous, Panayiota;Kirmizis, Antonis;Kyriakou, Dimitris;Luis, Bryan-Joseph San;Promponas, Vasilis J;Stavrou, Emmanouil | 16 | 2 | 389,551,500,001 | European Research Council (ERC-Stg) [N.260797] | Canada;Cyprus | BMC BIOLOGY | Cyprus | null | null | Univ Cyprus, Dept Biol Sci, CY-1678 Nicosia, Cyprus | 1741-7007 | Angelidou, G;Boone, C;Demosthenous, P;Kirmizis, A;Kyriakou, D;Luis, B J S;Promponas, V J;Stavrou, E | DEC 7 | kirmizis@ucy.ac.cy | <i>Saccharomyces cerevisiae</i>;functional characterisation;genetic interaction;long intergenic non-coding RNAs | 8 | J | Life Sciences & Biomedicine - Other Topics | <i>Saccharomyces cerevisiae</i>;adjacent genes;approach;background;BIDIRECTIONAL PROMOTERS;cellular role;complex organisms;conclusions;connection;diverse cellular processes;ECTOPIC EXPRESSION;eukaryotic genomes;evolution;Exo1-dependent pathway;expression;few lncRNAs;function;function independent;functional characterisation;functional significance;G-TAILS;GENERATION;genetic approach;genetic interaction;genetic interactions;GENOME-WIDE SCREEN;genomic location;GI network;GI profile;GIs;IDENTIFICATION;individual lncRNAs;lincRNA;lincRNAs;lncRNAs;Long intergenic non-coding RNAs;long intergenic non-coding RNAs (lincRNAs);majority;neighbouring genes;numerous long non-coding RNAs (lncRNAs);one;overall;pathways;protein-coding genes;redundant;results;Saccharomyces cerevisiae;SGA screens;SINGLE-STRANDED-DNA;Stable unannotated transcripts;SUT457;sut457 Delta cells;synthetic genetic array;synthetic genetic array (SGA);synthetic genetic interactions (GIs);systematic analysis;systematic application;telomerase RNA TLC1;Telomere;telomere biology;telomere length maintenance;telomere organisation;telomeric overhang accumulation;telomeric overhang homeostasis;trans-acting role;TRANSCRIPTION;Transcriptome studies;uncharacterised lincRNAs;well-described function;yeast;YEAST TELOMERASE RNA | Kyriakou, D | BIDIRECTIONAL PROMOTERS;EVOLUTION;G-TAILS;GENERATION;genetic interactions;GENOME-WIDE SCREEN;IDENTIFICATION;Long intergenic non-coding RNAs;PATHWAYS;SINGLE-STRANDED-DNA;Stable unannotated transcripts;synthetic genetic array;Telomere;TRANSCRIPTION;YEAST TELOMERASE RNA | null | [Kyriakou, Dimitris; Stavrou, Emmanouil; Demosthenous, Panayiota; Angelidou, Georgia; Promponas, Vasilis J.; Kirmizis, Antonis] Univ Cyprus, Dept Biol Sci, CY-1678 Nicosia, Cyprus. [Luis, Bryan-Joseph San; Boone, Charles] Univ Toronto, Donnelly Ctr, 160 Coll St, Toronto, ON M5S 3E1, Canada. | This work was supported by a grant to AK from the European Research Council (ERC-2010-Stg, N.260797, ChromatinModWeb). | adjacent genes;approach;background;cellular role;complex organisms;conclusions;connection;diverse cellular processes;ectopic expression;eukaryotic genomes;Exo1-dependent pathway;expression;few lncRNAs;function;function independent;functional significance;genetic approach;genomic location;GI network;GI profile;GIs;individual lncRNAs;lincRNA;lincRNAs;lncRNAs;long intergenic non-coding RNAs (lincRNAs);majority;neighbouring genes;numerous long non-coding RNAs (lncRNAs);one;overall;protein-coding genes;redundant;results;Saccharomyces cerevisiae;SGA screens;SUT457;sut457 Delta cells;synthetic genetic array (SGA);synthetic genetic interactions (GIs);systematic analysis;systematic application;telomerase RNA TLC1;telomere biology;telomere length maintenance;telomere organisation;telomeric overhang accumulation;telomeric overhang homeostasis;trans-acting role;Transcriptome studies;uncharacterised lincRNAs;well-described function;yeast | 10.1002/yea.1369;10.1007/s00412-013-0440-y;10.1007/s00438-007-0218-0;10.1016/0092-8674(89)90132-3;10.1016/j.bbagen.2013.10.035;10.1016/j.bbagrm.2015.10.010;10.1016/j.cell.2005.04.030;10.1016/j.cell.2005.12.044;10.1016/j.cell.2006.09.038;10.1016/j.cell.2012.01.033;10.1016/j.cell.2012.06.049;10.1016/j.cell.2013.07.047;10.1016/j.celrep.2015.04.023;10.1016/j.celrep.2016.05.043;10.1016/j.gde.2014.03.009;10.1016/j.gde.2015.12.005;10.1016/j.molcel.2008.09.027;10.1016/j.molcel.2008.10.019;10.1016/j.molcel.2009.05.015;10.1016/j.molcel.2012.05.028;10.1016/j.molcel.2013.10.032;10.1016/j.molcel.2014.01.006;10.1038/emboj.2009.108;10.1038/emboj.2010.155;10.1038/nature02538;10.1038/nature07728;10.1038/nature07747;10.1038/nature10118;10.1038/ncomms6576;10.1038/ng.524;10.1038/ng.846;10.1038/NMETH.1534;10.1038/nmeth.1936;10.1038/nprot.2014.160;10.1038/nrg.2015.10;10.1038/nsmb.1616;10.1038/srep19376;10.1073/pnas.0401263101;10.1073/pnas.0507783103;10.1073/pnas.0601091103;10.1073/pnas.0909641106;10.1073/pnas.1016459108;10.1074/jbc.M208347200;10.1093/bfgp/elv058;10.1093/hmg/ddu040;10.1093/nar/18.10.3091;10.1093/nar/27.12.2560;10.1101/gad.1125903;10.1101/gad.1199404;10.1101/gad.225102;10.1101/gad.458008;10.1101/gad.522509;10.1101/gr.6036807;10.1111/1574-6976.12054;10.1126/science.1065810;10.1126/science.1158441;10.1126/science.1180823;10.1126/science.1231143;10.1126/science.7544491;10.1126/science.7545955;10.1126/science.aac7557;10.1128/MCB.00418-07;10.1128/MCB.01417-07;10.1128/MCB.21.5.1819-1827.2001;10.1128/MCB.22.1.286-297.2002;10.1128/MCB.23.22.8202-8215.2003;10.1146/annurev.genet.39.073003.114751;10.1186/1471-2164-7-187;10.1242/jcs.033308;10.1371/journal.pgen.1000966;10.1371/journal.pgen.1001072;10.1371/journal.pgen.1002163;10.1371/journal.pgen.1002233;10.1371/journal.pgen.1002747;10.1371/journal.pone.0042028;10.1534/g3.111.000216;10.1534/genetics.104.027904;10.1534/genetics.111.137851;10.2144/000113687;10.4161/trns.2.3.16298;10.7554/eLife.01749;10.7554/eLife.07750;[10.1038/nmeth.1890, 10.1038/NMETH.1890];[10.1038/NMETH.2398, 10.1038/nmeth.2398] | Univ Cyprus | Angelidou, G;Boone, C;Demosthenous, P;Kirmizis, A;Kyriakou, D;Luis, B J S;Promponas, V J;Stavrou, E | Kyriakou, D: Univ Cyprus, Dept Biol Sci, CY-1678 Nicosia, Cyprus | Promponas, Vasilis J | N.260797 | 87 | null | Cyprus | Univ Cyprus;Univ Toronto | Kyriakou, Dimitris | Green Published, gold | BIDIRECTIONAL PROMOTERS;EVOLUTION;G-TAILS;GENERATION;GENOME-WIDE SCREEN;IDENTIFICATION;PATHWAYS;SINGLE-STRANDED-DNA;TRANSCRIPTION;YEAST TELOMERASE RNA | Kyriakou, Dimitris; Stavrou, Emmanouil; Demosthenous, Panayiota; Angelidou, Georgia; Luis, Bryan-Joseph San; Boone, Charles; Promponas, Vasilis J.; Kirmizis, Antonis; | null | Univ Cyprus, Dept Biol Sci, CY-1678 Nicosia, Cyprus;Univ Toronto, Donnelly Ctr, 160 Coll St, Toronto, ON M5S 3E1, Canada | Univ Cyprus, Dept Biol Sci, CY-1678 Nicosia, Cyprus;Univ Toronto, Donnelly Ctr, 160 Coll St, Toronto, ON M5S 3E1, Canada | null | genetic interaction;Long intergenic non-coding RNAs;Stable unannotated transcripts;synthetic genetic array;Telomere | null | 1859;1989;1990;1994;1995;1999;2001;2002;2003;2004;2005;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016 | 15 | Univ Cyprus, Dept Biol Sci, CY-1678 Nicosia, Cyprus | BMC Biol. | Kirmizis, Antonis | BMC | (GIs);(lincRNAs);(lncRNAs);(SGA);,;:;a;accordingly;accumulation;adjacent;an;analysis;and;annotated;application;approach;are;array;as;ascribed;assigning;associating;background;be;been;between;biology;by;cells;cellular;cerevisiae;complex;conclusions;connection;consistently;corresponds;could;Delta;demonstrate;demonstrating;determine;displays;distinct;diverse;ectopic;employ;essential;eukaryotic;even;exhibits;Exo1-dependent;expression;far;few;first;for;from;function;functional;functionally;furthermore;genes;genetic;genomes;genomic;GI;GIs;have;hence;here;homeostasis;however;identify;illuminated;implying;in;independent;individual;interactions;intergenic;is;it;its;length;less;lincRNA;lincRNAs;lncRNAs;location;long;maintenance;majority;many;may;most;neighbouring;network;non-coding;numerous;of;on;one;only;organisation;organisms;other;our;overall;overhang;pathway;performed;pervasively;processes;producing;profile;proposes;protein-coding;redundant;regulating;required;results;revealed;RNA;RNAs;role;Saccharomyces;screens;set;SGA;show;SIGNIFICANCE;studies;subsequently;suggesting;suppresses;SUT457;synthetic;systematic;telomerase;telomere;telomeric;that;the;their;therefore;these;this;through;thus;TLC1;to;trans-acting;transcribed;transcriptome;uncharacterised;uncover;validate;we;well-described;with;work;yeast | Univ Cyprus | Background: Transcriptome studies have revealed that many eukaryotic genomes are pervasively transcribed producing numerous long non-coding RNAs (lncRNAs). However, only a few lncRNAs have been ascribed a cellular role thus far, with most regulating the expression of adjacent genes. Even less lncRNAs have been annotated as essential hence implying that the majority may be functionally redundant. Therefore, the function of lncRNAs could be illuminated through systematic analysis of their synthetic genetic interactions (GIs). Results: Here, we employ synthetic genetic array (SGA) in Saccharomyces cerevisiae to identify GIs between long intergenic non-coding RNAs (lincRNAs) and protein-coding genes. We first validate this approach by demonstrating that the telomerase RNA TLC1 displays a GI network that corresponds to its well-described function in telomere length maintenance. We subsequently performed SGA screens on a set of uncharacterised lincRNAs and uncover their connection to diverse cellular