bluuebunny/crossref_metadata_2025_split huggingface dataset:
Shotgun Immunoproteomic Approach for the Discovery of Linear B Cell Epitopes in Biothreat Agents Francisella tularensis and Burkholderia pseudomallei
Authors: D’haeseleer Patrik , Collette Nicole M. , Lao Victoria , Segelke Brent W. , Branda Steven S. , Franco Magdalena 
Published: June 2021

AbstractPeptide-based subunit vaccines are coming to the forefront of current vaccine approaches, with safety and cost-effective production among their top advantages. Peptide vaccine formulations consist of multiple synthetic linear epitopes that together trigger desired immune responses that can result in robust immune memory. The advantages of peptide epitopes are their simple structure, ease of synthesis, and ability to stimulate immune responses by means that do not require complex 3D conformation. Identification of linear epitopes is currently an inefficient process that requires thorough characterization of previously identified full-length protein antigens, or laborious techniques involving genetic manipulation of organisms. In this study, we apply a newly developed generalizable screening method that enables efficient identification of B cell epitopes in the proteomes of pathogenic bacteria. As a test case, we used this method to identify epitopes in the proteome of Francisella tularensis (Ft), a Select Agent with a well-characterized immunoproteome. Our screen identified many peptides that map to known antigens, including verified and predicted outer membrane proteins and extracellular proteins, validating the utility of this approach. We then used the method to identify seroreactive peptides in the less characterized immunoproteome of Select Agent Burkholderia pseudomallei (Bp). This screen revealed known Bp antigens as well as proteins that have not been previously identified as antigens. The present workflow is easily adaptable to detecting peptide targets relevant to the immune systems of other mammalian species, including humans (depending upon the availability of convalescent sera from patients), and could aid in accelerating the discovery of B cell epitopes and development of vaccines to counter emerging biological threats.
Predicted Coronavirus Nsp5 Protease Cleavage Sites in the Human Proteome: A Resource for SARS-CoV-2 Research
Authors: Scott Benjamin M. , Lacasse Vincent , Blom Ditte G. , Tonner Peter D. , Blom Nikolaj S. 
Published: June 2021

AbstractBackgroundThe coronavirus nonstructural protein 5 (Nsp5) is a cysteine protease required for processing the viral polyprotein and is therefore crucial for viral replication. Nsp5 from several coronaviruses have also been found to cleave host proteins, disrupting molecular pathways involved in innate immunity. Nsp5 from the recently emerged SARS-CoV-2 virus interacts with and can cleave human proteins, which may be relevant to the pathogenesis of COVID-19. Based on the continuing global pandemic, and emerging understanding of coronavirus Nsp5-human protein interactions, we set out to predict what human proteins are cleaved by the coronavirus Nsp5 protease using a bioinformatics approach.ResultsUsing a previously developed neural network trained on coronavirus Nsp5 cleavage sites (NetCorona), we made predictions of Nsp5 cleavage sites in all human proteins. Structures of human proteins in the Protein Data Bank containing a predicted Nsp5 cleavage site were then examined, generating a list of 92 human proteins with a highly predicted and accessible cleavage site. Of those, 48 are expected to be found in the same cellular compartment as Nsp5. Analysis of this targeted list of proteins revealed molecular pathways susceptible to Nsp5 cleavage and therefore relevant to coronavirus infection, including pathways involved in mRNA processing, cytokine response, cytoskeleton organization, and apoptosis.ConclusionsThis study combines predictions of Nsp5 cleavage sites in human proteins with protein structure information and protein network analysis. We predicted cleavage sites in proteins recently shown to be cleaved in vitro by SARS-CoV-2 Nsp5, and we discuss how other potentially cleaved proteins may be relevant to coronavirus mediated immune dysregulation. The data presented here will assist in the design of more targeted experiments, to determine the role of coronavirus Nsp5 cleavage of host proteins, which is relevant to understanding the molecular pathology of SARS-CoV-2 infection.
Thin-film freeze-drying of a Norovirus vaccine candidate
Authors: Xu Haiyue , Bhowmik Tuhin , Gong Kevin , Anh Huynh Thu Ngoc , Williams Robert O. , Cui Zhengrong 
Published: June 2021

