bluuebunny/crossref_metadata_2025_split huggingface dataset:
A mechanistic framework for auxin dependent Arabidopsis root hair elongation to low external phosphate
Authors: Bhosale Rahul , Giri Jitender , Pandey Bipin K. , Giehl Ricardo F. H. , Hartmann Anja , Traini Richard , Truskina Jekaterina , Leftley Nicola , Hanlon Meredith , Swarup Kamal , Rashed Afaf , Voß Ute , Alonso Jose , Stepanova Anna , Yun Jeonga , Ljung Karin , Brown Kathleen M. , Lynch Jonathan P. , Dolan Liam , Vernoux Teva , Bishopp Anthony , Wells Darren , von Wirén Nicolaus , Bennett Malcolm J. , Swarup Ranjan 
Published: April 2018

AbstractPhosphate (P) is an essential macronutrient for plant growth. Roots employ adaptive mechanisms to forage for P in soil. Root hair elongation is particularly important since P is immobile. Here we report that auxin plays a critical role promoting root hair growth in Arabidopsis in response to low external P. Mutants disrupting auxin synthesis (taa1) and transport (aux1) attenuate the low P root hair response. Conversely, targeting AUX1 expression in lateral root cap and epidermal cells rescues this low P response in aux1. Hence auxin transport from the root apex to differentiation zone promotes auxin-dependent hair response to low P. Low external P results in induction of root hair expressed auxin-inducible transcription factors ARF19, RSL2, and RSL4. Mutants lacking these genes disrupt the low P root hair response. We conclude auxin synthesis, transport and response pathway components play critical roles regulating this low P root adaptive response.
Calculating curly arrows from ab initio wavefunctions
Authors: Liu Yu , Kilby Philip , Frankcombe Terry J. , Schmidt Timothy W. 
Published: April 2018

AbstractDespite being at the heart of chemical thought, the curly arrow notation of reaction mechanisms has been treated with suspicion—the connection with rigorous molecular quantum mechanics being unclear. The connection requires a view of the wavefunction that goes beyond molecular orbitals and rests on the most fundamental property of electrons. The antisymmetry of electronic wavefunctions requires that an N-electron wavefunction repeat itself in 3N dimensions, thus exhibiting tiles. Inspection of wavefunction tiles permits insight into structure and mechanism. Here, we demonstrate that analysis of the wavefunction tile along a reaction coordinate reveals the electron movements depicted by the curly arrow notation for several reactions. The Diels–Alder reaction is revealed to involve the separation and counter propagation of electron spins. This unprecedented method of extracting the movements of electrons during a chemical reaction is a breakthrough in connecting traditional depictions of chemical mechanism with state-of-the-art quantum chemical calculations.
Multi-petahertz electron interference in Cr:Al2O3 solid-state material
Authors: Mashiko Hiroki , Chisuga Yuta , Katayama Ikufumi , Oguri Katsuya , Masuda Hiroyuki , Takeda Jun , Gotoh Hideki 
Published: April 2018

AbstractLightwave-field-induced ultrafast electric dipole oscillation is promising for realizing petahertz (1015 Hz: PHz) signal processing in the future. In building the ultrahigh-clock-rate logic operation system, one of the major challenges will be petahertz electron manipulation accompanied with multiple frequencies. Here we study multi-petahertz interference with electronic dipole oscillations in alumina with chromium dopant (Cr:Al2O3). An intense near-infrared lightwave-field induces multiple electric inter-band polarizations, which are characterized by Fourier transform extreme ultraviolet attosecond spectroscopy. The interference results from the superposition state of periodic dipole oscillations of 667 to 383 attosecond (frequency of 1.5 to 2.6 PHz) measured by direct time-dependent spectroscopy and consists of various modulations on attosecond time scale through individual electron dephasing times of the Cr donor-like and Al2O3 conduction band states. The results indicate the possible manipulation of petahertz interference signal with multiple dipole oscillations using material band engineering and such a control will contribute to the study of ultrahigh-speed signal operation.
Tuning Ising superconductivity with layer and spin–orbit coupling in two-dimensional transition-metal dichalcogenides
Authors: de la Barrera Sergio C. , Sinko Michael R. , Gopalan Devashish P. , Sivadas Nikhil , Seyler Kyle L. , Watanabe Kenji , Taniguchi Takashi , Tsen Adam W. , Xu Xiaodong , Xiao Di , Hunt Benjamin M. 
Published: April 2018

