bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extended depth of focus multiphoton microscopy via incoherent pulse splitting
Authors: Chen Bingying , Chakraborty Tonmoy , Daetwyler Stephan , Manton James D. , Dean Kevin , Fiolka Reto 
Published: March 2020

AbstractWe present a phase mask that can be easily added to any multi-photon raster scanning microscope to extend the depth of focus five-fold at a small loss in lateral resolution. The method is designed for ultrafast laser pulses or other light-sources featuring a low coherence length. In contrast to other methods of focus extension, our approach uniquely combines low complexity, high light-throughput and multicolor capability. We characterize the point-spread function in a two-photon microscope and demonstrate fluorescence imaging of GFP labeled neurons in fixed brain samples as imaged with conventional and extended depth of focus two-photon microscopy.
Evolution of an interaction between disordered proteins resulted in increased heterogeneity of the binding transition state
Authors: Karlsson Elin , Paissoni Cristina , Erkelens Amanda M. , Tehranizadeh Zeinab Amiri , Sorgenfrei Frieda A. , Andersson Eva , Ye Weihua , Camilloni Carlo , Jemth Per 
Published: March 2020

AbstractIntrinsically disordered protein (IDP) domains often have multiple binding partners. Little is known regarding molecular changes in the binding mechanism when a new interaction evolves from low to high affinity. Here we compared the degree of native contacts in the transition state of the interaction of two IDP domains, low-affinity ancestral and high-affinity human NCBD and CID. We found that the coupled binding and folding mechanism of the domains is overall similar, but with a higher degree of native hydrophobic contact formation in the transition state of the ancestral complex while more heterogenous transient interactions, including electrostatic, and an increased disorder characterize the human complex. From an evolutionary perspective, adaptation to new binding partners for IDPs may benefit from this ability to exploit multiple alternative transient interactions while retaining the overall pathway.
Divergent evolution of a protein-protein interaction revealed through ancestral sequence reconstruction and resurrection
Authors: Laursen Louise , Čalyševa Jelena , Gibson Toby J. , Jemth Per 
Published: March 2020

AbstractThe postsynaptic density extends across the postsynaptic dendritic spine with Discs large (DLG) as the most abundant scaffolding protein. DLG dynamically alters the structure of the postsynaptic density, thus controlling the function and distribution of specific receptors at the synapse. PDZ domains make up one of the most abundant protein interaction domain families in animals. One important interaction governing postsynaptic architecture is that between the PDZ3 domain from DLG and cysteine-rich interactor of PDZ3 (CRIPT). However, little is know regarding functional evolution of the PDZ3:CRIPT interaction. Here, we subjected PDZ3 and CRIPT to ancestral sequence reconstruction, resurrection and biophysical experiments. We show that the PDZ3:CRIPT interaction is an ancient interaction, which was present in the last common ancestor of Eukaryotes, and that high affinity is maintained in most extant animal phyla. However, affinity is low in nematodes and insects, raising questions about the physiological function of the interaction in species from these animal groups. Our findings demonstrate how an apparently established protein-protein interaction involved in cellular scaffolding in bilaterians can suddenly be subject to dynamic evolution including possible loss of function.
Physical Interactions Driving the Activation/Inhibition of Calcium/Calmodulin Dependent Protein Kinase II
Authors: Asciutto Eliana K. , Pantano Sergio , General Ignacio J. 
Published: March 2020

AbstractCaMKII is a protein kinase whose function is regulated by the binding of the Calcium/Calmodulin complex (Ca2+/CaM). It is a major player in the Long Term Potentiation process where it acts as a molecular switch, oscillating between inhibited and active conformations. The mechanism for the switching is thought to be initiated by Ca2+/CaM binding, which allows the trans-phosphorylation of a subunit of CaMKII by a neighboring kinase, leading to the active state of the system. A combination of all-atom and coarse-grained MD simulations with free energy calculations, led us to reveal an interplay of electrostatic forces exerted by Ca2+/CaM on CaMKII, which initiate the activation process. The highly electrically charged Ca2+/CaM neutralizes basic regions in the linker domain of CaMKII, facilitating its opening and consequent activation. The emerging picture of CaMKII’s behavior highlights the preponderance of electrostatic interactions, which are modulated by the presence of Ca2+/CaM and the phosphorylation of key sites.
Structural Determinants of Phosphopeptide Binding to the N-Terminal Src Homology 2 Domain of the SHP2 Phosphatase
Authors: Anselmi M. , Calligari P. , Hub J.S. , Tartaglia M. , Bocchinfuso G. , Stella L. 
Published: March 2020