AbstractA bivalent Norovirus vaccine candidate has been developed that contains Norovirus strain GI.1 Norwalk-virus like particles (VLP) and strain GII.4 Consensus VLP adsorbed onto aluminum (oxy)hydroxide. In the present study, we tested the feasibility of converting the vaccine from a liquid suspension into dry powder by thin-film freeze-drying (TFFD). With the proper amount of trehalose and/or sucrose as cryoprotectant, TFFD can be applied to transform the Norovirus vaccine candidate into dry powders without causing antigen loss or particle aggregation, while maintaining the potency of the antigens within a specified acceptable range. In an accelerated stability study, the potency of the antigens was also maintained in the specified acceptable range after the dry powders were stored for eight weeks at 40°C, 75% relative humidity. The dry powder Norovirus vaccine offers the potential to eliminate the cold chain requirement for transport and/or storage of the vaccine.
Metabolomics of lung microdissections reveals region- and sex-specific metabolic effects of acute naphthalene exposure in mice
Authors: Stevens Nathanial C. , Edwards Patricia C. , Tran Lisa M. , Ding Xinxin , Van Winkle Laura S. , Fiehn Oliver 
Published: June 2021

AbstractNaphthalene is a ubiquitous environmental contaminant produced by combustion of fossil fuels and is a primary constituent of both mainstream and side stream tobacco smoke. Naphthalene elicits region-specific toxicity in airway club cells through cytochrome P450 (P450)-mediated bioactivation, resulting in depletion of glutathione and subsequent cytotoxicity. While effects of naphthalene in mice have been extensively studied, few experiments have characterized global metabolomic changes in the lung. In individual lung regions, we found metabolomic changes in microdissected mouse lung conducting airways and parenchyma obtained from animals sacrificed 2, 6, and 24 hours following naphthalene treatment. Data on 577 unique identified metabolites were acquired by accurate mass spectrometry-based assays focusing on lipidomics and non-targeted metabolomics of hydrophilic compounds. Statistical analyses revealed distinct metabolite profiles between the two major lung regions. In addition, the number and magnitude of statistically significant exposure-induced changes in metabolite abundance were different between lung airways and parenchyma for unsaturated lysophosphatidylcholines (LPCs), dipeptides, purines, pyrimidines, and amino acids. Importantly, temporal changes were found to be highly distinct for male and female mice, with males exhibiting predominant treatment-specific changes only at two hours post-exposure. In females, metabolomic changes persisted until six hours post-naphthalene treatment, which may explain the previously characterized higher susceptibility of female mice to naphthalene toxicity. In both males and females, treatment-specific changes corresponding to lung remodeling, oxidative stress response, and DNA damage were observed, which may provide insights into potential mechanisms contributing to the previously reported effects of naphthalene exposure in the lung.
Generation of ENSEMBL-based proteogenomics databases boosts the identification of non-canonical peptides
Authors: Umer Husen M. , Zhu Yafeng , Pfeuffer Julianus , Sachsenberg Timo , Lehtiö Janne , Branca Rui , Perez-Riverol Yasset 
Published: June 2021

AbstractSummaryWe have implemented the pypgatk package and the pgdb workflow to create proteogenomics databases based on ENSEMBL resources. The tools allow the generation of protein sequences from novel protein-coding transcripts by performing a three-frame translation of pseudogenes, lncRNAs, and other non-canonical transcripts, such as those produced by alternative splicing events. It also includes exonic out-of-frame translation from otherwise canonical protein-coding mRNAs. Moreover, the tool enables the generation of variant protein sequences from multiple sources of genomic variants including COSMIC, cBioportal, gnomAD, and mutations detected from sequencing of patient samples. pypgatk and pgdb provide multiple functionalities for database handling, notably optimized target/decoy generation by the algorithm DecoyPyrat. Finally, we perform a reanalysis of four public datasets in PRIDE by generating cell-type specific databases for 65 cell lines using the pypgatk and pgdb workflow, revealing a wealth of non-canonical or cryptic peptides amounting to more than 10% of the total number of peptides identified (43,501 out of 402,512).AvailabilityThe software is freely available. pypgatk: (https://github.com/bigbio/py-pgatk/), and pgdb: (https://github.com/nf-core/pgdb)ContactYasset Perez-Riverol (yperez@ebi.ac.uk), Rui Branca (rui.mamede-branca@ki.se)Supplementary informationSupplementary data are available online.
Optimization of Phosphate Limited Autoinduction Broth for 2-Stage Heterologous Protein Expression in E. coli
Authors: Menacho-Melgar Romel , Hennigan Jennifer N. , Lynch Michael D. 
Published: June 2021