AbstractSystems simultaneously exhibiting superconductivity and spin–orbit coupling are predicted to provide a route toward topological superconductivity and unconventional electron pairing, driving significant contemporary interest in these materials. Monolayer transition-metal dichalcogenide (TMD) superconductors in particular lack inversion symmetry, yielding an antisymmetric form of spin–orbit coupling that admits both spin-singlet and spin-triplet components of the superconducting wavefunction. Here, we present an experimental and theoretical study of two intrinsic TMD superconductors with large spin–orbit coupling in the atomic layer limit, metallic 2H-TaS2 and 2H-NbSe2. We investigate the superconducting properties as the material is reduced to monolayer thickness and show that high-field measurements point to the largest upper critical field thus reported for an intrinsic TMD superconductor. In few-layer samples, we find the enhancement of the upper critical field is sustained by the dominance of spin–orbit coupling over weak interlayer coupling, providing additional candidate systems for supporting unconventional superconducting states in two dimensions.
Functional crosstalk between histone H2B ubiquitylation and H2A modifications and variants
Authors: Wojcik Felix , Dann Geoffrey P. , Beh Leslie Y. , Debelouchina Galia T. , Hofmann Raphael , Muir Tom W. 
Published: April 2018

AbstractUbiquitylation of histone H2B at lysine residue 120 (H2BK120ub) is a prominent histone posttranslational modification (PTM) associated with the actively transcribed genome. Although H2BK120ub triggers several critical downstream histone modification pathways and changes in chromatin structure, less is known about the regulation of the ubiquitylation reaction itself, in particular with respect to the modification status of the chromatin substrate. Here we employ an unbiased library screening approach to profile the impact of pre-existing chromatin modifications on de novo ubiquitylation of H2BK120 by the cognate human E2:E3 ligase pair, UBE2A:RNF20/40. Deposition of H2BK120ub is found to be highly sensitive to PTMs on the N-terminal tail of histone H2A, a crosstalk that extends to the common histone variant H2A.Z. Based on a series of biochemical and cell-based studies, we propose that this crosstalk contributes to the spatial organization of H2BK120ub on gene bodies, and is thus important for transcriptional regulation.
Anchoring zero valence single atoms of nickel and iron on graphdiyne for hydrogen evolution
Authors: Xue Yurui , Huang Bolong , Yi Yuanping , Guo Yuan , Zuo Zicheng , Li Yongjun , Jia Zhiyu , Liu Huibiao , Li Yuliang 
Published: April 2018

AbstractElectrocatalysis by atomic catalysts is a major focus of chemical and energy conversion effort. Although transition-metal-based bulk electrocatalysts for electrochemical application on energy conversion processes have been reported frequently, anchoring the stable transition-metal atoms (e.g. nickel and iron) still remains a practical challenge. Here we report a strategy for fabrication of ACs comprising only isolated nickel/iron atoms anchored on graphdiyne. Our findings identify the very narrow size distributions of both nickel (1.23 Å) and iron (1.02 Å), typical sizes of single-atom nickel and iron. The precision of this method motivates us to develop a general approach in the field of single-atom transition-metal catalysis. Such atomic catalysts have high catalytic activity and stability for hydrogen evolution reactions.
In vivo guiding nitrogen-doped carbon nanozyme for tumor catalytic therapy
Authors: Fan Kelong , Xi Juqun , Fan Lei , Wang Peixia , Zhu Chunhua , Tang Yan , Xu Xiangdong , Liang Minmin , Jiang Bing , Yan Xiyun , Gao Lizeng 
Published: April 2018