processes. One of these lincRNAs, SUT457, exhibits a GI profile associating it to telomere organisation and we consistently demonstrate that SUT457 is required for telomeric overhang homeostasis through an Exo1-dependent pathway. Furthermore, the GI profile of SUT457 is distinct from that of its neighbouring genes suggesting a function independent to its genomic location. Accordingly, we show that ectopic expression of this lincRNA suppresses telomeric overhang accumulation in sut457 Delta cells assigning a trans-acting role for SUT457 in telomere biology. Conclusions: Overall, our work proposes that systematic application of this genetic approach could determine the functional significance of individual lncRNAs in yeast and other complex organisms. | G-5539-2010 | BIDIRECTIONAL PROMOTERS;EVOLUTION;G-TAILS;GENERATION;GENOME-WIDE SCREEN;IDENTIFICATION;PATHWAY;SINGLE-STRANDED-DNA;TRANSCRIPTION;YEAST TELOMERASE RNA | 0 | null | genetic interactions;Long intergenic non-coding RNAs;Stable unannotated transcripts;synthetic genetic array;Telomere | 16 | BIDIRECTIONAL PROMOTERS;EVOLUTION;G-TAILS;GENERATION;genetic interactions;GENOME-WIDE SCREEN;IDENTIFICATION;Long intergenic non-coding RNAs;PATHWAY;SINGLE-STRANDED-DNA;Stable unannotated transcripts;synthetic genetic array;Telomere;TRANSCRIPTION;YEAST TELOMERASE RNA | WOS:000389551500001 | Univ Cyprus, Nicosia, Cyprus;Univ Toronto, Toronto ON, Canada | Canada;Cyprus | 2,016 | null | 0000-0002-3748-8711;0000-0003-3352-4831 | null | null | English | null | ANNU REV GENET;BBA-GEN SUBJECTS;BBA-GENE REGUL MECH;BIOCHIM BIOPHYS ACTA;BIOTECHNIQUES;BMC GENOMICS;BRIEF FUNCT GENOMICS;CELL;CELL REP;CHROMOSOMA;CURR OPIN GENET DEV;ELIFE;EMBO J;FEMS MICROBIOL REV;GENE DEV;GENETICS;GENOME RES;HUM MOL GENET;J BIOL CHEM;J CELL SCI;MATH PROBLEMS ENG;MOL CELL;MOL CELL BIOL;MOL GENET GENOMICS;NAT COMMUN;NAT GENET;NAT METHODS;NAT PROTOC;NAT REV GENET;NAT STRUCT MOL BIOL;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PLOS GENET;PLOS ONE;SCI REP-UK;SCIENCE;TRANSCR-AUSTIN;YEAST | Angelidou, Georgia;Boone, Charles;Demosthenous, Panayiota;Kirmizis, Antonis;Kyriakou, Dimitris;Luis, Bryan-Joseph San;Promponas, Vasilis J;Stavrou, Emmanouil | 2024-03-11
ER | [Anonymous];Alcid, E A;Ard, R;Askree, S H;Baryshnikova, A;Ben-Shitrit, T;Berretta, J;Bertuch, A A;Blomen, V A;Bonetti, D;Bumgarner, S L;Camblong, J;Chang, H Y;Chen, Q J;Cong, L;Costanzo, M;David, L;Davis, C A;Denisenko, O;Dezwaan, D C;Dixon, S J;Downey, M;Fang, K;Feng, J L;Franke, J;Garvik, B;Grandin, N;Hass, E P;He, X L;Hezroni, H;Hongay, C F;Houalla, R;Houseley, J;Huber, F;Jensen, T H;Johnsson, P;Kashi, K;Kupiec, M;Lardenois, A;Larrivée, M;Laufer, C;Lopez, C R;Lue, N F;Luke, B;Luke-Glaser, S;Lundblad, V;Maringele, L;Marquardt, S;Marques, A C;Martens, J A;Mohankumar, S;Myers, C L;Nadal-Ribelles, M;Nagalakshmi, U;Neil, H;Ngo, H P;Niederer, R O;Ortega, L M;Pang, T L;Pfeiffer, V;Pfingsten, J S;Pinskaya, M;Ponjavic, J;Quinn, J J;Roguev, A;Ryan, C J;Sauvageau, M;Schmitt, M E;Singer, M S;Stellwagen, A E;Szappanos, B;Toesca, I;Tong, A H Y;Toogun, O A;Tuck, A C;Van Dijk, E L;Van Werven, F J;Vodenicharov, M D;Wellinger, R J;Wyers, F;Xu, Z Y;Yamashita, A;Yu, E Y;Zubko, M K | EE4DE | Nicosia, Cyprus | 17 | null | 2 | null | 27,927,215 | Angelidou, Georgia;Boone, Charles;Demosthenous, Panayiota;Kirmizis, Antonis;Kyriakou, Dimitris;Luis, Bryan-Joseph San;Promponas, Vasilis J;Stavrou, Emmanouil | BMC BIOL | Nicosia, Cyprus;Toronto ON, Canada |
Brás, J L A;Fontes, C M G A;Guerreiro, C I P D;Sequeira, A F;Vincentelli, R | 10.1186/s12896-016-0316-3 | 86 | 236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND | 4v1q4l4t6i43p41116d6w1b31r1a6o3u3o2v | Development of a gene synthesis platform for the efficient large scale production of small genes encoding animal toxins | Univ Lisbon | null | Fontes, CMGA (corresponding author), NZYTech Genes & Enzymes, Campus Lumiar,Estr Paco Lumiar,Edificio E,R-C, P-1649038 Lisbon, Portugal.;Fontes, CMGA (corresponding author), Univ Lisbon, CIISA, Fac Med Vet, Ave Univ Tecn, P-1300477 Lisbon, Portugal. | null | Bras, Joana L A;Fontes, Carlos M G A;Guerreiro, Catarina I P D;Sequeira, Ana Filipa;Vincentelli, Renaud | Biotechnology & Applied Microbiology | Fundacao para a Ciencia e a Tecnologia (Lisbon, Portugal); NZYTech [SFRH/BD/51602/2011]; VENOMICS project, European project through the Seventh Framework Program (FP7 HEALTH) [278346] | WOS | Fontes, CMGA | Aix Marseille Univ, Marseille, France;NZYTech Genes & Enzymes, Lisbon, Portugal;Univ Lisbon, Lisbon, Portugal | 16 | a;animal;Development;efficient;encoding;for;gene;genes;LARGE;of;Platform;production;scale;small;synthesis;the;toxins | 2 | Bras, Joana;Fontes, Carlos;Sequeira, Ana Filipa | BIOMED CENTRAL LTD | Aix Marseille Univ, AFMB, CNRS, UMR 7257, Campus Luminy,163 Ave Luminy, F-13288 Marseille 09, France;NZYTech Genes & Enzymes, Campus Lumiar,Estr Paco Lumiar,Edificio E,R-C, P-1649038 Lisbon, Portugal;Univ Lisbon, CIISA, Fac Med Vet, Ave Univ Tecn, P-1300477 Lisbon, Portugal;Univ Lisbon, CIISA, Fac Med Vet, Ave Univ Tecn, P-1300477 Lisbon, Portugal.; Fontes, CMGA (corresponding author), NZYTech Genes & Enzymes, Campus Lumiar,Estr Paco Lumiar,Edificio E,R-C, P-1649038 Lisbon, Portugal | Article | NZYTech Genes & Enzymes;Univ Lisbon | LONDON | null | null | Aix Marseille Univ;Fac Med Vet;NZYTech Genes & Enzymes;Univ Lisbon | Fundacao para a Ciencia e a Tecnologia (Lisbon, Portugal);NZYTech;VENOMICS project, European project through the Seventh Framework Program (FP7 HEALTH) | Fontes, CMGA (corresponding author), Univ Lisbon, CIISA, Fac Med Vet, Ave Univ Tecn, P-1300477 Lisbon, Portugal.; Fontes, CMGA (corresponding author), NZYTech Genes & Enzymes, Campus Lumiar,Estr Paco Lumiar,Edificio E,R-C, P-1649038 Lisbon, Portugal. | null | Bras, Joana L A;Fontes, Carlos M G A;Guerreiro, Catarina I P D;Sequeira, Ana Filipa;Vincentelli, Renaud | 11 | 3 | 390,272,700,002 | Fundacao para a Ciencia e a Tecnologia (Lisbon, Portugal);NZYTech [SFRH/BD/51602/2011];VENOMICS project, European project through the Seventh Framework Program (FP7 HEALTH) [278346] | France;Portugal | BMC BIOTECHNOLOGY | Portugal | null | null | Univ Lisbon, CIISA, Fac Med Vet, Ave Univ Tecn, P-1300477 Lisbon, Portugal | 1472-6750 | Brás, J L A;Fontes, C M G A;Guerreiro, C I P D;Sequeira, A F;Vincentelli, R | DEC 1 | cafontes@fmv.ulisboa.pt | development;efficient large scale production;gene synthesis platform;small genes encoding animal toxins | 5 | J | Biotechnology & Applied Microbiology | 96 genes encoding animal toxins;animal venoms;Assembly PCR;automated platform;available;background;CODON USAGE;conclusions;cost effective ligation independent;de novo gene synthesis;development;DNA-SYNTHESIS;dozens;drug discovery;effective Escherichia coli expression vector;efficient gene design algorithms;efficient large scale production;extraordinary potency;GENE DESIGN;GENE SYNTHESIS;gene synthesis platform;high levels;HIGH-FIDELITY;important tool;improved gene synthesis method;large libraries;large scale production;large scale recombinant expression;large-scale synthesis;lead molecules;leads;multiples genes;mutagenesis procedures;nucleic acids;OLIGONUCLEOTIDES;overlapping oligonucleotides;parallel;PCR;PCR-based protocol;pharmacological diversity;POLYMERASE;pools;recombinant DNA technology;recombinant protein expression;recombinant protein production;results;ROBUSTNESS;SEQUENCES;simultaneous synthesis;small genes encoding animal toxins;small genes encoding eukaryotic toxins;small genes encoding venom peptides;step;synthetic DNA;synthetic genes;synthetic genes encoding eukaryotic toxins will;synthetic nucleic acids;template;thousands;unexplored source;valuable;Venom peptides | Sequeira, A F | Assembly PCR;DNA-SYNTHESIS;GENE DESIGN;GENE SYNTHESIS;HIGH-FIDELITY;OLIGONUCLEOTIDES;PCR;POLYMERASE;SEQUENCES;Venom peptides | null | [Sequeira, Ana Filipa; Fontes, Carlos M. G. A.] Univ Lisbon, CIISA, Fac Med Vet, Ave Univ Tecn, P-1300477 Lisbon, Portugal. [Sequeira, Ana Filipa; Bras, Joana L. A.; Guerreiro, Catarina I. P. D.; Fontes, Carlos M. G. A.] NZYTech Genes & Enzymes, Campus Lumiar,Estr Paco Lumiar,Edificio E,R-C, P-1649038 Lisbon, Portugal. [Vincentelli, Renaud] Aix Marseille Univ, AFMB, CNRS, UMR 7257, Campus Luminy,163 Ave Luminy, F-13288 Marseille 09, France. | Ana Filipa Sequeira was supported by Fundacao para a Ciencia e a Tecnologia (Lisbon, Portugal) and NZYTech through the individual fellowship SFRH/BD/51602/2011. This work was supported by The VENOMICS project, European project grant No 278346 through the Seventh Framework Program (FP7 HEALTH 2011-2015). The VENOMICS project involves the collaboration between several research institutions and companies in Europe: AFMB, Aix-Marseille Universite (France), CEA Saclay (France), NZYTech (Portugal), Sistemas Genomicos (Spain), University de Liege (Belgium) and Zealand Pharma (Denmark). | 96 genes encoding animal toxins;animal venoms;automated platform;available;background;codon usage;conclusions;cost effective ligation independent;de novo gene synthesis;development;dozens;drug discovery;effective Escherichia coli expression vector;efficient gene design