bluuebunny/crossref_metadata_2025_split huggingface dataset:
Precision neoantigen discovery using large-scale immunopeptidomes and composite modeling of MHC peptide presentation
Authors: Pyke Rachel Marty , Mellacheruvu Datta , Dea Steven , Abbott Charles , Zhang Simo V. , Phillips Nick A. , Harris Jason , Bartha Gabor , Desai Sejal , McClory Rena , West John , Snyder Michael P. , Chen Richard , Boyle Sean Michael 
Published: May 2021

AbstractMajor histocompatibility complex (MHC)-bound peptides that originate from tumor-specific genetic alterations, known as neoantigens, are an important class of anti-cancer therapeutic targets. Accurately predicting peptide presentation by MHC complexes is a key aspect of discovering therapeutically relevant neoantigens. Technological improvements in mass-spectrometry-based immunopeptidomics and advanced modeling techniques have vastly improved MHC presentation prediction over the past two decades. However, improvement in the sensitivity and specificity of prediction algorithms is needed for clinical applications such as the development of personalized cancer vaccines, the discovery of biomarkers for response to checkpoint blockade and the quantification of autoimmune risk in gene therapies. Toward this end, we generated allele-specific immunopeptidomics data using 25 mono-allelic cell lines and createdSystematic HLA Epitope Ranking Pan Algorithm(SHERPA™), a pan-allelic MHC-peptide algorithm for predicting MHC-peptide binding and presentation. In contrast to previously published large-scale mono-allelic data, we used an HLA-null K562 parental cell line and a stable transfection of HLA alleles to better emulate native presentation. Our dataset includes five previously unprofiled alleles that expand MHC binding pocket diversity in the training data and extend allelic coverage in underprofiled populations. To improve generalizability, SHERPA systematically integrates 128 mono-allelic and 384 multi-allelic samples with publicly available immunoproteomics data and binding assay data. Using this dataset, we developed two features that empirically estimate the propensities of genes and specific regions within gene bodies to engender immunopeptides to represent antigen processing. Using a composite model constructed with gradient boosting decision trees, multiallelic deconvolution and 2.15 million peptides encompassing 167 alleles, we achieved a 1.44 fold improvement of positive predictive value compared to existing tools when evaluated on independent mono-allelic datasets and a 1.15 fold improvement when evaluating on tumor samples. With a high degree of accuracy, SHERPA has the potential to enable precision neoantigen discovery for future clinical applications.
Simplifying the development of portable, scalable, and reproducible workflows
Authors: Piccolo Stephen R. , Ence Zachary E. , Anderson Elizabeth C. , Chang Jeffrey T. , Bild Andrea H. 
Published: May 2021

AbstractCommand-line software plays a critical role in biology research. However, processes for installing and executing software differ widely. The Common Workflow Language (CWL) is a community standard that addresses this problem. Using CWL, tool developers can formally describe a tool’s inputs, outputs, and other execution details in a manner that fosters use of shared computational methods and reproducibility of complex analyses. CWL documents can include instructions for executing tools inside software containers—isolated, operating-system environments. Accordingly, CWL tools are portable—they can be executed on diverse computers—including personal workstations, high-performance clusters, or the cloud. This portability enables easier adoption of bioinformatics pipelines. CWL supports workflows, which describe dependencies among tools and using outputs from one tool as inputs to others. To date, CWL has been used primarily for batch processing of large datasets, especially in genomics. But it can also be used for analytical steps of a study. This article explains key concepts about CWL and software containers and provides examples for using CWL in biology research. CWL documents are text-based, so they can be created manually, without computer programming. However, ensuring that these documents confirm to the CWL specification may prevent some users from adopting it. To address this gap, we created ToolJig, a Web application that enables researchers to create CWL documents interactively. ToolJig validates information provided by the user to ensure it is complete and valid. After creating a CWL tool or workflow, the user can create “input-object” files, which store values for a particular invocation of a tool or workflow. In addition, ToolJig provides examples of how to execute the tool or workflow via a workflow engine.
CRISPR-Cas-mediated tethering recruits the yeastHMRmating-type locus to the nuclear periphery but fails to silence gene expression
Authors: Cliff Emily R. , Kirkpatrick Robin L. , Cunningham-Bryant Daniel , Fernandez Brianna , Zalatan Jesse G. 
Published: May 2021