AbstractNanomaterials with intrinsic enzyme-like activities (nanozymes), have been widely used as artificial enzymes in biomedicine. However, how to control their in vivo performance in a target cell is still challenging. Here we report a strategy to coordinate nanozymes to target tumor cells and selectively perform their activity to destruct tumors. We develop a nanozyme using nitrogen-doped porous carbon nanospheres which possess four enzyme-like activities (oxidase, peroxidase, catalase and superoxide dismutase) responsible for reactive oxygen species regulation. We then introduce ferritin to guide nitrogen-doped porous carbon nanospheres into lysosomes and boost reactive oxygen species generation in a tumor-specific manner, resulting in significant tumor regression in human tumor xenograft mice models. Together, our study provides evidence that nitrogen-doped porous carbon nanospheres are powerful nanozymes capable of regulating intracellular reactive oxygen species, and ferritinylation is a promising strategy to render nanozymes to target tumor cells for in vivo tumor catalytic therapy.
Competition between microtubule-associated proteins directs motor transport
Authors: Monroy Brigette Y. , Sawyer Danielle L. , Ackermann Bryce E. , Borden Melissa M. , Tan Tracy C. , Ori-McKenney Kassandra M. 
Published: April 2018

AbstractWithin cells, motor and non-motor microtubule-associated proteins (MAPs) simultaneously converge on the microtubule. How the binding activities of non-motor MAPs are coordinated and how they contribute to the balance and distribution of motor transport is unknown. Here, we examine the relationship between MAP7 and tau owing to their antagonistic roles in vivo. We find that MAP7 and tau compete for binding to microtubules, and determine a mechanism by which MAP7 displaces tau from the lattice. MAP7 promotes kinesin-based transport in vivo and strongly recruits kinesin-1 to the microtubule in vitro, providing evidence for direct enhancement of motor motility by a MAP. Both MAP7 and tau strongly inhibit kinesin-3 and have no effect on cytoplasmic dynein, demonstrating that MAPs differentially control distinct classes of motors. Overall, these results reveal a general principle for how MAP competition dictates access to the microtubule to determine the correct distribution and balance of motor activity.
Highly stable graphene-oxide-based membranes with superior permeability
Authors: Thebo Khalid Hussain , Qian Xitang , Zhang Qing , Chen Long , Cheng Hui-Ming , Ren Wencai 
Published: April 2018

AbstractIncreasing fresh water demand for drinking and agriculture is one of the grand challenges of our age. Graphene oxide (GO) membranes have shown a great potential for desalination and water purification. However, it is challenging to further improve the water permeability without sacrificing the separation efficiency, and the GO membranes are easily delaminated in aqueous solutions within few hours. Here, we report a class of reduced GO membranes with enlarged interlayer distance fabricated by using theanine amino acid and tannic acid as reducing agent and cross-linker. Such membranes show water permeance over 10,000 L m−2 h−1 bar−1, which is 10–1000 times higher than those of previously reported GO-based membranes and commercial membranes, and good separation efficiency, e.g., rhodamine B and methylene blue rejection of ~100%. Moreover, they show no damage or delamination in water, acid, and basic solutions even after months.
Greenland records of aerosol source and atmospheric lifetime changes from the Eemian to the Holocene
Authors: Schüpbach S. , Fischer H. , Bigler M. , Erhardt T. , Gfeller G. , Leuenberger D. , Mini O. , Mulvaney R. , Abram N. J. , Fleet L. , Frey M. M. , Thomas E. , Svensson A. , Dahl-Jensen D. , Kettner E. , Kjaer H. , Seierstad I. , Steffensen J. P. , Rasmussen S. O. , Vallelonga P. , Winstrup M. , Wegner A. , Twarloh B. , Wolff K. , Schmidt K. , Goto-Azuma K. , Kuramoto T. , Hirabayashi M. , Uetake J. , Zheng J. , Bourgeois J. , Fisher D. , Zhiheng D. , Xiao C. , Legrand M. , Spolaor A. , Gabrieli J. , Barbante C. , Kang J.-H. , Hur S. D. , Hong S. B. , Hwang H. J. , Hong S. , Hansson M. , Iizuka Y. , Oyabu I. , Muscheler R. , Adolphi F. , Maselli O. , McConnell J. , Wolff E. W. 
Published: April 2018