algorithms;extraordinary potency;gene synthesis;gene synthesis platform;high levels;important tool;improved gene synthesis method;large libraries;large scale production;large scale recombinant expression;large-scale synthesis;lead molecules;leads;multiples genes;mutagenesis procedures;nucleic acids;overlapping oligonucleotides;parallel;PCR-based protocol;pharmacological diversity;pools;recombinant DNA technology;recombinant protein expression;recombinant protein production;results;robustness;simultaneous synthesis;small genes encoding eukaryotic toxins;small genes encoding venom peptides;step;synthetic DNA;synthetic genes;synthetic genes encoding eukaryotic toxins will;synthetic nucleic acids;template;thousands;unexplored source;valuable | 10.1016/0378-1119(95)00511-4;10.1016/j.jbiotec.2006.01.015;10.1016/j.mimet.2010.02.013;10.1021/bi00416a027;10.1038/nprot.2006.103;10.1038/srep11302;10.1039/b822268c;10.1073/pnas.93.26.15012;10.1093/nar/30.10.e43;10.1093/nar/gkq163;10.1093/nar/gku405;10.1093/nar/gng143;10.1093/nar/gnh058;10.1093/nar/gnh094;10.1093/nar/gnh160;10.1093/nar/gni053;10.1093/protein/2.5.387;10.1128/AEM.63.11.4504-4510.1997;10.1371/journal.pone.0029678 | Univ Lisbon | Brás, J L A;Fontes, C M G A;Guerreiro, C I P D;Sequeira, A F;Vincentelli, R | Sequeira, A F: Univ Lisbon, CIISA, Fac Med Vet, Ave Univ Tecn, P-1300477 Lisbon, Portugal | null | 278346;SFRH/BD/51602/2011 | 20 | null | Portugal | Aix Marseille Univ;NZYTech Genes & Enzymes;Univ Lisbon | Sequeira, Ana Filipa | Green Published, gold | DNA-SYNTHESIS;HIGH-FIDELITY;OLIGONUCLEOTIDES;PCR;POLYMERASE;SEQUENCES | Sequeira, Ana Filipa; Bras, Joana L. A.; Guerreiro, Catarina I. P. D.; Vincentelli, Renaud; Fontes, Carlos M. G. A.; | null | Aix Marseille Univ, AFMB, CNRS, UMR 7257, Campus Luminy,163 Ave Luminy, F-13288 Marseille 09, France;NZYTech Genes & Enzymes, Campus Lumiar,Estr Paco Lumiar,Edificio E,R-C, P-1649038 Lisbon, Portugal;Univ Lisbon, CIISA, Fac Med Vet, Ave Univ Tecn, P-1300477 Lisbon, Portugal | Aix Marseille Univ, AFMB, CNRS, UMR 7257, Campus Luminy,163 Ave Luminy, F-13288 Marseille 09, France;NZYTech Genes & Enzymes, Campus Lumiar,Estr Paco Lumiar,Edificio E,R-C, P-1649038 Lisbon, Portugal;Univ Lisbon, CIISA, Fac Med Vet, Ave Univ Tecn, P-1300477 Lisbon, Portugal | null | Assembly PCR;GENE DESIGN;Gene synthesis;Venom peptides | null | 1988;1989;1994;1995;1996;1997;2002;2003;2004;2005;2006;2009;2010;2012;2014;2015 | 2 | NZYTech Genes & Enzymes, Campus Lumiar,Estr Paco Lumiar,Edificio E,R-C, P-1649038 Lisbon, Portugal;Univ Lisbon, CIISA, Fac Med Vet, Ave Univ Tecn, P-1300477 Lisbon, Portugal | BMC Biotechnol. | Fontes, Carlos M G A | BIOMED CENTRAL LTD | ,;96;:;a;accurate;acids;addition;algorithms;allow;allows;an;and;animal;applied;assemble;automated;available;background;becoming;but;classical;cloning;codon;coli;conclusions;cost;coupled;de;demonstrated;describe;design;developed;development;directly;discovery;diversity;DNA;dozens;drug;effective;efficient;encoding;Escherichia;eukaryotic;exploring;expression;extraordinary;fields;for;from;gene;generate;generating;genes;here;high;important;improved;in;including;incorporates;increasingly;independent;integrate;into;is;it;large;large-scale;lead;leads;levels;libraries;ligation;many;method;molecules;multiples;mutagenesis;no;novo;nucleic;of;oligonucleotides;optimize;optimized;overlapping;parallel;PCR-based;peptides;pharmacological;platform;pools;potency;procedures;production;protein;protocol;quickly;recombinant;replacing;results;robustness;scale;simultaneous;simultaneously;small;source;step;synthesis;synthesise;synthetic;technology;template;that;the;this;thousands;through;to;tool;toxins;unexplored;usage;uses;valuable;vector;venom;venoms;was;we;when;which;will;with | NZYTech Genes & Enzymes;Univ Lisbon | Background: Gene synthesis is becoming an important tool in many fields of recombinant DNA technology, including recombinant protein production. De novo gene synthesis is quickly replacing the classical cloning and mutagenesis procedures and allows generating nucleic acids for which no template is available. In addition, when coupled with efficient gene design algorithms that optimize codon usage, it leads to high levels of recombinant protein expression. Results: Here, we describe the development of an optimized gene synthesis platform that was applied to the large scale production of small genes encoding venom peptides. This improved gene synthesis method uses a PCR-based protocol to assemble synthetic DNA from pools of overlapping oligonucleotides and was developed to synthesise multiples genes simultaneously. This technology incorporates an accurate, automated and cost effective ligation independent cloning step to directly integrate the synthetic genes into an effective Escherichia coli expression vector. The robustness of this technology to generate large libraries of dozens to thousands of synthetic nucleic acids was demonstrated through the parallel and simultaneous synthesis of 96 genes encoding animal toxins. Conclusions: An automated platform was developed for the large-scale synthesis of small genes encoding eukaryotic toxins. Large scale recombinant expression of synthetic genes encoding eukaryotic toxins will allow exploring the extraordinary potency and pharmacological diversity of animal venoms, an increasingly valuable but unexplored source of lead molecules for drug discovery. | null | DNA-SYNTHESIS;HIGH-FIDELITY;OLIGONUCLEOTIDES;PCR;POLYMERASE;SEQUENCE | 0 | null | Assembly PCR;GENE DESIGN;Gene synthesis;Venom peptides | 13 | Assembly PCR;DNA SYNTHESIS;GENE DESIGN;GENE SYNTHESIS;HIGH-FIDELITY;OLIGONUCLEOTIDES;PCR;POLYMERASE;SEQUENCE;Venom peptides | WOS:000390272700002 | Aix Marseille Univ, Marseille, France;NZYTech Genes & Enzymes, Lisbon, Portugal;Univ Lisbon, Lisbon, Portugal | France;Portugal | 2,016 | null | 0000-0001-8445-6221;0000-0002-1141-5530;0000-0002-1219-9753 | null | null | English | null | APPL ENVIRON MICROB;BIOCHEMISTRY-US;BIOTECHNIQUES;GENE;J BIOTECHNOL;J MICROBIOL METH;MOL BIOSYST;NAT PROTOC;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;PLOS ONE;PROTEIN ENG;SCI REP-UK | Bras, Joana L A;Fontes, Carlos M G A;Guerreiro, Catarina I P D;Sequeira, Ana Filipa;Vincentelli, Renaud | 2024-03-11
ER | Ashman, K;Binkowski, B F;Carr, P A;Gao, X X;Gordeeva, T L;Hayashi, N;Hoover, D M;Leproust, E M;Stemmer, W P C;Strizhov, N;Takagi, M;Tian, J D;Tindall, K R;Wan, W;Wu, G;Xiong, A S;Yang, D F;Young, L;Zampini, M | EF4CR | Lisbon, Portugal;Lisbon, Portugal. | 4 | null | 3 | null | 27,905,914 | Bras, Joana L A;Fontes, Carlos M G A;Guerreiro, Catarina I P D;Sequeira, Ana Filipa;Vincentelli, Renaud | BMC BIOTECHNOL | Lisbon, Portugal;Marseille, France |
Bennett, M R;Gupta, C;Josic, K;Ott, W;Veliz-Cuba, A | 10.1088/1478-3975/13/6/066007 | 066007 | TEMPLE CIRCUS, TEMPLE WAY, BRISTOL BS1 6BE, ENGLAND | 5h3f2c7x6b22l4t672fb1x594l21d1ln56 | Effects of cell cycle noise on excitable gene circuits | Univ Dayton | null | Ott, W (corresponding author), Univ Houston, Dept Math, Houston, TX 77004 USA. | null | Bennett, Matthew R;Gupta, Chinmaya;Josic, Kresimir;Ott, William;Veliz-Cuba, Alan | Biochemistry & Molecular Biology;Biophysics | NIH [4R01GM104974]; NSF [DMS 1413437]; Welch Foundation [C-1729]; Direct For Mathematical & Physical Scien; Division Of Mathematical Sciences [1413437] Funding Source: National Science Foundation | WOS | Ott, W | Rice Univ, Houston, TX USA;Univ Dayton, Dayton, OH USA;Univ Houston, Houston, TX USA | 13 | cell;circuits;cycle;Effects;excitable;gene;noise;of;on | 1 | Veliz-Cuba, Alan | IOP PUBLISHING LTD | Rice Univ, Dept Bioengn, Houston, TX 77251 USA;Rice Univ, Dept Biosci, Houston, TX 77251 USA;Univ Dayton, Dept Math, Dayton, OH 45469 USA;Univ Houston, Dept Biol & Biochem, Houston, TX 77004 USA;Univ Houston, Dept Math, Houston, TX 77004 USA | Article | Univ Houston | BRISTOL | null | null | Rice Univ;Univ Dayton;Univ Houston | Direct For Mathematical & Physical Scien;Division Of Mathematical Sciences;NIH;NSF;Welch Foundation | Ott, W (corresponding author), Univ Houston, Dept Math, Houston, TX 77004 USA. | null | Bennett, Matthew R;Gupta, Chinmaya;Josic, Kresimir;Ott, William;Veliz-Cuba, Alan | 11 | 5 | 390,359,500,001 | Direct For Mathematical & Physical Scien;Division Of Mathematical Sciences [1413437] Funding Source: National Science Foundation;NIH [4R01GM104974];NSF [DMS 1413437];Welch Foundation [C-1729] | USA | PHYSICAL BIOLOGY | USA | null | null | Univ Dayton, Dept Math, Dayton, OH 45469 USA | 1478-3967 | Bennett, M R;Gupta, C;Josic, K;Ott, W;Veliz-Cuba, A | DEC | ott@math.uh.edu | cell cycle noise;Effects;excitable gene circuits | 5 | J | Biochemistry & Molecular Biology;Biophysics | BACILLUS-SUBTILIS;bistable genetic switches;bistable switch;bistable systems;cell cycle noise;cell division;concentration effect;daughter cells;delay;differentiation;Effects;ESCHERICHIA-COLI;excitable circuits;excitable gene circuits;excitable system;expression;EXTRINSIC FLUCTUATIONS;gene circuit dynamics;gene networks;genetic oscillators;IMPACT;INDUCED RESONANCE;KINETIC-ANALYSIS;metastability;metastable states;noise sources;STOCHASTICITY;synthetic genetic oscillator;temporal