AbstractAutoinducible, 2-stage protein expression leveraging phosphate inducible promoters has been recently shown to enable not only high protein titers but also consistent performance across scales from screening systems (microtiter plates) to instrumented bioreactors. However, to date small scale production using microtiter plates and shake flasks rely on a complex autoinduction broth (AB) that requires making numerous media components, not all amenable to autoclaving. In this report, we develop a simpler media formulation (AB-2) with just a few autoclavable components. We show that AB-2 is robust to small changes in its composition and performs equally, if not better, than AB across different scales. AB-2 will facilitate adoption of phosphate limited 2-stage protein expression protocols.
Populus ERF85 balances xylem cell expansion and secondary cell wall formation in hybrid aspen
Authors: Seyfferth Carolin , Wessels Bernard A. , Vahala Jorma , Kangasjärvi Jaakko , Delhomme Nicolas , Hvidsten Torgeir R. , Tuominen Hannele , Lundberg-Felten Judith 
Published: June 2021

AbstractSecondary growth relies on precise and specialized transcriptional networks that determine cell division, differentiation, and maturation of xylem cells. We identify a novel role for the ethylene induced Populus ETHYLENE RESPONSE FACTOR ERF85 (Potri.015G023200) in balancing xylem cell expansion and secondary cell wall (SCW) formation in hybrid aspen (Populus tremula x tremuloides). Expression of ERF85 is high in phloem and cambium cells and during expansion of xylem cells, while it is low in maturing xylem tissue. Extending ERF85 expression into SCW forming zones of woody tissues through ectopic expression reduced wood density and SCW thickness of xylem fibers but increased fiber diameter. Xylem transcriptomes from the transgenic trees revealed transcriptional induction of genes involved in cell expansion, translation and growth. Expression of genes associated with plant vascular development and biosynthesis of SCW chemical components such as xylan and lignin, was downregulated in the transgenic trees. Our results suggest that ERF85 activates genes related with xylem cell expansion, while preventing transcriptional activation of genes related to SCW formation. The importance of precise spatial expression of ERF85 during wood development together with the observed phenotypes in response to ectopic ERF85 expression suggests that ERF85 functions as a switch between different phases of xylem differentiation during wood formation.
Genetic and phylogenetic uncoupling of structure and function in human transmodal cortex
Authors: Valk Sofie L. , Xu Ting , Paquola Casey , Park Bo-yong , Bethlehem Richard A.I. , Vos de Wael Reinder , Royer Jessica , Masouleh Shahrzad Kharabian , Bayrak Şeyma , Kochunov Peter , Yeo B.T. Thomas , Margulies Daniel , Smallw Jonathan , Eickhoff Simon B. , Bernhardt Boris C. 
Published: June 2021

ABSTRACTBrain structure scaffolds intrinsic function, supporting cognition and ultimately behavioral flexibility. However, it remains unclear how a static, genetically controlled architecture supports flexible cognition and behavior. Here, we synthesize genetic, phylogenetic and cognitive analyses to understand how the macroscale organization of structure-function coupling across the cortex can inform its role in cognition. In humans, structure-function coupling was highest in regions of unimodal cortex and lowest in transmodal cortex, a pattern that was mirrored by a reduced alignment with heritable connectivity profiles. Structure-function uncoupling in non-human primates had a similar spatial distribution, but we observed an increased coupling between structure and function in association regions in macaques relative to humans. Meta-analysis suggested regions with the least genetic control (low heritable correspondence and different across primates) are linked to social cognition and autobiographical memory. Our findings establish the genetic and evolutionary uncoupling of structure and function in different transmodal systems may support the emergence of complex, culturally embedded forms of cognition.
Identification of candidate biomarkers and pathways associated with type 1 diabetes mellitus using bioinformatics analysis
Authors: Vastrad Basavaraj , Vastrad Chanabasayya 
Published: June 2021