AbstractTo investigate the relationship between genome structure and function, we have developed a programmable CRISPR-Cas system for nuclear peripheral recruitment in yeast. We benchmarked this system at theHMRandGAL2loci, both well-characterized model systems for localization to the nuclear periphery. Using microscopy and gene silencing assays, we demonstrate that CRISPR-Cas-mediated tethering can recruit theHMRlocus but does not silence reporter gene expression. A previously reported Gal4-mediated tethering system does silence gene expression, and we demonstrate that the silencing phenotype has an unexpected dependence on the structure of the protein tether. The CRISPR-Cas system was unable to recruitGAL2to the nuclear periphery. Our results reveal potential challenges for synthetic genome structure perturbations and suggest that distinct functional effects can arise from subtle structural differences in how genes are recruited to the periphery.
TransposonUltimate: software for transposon classification, annotation and detection
Authors: Riehl Kevin , Riccio Cristian , Miska Eric A. , Hemberg Martin 
Published: May 2021

AbstractMotivationMost genomes harbor a large number of transposons, and they play an important role in evolution and gene regulation. They are also of interest to clinicians as they are involved in several diseases, including cancer and neurodegeneration. Although several methods for transposon identification are available, they are often highly specialised towards specific tasks or classes of transposons, and they lack common standards such as a unified taxonomy scheme and output file format. Moreover, many methods are difficult to install, poorly documented, and difficult to reproduce.ResultsWe present TransposonUltimate, a powerful bundle of three modules for transposon classification, annotation, and detection of transposition events. TransposonUltimate comes as a Conda package under the GPL-3.0 licence, is well documented and it is easy to install. We benchmark the classification module on the largeTransposonDBcovering over 891,051 sequences to demonstrate that it outperforms the currently best existing solutions. The annotation and detection modules combine sixteen existing softwares, and we illustrate its use by annotatingCaenorhabditis elegans,Rhizophagus irregularisandOryza sativa subs. japonicagenomes. Finally, we use the detection module to discover 29,554 transposition events in the genomes of twenty wild type strains ofCaenorhabditis elegans.AvailabilityRunning software and source code available onhttps://github.com/DerKevinRiehl/TransposonClassifierRFSB. Databases, assemblies, annotations and further findings can be downloaded fromhttps://cellgeni.cog.sanger.ac.uk/browser.html?shared=transposonultimate.
A novel framework for single-cell Hi-C clustering based on graph-convolution-based imputation and two-phase-based feature extraction
Authors: Zhen Caiwei , Wang Yuxian , Han Lu , Li Jingyi , Peng Jinghao , Wang Tao , Hao Jianye , Shang Xuequn , Wei Zhongyu , Peng Jiajie 
Published: May 2021

ABSTRACTThe three-dimensional genome structure plays a key role in cellular function and gene regulation. Singlecell Hi-C technology can capture genome structure information at the cell level, which provides the opportunity to study how genome structure varies among different cell types. However, few methods are well designed for single-cell Hi-C clustering, because of high sparsity, noise and heterogeneity of single-cell Hi-C data. In this manuscript, we propose a novel framework, named ScHiC-Rep, for singlecell Hi-C data representation and clustering. ScHiC-Rep mainly contains two parts: data imputation and feature extraction. In the imputation part, a novel imputation workflow is proposed, including graph convolution-based, random walk with restart-based and genomic neighbor-based imputation. In the feature extraction part, a two-phase feature extraction method is proposed, including linear phase for chromosome level and non-linear phase for cell level feature extraction. The evaluation results show that the proposed framework outperforms existing state-of-the-art approaches on both human and mouse datasets.
Breaking the Scale: Allometric scaling analysis in Carnivoran families
Authors: Navaratnam Stefanie , Phillips Julie Baker 
Published: May 2021

