bluuebunny/crossref_metadata_2025_split huggingface dataset:
Allelic diversity study of functional genes in East Africa bread wheat highlights opportunities for genetic improvement
Authors: Wamalwa Mercy , Tadesse Zerihun , Muthui Lucy , Yao Nasser , Zegeye Habtemariam , Randhawa Mandeep , Wanyera Ruth , Uauy Cristobal , Shorinola Oluwaseyi 
Published: May 2020

AbstractWheat (Triticum aestivumL.) is a major staple crop in East Africa (EA) providing 9% and 10% of daily calories and protein intake, respectively. However, EA countries depend on import to meet 55% of their domestic wheat supplies due to increasing demands and low domestic yields. To determine the beneficial gene pool currently exploited for wheat improvement in EA, we examined the allelic diversity of 42 genes of breeding importance in a collection of 239 wheat cultivars and breeding lines from Kenya and Ethiopia using KASP markers. The assayed genes have been shown to control variations in plant height, thousand kernel weight (TKW), grain protein content, pre-harvest sprouting (PHS), disease resistance and flowering time. We observed the beneficial alleles of some major genes includingRht-D1, Gpc-B1, Yr5, Yr15, Sr26, andFhb1to be missing or present at low frequencies in this population. Furthermore, we validated the effects of the majorRht-1alleles andTaCKX-6Ain controlling variation in plant height and thousand kernel weight, respectively, under EA conditions. Our results uncover hitherto unexploited allelic diversity that can be used to improve the genetic potential of EA wheat germplasm. This will inform strategies to rapidly mobilize these beneficial alleles for wheat improvement in EA.
TripletProt: Deep Representation Learning of Proteins based on Siamese Networks
Authors: Nourani Esmaeil , Asgari Ehsaneddin , McHardy Alice C. , Mofrad Mohammad R.K. 
Published: May 2020

AbstractWe introduce TripletProt, a new approach for protein representation learning based on the Siamese neural networks. We evaluate TripletProt comprehensively in protein functional annotation tasks including sub-cellular localization (14 categories) and gene ontology prediction (more than 2000 classes), which are both challenging multi-class multi-label classification machine learning problems. We compare the performance of TripletProt with the state-of-the-art approaches including recurrent language model-based approach (i.e., UniRep), as well as protein-protein interaction (PPI) network and sequence-based method (i.e., DeepGO). Our TripletProt showed an overall improvement of F1 score in the above mentioned comprehensive functional annotation tasks, solely relying on the PPI network. TripletProt and in general Siamese Network offer great potentials for the protein informatics tasks and can be widely applied to similar tasks.
A Homology Independent Sequence Replacement Strategy in Human Cells Using a CRISPR Nuclease
Authors: Danner Eric , Lebedin Mikhail , de la Rosa Kathrin , Kühn Ralf 
Published: May 2020

AbstractPrecision genomic alterations largely rely on Homology Directed Repair (HDR), but targeting without homology using the Non-Homologous End Joining (NHEJ) pathway has gained attention as a promising alternative. Previous studies demonstrated precise insertions formed by the ligation of donor DNA into a targeted genomic double strand break in both dividing and non-dividing cells. Here we extend this idea and use NHEJ repair to replace genomic segments with donor sequences; we name this method ‘Replace’ editing (Rationalend-joiningprotocol deliveringatargeted sequenceexchange). Using CRISPR/Cas9 we create two genomic breaks and ligate a donor sequence in-between. This exchange of a genomic for a donor sequence uses neither microhomology nor homology arms. We target four loci and show successful exchange of exons in 16% to 54% of cells. Using linear amplification methods and deep sequencing pipelines we quantify the diversity of outcomes following Replace editing and profile mutations formed at the ligated interfaces. The ability to replace exons or other genomic sequences in cells not efficiently modified by HDR holds promise for both basic research and medicine.
Reimplementing Unirep in JAX
Authors: Ma Eric J. , Kummer Arkadij 
Published: May 2020

AbstractUniRep is a recurrent neural network model trained on 24 million protein sequences, and has shown utility in protein engineering. The original model, however, has rough spots in its implementation, and a convenient API is not available for certain tasks. To rectify this, we reimplemented the model in JAX/NumPy, achieving near-100X speedups in forward pass performance, and implemented a convenient API for specialized tasks. In this article, we wish to document our model reimplementation process with the goal of educating others interested in learning how to dissect a deep learning model, and engineer it for robustness and ease of use.
3D ultrastructural study of synapses in the human entorhinal cortex
Authors: Domínguez-Álvaro M , Montero-Crespo M , Blazquez-Llorca L , DeFelipe J , Alonso-Nanclares L 
Published: May 2020