correlations;three-states stochastic model;transcriptional;transcriptional delay;transitions | Veliz-Cuba, A | BACILLUS-SUBTILIS;bistable switch;BISTABLE SYSTEMS;cell cycle noise;delay;DIFFERENTIATION;ESCHERICHIA-COLI;excitable system;EXPRESSION;EXTRINSIC FLUCTUATIONS;INDUCED RESONANCE;KINETIC-ANALYSIS;metastability;STOCHASTICITY;synthetic genetic oscillator;transcriptional | null | [Veliz-Cuba, Alan] Univ Dayton, Dept Math, Dayton, OH 45469 USA. [Gupta, Chinmaya; Josic, Kresimir; Ott, William] Univ Houston, Dept Math, Houston, TX 77004 USA. [Bennett, Matthew R.; Josic, Kresimir] Rice Univ, Dept Biosci, Houston, TX 77251 USA. [Bennett, Matthew R.; Josic, Kresimir] Rice Univ, Dept Bioengn, Houston, TX 77251 USA. [Josic, Kresimir] Univ Houston, Dept Biol & Biochem, Houston, TX 77004 USA. | This work was partially supported by NIH grant 4R01GM104974 (AVC, MRB, KJ, WO), NSF grant DMS 1413437 (CG, WO), and Welch Foundation grant C-1729. | bistable genetic switches;cell cycle noise;cell division;concentration effect;daughter cells;excitable circuits;gene circuit dynamics;gene networks;genetic oscillators;impact;metastable states;noise sources;temporal correlations;three-states stochastic model;transcriptional delay;transitions | 10.1007/s00203-002-0476-5;10.1007/s00285-008-0178-y;10.1016/j.cell.2009.07.046;10.1016/j.mbs.2012.01.001;10.1016/S0006-3495(01)75949-8;10.1038/msb.2008.31;10.1038/nature02298;10.1038/nature04281;10.1038/nature04588;10.1038/nature07389;10.1038/nature07616;10.1038/nature09326;10.1038/ng.110;10.1038/ng.281;10.1038/ng.729;10.1038/ng1616;10.1038/ng869;10.1038/nsmb.2336;10.1049/sb:20045016;10.1063/1.4878662;10.1073/pnas.0503858102;10.1073/pnas.0806349105;10.1073/pnas.0808831105;10.1073/pnas.0831229100;10.1073/pnas.1018832108;10.1073/pnas.1102106108;10.1073/pnas.162041399;10.1080/07362990500397715;10.1091/mbc.11.1.369;10.1103/PhysRevE.86.031145;10.1103/PhysRevE.86.056202;10.1103/PhysRevE.91.012139;10.1103/PhysRevLett.102.068105;10.1103/PhysRevLett.111.058104;10.1111/j.1365-2958.2005.04592.x;10.1126/science.1070919;10.1126/science.1098641;10.1126/science.1137455;10.1126/science.1140818;10.1137/060666457;10.1142/S0219493705001389;10.1146/annurev.genet.42.110807.091601;10.1186/1752-0509-6-66;10.1371/journal.pcbi.0020117;10.1371/journal.pcbi.1002010;10.1371/journal.pcbi.1002264;10.1371/journal.pcbi.1003161;10.1371/journal.pcbi.1004674;10.1371/journal.pone.0121681;10.1371/journal.ppat.1003288;10.1534/genetics.167.1.523 | Univ Dayton | Bennett, M R;Gupta, C;Josic, K;Ott, W;Veliz-Cuba, A | Veliz-Cuba, A: Univ Dayton, Dept Math, Dayton, OH 45469 USA | null | 1413437;4R01GM104974;C-1729;DMS 1413437 | 53 | null | USA | Rice Univ;Univ Dayton;Univ Houston | Veliz-Cuba, Alan | Green Accepted, Green Submitted | BACILLUS-SUBTILIS;BISTABLE SYSTEMS;DELAY;DIFFERENTIATION;ESCHERICHIA-COLI;EXPRESSION;EXTRINSIC FLUCTUATIONS;INDUCED RESONANCE;KINETIC-ANALYSIS;STOCHASTICITY | Veliz-Cuba, Alan; Gupta, Chinmaya; Bennett, Matthew R.; Josic, Kresimir; Ott, William; | null | Rice Univ, Dept Bioengn, Houston, TX 77251 USA;Rice Univ, Dept Biosci, Houston, TX 77251 USA;Univ Dayton, Dept Math, Dayton, OH 45469 USA;Univ Houston, Dept Biol & Biochem, Houston, TX 77004 USA;Univ Houston, Dept Math, Houston, TX 77004 USA | Rice Univ, Dept Bioengn, Houston, TX 77251 USA;Rice Univ, Dept Biosci, Houston, TX 77251 USA;Univ Dayton, Dept Math, Dayton, OH 45469 USA;Univ Houston, Dept Biol & Biochem, Houston, TX 77004 USA;Univ Houston, Dept Math, Houston, TX 77004 USA | 1478-3975 | bistable switch;cell cycle noise;excitable system;metastability;synthetic genetic oscillator;transcription | 6 | 1998;2000;2001;2002;2003;2004;2005;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015 | 3 | Univ Houston, Dept Math, Houston, TX 77004 USA | Phys. Biol. | Ott, William | IOP PUBLISHING LTD | ,;a;accurately;after;and;assess;be;between;bistable;by;captured;cell;cells;circuit;circuits;concentration;correlations;cycle;daughter;delay;division;dynamics;effect;excitable;explain;find;for;gene;genetic;impact;in;induced;intensifies;just;likely;metastable;model;most;must;networks;noise;occur;of;on;order;oscillators;presence;properly;quantify;sources;states;stochastic;switches;temporal;that;the;this;three-states;to;transcriptional;transitions;we;with;within | Univ Houston | We assess the impact of cell cycle noise on gene circuit dynamics. For bistable genetic switches and excitable circuits, we find that transitions between metastable states most likely occur just after cell division and that this concentration effect intensifies in the presence of transcriptional delay. We explain this concentration effect with a three-states stochastic model. For genetic oscillators, we quantify the temporal correlations between daughter cells induced by cell division. Temporal correlations must be captured properly in order to accurately quantify noise sources within gene networks. | null | BACILLUS-SUBTILIS;BISTABLE SYSTEM;DELAY;DIFFERENTIATION;ESCHERICHIA-COLI;EXPRESSION;EXTRINSIC FLUCTUATIONS;INDUCED RESONANCE;KINETIC-ANALYSIS;STOCHASTICITY | 0 | null | bistable switch;cell cycle noise;excitable system;metastability;synthetic genetic oscillator;transcriptional | 13 | ESCHERICHIA-COLI;BACILLUS-SUBTILIS;bistable switch;BISTABLE SYSTEM;cell cycle noise;delay;DIFFERENTIATION;excitable system;EXPRESSION;EXTRINSIC FLUCTUATIONS;INDUCED RESONANCE;KINETIC-ANALYSIS;metastability;STOCHASTICITY;synthetic genetic oscillator;TRANSCRIPTION | WOS:000390359500001 | Rice Univ, Houston, TX USA;Univ Dayton, Dayton, OH USA;Univ Houston, Houston, TX USA | USA | 2,016 | null | 0000-0002-9860-8772 | null | null | English | null | ANNU REV GENET;ARCH MICROBIOL;BIOPHYS J;BMC SYST BIOL;GENETICS;J CHEM PHYS;J MATH BIOL;MATH BIOSCI;MOL BIOL CELL;MOL MICROBIOL;MOL SYST BIOL;NAT GENET;NAT STRUCT MOL BIOL;NATURE;P NATL ACAD SCI USA;PHYS REV E;PHYS REV LETT;PLOS COMPUT BIOL;PLOS ONE;PLOS PATHOG;SCIENCE;SIAM REV;STOCH ANAL APPL;STOCH DYNAM;SYSTEMS BIOL | Bennett, Matthew R;Gupta, Chinmaya;Josic, Kresimir;Ott, William;Veliz-Cuba, Alan | 2024-03-11
ER | Acar, M;Arkin, A;Barrio, M;Becskei, A;Bratsun, D;Brett, T;Chen, K C;Davidson, C J;Dunlop, M J;Dupin, E;Dykman, M I;Eldar, A;Elowitz, M B;Endres, R G;Fischer, M;Garcia-Monco, J C;Gupta, C;He, E;Hensel, Z;Higham, D J;Hilfinger, A;Hong, T;Huh, D;Josic, K;Kepler, T B;Lu, T;Maamar, H;Mather, W;Meeks, J C;Mier-Y-Teran-Romero, L;O'Brien, E L;Ozbudak, E M;Raser, J M;Roberts, E;Schlicht, R;Schwartz, I B;Shahrezaei, V;St-Pierre, F;Stricker, J;Swain, P S;Süel, G M;Thattai, M;Tigges, M;Turcotte, M;Veliz-Cuba, A;Volfson, D;Zopf, C J | EF5GU | Houston, TX USA | 4 | null | 3 | null | 27,902,489 | Bennett, Matthew R;Gupta, Chinmaya;Josic, Kresimir;Ott, William;Veliz-Cuba, Alan | PHYS BIOL | Dayton, OH USA;Houston, TX USA |
Cheng, H;Wang, L Y;Wei, K;Zhang, C C;Zhang, L Q | 10.1186/s40529-016-0143-9 | 31 | CAMPUS, 4 CRINAN ST, LONDON, N1 9XW, ENGLAND | 1h6s1t2ati3p1h1g3m2e4b0546e665b6h1e6b | Accumulation of catechins and expression of catechin synthetic genes in <i>Camellia sinensis</i> at different developmental stages | Minist Agr | null | Cheng, H (corresponding author), Minist Agr, Key Lab Tea Biol & Resources Utilizat, Chinese Acad Agr Sci, Tea Res Inst,Natl Ctr Tea Improvement, 9 Meiling South Rd, Hangzhou 310008, Zhejiang, Peoples R China. | null | Cheng, Hao;Wang, Li-Yuan;Wei, Kang;Zhang, Cheng-Cai;Zhang, Li-Qun | Plant Sciences | National Natural Science Foundation of China [31470396]; Natural Science Foundation of Zhejiang Province [LY14C020001]; Earmarked Fund for China Agriculture Research System [CARS-23] | WOS | Cheng, H | Minist Agr, Zhejiang, Peoples R China | 57 | <i>Camellia;accumulation;and;at;catechin;catechins;developmental;Different;expression;genes;in;of;sinensis</i>;stages;synthetic | 1 | Zhang, Chengcai;Zhang, Liqun | SPRINGEROPEN | Minist Agr, Key Lab Tea Biol & Resources Utilizat, Chinese Acad Agr Sci, Tea Res Inst,Natl Ctr Tea Improvement, 9 Meiling South Rd, Hangzhou 310008, Zhejiang, Peoples R China | Article | Minist Agr | LONDON | null | null | Minist Agr | Earmarked Fund for China Agriculture Research System;National Natural Science Foundation of China;Natural Science Foundation of Zhejiang Province | Cheng, H (corresponding author), Minist Agr, Key Lab Tea Biol & Resources Utilizat, Chinese Acad Agr Sci, Tea Res Inst,Natl Ctr Tea Improvement, 9 Meiling South Rd, Hangzhou 310008, Zhejiang, Peoples R China. | null | Cheng, Hao;Wang, Li-Yuan;Wei, Kang;Zhang, Cheng-Cai;Zhang, Li-Qun | 40 | 1 | 388,583,300,001 | Earmarked Fund for China Agriculture Research System [CARS-23];National Natural Science Foundation of China [31470396];Natural Science Foundation of Zhejiang Province [LY14C020001] | China | BOTANICAL STUDIES | China | null | null | Minist Agr, Key Lab Tea Biol & Resources Utilizat, Chinese Acad Agr Sci, Tea Res Inst,Natl Ctr Tea Improvement, 9 Meiling South Rd, Hangzhou 310008, Zhejiang, Peoples R China | null | Cheng, H;Wang, L Y;Wei, K;Zhang, C C;Zhang, L Q | OCT 24 | chenghao@tricaas.com | <i>Camellia sinensis</i>;accumulation;catechin synthetic genes;catechins;different developmental stages;expression | 5 | J | Plant