AbstractType 1 diabetes mellitus (T1DM) is a metabolic disorder for which the underlying molecular mechanisms remain largely unclear. This investigation aimed to elucidate essential candidate genes and pathways in T1DM by integrated bioinformatics analysis. In this study, differentially expressed genes (DEGs) were analyzed using DESeq2 of R package from GSE162689 of the Gene Expression Omnibus (GEO). Gene ontology (GO) enrichment analysis, REACTOME pathway enrichment analysis, and construction and analysis of protein-protein interaction (PPI) network, modules, miRNA-hub gene regulatory network and TF-hub gene regulatory network, and validation of hub genes were then performed. A total of 952 DEGs (477 up regulated and 475 down regulated genes) were identified in T1DM. GO and REACTOME enrichment result results showed that DEGs mainly enriched in multicellular organism development, detection of stimulus, diseases of signal transduction by growth factor receptors and second messengers, and olfactory signaling pathway. The top hub genes such as MYC, EGFR, LNX1, YBX1, HSP90AA1, ESR1, FN1, TK1, ANLN and SMAD9 were screened out as the critical genes among the DEGs from the PPI network, modules, miRNA-hub gene regulatory network and TF-hub gene regulatory network. Receiver operating characteristic curve (ROC) analysis and RT-PCR confirmed that these genes were significantly associated with T1DM. In conclusion, the identified DEGs, particularly the hub genes, strengthen the understanding of the advancement and progression of T1DM, and certain genes might be used as candidate target molecules to diagnose, monitor and treat T1DM.
Genomics analysis of hexanoic acid exposure in Drosophila species
Authors: Drum Z.A. , Lanno S.M. , Gregory S.M. , Shimshak S.J. , Ahamed M. , Barr W. , Bekele B. , Biester A. , Castro C. , Connolly L. , DelGaudio N. , Humphrey W. , Karimi H. , Karolczak S. , Lawrence T. , McCracken A. , Miller-Medzon N. , Murphy L. , Park C. , Park S. , Qiu C. , Serra K. , Snyder G. , Strauss A. , Tang S. , Vyzas C. , Coolon Joseph D. 
Published: June 2021

AbstractDrosophila sechellia is a dietary specialist endemic to the Seychelles islands that has evolved to consume the fruit of Morinda citrifolia. When ripe, the fruit of M. citrifolia contains octanoic acid and hexanoic acid, two medium chain fatty acid volatiles that deter and are toxic to generalist insects. D. sechellia has evolved resistance to these volatiles allowing it to feed almost exclusively on this host plant. The genetic basis of octanoic acid resistance has been the focus of multiple recent studies, but the mechanisms that govern hexanoic acid resistance in D. sechellia remain unknown. To understand how D. sechellia has evolved to specialize on M. citrifolia fruit and avoid the toxic effects of hexanoic acid, we exposed adult D. sechellia, D. melanogaster and D. simulans to hexanoic acid and performed RNA sequencing comparing their transcriptional responses to identify D. sechellia specific responses. Our analysis identified many more genes responding transcriptionally to hexanoic acid in the susceptible generalist species than in the specialist D. sechellia. Interrogation of the sets of differentially expressed genes showed that generalists regulated the expression of many genes involved in metabolism and detoxification whereas the specialist primarily downregulated genes involved in the innate immunity. Using these data we have identified interesting candidate genes that may be critically important in aspects of adaptation to their food source that contains high concentrations of HA. Understanding how gene expression evolves during dietary specialization is crucial for our understanding of how ecological communities are built and how evolution shapes trophic interactions.
Parallel and non-parallel divergence within polymorphic populations of brook stickleback,Culaea inconstans(Actinopterygii: Gasterosteidae)
Authors: Willerth Kaitlyn , Franks Emily , Mee Jonathan A. 
Published: June 2021