ABSTRACTSH2 domain-containing tyrosine phosphatase 2 (SHP2), encoded byPTPN11, plays a fundamental role in the modulation of several signaling pathways. Germline and somatic mutations inPTPN11are associated with different rare diseases and hematologic malignancies, and recent studies have individuated SHP2 as a central node in oncogenesis and cancer drug resistance. SHP2 structure includes two Src homology 2 domains (N-SH2 and C-SH2) followed by a catalytic protein tyrosine phosphatase (PTP) domain. Under basal conditions, the N-SH2 domain blocks the active site, inhibiting phosphatase activity. Association of the N-SH2 domain with binding partners containing short amino acid motifs comprising a phosphotyrosine residue (pY) leads to N-SH2/PTP dissociation and SHP2 activation. Considering the relevance of SHP2 in signaling and disease and the central role of the N-SH2 domain in its allosteric regulation mechanism, we performed microsecond-long molecular dynamics simulations of the N-SH2 domain complexed to 12 different peptides, to define the structural and dynamical features determining the binding affinity and specificity of the domain. Phosphopeptide residues at position −2 to +5, with respect to pY, have significant interactions with the SH2 domain. In addition to the strong interaction of the pY residue with its conserved binding pocket, the complex is stabilized hydrophobically by insertion of residues +1, +3 and +5 in an apolar groove of the domain, and interaction of residue −2 with both the pY and a protein surface residue. Additional interactions are provided by hydrogen bonds formed by the backbone of residues −1, +1, +2 and +4. Finally, negatively charged residues at position +2 and +4 are involved in electrostatic interactions with two lysines (Lys89 and Lys91) specific of the SHP2 N-SH2 domain. Interestingly, the MD simulations illustrated a previously undescribed conformational flexibility of the domain, involving the core β-sheet and the loop that closes the pY binding pocket.
Evaluating the transcriptional fidelity of cancer models
Authors: Peng Da , Gleyzer Rachel , Tai Wen-Hsin , Kumar Pavithra , Bian Qin , Issacs Bradley , da Rocha Edroaldo Lummertz , Cai Stephanie , DiNapoli Kathleen , Huang Franklin W , Cahan Patrick 
Published: March 2020

ABSTRACTBackgroundCancer researchers use cell lines, patient derived xenografts, engineered mice, and tumoroids as models to investigate tumor biology and to identify therapies. The generalizability and power of a model derives from the fidelity with which it represents the tumor type under investigation, however, the extent to which this is true is often unclear. The preponderance of models and the ability to readily generate new ones has created a demand for tools that can measure the extent and ways in which cancer models resemble or diverge from native tumors.MethodsWe developed a machine learning based computational tool, CancerCellNet, that measures the similarity of cancer models to 22 naturally occurring tumor types and 36 subtypes, in a platform and species agnostic manner. We applied this tool to 657 cancer cell lines, 415 patient derived xenografts, 26 distinct genetically engineered mouse models, and 131 tumoroids. We validated CancerCellNet by application to independent data, and we tested several predictions with immunofluorescence.ResultsWe have documented the cancer models with the greatest transcriptional fidelity to natural tumors, we have identified cancers underserved by adequate models, and we have found models with annotations that do not match their classification. By comparing models across modalities, we report that, on average, genetically engineered mice and tumoroids have higher transcriptional fidelity than patient derived xenografts and cell lines in four out of five tumor types. However, several patient derived xenografts and tumoroids have classification scores that are on par with native tumors, highlighting both their potential as faithful model classes and their heterogeneity.ConclusionsCancerCellNet enables the rapid assessment of transcriptional fidelity of tumor models. We have made CancerCellNet available as freely downloadable software and as a web application that can be applied to new cancer models that allows for direct comparison to the cancer models evaluated here.
Computational Investigation Of Structural Interfaces Of Protein Complexes With Short Linear Motifs
Authors: Upadhyayula Raghavender Surya 
Published: March 2020