ABSTRACTThe analysis of scaling relationships, allometric scaling, has a long history of importance for modelling and predicting biological phenomena. Individual organisms are not truly independent, and as a result phylogenetic corrections are necessary to increase the accuracy of scaling relationships. The relationships between body mass and gestation length have not been previously reported at the Family level, as it was previously thought species had insufficient time to diverge evolutionarily leaving phylogenetic corrections unnecessary. Using a Carnivora supertree, we perform a phylogenetically generalised least squares (PGLS) analysis using life history information largely from the Pantheria dataset. Our results suggest that allometric relationships are maintained in four families: Canidae, Felidae, Herpestidae and Otariidae. Conversely, several evolutionary mechanisms may contribute to the lack of a significant scaling parameter in other families, such as diverse reproductive strategies or positive selection for genes affecting adiposity. In addition, low sample sizes or the inclusion of paternal body masses could alter the presence of significant scaling. Our results suggests that PGLS analyses are informative at the family level, and the absence of scaling can provide insight to understanding of the evolutionary mechanisms that work on the family taxonomic level or below.CCS CONCEPTS• Applied computing → Molecular evolution; • Computing methodologies → Modeling methodologies.ACM Reference FormatStefanie Navaratnam and Julie Baker Phillips. 2021. Breaking the Scale: Allometric scaling analysis in Carnivoran families. InBCB: ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, August 01–04, 2021, Virtual due to COVID-19.ACM, New York, NY, USA, 7 pages.https://doi.org/10.1145/1122445.1122456
Molecular and cell biological analysis of SwrB inBacillus subtilis
Authors: Phillips Andrew M. , Sanchez Sandra , Sysoeva Tatyana A. , Burton Briana M. , Kearns Daniel B. 
Published: May 2021

ABSTRACTSwarming motility is flagellar-mediated movement over a solid surface and Bacillus subtilis cells require an increase in flagellar density to swarm. SwrB is a protein of unknown function required for swarming that is necessary to increase the number of flagellar hooks but not basal bodies. Previous work suggested that SwrB activates flagellar type III secretion but the mechanism by which it might perform this function is unknown. Here we show that SwrB likely acts sub-stoichiometrically as it localizes as puncta at the membrane in numbers fewer than that of flagellar basal bodies. Moreover the action of SwrB is likely transient as puncta of SwrB were not dependent on the presence of the basal bodies and rarely co-localized with flagellar hooks. Random mutagenesis of the SwrB sequence found that a histidine within the transmembrane segment was conditionally required for activity and punctate localization. Finally, three hydrophobic residues that precede a cytoplasmic domain of poor conservation abolished SwrB activity when mutated and caused aberrant migration during electrophoresis. Our data are consistent with a model in which SwrB interacts with the flagellum, changes conformation to activate type III secretion, and departs.IMPORTANCEType III secretion systems (T3SS) are elaborate nanomachines that form the core of the bacterial flagellum and injectisome of pathogens. The machines not only secrete proteins like virulence factors but also secrete the structural components for their own assembly. Moroever, proper construction requires complex regulation to ensure that the parts are roughly secreted in the order in which they are assembled. Here we explore a poorly understood activator the flagellar T3SS activation inBacillus subtiliscalled SwrB. To aid mechanistic understanding, we determine the rules for subcellular punctate localization, the topology with respect to the membrane, and critical residues required for SwrB function.
Identification of residues in Lassa virus glycoprotein 1 involved in receptor switch
Authors: Guo Jiao , Jia Xiaoying , Liu Yang , Cao Junyuan , Xiao Gengfu , Wang Wei 
Published: May 2021

ABSTRACTLassa virus (LASV) is an enveloped, negative-sense RNA virus that causes Lassa hemorrhagic fever, for which there are limited treatment options. Successful LASV entry requires the viral glycoprotein 1 (GP1) to undergo a receptor switch from its primary receptor alpha-dystroglycan (α-DG) to its endosomal receptor lysosome-associated membrane protein 1 (LAMP1). A conserved histidine triad in LASV GP1 has been reported to be responsible for receptor switch. To test the hypothesis that other non-conserved residues also contribute to receptor switch, we constructed a series of GP1 mutant proteins and tested them for binding to LAMP1. Four residues, L84, K88, L107, and H170, were identified as critical for receptor switch. Substituting any of the four residues with the corresponding lymphocytic choriomeningitis virus residue (L84N, K88E, L10F, and H170S) reduced the binding affinity of GP1LASVfor LAMP1. Moreover, all the mutations caused decreases in GPC-mediated membrane fusion at both pH 4.5 and 5.2. The infectivity of pseudotyped viruses bearing either GPCL84Nor GPCK88Edecreased sharply in multiple cell types, whereas L107F and H170S had only mild effects on infectivity. Notably, in LAMP1 knockout cells, all four mutants showed reduced pseudovirus infectivity. Using biolayer light interferometry assay, we found that all four mutants had decreased binding affinity to LAMP1, in the order L84N > L107F > K88E > H170S.IMPORTANCELassa virus requires pH-dependent receptor switch to infect host cells; however, the underlying molecular mechanisms of this process are not well known. Here, we identify four residues, L84, K88, L107, and H170 that contribute to the interaction with the second receptor lysosome-associated membrane protein 1 (LAMP1). Mutant any of the four residues would impair the binding affinity to LAMP1, decrease the glycoprotein mediated membrane fusion, and reduce the pseudovirus infectivity.
The host factor ANP32A is required for influenza A virus vRNA and cRNA synthesis
Authors: Nilsson-Payant Benjamin E. , tenOever Benjamin R. , te Velthuis Aartjan J.W. 
Published: May 2021