AbstractStudying parallel evolution allows us to draw conclusions about the repeatability of adaptive evolution. Whereas populations likely experience similar selective pressures in similar environments, it is not clear if this will always result in parallel divergence of ecologically relevant traits. Our study investigates the extent of parallelism associated with the evolution of pelvic spine reduction in brook stickleback populations. We find that populations with parallel divergence in pelvic spine morphology do not exhibit parallel divergence in head and body morphology but do exhibit parallel divergence in diet. In addition, we compare these patterns associated with pelvic reduction in brook stickleback to well-studied patterns of divergence between spined and unspined threespine stickleback. Whereas spine reduction is associated with littoral habitats and a benthic diet in threespine stickleback, spine reduction in brook stickleback is associated with a planktonic diet. Hence, we find that pelvic spine divergence is associated with largely non-parallel ecological consequences across species.
Comparative population genomics in two sympatric species ofStrophostyles(Fabaceae) with contrasting life histories
Authors: Herron Sterling A. , Harris Zachary N. , Rubin Matthew J. , Miller Allison J. 
Published: June 2021

ABSTRACTPREMISE OF THE STUDYLife history is an important predictor of population genetic variation, although this link remains unexplored in numerous important plant lineages. One such lineage is the legume genusStrophostyles, which contains both annual and herbaceous perennial vines native to eastern North America. Specifically, it remains to be determined whetherStrophostylesspecies with different life histories show different patterns of genetic differentiation and diversity, as well as if these species hybridize across their range.METHODSHere we sampled the perennialStrophostyles helvolaand annualS. leiospermain five sites across a latitudinal transect in the central United States, including three sites where the species occur in sympatry. Using genotyping-by-sequencing, we identified 5556 polymorphic SNPs across 166 individuals.KEY RESULTSThere is no evidence thatStrophostyles helvolaandS. leiospermahybridize in the populations examined. Within species,Strophostyles helvola(perennial) displays admixture among populations, whileS. leiosperma(annual) does not, although both species show more genetic diversity among rather than within populations. Patterns of genetic diversity are varied across populations of both species, with both heterozygote excess and deficiency.CONCLUSIONSThe complex patterns of genetic differentiation and diversity warrant further investigation of life history and population dynamics inStrophostyles, particularly mating system and modes of gene flow. This study exemplifies the diversity of population genetic patterns even within a small genus, and it reinforces the need to characterize such diversity in non-model systems to gain a more complete understanding of how life history contributes to population genetics.
Removing Thermostat Distortions of Protein Dynamics in Constant-Temperature Molecular Dynamics Simulations
Authors: Hicks Alan , MacAinsh Matthew , Zhou Huan-Xiang 
Published: June 2021

ABSTRACTMolecular dynamics simulations are widely used to determine equilibrium and dynamic properties of proteins. Nearly all simulations nowadays are carried out at constant temperature, with a Langevin thermostat among the most widely used. Thermostats distort protein dynamics, but whether or how such distortions can be corrected has long been an open question. Here we show that constant-temperature simulations with a Langevin thermostat dilate protein dynamics and present a correction scheme to remove the dynamic distortions. Specifically, ns-scale time constants for overall rotation are dilated significantly but sub-ns time constants for internal motions are dilated modestly, while all motional amplitudes are unaffected. The correction scheme involves contraction of the time constants, with the contraction factor a linear function of the time constant to be corrected. The corrected dynamics of eight proteins are validated by NMR data for rotational diffusion and for backbone amide and side-chain methyl relaxation. The present work demonstrates that, even for complex systems like proteins with dynamics spanning multiple timescales, one can predict how thermostats distort protein dynamics and remove such distortions. The correction scheme will have wide applications, facilitating force-field parameterization and propelling simulations to be on par with NMR and other experimental techniques in determining dynamic properties of proteins.TOC graphic