Sciences | (-)-epicatechin gallate;(-)-epigallocatechin gallate;<i>Camellia sinensis</i>;accumulation;affect total catechin accumulation;amounts;analyzed;ANRs;Anthocyanidin reductase;anthocyanidin reductase 1;anthocyanidin reductase 2;Anthocyanidin synthase;background;biosynthesis;Camellia sinensis;catechin;catechin synthetic genes;Catechins;Chalcone synthase;chalcone synthase 1;chalcone synthase 3;close correlations;conclusion;conversion;correlation analysis;different developmental stages;different stages;earlier steps;enzymes;expression;expressions;findings;gallocatechin gallate;galloylated catechins;gene expression;GREEN;identified;key genes;LAR;LEAVES;Leucoanthocyanidin reductase;leucoanthocyanidin reductase genes;main polyphenol compounds;METABOLISM;MOLECULAR-CLONING;PHENOLIC-COMPOUNDS;play important roles;product accumulation;relationship;relative expressions;results;synergistic changes;synthesis genes;synthetic genes;tea (Camellia sinensis);TEA CATECHINS;tea leaves;total catechin contents | Zhang, L Q | Anthocyanidin reductase;Anthocyanidin synthase;BIOSYNTHESIS;Camellia sinensis;Catechins;Chalcone synthase;ENZYMES;GREEN;Leucoanthocyanidin reductase;METABOLISM;MOLECULAR-CLONING;PHENOLIC-COMPOUNDS;TEA CATECHINS | null | [Zhang, Li-Qun; Wei, Kang; Cheng, Hao; Wang, Li-Yuan; Zhang, Cheng-Cai] Minist Agr, Key Lab Tea Biol & Resources Utilizat, Chinese Acad Agr Sci, Tea Res Inst,Natl Ctr Tea Improvement, 9 Meiling South Rd, Hangzhou 310008, Zhejiang, Peoples R China. | This work was supported by the National Natural Science Foundation of China (31470396), the Natural Science Foundation of Zhejiang Province (LY14C020001) and the Earmarked Fund for China Agriculture Research System (CARS-23). | (-)-epicatechin gallate;(-)-epigallocatechin gallate;accumulation;affect total catechin accumulation;amounts;analyzed;ANRs;anthocyanidin reductase;anthocyanidin reductase 1;anthocyanidin reductase 2;anthocyanidin synthase;background;biosynthesis;catechin;Catechins;chalcone synthase 1;chalcone synthase 3;close correlations;conclusion;conversion;correlation analysis;different developmental stages;different stages;earlier steps;expression;expressions;findings;gallocatechin gallate;galloylated catechins;gene expression;identified;key genes;LAR;leaves;leucoanthocyanidin reductase genes;main polyphenol compounds;play important roles;product accumulation;relationship;relative expressions;results;synergistic changes;synthesis genes;synthetic genes;tea (Camellia sinensis);tea leaves;total catechin contents | 10.1002/ijc.22419;10.1002/jsfa.2368;10.1007/BF02980469;10.1007/s10142-008-0098-3;10.1007/s11032-011-9653-z;10.1016/j.abb.2003.12.011;10.1016/j.abb.2004.08.003;10.1016/j.foodchem.2010.08.029;10.1016/j.foodchem.2013.09.043;10.1016/j.jplph.2011.01.003;10.1016/j.phytochem.2006.09.030;10.1016/j.phytochem.2010.01.010;10.1016/j.plantsci.2003.12.010;10.1016/j.plaphy.2008.11.002;10.1016/j.scienta.2011.10.017;10.1016/j.tplants.2006.11.006;10.1016/S0969-2126(01)00695-5;10.1021/jf026227q;10.1021/jf0354848;10.1038/sj.onc.1209227;10.1046/j.1365-313X.1999.00365.x;10.1074/jbc.M302783200;10.1080/10408690390826464;10.1093/ajcn/71.6.1698S;10.1093/jxb/erg199;10.1104/pp.105.064238;10.1104/pp.112.212050;10.1111/j.1365-313X.2012.04908.x;10.1111/tpj.12140;10.1207/S15327914NC4502_13;10.1271/bbb.67.2683;10.5511/PLANTBIOTECHNOLOGY.21.377] | Minist Agr | Cheng, H;Wang, L Y;Wei, K;Zhang, C C;Zhang, L Q | Zhang, L Q: Minist Agr, Key Lab Tea Biol & Resources Utilizat, Chinese Acad Agr Sci, Tea Res Inst,Natl Ctr Tea Improvement, 9 Meiling South Rd, Hangzhou 310008, Zhejiang, Peoples R China | Zhang, Chengcai;Zhang, Liqun | 31470396;CARS-23;LY14C020001 | 36 | null | China | Minist Agr | Zhang, Li-Qun | gold, Green Published | ANTHOCYANIDIN SYNTHASE;BIOSYNTHESIS;CHALCONE SYNTHASE;ENZYMES;GREEN;LEUCOANTHOCYANIDIN REDUCTASE;METABOLISM;MOLECULAR-CLONING;PHENOLIC-COMPOUNDS;TEA CATECHINS | Zhang, Li-Qun; Wei, Kang; Cheng, Hao; Wang, Li-Yuan; Zhang, Cheng-Cai; | null | Minist Agr, Key Lab Tea Biol & Resources Utilizat, Chinese Acad Agr Sci, Tea Res Inst,Natl Ctr Tea Improvement, 9 Meiling South Rd, Hangzhou 310008, Zhejiang, Peoples R China | Minist Agr, Key Lab Tea Biol & Resources Utilizat, Chinese Acad Agr Sci, Tea Res Inst,Natl Ctr Tea Improvement, 9 Meiling South Rd, Hangzhou 310008, Zhejiang, Peoples R China | 1999-3110 | Anthocyanidin reductase;Anthocyanidin synthase;Camellia sinensis;Catechin;Chalcone synthase;Leucoanthocyanidin reductase | null | 1988;1990;1992;1994;1999;2000;2002;2003;2004;2005;2006;2007;2009;2010;2011;2012;2013;2014 | 36 | Minist Agr, Key Lab Tea Biol & Resources Utilizat, Chinese Acad Agr Sci, Tea Res Inst,Natl Ctr Tea Improvement, 9 Meiling South Rd, Hangzhou 310008, Zhejiang, Peoples R China | Bot. Stud. | Zhang, Cheng-Cai | SPRINGEROPEN | (-)-epicatechin;(-)-epigallocatechin;(Camellia;,;1;2;3;:;accumulation;affect;amounts;analysis;analyzed;and;ANRs;anthocyanidin;are;background;based;between;biosynthesis;both;catechin;Catechins;chalcone;changes;close;compounds;conclusion;contents;conversion;correlated;correlation;correlations;developmental;differed;different;earlier;except;expression;expressions;findings;for;gallate;gallocatechin;galloylated;gene;genes;identified;important;in;key;LAR;largely;leaves;leucoanthocyanidin;levels;main;may;of;on;our;play;polyphenol;positively;product;reductase;regulate;relationship;relative;results;roles;showed;significantly;sinensis);stages;steps;suggest;suggesting;synergistic;synthase;synthesis;synthetic;tea;that;the;their;to;total;understand;was;were;while;with | Minist Agr | Background: Catechins are the main polyphenol compounds in tea (Camellia sinensis). To understand the relationship between gene expression and product accumulation, the levels of catechins and relative expressions of key genes in tea leaves of different developmental stages were analyzed. Results: The amounts of catechins differed significantly in leaves of different stages, except for gallocatechin gallate. Close correlations between the expression of synthesis genes and the accumulation of catechins were identified. Correlation analysis showed that the expressions of chalcone synthase 1, chalcone synthase 3, anthocyanidin reductase 1, anthocyanidin reductase 2 and leucoanthocyanidin reductase genes were significantly and positively correlated with total catechin contents, suggesting their expression may largely affect total catechin accumulation. Anthocyanidin synthase was significantly correlated with catechin. While both ANRs and LAR were significantly and positively correlated with the contents of (-)-epigallocatechin gallate and (-)-epicatechin gallate. Conclusion: Our results suggest synergistic changes between the expression of synthetic genes and the accumulation of catechins. Based on our findings, anthocyanidin synthase may regulate earlier steps in the conversion of catechin, while the anthocyanidin reductase and leucoanthocyanidin reductase genes may both play important roles in the biosynthesis of galloylated catechins. | HTS-7417-2023;JDN-3523-2023;Q-7646-2019 | ANTHOCYANIDIN SYNTHASE;BIOSYNTHESIS;CHALCONE SYNTHASE;ENZYMES;GREEN;LEUCOANTHOCYANIDIN REDUCTASE;METABOLISM;MOLECULAR-CLONING;PHENOLIC-COMPOUNDS;TEA CATECHINS | 7 | null | Anthocyanidin reductase;Anthocyanidin synthase;Camellia sinensis;Catechins;Chalcone synthase;Leucoanthocyanidin reductase | 8 | Anthocyanidin reductase;Anthocyanidin synthase;BIOSYNTHESIS;Camellia sinensis;Catechin;Chalcone synthase;ENZYMES;GREEN;Leucoanthocyanidin reductase;METABOLISM;MOLECULAR-CLONING;PHENOLIC-COMPOUNDS;TEA CATECHINS | WOS:000388583300001 | Minist Agr, Zhejiang, Peoples R China | China | 2,016 | null | 0000-0001-6938-3861;0000-0002-2103-6294 | null | null | English | null | AM J CLIN NUTR;and Unsubstituted Flavans;ARCH BIOCHEM BIOPHYS;BASIC LIFE SCI;BIOSCI BIOTECH BIOCH;CRIT REV FOOD SCI;FOOD CHEM;FUNCT INTEGR GENOMIC;INFORM MANAGEMENT SC;INT J CANCER;J AGR FOOD CHEM;J BIOL CHEM;J EXP BOT;J PLANT PHYSIOL;J SCI FOOD AGR;MOL BREEDING;NUTR CANCER;ONCOGENE;PHYTOCHEMISTRY;PHYTOPARASITICA;PLANT BIOTECHNOL-NAR;PLANT CELL PHYSIOL;PLANT J;PLANT PHYSIOL;PLANT PHYSIOL BIOCH;PLANT SCI;SCI HORTIC-AMSTERDAM;STRUCTURE;TRENDS PLANT SCI | Cheng, Hao;Wang, Li-Yuan;Wei, Kang;Zhang, Cheng-Cai;Zhang, Li-Qun | 2024-03-11
ER | Ashihara, H;Bigelow, R L H;Bogs, J;Dare, A P;Del Rio, D;Eungwanichayapant, P D;Gulati, A;Henning, S M;Higdon, J V;Jiang, C G;Kamiishi, Y;Kurauchi, T;Lea, A G H;Mamati, G E;Matern, U;Morita, Y;Mukhtar, H;Pang, Y Z;Park, J S;Pourcel, L;Punyasiri, P A N;Rani, A;Saito, K;She, H;Solovchenko, A;Stafford H.A.;Suzuki, T;Takeuchi, A;Tanner, G J;Thomasset, S C;Tsuda S.;Wang, L Y;Wang, Y S;Wei, K;Wilmouth, R C;Xie, D Y | ED1DD | Zhejiang, Peoples R China | 40 | null | 1 | null | 28,597,441 | Cheng, Hao;Wang, Li-Yuan;Wei, Kang;Zhang, Cheng-Cai;Zhang, Li-Qun | BOT STUD | Zhejiang, Peoples R China |