ABSTRACTInfluenza A viruses are negative-sense RNA viruses that rely on their own viral replication machinery to replicate and transcribe their segmented single-stranded RNA genome. The viral ribonucleoprotein complexes in which viral RNA is replicated consist of a nucleoprotein scaffold around which the RNA genome is bound, and a heterotrimeric RNA-dependent RNA polymerase that catalyzes viral replication. The RNA polymerase copies the viral RNA (vRNA) via a replicative intermediate, called the complementary RNA (cRNA), and subsequently uses this cRNA to make more vRNA copies. To ensure that new cRNA and vRNA molecules are associated with ribonucleoproteins in which they can be amplified, the active RNA polymerase recruits a second polymerase to encapsidate the cRNA or vRNA. Host factor ANP32A has been shown to be essential for viral replication and to facilitate the formation of a dimer between viral RNA polymerases and differences between mammalian and avian ANP32A proteins are sufficient to restrict viral replication. It has been proposed that ANP32A is only required for the synthesis of vRNA molecules from a cRNA, but not vice versa. However, this view does not match recent molecular evidence. Here we use minigenome assays, virus infections, and viral promoter mutations to demonstrate that ANP32A is essential for both vRNA and cRNA synthesis. Moreover, we show that ANP32 is not only needed for the actively replicating polymerase, but also for the polymerase that is encapsidating nascent viral RNA products. Overall, these results provide new insights into influenza A virus replication and host adaptation.IMPORTANCEZoonotic avian influenza A viruses pose a constant threat to global health and they have the potential to cause highly pathogenic pandemic outbreaks. Species variations in host factor ANP32A play a key role in supporting the activity of avian influenza A virus RNA polymerases in mammalian hosts. Here we show that ANP32A acts at two stages in the influenza A virus replication cycle, supporting recent structural experiments and in line with its essential role. Understanding how ANP32A supports viral RNA polymerase activity and how it supports avian polymerase function in mammalian hosts is important for understanding influenza A virus replication and the development of antiviral strategies against influenza A viruses.
A multisensory circuit for gating intense aversive experiences
Authors: Asok Arun , Leroy Félix , Parro Cameron , de Solis Christopher A. , Ford Lenzie , Fitzpatrick Michelle N. , Kalmbach Abigail , Neve Rachael , Rayman Joseph B , Kandel Eric R. 
Published: May 2021

AbstractThe ventral hippocampus (vHPC) is critical for both learned and innate fear, but how discrete projections control different types of fear is poorly understood. Here, we report a novel excitatory circuit from a subpopulation of the ventral hippocampus CA1 subfield (vCA1) to the inhibitory peri-paraventricular nucleus of the hypothalamus (pPVN) which then routes to the periaqueductal grey (PAG). We find that vCA1→pPVN projections modulatebothlearned and innate fear. Fiber photometric calcium recordings reveal that activity in vCA1→pPVN projections increases during the first moments of exposure to an unconditioned threat. Chemogenetic or optogenetic silencing of vCA1→pPVN cell bodies or vCA1→pPVN axon terminals in the pPVN enhances the initial magnitude of both active and passive unconditioned defensive responses, irrespective of the sensory modalities engaged by a particular innate threat. Moreover, silencing produces a dramatic impact on learned fear without affecting milder anxiety-like behaviors. We also show that vCA1→pPVN projections monosynaptically route to the PAG, a key brain region that orchestrates the fear response. Surprisingly, optogenetic silencing of vCA1 terminals in the pPVN titrates the level of c-Fos neural activity in the PAG differently for learned versus innate threats. Together, our results show how a novel vCA1→pPVN circuit modulates neuronal activity in the PAG to regulate both learned and innate fear. These findings have implications for how initial trauma processing may influence maladaptive defensive behaviors across fear and trauma-related disorders.One Sentence SummaryA multisensory gate for high intensity aversive experiences.
INfrastructure for a PHAge REference Database: Identification of large-scale biases in the current collection of phage genomes
Authors: Cook Ryan , Brown Nathan , Redgwell Tamsin , Rihtman Branko , Barnes Megan , Clokie Martha , Stekel Dov J. , Hobman Jon , Jones Michael A. , Millard Andrew 
Published: May 2021