AbstractProtein complexes with short linear motifs (SLiMs) are known to play important regulatory functions in eukaryotes. In this investigation, I have studied the structures deposited in PDB with SLiMs. The structures Were grouped into three broad categories of protein-protein, protein-peptide and the rest as others. Protein-peptide complexes Were found to be most highly represented. The interfaces Were evaluated for geometric features and conformational variables. It was observed that protein-protein and protein-peptide complexes show characteristic differences in residue pairings, which Were quantified by evaluating normalized contact residue pairing frequencies. Interface residues adopt characteristic canonical residue conformations in the Ramachandran space, with a pronounced preference for positive ϕ conformations. It was observed that phosphorylated residues have an unusual propensity to adopt the unusual positive ϕ conformations at the interface.
Antimicrobial Resistance Profile andmcr-1Gene Detection inSalmonellaIsolates from Poultry in Bangladesh: Molecular and Bioinformatics Characterization
Authors: Uddin Md Bashir , Hossain S M Bayejed , Hasan Mahmudul , Alam Mohammad Nurul , Debnath Mita , Begum Ruhena , Roy Sawrab , Harun-Al-Rashid Ahmed , Chowdhury Md. Shahidur Rahman , Rahman Md. Mahfujur , Hossain Md. Mukter , Chowdhury Mohammed Yousuf Elahi , Ahmed Syed Sayeem Uddin 
Published: March 2020

AbstractAntimicrobial resistance genemcr-1has been disseminated globally since its first discovery in Southern China in late 2015. However, themcr-1 gene had not been identified previously inSalmonellaisolates from poultry in Bangladesh. Here, we aimed to explore antimicrobial resistance genemcr-1inSalmonellaisolates. Eighty twoSalmonellaisolates were isolated and characterized from suspected poultry specimens received from different zones of the country. A phenotypic disc diffusion assay with 15 antimicrobial agents was performed following CLSI standard. The disk diffusion assay showed that, all of the isolates presented high resistance to colistin (92.68%), oxytetracycline (86.59%), co-trimoxazole (76.83%), ciprofloxacin (73.17%) and enrofloxacin (65.85%). Further, randomly selected 10Salmonellaisolates were analyzed by polymerase chain reaction (PCR) targeting genus-specificinvAand antimicrobial (colistin) resistancemcr-1 genes. Five were confirmed for the presence of themcr-1gene belonging toSalmonellaspp. Further, sequencing followed by phylogenetic analysis revealed divergent evolutionary relation between the LptA and MCR proteins rendering them resistant to colistin. Three-dimensional homology structures of MCR-1 proteins were constructed and verified using different bioinformatics tools. Moreover, molecular docking interactions suggested that, MCR-1 and LptA share a similar substrate binding cavity which could be validated for the functional analysis. The results represent here is the first molecular andin silicoanalysis of colistin resistancemcr-1gene ofSalmonellain poultry in Bangladesh, which may emphasize the importance of the study on antibiotic resistance genes requiring for national monitoring and strategic surveillance in the country.
A novel rare c. -39C>T mutation in thePROS15’UTR causing PS deficiency by creating a new upstream translation initiation codon and inhibiting the production of the natural protein
Authors: Labrouche-Colomer Sylvie , Soukarieh Omar , Proust Carole , Mouton Christine , Huguenin Yoann , Roux Maguelonne , Besse Céline , Boland Anne , Olaso Robert , Constans Joël , Deleuze Jean-François , Morange Pierre-Emmanuel , Jaspard-Vinassa Béatrice , Trégouët David-Alexandre ,   on behalf of the GenMed consortium
Published: March 2020

SummaryInherited Protein S deficiency (PSD) (MIM176880) is a rare automosal dominant disorder caused by rare mutations, mainly located in the coding sequence of the structuralPROS1gene, and associated with an increased risk of venous thromboembolism. To identify the molecular defect underlying PSD observed in an extended French pedigree with 7 PSD affected members in who no candidate deleteriousPROS1mutation was detected by Sanger sequencing ofPROS1exons and their flanking intronic regions or via a MLPA approach, a whole genome sequencing strategy was adopted. This led to the identification of a never reported C to T substitution at c.-39 from the natural ATG codon of thePROS1gene that completely segregates with PSD in the whole family. This substitution ACG->ATG creates a new start codon upstream of the main ATG. We experimentally demonstrated that the variant generates a novel overlapping ORF and inhibits the translation of the wild type protein from the main ORF in HeLa cells. This work describes the first example of 5’UTRPROS1mutation causing PSD through the creation of an upstream ORF, a mutation that is not predicted to be deleterious by standard annotation softwares.
Left-handed DNA-PAINT for improved superresolution imaging in the nucleus
Authors: Geertsema H.J. , Aimola G. , Fabricius V. , Fuerste J.P. , Kaufer B.B. , Ewers H. 
Published: March 2020