Chaput, J C;Dunn, M R | 10.1002/cbic.201600338 | null | POSTFACH 101161, 69451 WEINHEIM, GERMANY | 2r356d4rb3k4p3w436i1m5hk4f3f364p425647 | Reverse Transcription of Threose Nucleic Acid by a Naturally Occurring DNA Polymerase | Univ Calif Irvine | null | Chaput, JC (corresponding author), Univ Calif Irvine, Dept Pharmaceut Sci, Irvine, CA 92697 USA. | null | Chaput, John C;Dunn, Matthew R | Biochemistry & Molecular Biology;Chemistry, Medicinal | Defense Advanced Research Projects Agency (DARPA) Folded Non-Natural Polymers with Biological Function (Fold F(x)) Program [N66001-14-2-4054]; National Science Foundation [1615804, 1607111]; Division Of Chemistry; Direct For Mathematical & Physical Scien [1615804] Funding Source: National Science Foundation | WOS | Chaput, J C | Univ Calif Irvine, Irvine, CA USA | 17 | a;acid;by;DNA;Naturally;Nucleic;Occurring;of;polymerase;reverse;Threose;transcription | 1 | Dunn, Matthew | WILEY-V C H VERLAG GMBH | Univ Calif Irvine, Dept Pharmaceut Sci, Irvine, CA 92697 USA | Article | Univ Calif Irvine | WEINHEIM | null | null | Univ Calif Irvine | Defense Advanced Research Projects Agency (DARPA) Folded Non-Natural Polymers with Biological Function (Fold F(x)) Program;Direct For Mathematical & Physical Scien;Division Of Chemistry;National Science Foundation | Chaput, JC (corresponding author), Univ Calif Irvine, Dept Pharmaceut Sci, Irvine, CA 92697 USA. | 1808 | Chaput, John C;Dunn, Matthew R | 51 | 1 | 385,700,900,003 | Defense Advanced Research Projects Agency (DARPA) Folded Non-Natural Polymers with Biological Function (Fold F(x)) Program [N66001-14-2-4054];Direct For Mathematical & Physical Scien [1615804] Funding Source: National Science Foundation;Division Of Chemistry;National Science Foundation [1615804, 1607111] | USA | CHEMBIOCHEM | USA | null | null | Univ Calif Irvine, Dept Pharmaceut Sci, Irvine, CA 92697 USA | 1439-4227 | Chaput, J C;Dunn, M R | OCT 4 | jchaput@uci.edu | DNA Polymerase;reverse Transcription;Threose Nucleic Acid | 2 | J | Biochemistry & Molecular Biology;Pharmacology & Pharmacy | affinity;amplification;aptamer;backbone structures;BINDING;Bst;bst DNA polymerase;CAPILLARY-ELECTROPHORESIS;catalytic activity;catalytic efficiency;CDNA;coding;decoding genetic information;directed evolution;DNA;DNA polymerase;enzyme's substrate specificity;faithful threose nucleic acid (TNA)-dependent DNA polymerase;fidelity;functional XNA molecules;functions;Geobacillus stearothermophilus (Bst) DNA polymeraseI functions;human alpha-thrombin;IN-VITRO SELECTION;manganese ions;MICROSCALE THERMOPHORESIS;nature;PCR;Polymerase Engineering;problematic;process;recent advances;replication;replication cycle;reverse;reverse transcription;selective amplification step;SELEX;SSII;standard magnesium-dependent conditions;successes;SuperscriptII (SSII);synthetic genetic polymers;synthetic genetics;SYSTEM;templates;threefold fewer mutations;Threose Nucleic Acid;TNA;TNA aptamer;TNA aptamers;TNA reverse transcriptase;vitro selection;xenonucleic acid (XNA) polymers;XNA back;XNA polymerases;XNA polymers | Dunn, M R | AFFINITY;aptamer;CAPILLARY-ELECTROPHORESIS;directed evolution;IN-VITRO SELECTION;MICROSCALE THERMOPHORESIS;REPLICATION;reverse transcription;SELEX;SYNTHETIC GENETIC POLYMERS;synthetic genetics;SYSTEM;TEMPLATES;threose nucleic acid;TNA | 1804 | [Dunn, Matthew R.; Chaput, John C.] Univ Calif Irvine, Dept Pharmaceut Sci, Irvine, CA 92697 USA. | We would like to thank Andrew Larsen and the Chaput Laboratory members for helpful insight and comments on manuscript preparation. This work was supported by the Defense Advanced Research Projects Agency (DARPA) Folded Non-Natural Polymers with Biological Function (Fold F(x)) Program under award number N66001-14-2-4054 and by grants from the National Science Foundation (1615804 and 1607111). | amplification;backbone structures;binding;Bst;bst DNA polymerase;catalytic activity;catalytic efficiency;cDNA;coding;decoding genetic information;DNA;enzyme's substrate specificity;faithful threose nucleic acid (TNA)-dependent DNA polymerase;fidelity;functional XNA molecules;functions;Geobacillus stearothermophilus (Bst) DNA polymeraseI functions;human alpha-thrombin;manganese ions;nature;PCR;polymerase engineering;problematic;process;recent advances;replication;replication cycle;reverse;selective amplification step;SSII;standard magnesium-dependent conditions;successes;SuperscriptII (SSII);threefold fewer mutations;TNA aptamer;TNA aptamers;TNA reverse transcriptase;vitro selection;xenonucleic acid (XNA) polymers;XNA back;XNA polymerases;XNA polymers | 10.1016/j.bmcl.2016.03.118;10.1016/j.cbpa.2012.05.198;10.1016/j.chembiol.2012.10.011;10.1016/j.febslet.2013.10.040;10.1016/j.jmb.2006.06.050;10.1016/j.molstruc.2014.03.009;10.1016/j.ymeth.2012.12.005;10.1021/ac049857v;10.1021/ac050836q;10.1021/acschembio.5b00949;10.1021/ja028589k;10.1021/ja037832s;10.1021/ja0428255;10.1021/ja052406n;10.1021/ja3118703;10.1021/jacs.5b08144;10.1038/nature13982;10.1038/ncomms11235;10.1073/pnas.0704211104;10.1073/pnas.071052198;10.1073/pnas.86.11.4076;10.1073/pnas.90.12.5428;10.1089/adt.2011.0380;10.1126/science.1217622;10.1126/science.290.5495.1347;10.1139/V08-089;10.1371/journal.pone.0004949;10.2307/3429233;[10.1038/NCHEM.1241, 10.1038/nchem.1241];[10.1038/NCHEM.2493, 10.1038/nchem.2493] | Univ Calif Irvine | Chaput, J C;Dunn, M R | Dunn, M R: Univ Calif Irvine, Dept Pharmaceut Sci, Irvine, CA 92697 USA | Dunn, Matthew | 1607111;1615804;N66001-14-2-4054 | 30 | null | USA | Univ Calif Irvine | Dunn, Matthew R | null | AFFINITY;CAPILLARY-ELECTROPHORESIS;DIRECTED EVOLUTION;IN-VITRO SELECTION;MICROSCALE THERMOPHORESIS;REPLICATION;SYNTHETIC GENETIC POLYMERS;SYSTEM;TEMPLATES;TNA | Dunn, Matthew R.; Chaput, John C.; | null | Univ Calif Irvine, Dept Pharmaceut Sci, Irvine, CA 92697 USA | Univ Calif Irvine, Dept Pharmaceut Sci, Irvine, CA 92697 USA | 1439-7633 | aptamer;reverse transcription;SELEX;synthetic genetics;threose nucleic acid | 19 | 1981;1989;1993;2000;2001;2003;2004;2005;2006;2007;2008;2009;2011;2012;2013;2014;2015;2016 | 37 | Univ Calif Irvine, Dept Pharmaceut Sci, Irvine, CA 92697 USA | ChemBioChem | Chaput, John C | WILEY-V C H VERLAG GMBH | (Bst);(SSII);(TNA)-dependent;(XNA);,;a;acid;activity;advances;alpha-thrombin;also;amplification;an;and;approximate;aptamer;aptamers;as;back;backbone;been;best;binding;bst;by;can;catalytic;cDNA;coding;conditions;cycle;decoding;demonstrate;despite;distinct;DNA;efficiency;efficient;enabled;engineered;engineering;enzyme's;evolving;faithful;fewer;fidelity;for;found;from;functional;functions;further;generates;genetic;Geobacillus;has;have;here;human;in;information;into;introducing;ions;isolated;limited;magnesium-dependent;manganese;molecules;more;mutations;nature;notably;nucleic;of;particular;PCR;polymerase;polymeraseI;polymerases;polymers;previously;problematic;process;recent;relax;remains;replication;requires;reverse;selection;selective;show;specificity;SSII;standard;stearothermophilus;step;structures;substrate;successes;SuperscriptII;support;than;that;the;these;those;threefold;threose;TNA;to;transcribing;transcriptase;twofold;under;vitro;was;we;whereas;which;with;xenonucleic;XNA | Univ Calif Irvine | Recent advances in polymerase engineering have enabled the replication of xenonucleic acid (XNA) polymers with backbone structures distinct from those found in nature. By introducing a selective amplification step into the replication cycle, functional XNA molecules have been isolated by in vitro selection with binding and catalytic activity. Despite these successes, coding and decoding genetic information in XNA polymers remains limited by the fidelity and catalytic efficiency of engineered XNA polymerases. In particular, the process of reverse transcribing XNA back into DNA for amplification by PCR has been problematic. Here, we show that Geobacillus stearothermophilus (Bst) DNA polymeraseI functions as an efficient and faithful threose nucleic acid (TNA)-dependent DNA polymerase. Bst DNA polymerase generates approximate to twofold more cDNA with threefold fewer mutations than SuperscriptII (SSII), which was previously the best TNA reverse transcriptase. Notably, Bst also functions under standard magnesium-dependent conditions, whereas SSII requires manganese ions to relax the enzyme's substrate specificity. We further demonstrate that Bst DNA polymerase can support the in vitro selection of TNA aptamers by evolving a TNA aptamer to human alpha-thrombin. | J-3750-2014 | AFFINITY;CAPILLARY-ELECTROPHORESIS;DIRECTED EVOLUTION;IN-VITRO SELECTION;MICROSCALE THERMOPHORESIS;REPLICATION;SYNTHETIC GENETIC POLYMERS;SYSTEM;TEMPLATES;TNA | 6 | null | aptamer;reverse transcription;SELEX;synthetic genetics;threose nucleic acid | 5 | AFFINITY;aptamer;CAPILLARY-ELECTROPHORESIS;directed evolution;IN-VITRO SELECTION;MICROSCALE THERMOPHORESIS;REPLICATION;reverse transcription;SELEX;SYNTHETIC GENETIC POLYMERS;synthetic genetics;SYSTEM;TEMPLATES;THREOSE NUCLEIC-ACID;TNA | WOS:000385700900003 | Univ Calif Irvine, Irvine, CA USA | USA | 2,016 | null | 0000-0002-8391-7409 | null | null | English | null | ACS CHEM BIOL;ANAL CHEM;ASSAY DRUG DEV TECHN;BIOORG MED CHEM LETT;CAN J CHEM;CHEM BIOL;CURR OPIN CHEM BIOL;ENVIRON HEALTH PERSP;FEBS LETT;J AM CHEM SOC;J MOL BIOL;J MOL STRUCT;METHODS;NAT CHEM;NAT COMMUN;NATURE;P NATL ACAD SCI USA;PLOS ONE;SCIENCE | Chaput, John C;Dunn, Matthew R | 2024-03-11