AbstractBackgroundWith advances in sequencing technology and decreasing costs, the number of bacteriophage genomes that have been sequenced has increased markedly in the last decade.Materials and MethodsWe developed an automated retrieval and analysis system for bacteriophage genomes, INPHARED (https://github.com/RyanCook94/inphared), that provides data in a consistent format.ResultsAs of January 2021, 14,244 complete phage genomes have been sequenced. The data set is dominated by phages that infect a small number of bacterial genera, with 75% of phages isolated only on 30 bacterial genera. There is further bias with significantly more lytic phage genomes than temperate within the database, resulting in ~54% of temperate phage genomes originating from just three host genera. Within phage genomes, putative antibiotic resistance genes were found in higher frequencies in temperate phages than lytic phages.ConclusionWe provide a mechanism to reproducibly extract complete phage genomes and highlight some of the biases within this data, that underpins our current understanding of phage genomes.
Phylogenomic study ofStaphylococcus aureusandStaphylococcus haemolyticusclinical isolates from Egypt
Authors: Montelongo Cesar , Mores Carine R. , Putonti Catherine , Wolfe Alan J. , Abouelfetouh Alaa 
Published: May 2021

AbstractAntibiotic resistantStaphylococcusinfections are a global concern, with increasing cases of resistantStaphylococcus aureusandStaphylococcus haemolyticusfound circulating in the Middle East. While extensive surveys have described the prevalence of resistant infections in Europe, Asia, and North America, the population structure of resistant staphylococcal Middle Eastern clinical isolates is poorly characterized. We performed whole genome sequencing of 56S. aureusand 10S. haemolyticusisolates from Alexandria Main University Hospital. Supplemented with additional publicly available genomes from the region (34S. aureusand 6S. haemolyticus), we present the largest genomic study of staphylococcal Middle Eastern isolates. These genomes include 20S. aureusmultilocus sequence typing (MLST) types and 9S. haemolyticusMLSTs, including 3 and 1 new MLSTs, respectively. Phylogenomic analyses of each species core genome largely mirrored MLSTs, irrespective of geographical origin. The hospital-acquiredspat037/SCCmecIII/MLST CC8 clone represented the largest clade, comprising 22% ofS. aureusisolates. Similar to other regional genome surveys ofS. aureus, the Middle Eastern isolates have an open pangenome, a strong indicator of gene exchange of virulence factors and antibiotic resistance genes with other reservoirs. We recommend stricter implementation of antibiotic stewardship and infection control plans in the region.Impact StatementStaphylococci are under-studied despite their prevalence within the Middle East. Methicillin-resistantStaphylococcus aureus(MRSA) is endemic to hospitals in this region, as are other antibiotic-resistant strains ofS. aureusandS. haemolyticus. To provide insight into the strains currently in circulation within Egypt, we performed whole genome sequencing of 56S. aureusand 10S. haemolyticusisolates from Alexandria Main University Hospital (AMUH). Through analysis of these genomes, as well as other genomes of isolates from the Middle East, we were able to produce a more complete picture of the current diversity than traditional molecular typing strategies. Furthermore, theS. haemolyticusgenome analyses provide the first insight into strains found in Egypt. Our analysis of resistance and virulence mechanisms carried by these strains provides invaluable insight into future plans of antibiotic stewardship and infection control within the region.Data SummaryRaw sequencing reads and assembled genomes can be found at BioProject Accession number PRJNA648411 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA648411).