AbstractThe entorhinal cortex (EC) is a brain region that has been shown to be essential for memory functions and spatial navigation. However, detailed 3D synaptic morphology analysis and identification of postsynaptic targets at the ultrastructural level have not been performed before in the human EC. In the present study, we used Focused Ion Beam/Scanning Electron Microscopy (FIB/SEM) to perform a three-dimensional analysis of the synapses in the neuropil of medial EC in layers II and III from human brain autopsies. Specifically, we studied synaptic structural parameters of3561synapses, which were fully reconstructed in 3D. We analyzed the synaptic density, 3D spatial distribution, and type (excitatory and inhibitory), as well as the shape and size of each synaptic junction. Moreover, the postsynaptic targets of synapses could be clearly determined. The present work constitutes a detailed description of the synaptic organization of the human EC, which is a necessary step to better understand the functional organization of this region in both health and disease.Significance StatementThe present study represents the first attempt to unveil the detailed synaptic organization of the neuropil of the human entorhinal cortex — a brain region that is essential for memory function and spatial navigation. Using 3D electron microscopy, we have characterized the synaptic morphology and identified the postsynaptic targets of thousands of synapses. The results provide a new, large, quantitative ultrastructure dataset of the synaptic organization of the human entorhinal cortex. These data provide critical information to better understand synaptic functionality in the human brain.HighlightEstimation of the number of synapses, as well as determination of their type, shapes, sizes and postsynaptic targets, provides critical data to better understand synaptic functionality. This study provides a new, large, quantitative ultrastructure dataset of the synaptic organization of the human entorhinal cortex using 3D electron microscopy.
G protein-coupled receptor signaling regulates ER-mitochondria contacts
Authors: Lim Youngshin , Cho Il-Taeg , Rennke Helmut G. , Cho Ginam 
Published: May 2020

AbstractInteractions between the endoplasmic reticulum (ER) and mitochondria (Mito) are crucial for many cellular functions, and their interaction levels change dynamically depending on the cellular environment. Little is known about how the interactions between these organelles are regulated within the cell. Here we screened a compound library to identify chemical modulators for ER-Mito contacts. Multiple agonists of G-protein coupled receptors (GPCRs), beta-adrenergic receptors (β-ARs) in particular, scored in this screen. Analyses in multiple orthogonal assays validated that GPCR activation promotes physical and functional interactions between the two organelles. Furthermore, we have elucidated potential downstream effectors mediating GPCR-induced ER-Mito contacts. Given the role of GPCRs in sensing various extracellular signals and subsequently eliciting appropriate cellular responses, our data provide significant insights into the roles of ER-Mito contacts in maintaining cellular homeostasis and in responding to physiological demands or stresses.
Thermostable mutants of glycoside hydrolase family 6 cellobiohydrolase from the basidiomycetePhanerochaete chrysosporium
Authors: Yamaguchi Sora , Sunagawa Naoki , Tachioka Mikako , Igarashi Kiyohiko , Samejima Masahiro 
Published: May 2020

AbstractThermal inactivation of saccharifying enzymes is a crucial issue for the efficient utilization of cellulosic biomass as a renewable resource. Cellobiohydrolases (CBHs) is a kind of cellulase. In general, CBHs belonging to glycoside hydrolase (GH) family 6 (Cel6) act synergistically with CBHs of GH family 7 (Cel7) and other carbohydrate-active enzymes during the degradation of cellulosic biomass. However, while the catalytic rate of enzymes generally becomes faster at higher temperatures, Cel6 CBHs are inactivated at lower temperatures than Cel7 CBHs, and this represents a limiting factor for industrial utilization. In this study, we produced a series of mutants of the glycoside hydrolase family 6 cellobiohydrolasePcCel6A from the fungusPhanerochaete chrysosporium, and compared their thermal stability. Eight mutants from a random mutagenesis library and one rationally designed mutant were selected as candidate thermostable mutants and produced by heterologous expression in the yeastPichia pastoris. Comparison of the hydrolytic activities at 50 and 60°C indicated that the thermal stability ofPcCel6A is influenced by the number and position of cysteine residues that are not involved in disulfide bonds.
The SARS-CoV-2 conserved macrodomain is a mono-ADP-ribosylhydrolase
Authors: Alhammad Yousef M.O. , Kashipathy Maithri M. , Roy Anuradha , Gagné Jean-Philippe , McDonald Peter , Gao Philip , Nonfoux Louis , Battaile Kevin P. , Johnson David K. , Holmstrom Erik D. , Poirier Guy G. , Lovell Scott , Fehr Anthony R. 
Published: May 2020

ABSTRACTSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other SARS-like-CoVs encode 3 tandem macrodomains within non-structural protein 3 (nsp3). The first macrodomain, Mac1, is conserved throughout CoVs, and binds to and hydrolyzes mono-ADP-ribose (MAR) from target proteins. Mac1 likely counters host-mediated anti-viral ADP-ribosylation, a posttranslational modification that is part of the host response to viral infections. Mac1 is essential for pathogenesis in multiple animal models of CoV infection, implicating it as a virulence factor and potential therapeutic target. Here we report the crystal structure of SARS-CoV-2 Mac1 in complex with ADP-ribose. SARS-CoV-2, SARS-CoV and MERS-CoV Mac1 exhibit similar structural folds and all 3 proteins bound to ADP-ribose with low μM affinities. Importantly, using ADP-ribose detecting binding reagents in both a gel-based assay and novel ELISA assays, we demonstrated de-MARylating activity for all 3 CoV Mac1 proteins, with the SARS-CoV-2 Mac1 protein leading to a more rapid loss of substrate compared to the others. In addition, none of these enzymes could hydrolyze poly-ADP-ribose. We conclude that the SARS-CoV-2 and other CoV Mac1 proteins are MAR-hydrolases with similar functions, indicating that compounds targeting CoV Mac1 proteins may have broad anti-CoV activity.IMPORTANCESARS-CoV-2 has recently emerged into the human population and has led to a worldwide pandemic of COVID-19 that has caused greater than 900 thousand deaths worldwide. With, no currently approved treatments, novel therapeutic strategies are desperately needed. All coronaviruses encode for a highly conserved macrodomain (Mac1) that binds to and removes ADP-ribose adducts from proteins in a dynamic post-translational process increasingly recognized as an important factor that regulates viral infection. The macrodomain is essential for CoV pathogenesis and may be a novel therapeutic target. Thus, understanding its biochemistry and enzyme activity are critical first steps for these efforts. Here we report the crystal structure of SARS-CoV-2 Mac1 in complex with ADP-ribose, and describe its ADP-ribose binding and hydrolysis activities in direct comparison to SARS-CoV and MERS-CoV Mac1 proteins. These results are an important first step for the design and testing of potential therapies targeting this unique protein domain.
An integratedin silicoimmuno-genetic analytical platform provides insights into COVID-19 serological and vaccine targets
Authors: Ward Daniel , Higgins Matthew , Phelan Jody E. , Hibberd Martin L. , Campino Susana , Clark Taane G 
Published: May 2020

ABSTRACTBackgroundThe COVID-19 pandemic, caused by the SARS-CoV-2 virus, has a major global health and socio-economic burden. It has instigated the mobilisation of resources into the development of control tools, such as diagnostics and vaccines. The poor performance of some diagnostic serological tools has emphasised the need for up to date immune-informatic analyses to inform the selection of viable targets for further study. This requires the integration and analysis of genetic and immunological data for SARS-CoV-2 and its homology with other human coronavirus species to understand cross-reactivity.MethodsWe have developed an online “immuno-analytics” resource to facilitate SARS-CoV-2 research, combining an extensive B/T-cell epitope mapping and prediction meta-analysis, and human CoV sequence homology mapping and protein database annotation, with an updated variant database and geospatial tracking for >7,800 non-synonymous mutation positions derived from >150,000 whole genome sequences. To demonstrate its utility, we present an integrated analysis of SARS-CoV-2 spike and nucleocapsid proteins, both being vaccine and serological diagnostic targets, including an analysis of changes in relevant mutation frequencies over time.ResultsOur analysis reveals that the nucleocapsid protein in its native form appears to be a sub-optimal target for use in serological diagnostic platforms. The most frequent mutations were the spike protein D614G and nsp12 L314P, which were common (>86%) across all the geographical regions. Some mutations in the spike protein (e.g. A222V and L18F) have increased in frequency in Europe during the latter half of 2020, detected using our automated algorithms. The tool also suggests that orf3a proteins may be a suitable alternative target for diagnostic serologic assays in a post-vaccine surveillance setting.ConclusionsThe immuno-analytics tool can be accessed online (http://genomics.lshtm.ac.uk/immuno) and will serve as a useful resource for biological discovery and surveillance in the fight against SARS-CoV-2. Further, the tool may be adapted to inform on biological targets in future outbreaks, including potential emerging human coronaviruses that spill over from animal hosts.
Performance of Abbott ID NOW COVID-19 rapid nucleic acid amplification test in nasopharyngeal swabs transported in viral media and dry nasal swabs, in a New York City academic institution
Authors: Basu Atreyee , Zinger Tatyana , Inglima Kenneth , Woo Kar-mun , Atie Onome , Yurasits Lauren , See Benjamin , Aguero-Rosenfeld Maria E. 
Published: May 2020