AbstractDNA point accumulation in nanoscale topography (DNA-PAINT) advances super-resolution microscopy with superior resolution and multiplexing capabilities. However, cellular DNA may interfere with this single-molecule localization technique based on DNA-DNA hybridization. Here, we introduce left-handed DNA (L-DNA) oligomers that do not hybridize to naturally present R-DNA and demonstrate that L-DNA PAINT has the same specificity and multiplexing capability as R-DNA PAINT, but greatly improves specific visualization of nuclear target molecules.
Induced Pluripotent Stem Cell-derived CAR-Macrophage Cells with Antigen-dependent Anti-Cancer Cell Functions for Liquid and Solid Tumors
Authors: Zhang Li , Tian Lin , Dai Xiaoyang , Yu Hua , Wang Jiajia , Lei Anhua , Zhao Wei , Zhu Yuqing , Sun Zhen , Zhang Hao , Church George M. , Huang He , Weng Qinjie , Zhang Jin 
Published: March 2020

AbstractThe Chimera antigen receptor (CAR)-T cell therapy has gained great success in the clinic. However, there are still major challenges for its wider applications in a variety of cancer types including lack of effectiveness due to the highly complex tumor microenvironment, and the forbiddingly high cost due to personalized manufacturing procedures. In order to overcome these hurdles, numerous efforts have been spent focusing on optimizing Chimera Antigen Receptors, engineering and improving T cell capacity, exploiting features of subsets of T cell or NK cells, or making off-the-shelf universal T cells. Here, we developed induced pluripotent stem cells (iPSCs)-derived, CAR-expressing macrophage cells (CAR-iMac). These cells showed antigen-dependent macrophage functions such as expression and secretion of cytokines, polarization toward the pro-inflammatory/anti-tumor state, and phagocytosis of tumor cells, as well as somein vivoanti-cancer cell activity for both liquid and solid tumors. This technology platform for the first time provides an unlimited source of iPSC-derived engineered CAR-macrophage cells which could be utilized to eliminate cancer cells or modulate the tumor microenvironment in liquid and solid tumor immunotherapy.One sentence summaryWe developed CAR-expressing iPSC-induced macrophage cells that have antigen-dependent phagocytosis and pro-inflammatory functions and anti-cancer cell activity for both liquid and solid tumor cells.
Differential small RNA responses against co-infecting insect-specific viruses inAedes albopictusmosquitoes
Authors: Frangeul Lionel , Blanc Hervé , Saleh Maria-Carla , Suzuki Yasutsugu 
Published: March 2020

AbstractThe mosquito antiviral response has been mainly studied in the case of arthropod-borne virus (arbovirus) infection in female mosquitoes. However, in nature, both female and male mosquitoes are abundantly infected with insect-specific viruses (ISVs). ISVs are capable of infecting the reproductive organs of both sexes and are maintained primarily by vertical transmission. Since the RNA interference (RNAi)-mediated antiviral response plays an important antiviral role in mosquitoes, ISVs constitute a relevant model to study sex-dependent antiviral responses. Using a naturally generated viral stock containing three distinct ISVs,Aedesflavivirus (AEFV), Menghai Rhabdovirus (MERV) and Shinobi tetra virus (SHTV), we infected adultAedes albopictusfemales and males and generated small RNA libraries from ovaries, testes, and the remainder of the body. Overall, both female and male mosquitoes showed unique small RNA profiles to each co-infecting ISV regardless the sex or tissue tested. While all three ISVs generated virus-derived siRNAs, only MERV generated virus-derived piRNAs. We also studied the expression of PIWI genes in reproductive tissues and carcasses. Piwi1-4 were abundantly expressed in ovaries and testes in contrast to Piwi5-9, suggesting that Piwi 5-9 are involved in exogenous viral piRNA production. Together, our results show that ISV-infectedAedes albopictusproduce viral small RNAs in a virus-specific manner and that male mosquitoes mount a similar small RNA-mediated antiviral response to that of females.
Individualized System for Augmenting Ventilator Efficacy (iSAVE): A Rapidly deployable system to expand ventilator capacity
Authors: Srinivasan Shriya , Ramadi Khalil B , Vicario Francesco , Gwynne Declan , Hayward Alison , Langer Robert , Frassica Joseph J. , Baron Rebecca M. , Traverso Giovanni 
Published: March 2020