AbstractThe Northern Hemisphere experienced dramatic changes during the last glacial, featuring vast ice sheets and abrupt climate events, while high northern latitudes during the last interglacial (Eemian) were warmer than today. Here we use high-resolution aerosol records from the Greenland NEEM ice core to reconstruct the environmental alterations in aerosol source regions accompanying these changes. Separating source and transport effects, we find strongly reduced terrestrial biogenic emissions during glacial times reflecting net loss of vegetated area in North America. Rapid climate changes during the glacial have little effect on terrestrial biogenic aerosol emissions. A strong increase in terrestrial dust emissions during the coldest intervals indicates higher aridity and dust storm activity in East Asian deserts. Glacial sea salt aerosol emissions in the North Atlantic region increase only moderately (50%), likely due to sea ice expansion. Lower aerosol concentrations in Eemian ice compared to the Holocene are mainly due to shortened atmospheric residence time, while emissions changed little.
Incorporation of bridged nucleic acids into CRISPR RNAs improves Cas9 endonuclease specificity
Authors: Cromwell Christopher R. , Sung Keewon , Park Jinho , Krysler Amanda R. , Jovel Juan , Kim Seong Keun , Hubbard Basil P. 
Published: April 2018

AbstractOff-target DNA cleavage is a paramount concern when applying CRISPR-Cas9 gene-editing technology to functional genetics and human therapeutic applications. Here, we show that incorporation of next-generation bridged nucleic acids (2′,4′-BNANC[N-Me]) as well as locked nucleic acids (LNA) at specific locations in CRISPR-RNAs (crRNAs) broadly reduces off-target DNA cleavage by Cas9 in vitro and in cells by several orders of magnitude. Using single-molecule FRET experiments we show that BNANC incorporation slows Cas9 kinetics and improves specificity by inducing a highly dynamic crRNA–DNA duplex for off-target sequences, which shortens dwell time in the cleavage-competent, “zipped” conformation. In addition to describing a robust technique for improving the precision of CRISPR/Cas9-based gene editing, this study illuminates an application of synthetic nucleic acids.
Phosphatase activity tunes two-component system sensor detection threshold
Authors: Landry Brian P. , Palanki Rohan , Dyulgyarov Nikola , Hartsough Lucas A. , Tabor Jeffrey J. 
Published: April 2018

AbstractTwo-component systems (TCSs) are the largest family of multi-step signal transduction pathways in biology, and a major source of sensors for biotechnology. However, the input concentrations to which biosensors respond are often mismatched with application requirements. Here, we utilize a mathematical model to show that TCS detection thresholds increase with the phosphatase activity of the sensor histidine kinase. We experimentally validate this result in engineered Bacillus subtilis nitrate and E. coli aspartate TCS sensors by tuning their detection threshold up to two orders of magnitude. We go on to apply our TCS tuning method to recently described tetrathionate and thiosulfate sensors by mutating a widely conserved residue previously shown to impact phosphatase activity. Finally, we apply TCS tuning to engineer B. subtilis to sense and report a wide range of fertilizer concentrations in soil. This work will enable the engineering of tailor-made biosensors for diverse synthetic biology applications.
HATRIC-based identification of receptors for orphan ligands
Authors: Sobotzki Nadine , Schafroth Michael A. , Rudnicka Alina , Koetemann Anika , Marty Florian , Goetze Sandra , Yamauchi Yohei , Carreira Erick M. , Wollscheid Bernd 
Published: April 2018

AbstractCellular responses depend on the interactions of extracellular ligands, such as nutrients, growth factors, or drugs, with specific cell-surface receptors. The sensitivity of these interactions to non-physiological conditions, however, makes them challenging to study using in vitro assays. Here we present HATRIC-based ligand receptor capture (HATRIC-LRC), a chemoproteomic technology that successfully identifies target receptors for orphan ligands on living cells ranging from small molecules to intact viruses. HATRIC-LRC combines a click chemistry-based, protein-centric workflow with a water-soluble catalyst to capture ligand-receptor interactions at physiological pH from as few as 1 million cells. We show HATRIC-LRC utility for general antibody target validation within the native nanoscale organization of the surfaceome, as well as receptor identification for a small molecule ligand. HATRIC-LRC further enables the identification of complex extracellular interactomes, such as the host receptor panel for influenza A virus (IAV), the causative agent of the common flu.
Horizontal antimicrobial resistance transfer drives epidemics of multiple Shigella species
Authors: Baker Kate S. , Dallman Timothy J. , Field Nigel , Childs Tristan , Mitchell Holly , Day Martin , Weill François-Xavier , Lefèvre Sophie , Tourdjman Mathieu , Hughes Gwenda , Jenkins Claire , Thomson Nicholas 
Published: April 2018