AbstractThe recent emergence of the SARS-CoV-2 pandemic has posed formidable challenges for clinical laboratories seeking reliable laboratory diagnostic confirmation. The swift advance of the crisis in the United States has led to Emergency Use Authorization (EUA) facilitating the availability of molecular diagnostic assays without the more rigorous examination to which tests are normally subjected prior to FDA approval. Our laboratory currently uses two real time RT-PCR platforms, the Roche Cobas SARS-CoV2 and the Cepheid Xpert Xpress SARS-CoV-2. Both platforms demonstrate comparable performance; however, the run times for each assay are 3.5 hours and 45 minutes, respectively. In search for a platform with shorter turnaround time, we sought to evaluate the recently released Abbott ID NOW COVID-19 assay which is capable of producing positive results in as little as 5 minutes. We present here the results of comparisons between Abbott ID NOW COVID-19 and Cepheid Xpert Xpress SARS-CoV-2 using nasopharyngeal swabs transported in viral transport media and comparisons between Abbott ID NOW COVID-19 and Cepheid Xpert Xpress SARS-CoV-2 using nasopharyngeal swabs transported in viral transport media for Cepheid and dry nasal swabs for Abbott ID NOW. Regardless of method of collection and sample type, Abbott ID NOW COVID-19 had negative results in a third of the samples that tested positive by Cepheid Xpert Xpress when using nasopharyngeal swabs in viral transport media and 45% when using dry nasal swabs.
Connecting structure to function with the recovery of over 1000 high-quality activated sludge metagenome-assembled genomes encoding full-length rRNA genes using long-read sequencing
Authors: Singleton Caitlin M , Petriglieri Francesca , Kristensen Jannie M , Kirkegaard Rasmus H , Michaelsen Thomas Y , Andersen Martin H , Kondrotaite Zivile , Karst Søren M , Dueholm Morten S , Nielsen Per H , Albertsen Mads 
Published: May 2020

AbstractMicroorganisms are critical to water recycling, pollution removal and resource recovery processes in the wastewater industry. While the structure of this complex community is increasingly understood based on 16S rRNA gene studies, this structure cannot currently be linked to functional potential due to the absence of high-quality metagenome-assembled genomes (MAGs) with full-length rRNA genes for nearly all species. Here, we sequence 23 Danish full-scale wastewater treatment plant metagenomes, producing >1 Tbp of long-read and >0.9 Tbp of short-read data. We recovered 1083 high-quality MAGs, including 57 closed circular genomes. The MAGs accounted for ~30% of the community, and meet the stringent MIMAG high-quality draft requirements including full-length rRNA genes. We show how novel high-quality MAGs in combination with >13 years of amplicon data, Raman microspectroscopy and fluorescence in situ hybridisation can be used to uncover abundant undescribed lineages belonging to important functional groups.
Knowledge syntheses in medical education: A bibliometric analysis
Authors: Maggio Lauren A. , Costello Joseph A. , Norton Candace , Driessen Erik W. , Artino Anthony R. 
Published: May 2020