AbstractThe COVID-19 pandemic is overwhelming healthcare systems worldwide. A significant portion of COVID-19 patients develop pneumonia and acute respiratory distress syndrome (ARDS), necessitating ventilator support. Some health systems do not have the capacity to accommodate this surge in ventilator demand, leading to shortages and inevitable mortality. Some clinicians have, of necessity, jerry-rigged ventilators to support multiple patients, but these devices lack protected air streams or individualized controls for each patient. Moreover, some have not been tested under conditions of ARDS. We have developed the Individualized System for Augmenting Ventilator Efficacy (iSAVE), a rapidly deployable platform to more safely use a single ventilator to simultaneously support multiple critically-ill patients. The iSAVE enables patient-specific volume and pressure control and incorporates safety features to mitigate cross-contamination between patients and flow changes due to patient interdependencies within the respiratory circuit. Here we demonstrate through simulated andin vivopig evaluation the capacity of the iSAVE to support a range of respiratory clinical states. By leveraging off-the-shelf components that are readily available to intensive care unit (ICU) caregivers, the iSAVE could potentially be translated for human application to expand the ventilation capacity of hospitals using existing ventilators, minimizing the need to procure additional ventilators.
Dynamic effects of genetic variation on gene expression revealed following hypoxic stress in cardiomyocytes
Authors: Ward Michelle C. , Banovich Nicholas E. , Sarkar Abhishek , Stephens Matthew , Gilad Yoav 
Published: March 2020

AbstractOne life-threatening outcome of cardiovascular disease is myocardial infarction, where cardiomyocytes are deprived of oxygen. To study inter-individual differences in response to hypoxia, we established anin vitromodel of induced pluripotent stem cell-derived cardiomyocytes from 15 individuals. We measured gene expression levels, chromatin accessibility, and methylation levels in four culturing conditions that correspond to normoxia, hypoxia and short or long-term re-oxygenation. We characterized thousands of gene regulatory changes as the cells transition between conditions. Using available genotypes, we identified 1,573 genes with acisexpression quantitative locus (eQTL) in at least one condition, as well as 367 dynamic eQTLs, which are classified as eQTLs in at least one, but not in all conditions. A subset of genes with dynamic eQTLs is associated with complex traits and disease. Our data demonstrate how dynamic genetic effects on gene expression, which are likely relevant for disease, can be uncovered under stress.
Cryo-EM structures of SERCA2b reveal the mechanism of regulation by the luminal extension tail
Authors: Zhang Yuxia , Inoue Michio , Tsutsumi Akihisa , Watanabe Satoshi , Nishizawa Tomohiro , Nagata Kazuhiro , Kikkawa Masahide , Inaba Kenji 
Published: March 2020

AbstractSERCA2b is a Ca2+-ATPase that pumps Ca2+from the cytosol into the ER and maintains the cellular calcium homeostasis. Herein, we present cryo-EM structures of human SERCA2b in E1·2Ca2+-AMPPCP and E2-BeF3-states at 2.9 and 2.8 Å resolutions, respectively. The structures revealed that the luminal extension tail (LE) characteristic of SERCA2b runs parallel to the lipid-water boundary near the luminal ends of transmembrane (TM) helices TM10 and TM7, and approaches the luminal loop flanked by TM7 and TM8. Upon deletion of the LE, the cytosolic- and TM-domain arrangement of SERCA2b resembled that of SERCA1a, resulting in multiple conformations. The LE regulates the conformational transition between the E1·2Ca2+-ATP and E2P states, explaining the different kinetic properties of SERCA2b from other isoforms lacking the LE.One sentence summaryCryo-EM structures of SERCA2b at 2.8-2.9 Å resolutions reveal how the luminal extension tail regulates its activity.