ER | Chaput, J C;Chen, J J;Chen, T J;Culbertson, M C;Dunn, M R;Ghadessy, F J;Horhota, A;Jerabek-Willemsen, M;Larsen, A C;Mendonsa, S D;Mosing, R K;Ong, J L;Peng, C G;Pinheiro, V B;Schöning, K U;Seidel, S A I;Shi, C;Tabor, S;Taylor, A I;Tsai, C H;Wong, I;Yu, H Y;Zakour, R A | DZ2VX | Irvine, CA USA | 46 | null | 1 | null | 27,383,648 | Chaput, John C;Dunn, Matthew R | CHEMBIOCHEM | Irvine, CA USA |
Ma, D C;Peng, S G;Xie, Z | 10.1038/ncomms13056 | 13056 | MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND | 3d352s6h4me3ej6b68t2p4x4g3m3o1l58o61 | Integration and exchange of split dCas9 domains for transcriptional controls in mammalian cells | Tsinghua Univ | null | Xie, Z (corresponding author), Tsinghua Univ, Bioinformat Div, Ctr Synthet & Syst Biol, Dept Automat,Tsinghua Natl Lab Informat Sci & Tec, Beijing 100084, Peoples R China.;Xie, Z (corresponding author), Tsinghua Univ, MOE Key Lab Bioinformat, Beijing 100084, Peoples R China. | null | Ma, Dacheng;Peng, Shuguang;Xie, Zhen | Multidisciplinary Sciences | National Key Basic Research Program of China [2014CB745200]; Basic Research Program of Tsinghua National Lab for Information Science and Technology | WOS | Xie, Z | Tsinghua Univ, Beijing, Peoples R China | 7 | and;Cells;controls;dCas9;DOMAINS;Exchange;for;in;integration;mammalian;of;split;Transcriptional | 1 | null | NATURE PUBLISHING GROUP | Tsinghua Univ, Bioinformat Div, Ctr Synthet & Syst Biol, Dept Automat,Tsinghua Natl Lab Informat Sci & Tec, Beijing 100084, Peoples R China;Tsinghua Univ, MOE Key Lab Bioinformat, Beijing 100084, Peoples R China;Tsinghua Univ, MOE Key Lab Bioinformat, Beijing 100084, Peoples R China.; Xie, Z (corresponding author), Tsinghua Univ, Bioinformat Div, Ctr Synthet & Syst Biol, Dept Automat,Tsinghua Natl Lab Informat Sci & Tec, Beijing 100084, Peoples R China | Article | Tsinghua Univ | LONDON | null | null | Tsinghua Univ | Basic Research Program of Tsinghua National Lab for Information Science and Technology;National Key Basic Research Program of China | Xie, Z (corresponding author), Tsinghua Univ, MOE Key Lab Bioinformat, Beijing 100084, Peoples R China.; Xie, Z (corresponding author), Tsinghua Univ, Bioinformat Div, Ctr Synthet & Syst Biol, Dept Automat,Tsinghua Natl Lab Informat Sci & Tec, Beijing 100084, Peoples R China. | null | Ma, Dacheng;Peng, Shuguang;Xie, Zhen | 57 | 2 | 385,542,700,001 | Basic Research Program of Tsinghua National Lab for Information Science and Technology;National Key Basic Research Program of China [2014CB745200] | China | NATURE COMMUNICATIONS | China | null | null | Tsinghua Univ, MOE Key Lab Bioinformat, Beijing 100084, Peoples R China | 2041-1723 | Ma, D C;Peng, S G;Xie, Z | OCT 3 | zhenxie@tsinghua.edu.cn | Exchange;integration;mammalian cells;split dCas9 domains;transcriptional controls | 3 | J | Science & Technology - Other Topics | activating two different genes;application;Cas9;cell-type specific microRNAs;CIRCUITS;CLEAVAGE;complex;complex transcription controls;CRISPR;CRISPR-Cas technology;CRISPR-Cas therapeutic circuits;CRYSTAL-STRUCTURE;dCas9 functions;differential regulations;Exchange;existing viral delivery vehicles;expression;integrating multiple split dCas9 domains;integration;logic;mammalian cells;multiple molecular signals;new biomedical applications;one gene;precise regulation;programmable;PROTEIN;response;restrictive cargo size;RNA;sensory switches;size;split dCas9 domains;synthetic circuits;synthetic gene circuits will;SYSTEM;transcriptional controls;valuable split-dCas9 toolkit | Ma, D C | CAS9;CLEAVAGE;COMPLEX;CRISPR;CRYSTAL-STRUCTURE;EXPRESSION;PROTEIN;RNA;SYSTEM | null | [Ma, Dacheng; Peng, Shuguang; Xie, Zhen] Tsinghua Univ, MOE Key Lab Bioinformat, Beijing 100084, Peoples R China. [Ma, Dacheng; Peng, Shuguang; Xie, Zhen] Tsinghua Univ, Bioinformat Div, Ctr Synthet & Syst Biol, Dept Automat,Tsinghua Natl Lab Informat Sci & Tec, Beijing 100084, Peoples R China. | We thank members of Xie Lab for helpful discussions. We thank Lei Stanley Qi for providing the Cas9-Suntag and ScFv-GB1 constructs as gifts. The research is supported by the National Key Basic Research Program of China (2014CB745200) and Basic Research Program of Tsinghua National Lab for Information Science and Technology (Z.X.). | activating two different genes;application;cell-type specific microRNAs;circuits;complex transcription controls;CRISPR-Cas technology;CRISPR-Cas therapeutic circuits;dCas9 functions;differential regulations;existing viral delivery vehicles;integrating multiple split dCas9 domains;logic;multiple molecular signals;new biomedical applications;one gene;precise regulation;programmable;response;restrictive cargo size;sensory switches;size;split dCas9 domains;synthetic circuits;synthetic gene circuits will;valuable split-dCas9 toolkit | 10.1007/s11051-014-2826-z;10.1016/j.biortech.2014.07.104;10.1016/j.cell.2013.02.022;10.1016/j.cell.2013.06.044;10.1016/j.cell.2014.02.001;10.1016/j.cell.2014.09.039;10.1016/j.cell.2014.11.052;10.1016/j.cell.2015.08.007;10.1016/j.celrep.2016.01.019;10.1016/j.molcel.2014.04.022;10.1021/sb400081r;10.1038/nature13579;10.1038/nature14592;10.1038/nbt.3149;10.1038/nbt.3245;10.1038/nbt.3528;10.1038/nchembio.1753;10.1038/ncomms12009;10.1038/nm0996-1028;10.1038/srep03355;10.1038/srep10777;10.1073/pnas.1208507109;10.1073/pnas.1501698112;10.1093/nar/gkv601;10.1126/science.1205527;10.1126/science.1225829;10.1126/science.1231143;[10.1038/NCHEMBIO.1793, 10.1038/nchembio.1793];[10.1038/NMETH.2969, 10.1038/nmeth.2969];[10.1038/NMETH.3580, 10.1038/nmeth.3580] | Tsinghua Univ | Ma, D C;Peng, S G;Xie, Z | Ma, D C: Tsinghua Univ, MOE Key Lab Bioinformat, Beijing 100084, Peoples R China | Xie, Zhen | 2014CB745200 | 30 | null | China | Tsinghua Univ | Ma, Dacheng | Green Published, gold | CAS9;CLEAVAGE;COMPLEX;CRISPR;CRYSTAL-STRUCTURE;EXPRESSION;PROTEIN;RNA;SYSTEM | Ma, Dacheng; Peng, Shuguang; Xie, Zhen; | null | Tsinghua Univ, Bioinformat Div, Ctr Synthet & Syst Biol, Dept Automat,Tsinghua Natl Lab Informat Sci & Tec, Beijing 100084, Peoples R China;Tsinghua Univ, MOE Key Lab Bioinformat, Beijing 100084, Peoples R China | Tsinghua Univ, Bioinformat Div, Ctr Synthet & Syst Biol, Dept Automat,Tsinghua Natl Lab Informat Sci & Tec, Beijing 100084, Peoples R China;Tsinghua Univ, MOE Key Lab Bioinformat, Beijing 100084, Peoples R China | null | null | null | 1996;2011;2012;2013;2014;2015;2016 | 38 | Tsinghua Univ, Bioinformat Div, Ctr Synthet & Syst Biol, Dept Automat,Tsinghua Natl Lab Informat Sci & Tec, Beijing 100084, Peoples R China;Tsinghua Univ, MOE Key Lab Bioinformat, Beijing 100084, Peoples R China | Nat. Commun. | Xie, Zhen | NATURE PUBLISHING GROUP | ,;a;activating;addition;allowing;and;application;applications;biomedical;by;cargo;cell-type;challenging;circuits;complex;construct;controls;CRISPR-Cas;dCas9;delivery;different;differential;domains;due;engineer;exchanging;existing;expand;functions;gene;genes;here;however;in;inspire;integrating;is;logic;may;microRNAs;molecular;multiple;new;of;on;one;or;precise;programmable;provide;reduce;regulation;regulations;response;restrictive;sensory;signals;size;specific;split;split-dCas9;still;switches;synthetic;technology;the;therapeutic;therefore;to;toolkit;transcription;two;useful;using;valuable;vehicles;viral;we;which;will | Tsinghua Univ | Programmable and precise regulation of dCas9 functions in response to multiple molecular signals by using synthetic gene circuits will expand the application of the CRISPR-Cas technology. However, the application of CRISPR-Cas therapeutic circuits is still challenging due to the restrictive cargo size of existing viral delivery vehicles. Here, we construct logic AND circuits by integrating multiple split dCas9 domains, which is useful to reduce the size of synthetic circuits. In addition, we engineer sensory switches by exchanging split dCas9 domains, allowing differential regulations on one gene, or activating two different genes in response to cell-type specific microRNAs. Therefore, we provide a valuable split-dCas9 toolkit to engineer complex transcription controls, which may inspire new biomedical applications. | GPW-5925-2022 | CAS9;CLEAVAGE;COMPLEX;CRISPR;CRYSTAL-STRUCTURE;EXPRESSION;PROTEIN;RNA;SYSTEM | 4 | null | null | 7 | CAS9;CLEAVAGE;COMPLEX;CRISPR;CRYSTAL-STRUCTURE;EXPRESSION;PROTEIN;RNA;SYSTEM | WOS:000385542700001 | Tsinghua Univ, Beijing, Peoples R China | China | 2,016 | null | null | null | null | English | null | ACS SYNTH BIOL;BIORESOURCE TECHNOL;CELL;CELL REP;J NANOPART RES;MOL CELL;NAT BIOTECHNOL;NAT CHEM BIOL;NAT COMMUN;NAT MED;NAT METHODS;NATURE;NUCLEIC ACIDS RES;P NATL ACAD SCI USA;SCI REP-UK;SCIENCE | Ma, Dacheng;Peng, Shuguang;Xie, Zhen | 2024-03-11
ER | Anders, C;Cong, L;Davis, K M;Farzadfard, F;Fine, E J;Gasiunas, G;Gilbert, L A;Gutschner, T;Jinek, M;Kiani, S;Kleinstiver, B P;Li, Y;Mashiko, D;Nguyen, D P;Nihongaki, Y;Nishimasu, H;Nissim, L;Oakes, B L;Polstein, L R;Qi, L S;Rivera, V M;Tanenbaum, M E;Truong, D J J;Wright, A V;Xie, Z;Yuan, Y;Zalatan, J G;Zetsche, B | DZ0PR | Beijing, Peoples R China;Beijing, Peoples R China. | 47 | null | 1 | null | 27,694,915 | Ma, Dacheng;Peng, Shuguang;Xie, Zhen | NAT COMMUN | Beijing, Peoples R China |