AbstractHorizontal gene transfer has played a role in developing the global public health crisis of antimicrobial resistance (AMR). However, the dynamics of AMR transfer through bacterial populations and its direct impact on human disease is poorly elucidated. Here, we study parallel epidemic emergences of multiple Shigella species, a priority AMR organism, in men who have sex with men to gain insight into AMR emergence and spread. Using genomic epidemiology, we show that repeated horizontal transfer of a single AMR plasmid among Shigella enhanced existing and facilitated new epidemics. These epidemic patterns contrasted with slighter, slower increases in disease caused by organisms with vertically inherited (chromosomally encoded) AMR. This demonstrates that horizontal transfer of AMR directly affects epidemiological outcomes of globally important AMR pathogens and highlights the need for integration of genomic analyses into all areas of AMR research, surveillance and management.
Cell-free prediction of protein expression costs for growing cells
Authors: Borkowski Olivier , Bricio Carlos , Murgiano Michela , Rothschild-Mancinelli Brooke , Stan Guy-Bart , Ellis Tom 
Published: April 2018

AbstractTranslating heterologous proteins places significant burden on host cells, consuming expression resources leading to slower cell growth and productivity. Yet predicting the cost of protein production for any given gene is a major challenge, as multiple processes and factors combine to determine translation efficiency. To enable prediction of the cost of gene expression in bacteria, we describe here a standard cell-free lysate assay that provides a relative measure of resource consumption when a protein coding sequence is expressed. These lysate measurements can then be used with a computational model of translation to predict the in vivo burden placed on growing E. coli cells for a variety of proteins of different functions and lengths. Using this approach, we can predict the burden of expressing multigene operons of different designs and differentiate between the fraction of burden related to gene expression compared to action of a metabolic pathway.
Microfabricated electrodes unravel the role of interfaces in multicomponent copper-based CO2 reduction catalysts
Authors: Larrazábal Gastón O. , Shinagawa Tatsuya , Martín Antonio J. , Pérez-Ramírez Javier 
Published: April 2018

AbstractThe emergence of synergistic effects in multicomponent catalysts can result in breakthrough advances in the electrochemical reduction of carbon dioxide. Copper-indium catalysts show high performance toward carbon monoxide production but also extensive structural and compositional changes under operation. The origin of the synergistic effect and the nature of the active phase are not well understood, thus hindering optimization efforts. Here we develop a platform that sheds light into these aspects, based on microfabricated model electrodes that are evaluated under conventional experimental conditions. The relationship among the electrode performance, geometry and composition associates the high carbon monoxide evolution activity of copper-indium catalysts to indium-poor bimetallic phases, which are formed upon exposure to reaction conditions in the vicinity of the interfaces between copper oxide and an indium source. The exploratory extension of this approach to the copper-tin system demonstrates its versatility and potential for the study of complex multicomponent electrocatalysts.
Micro-CT X-ray imaging exposes structured diffusion barriers within biofilms
Authors: Keren-Paz Alona , Brumfeld Vlad , Oppenheimer-Shaanan Yaara , Kolodkin-Gal Ilana 
Published: April 2018

AbstractIn nature, bacteria predominantly exist as highly structured biofilms, which are held together by extracellular polymeric substance and protect their residents from environmental insults, such as antibiotics. The mechanisms supporting this phenotypic resistance are poorly understood. Recently, we identified a new mechanism maintaining biofilms - an active production of calcite minerals. In this work, a high-resolution and robust µCT technique is used to study the mineralized areas within intact bacterial biofilms. µCT is a vital tool for visualizing bacterial communities that can provide insights into the relationship between bacterial biofilm structure and function. Our results imply that dense and structured calcium carbonate lamina forms a diffusion barrier sheltering the inner cell mass of the biofilm colony. Therefore, µCT can be employed in clinical settings to predict the permeability of the biofilms. It is demonstrated that chemical interference with urease, a key enzyme in biomineralization, inhibits the assembly of complex bacterial structures, prevents the formation of mineral diffusion barriers and increases biofilm permeability. Therefore, biomineralization enzymes emerge as novel therapeutic targets for highly resistant infections.