AbstractPurposeThis bibliometric analysis maps the landscape of knowledge syntheses in medical education. It provides scholars with a roadmap for understanding where the field has been and where it might go in the future. In particular, this analysis details the venues in which knowledge syntheses are published, the types of syntheses conducted, citation rates they produce, and altmetric attention they garner.MethodIn 2020, the authors conducted a bibliometric analysis of knowledge syntheses published in 14 core medical education journals from 1999 to 2019. To characterize the studies, metadata was extracted from Pubmed, Web of Science, Altmetrics Explorer, and Unpaywall.ResultsThe authors analyzed 963 knowledge syntheses representing 3.1% of total articles published (n=30,597). On average, 45.9 knowledge syntheses were published annually (SD=35.85, Median=33), and there was an overall 2,620% increase in the number of knowledge syntheses published from 1999 to 2019. The journals each published, on average, a total of 68.8 knowledge syntheses (SD=67.2, Median=41) withMedical Educationpublishing the most (n=189; 19%). Twenty-one knowledge synthesis types were identified; the most prevalent types were systematic reviews (n=341; 35.4%) and scoping reviews (n=88; 9.1%). Knowledge syntheses were cited an average of 53.80 times (SD=107.12, Median=19) and received a mean Altmetric Attention Score of 14.12 (SD=37.59, Median=6).ConclusionsThere has been considerable growth in knowledge syntheses in medical education over the past 20 years, contributing to medical education’s evidence base. Beyond this increase in volume, researchers have introduced methodological diversity in these publications, and the community has taken to social media to share knowledge syntheses. Implications for the field, including the impact of synthesis types and their relationship to knowledge translation, are discussed.
A miR-494 dependent feedback loop regulates ER stress
Authors: Chatterjee Namita , Espinosa-Diez Cristina , Anand Sudarshan 
Published: May 2020

AbstractDefects in stress responses are important contributors in many chronic conditions including cancer, cardiovascular disease, diabetes, and obesity-driven pathologies like non-alcoholic steatohepatitis (NASH). Specifically, endoplasmic reticulum (ER) stress is linked with these pathologies and control of ER stress can ameliorate tissue damage. MicroRNAs have a critical role in regulating diverse stress responses including ER stress. Here we show that miR-494 plays a functional role during ER stress. ER stress inducers (tunicamycin & thapsigargin) robustly increase the expression of miR-494in vitroin an ATF6 dependent manner. Surprisingly, miR-494 pretreatment dampens the induction and magnitude of ER stress in response to tunicamycin in endothelial cells. Conversely, inhibition of miR-494 increases ER stressde novoand amplifies the effects of ER stress inducers. Using Mass Spectrometry (TMT-MS) we identified 23 proteins that are downregulated by both tunicamycin and miR-494. Among these, we found 6 transcripts which harbor a putative miR-494 binding site. We validated the anti-apoptotic geneBIRC5(survivin) as one of the targets of miR-494 during ER stress. Finally, induction of ER stressin vivoincreases miR-494 expression in the liver. Pretreatment of mice with a miR-494 plasmid via hydrodynamic injection decreased ER stress in response to tunicamycin in part by decreasing inflammatory chemokines and cytokines. In summary, our data indicates that ER stress driven miR-494 may act in a feedback inhibitory loop to dampen downstream ER stress signaling. We propose that RNA-based approaches targeting miR-494 or its targets may be attractive candidates for inhibiting ER stress dependent pathologies in human disease.
Structures of the stator complex that drives rotation of the bacterial flagellum
Authors: Deme Justin C. , Johnson Steven , Vickery Owen , Muellbauer Amy , Monkhouse Holly , Griffiths Thomas , James Rory Hennell , Berks Ben C. , Coulton James W. , Stansfeld Phillip J. , Lea Susan M. 
Published: May 2020

SummaryThe bacterial flagellum is the proto-typical protein nanomachine and comprises a rotating helical propeller attached to a membrane-embedded motor complex1. The motor consists of a central rotor surround by stator units that couple ion flow across the cytoplasmic membrane to torque generation. Here we present the structures of stator complexes from multiple bacterial species, allowing interpretation of the extensive body of data on stator mechanism. The structures reveal an unexpected asymmetric A5B2subunit assembly in which the five A subunits enclose the two B subunits. Comparison to novel structures of other ion-driven motors indicates that this A5B2architecture is fundamental to bacterial systems that couple energy from ion-flow to generate mechanical work at a distance, and suggests that such events involve rotation in the motor structures.