Bojar, D;Fussenegger, M | 10.1016/j.cbpa.2016.05.012 | null | THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, OXON, ENGLAND | 61505c6l6f6k93w5603x122m2x2m1x3e2f4l6q | The best of both worlds: reaping the benefits from mammalian and bacterial therapeutic circuits | Swiss Fed Inst Technol | null | Fussenegger, M (corresponding author), Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Mattenstr 26, CH-4058 Basel, Switzerland.;Fussenegger, M (corresponding author), Univ Basel, Fac Life Sci, Mattenstr 26, CH-4058 Basel, Switzerland. | null | Bojar, Daniel;Fussenegger, Martin | Biochemistry & Molecular Biology;Biophysics | null | WOS | Fussenegger, M | Swiss Fed Inst Technol, Basel, Switzerland;Univ Basel, Basel, Switzerland | 34 | :;and;Bacterial;benefits;best;both;circuits;From;mammalian;of;reaping;the;therapeutic;worlds | 1 | Bojar, Daniel | ELSEVIER SCI LTD | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Mattenstr 26, CH-4058 Basel, Switzerland;Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Mattenstr 26, CH-4058 Basel, Switzerland.; Fussenegger, M (corresponding author), Univ Basel, Fac Life Sci, Mattenstr 26, CH-4058 Basel, Switzerland;Univ Basel, Fac Life Sci, Mattenstr 26, CH-4058 Basel, Switzerland | Review | Swiss Fed Inst Technol;Univ Basel | OXFORD | null | null | Swiss Fed Inst Technol;Univ Basel | null | Fussenegger, M (corresponding author), Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Mattenstr 26, CH-4058 Basel, Switzerland.; Fussenegger, M (corresponding author), Univ Basel, Fac Life Sci, Mattenstr 26, CH-4058 Basel, Switzerland. | 19 | Bojar, Daniel;Fussenegger, Martin | 24 | 2 | 389,103,600,003 | null | Switzerland | CURRENT OPINION IN CHEMICAL BIOLOGY | Switzerland | null | null | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Mattenstr 26, CH-4058 Basel, Switzerland | 1367-5931 | Bojar, D;Fussenegger, M | OCT | martin.fussenegger@bsse.ethz.ch | bacterial therapeutic circuits | 2 | J | Biochemistry & Molecular Biology;Biophysics | action;bacterial cells;bacterial therapeutic circuits;biological control mechanisms;BIOLOGY;biomedical achievements;common mode;DETECT;Diagnosis;diseases;extensive array;future;Gene circuits;glucose;highlighting new tools;homeostasis;innovative diagnostics;mechanisms;medicine;microbes;MODELS;novel constellations;panoply;PARTS;plethora;potentialities;rational manner;recent therapeutic gene circuits;recombining;review;staggering variety;synthetic biology;synthetic gene circuits;T-CELLS;taking apart natural systems;therapeutic gene circuits;therapies;therapy;tomorrow;TRANSGENE EXPRESSION;two decades | Bojar, D | DETECT;Gene circuits;GLUCOSE;HOMEOSTASIS;MECHANISMS;MICROBES;MODELS;Synthetic biology;T-CELLS;TRANSGENE EXPRESSION | 11 | [Bojar, Daniel; Fussenegger, Martin] Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Mattenstr 26, CH-4058 Basel, Switzerland. [Fussenegger, Martin] Univ Basel, Fac Life Sci, Mattenstr 26, CH-4058 Basel, Switzerland. | null | action;bacterial cells;biological control mechanisms;biology;biomedical achievements;common mode;diagnosis;diseases;extensive array;future;highlighting new tools;innovative diagnostics;medicine;novel constellations;panoply;parts;plethora;potentialities;rational manner;recent therapeutic gene circuits;recombining;review;staggering variety;synthetic biology;synthetic gene circuits;taking apart natural systems;therapeutic gene circuits;therapies;therapy;tomorrow;two decades | 10.1002/anie.201412204;10.1007/978-1-59745-323-3_15;10.1007/s00253-015-6867-8;10.1007/s11693-014-9154-6;10.1016/j.amjcard.2005.07.008;10.1016/j.cbpa.2013.10.006;10.1016/j.cbpa.2015.05.018;10.1016/j.cell.2014.10.002;10.1016/j.cell.2014.10.004;10.1016/j.coi.2015.06.015;10.1016/j.copbio.2015.05.004;10.1016/j.febslet.2014.05.003;10.1016/j.molcel.2014.06.007;10.1016/j.tibtech.2015.05.001;10.1016/S1081-1206(10)60305-5;10.1021/sb3000595;10.1021/sb4000417;10.1021/sb500090b;10.1021/sb500258b;10.1038/35002125;10.1038/35002131;10.1038/463288a;10.1038/msb.2010.99;10.1038/msb.2011.55;10.1038/msb.2012.71;10.1038/mt.2010.24;10.1038/nature11149;10.1038/nbt.1617;10.1038/nbt1211;10.1038/ncomms5408;10.1038/ncomms6392;10.1038/nrg1637;10.1038/nrg3094;10.1038/nrm2698;10.1038/nrm3767;10.1038/sj.ijir.3900567;10.1039/c5an01181g;10.1056/NEJMoa1215134;10.1073/pnas.1001721107;10.1073/pnas.1216801110;10.1073/pnas.1222878110;10.1073/pnas.1414558112;10.1093/nar/gku545;10.1093/nar/gkv326;10.1098/rsif.2014.1000;10.1098/rstb.2014.0374;10.1111/ajt.13330;10.1126/science.1192128;10.1126/science.1203535;10.1126/science.1205527;10.1126/science.1216753;10.1126/science.aab4077;10.1126/scitranslmed.aaa3519;10.1186/2045-7022-3-3;10.2337/diacare.24.1.131;[10.1038/NNANO.2009.457, 10.1038/nnano.2009.457] | Swiss Fed Inst Technol | Bojar, D;Fussenegger, M | Bojar, D: Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Mattenstr 26, CH-4058 Basel, Switzerland | Bojar, Daniel | null | 60 | null | Switzerland | Swiss Fed Inst Technol;Univ Basel | Bojar, Daniel | null | DETECT;GENE CIRCUITS;GLUCOSE;HOMEOSTASIS;MECHANISMS;MICROBES;MODELS;SYNTHETIC BIOLOGY;T-CELLS;TRANSGENE EXPRESSION | Bojar, Daniel; Fussenegger, Martin; | null | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Mattenstr 26, CH-4058 Basel, Switzerland;Univ Basel, Fac Life Sci, Mattenstr 26, CH-4058 Basel, Switzerland | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Mattenstr 26, CH-4058 Basel, Switzerland;Univ Basel, Fac Life Sci, Mattenstr 26, CH-4058 Basel, Switzerland | 1879-0402 | null | null | 2000;2001;2005;2006;2007;2008;2009;2010;2011;2012;2013;2014;2015;2016 | 9 | Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Mattenstr 26, CH-4058 Basel, Switzerland;Univ Basel, Fac Life Sci, Mattenstr 26, CH-4058 Basel, Switzerland | Curr. Opin. Chem. Biol. | Fussenegger, Martin | ELSEVIER SCI LTD | ,;a;achievements;action;also;an;and;apart;array;as;assembled;bacterial;biological;biology;biomedical;but;by;cells;circuits;common;constellations;control;covers;created;decades;describe;designed;diagnosis;diagnostics;diseases;engineered;extensive;field;for;future;gene;has;highlighting;holds;implemented;in;innovative;is;it;last;mammalian;manner;mechanisms;mediated;medicine;mode;most;natural;new;not;novel;of;only;panoply;parts;plethora;potentialities;rational;recent;recombining;review;revolutionized;staggering;such;synthetic;systematic;systems;taking;that;the;therapeutic;therapies;therapy;this;tomorrow;tools;two;unlocked;variety;we | Swiss Fed Inst Technol;Univ Basel | Synthetic biology has revolutionized the field of biology in the last two decades. By taking apart natural systems and recombining engineered parts in novel constellations, it has not only unlocked a staggering variety of biological control mechanisms but it has also created a panoply of biomedical achievements, such as innovative diagnostics and therapies. The most common mode of action in the field of synthetic biology is mediated by synthetic gene circuits assembled in a systematic and rational manner. This review covers the most recent therapeutic gene circuits implemented in mammalian and bacterial cells designed for the diagnosis and therapy of an extensive array of diseases. Highlighting new tools for therapeutic gene circuits, we describe a future that holds a plethora of potentialities for the medicine of tomorrow. | U-4976-2017 | DETECT;GENE CIRCUITS;GLUCOSE;HOMEOSTASIS;MECHANISM;MICROBES;MODEL;SYNTHETIC BIOLOGY;T-CELLS;TRANSGENE EXPRESSION | 0 | null | null | 9 | DETECTION;Gene circuits;GLUCOSE;HOMEOSTASIS;MECHANISM;MICROBES;MODEL;Synthetic biology;T-CELLS;TRANSGENE EXPRESSION | WOS:000389103600003 | Swiss Fed Inst Technol, Basel, Switzerland;Univ Basel, Basel, Switzerland | Switzerland | 2,016 | null | 0000-0002-3008-7851 | null | null | English | null | ACS SYNTH BIOL;AM J CARDIOL;AM J TRANSL RES;AM J TRANSPLANT;ANALYST;ANGEW CHEM INT EDIT;ANN ALLERG ASTHMA IM;APPL MICROBIOL BIOT;CELL;Clin Transl Allergy;CURR OPIN BIOTECH;CURR OPIN CHEM BIOL;CURR OPIN IMMUNOL;DIABETES CARE;FEBS LETT;INT J IMPOT RES;J R SOC INTERFACE;Journal of Molecular Biology;METHODS MOL BIOL;MOL CELL;MOL SYST BIOL;MOL THER;NAT BIOTECHNOL;NAT COMMUN;NAT NANOTECHNOL;NAT REV GENET;NAT REV MOL CELL BIO;NATURE;NEW ENGL J MED;NUCLEIC ACIDS RES;P NATL ACAD SCI;P NATL ACAD SCI USA;PHILOS T R SOC B;SCI TRANSL MED;SCIENCE;Syst Synth Biol;TRENDS BIOTECHNOL | Bojar, Daniel;Fussenegger, Martin | 2024-03-11
ER | Alcaine, S D;Archer, E J;Ausländer, D;Ausländer, S;Benner, S A;Bernstein, I L;Borrero, J;Burnett, A L;Chakravarti, D;Chappell, J;Chen, Y Y;Church, G M;Claesen, J;Culler, S J;Danino, T;Elowitz, M B;Fernandes, R;Folcher, M;Gardner, T S;Glovsky M Michael;Green, A A;Grupp, S A;Gupta, S;Haellman V.;Heinzerling Lucie;June, C H;Kemmer, C;Kim, T;Kis, Z;Kitabchi, A E;Kwok, R;Mak, I W Y;Mckinlay, J B;Morgan, R A;Nissim, L;Pardee, K;Piñero-Lambea, C;Purnick, P E M;Saeidi, N;Saxena, P;Scholman, T;Schukur, L;Seok, J;Singh Vijai;Stanley, S A;Swofford, C A;Wang, H;Weber, W;Wu, C Y;Wu, H C;Xiang, S L;Xie, M Q;Xie, Z;Ye, H F | ED8EA | Basel, Switzerland;Basel, Switzerland. | 9 | null | 2 | null | 27,236,825 | Bojar, Daniel;Fussenegger, Martin | CURR OPIN CHEM BIOL | Basel, Switzerland |