bluuebunny/crossref_metadata_2025_split huggingface dataset:
VarSAn: Associating pathways with a set of genomic variants using network analysis
Authors: Xie Xiaoman , Kendzior Matthew C. , Ge Xiyu , Mainzer Liudmila S. , Sinha Saurabh 
Published: December 2020

ABSTRACTThere is a pressing need today to mechanistically interpret sets of genomic variants associated with diseases. Here we present a tool called ‘VarSAn’ that uses a network analysis algorithm to identify pathways relevant to a given set of variants. VarSAn analyzes a configurable network whose nodes represent variants, genes and pathways, using a Random Walk with Restarts algorithm to rank pathways for relevance to the given variants, and reports p-values for pathway relevance. It treats non-coding and coding variants differently, properly accounts for the number of pathways impacted by each variant and identifies relevant pathways even if many variants do not directly impact genes of the pathway. We use VarSAn to identify pathways relevant to variants related to cancer and several other diseases, as well as drug response variation. We find VarSAn’s pathway ranking to be complementary to the standard approach of enrichment tests on genes related to the query set. We adopt a novel benchmarking strategy to quantify its advantage over this baseline approach. Finally, we use VarSAn to discover key pathways, including the VEGFA-VEGFR2 pathway, related to de novo variants in patients of Hypoplastic Left Heart Syndrome, a rare and severe congenital heart defect.
Microcircuit synchronization and heavy tailed synaptic weight distribution in preBötzinger Complex contribute to generation of breathing rhythm
Authors: Slepukhin Valentin M. , Ashhad Sufyan , Feldman Jack L. , Levine Alex J. 
Published: December 2020

ABSTRACTThe preBötzinger Complex, the mammalian inspiratory rhythm generator, encodes inspiratory time as motor pattern. Spike synchronization throughout this sparsely connected network generates inspiratory bursts albeit with variable latencies after preinspiratory activity onset in each breathing cycle. Using preBötC rhythmogenic microcircuit minimal models, we examined the variability in probability and latency to burst, mimicking experiments. Among various physiologically plausible graphs of 1000 point neurons with experimentally determined neuronal and synaptic parameters, directed Erdős-Rényi graphs best captured the experimentally observed dynamics. Mechanistically, preBötC (de)synchronization and oscillatory dynamics are regulated by the efferent connectivity of spiking neurons that gates the amplification of modest preinspiratory activity through input convergence. Furthermore, to replicate experiments, a lognormal distribution of synaptic weights was necessary to augment the efficacy of convergent coincident inputs. These mechanisms enable exceptionally robust yet flexible preBötC attractor dynamics that, we postulate, represent universal temporal-processing and decision-making computational motifs throughout the brain.
Brucella oviscysteine biosynthesis contributes to peroxide stress survival and fitness in the intracellular niche
Authors: Varesio Lydia M. , Fiebig Aretha , Crosson Sean 
Published: December 2020

AbstractBrucella ovisis an ovine intracellular pathogen with tropism for the male genital tract. To establish and maintain infection,B. ovismust survive stressful conditions inside host cells, including low pH, nutrient limitation, and reactive oxygen species. These same conditions are often encountered in axenic cultures during stationary phase. Studies of stationary phase may thus inform understanding ofBrucellainfection biology, yet the genes and pathways that are important inBrucellastationary phase physiology remain poorly defined. We measured fitness of a barcoded pool ofB. ovisTn-himarmutants as a function of growth phase and identifiedcysEas a determinant of fitness in stationary phase. CysE catalyzes the first step in cysteine biosynthesis from serine, and we provide genetic evidence that two related enzymes, CysK1 and CysK2, function redundantly to catalyze cysteine synthesis at steps downstream of CysE. Deleting eithercysE(ΔcysE) or bothcysK1andcysK2(ΔcysK1ΔcysK2) results in premature entry into stationary phase, reduced culture yield and sensitivity to exogenous hydrogen peroxide. These phenotypes can be chemically complemented by cysteine or glutathione. ΔcysEand ΔcysK1ΔcysK2strains have no defect in host cell entryin vitrobut have significantly diminished intracellular fitness between 2 and 24 hours post infection. Our study has uncovered unexpected redundancy at the CysK step of cysteine biosynthesis inB. ovis, and demonstrates that cysteine anabolism is a determinant of peroxide stress survival and fitness in the intracellular niche.
Functional architecture of the pancreatic islets reveals first responder cells which drive the first-phase [Ca2+] response
Authors: Kravets Vira , Dwulet JaeAnn M. , Schleicher Wolfgang E. , Hodson David J. , Davis Anna M. , Pyle Laura , Piscopio Robert A. , Sticco-Ivins Maura , Benninger Richard K.P. 
Published: December 2020

AbstractInsulin-secreting β-cells are functionally heterogeneous. Whether there exist cells driving the first-phase calcium response in individual islets, has not been examined. We examine ‘first responder’ cells, defined by the earliest [Ca2+] response during first-phase [Ca2+] elevation, distinct from previously identified “hub” and “leader” cells. First responder cells showed characteristics of high membrane excitability and lower electrical coupling to their neighbors. The first-phase response time of β-cells in the islet was spatially organized, dependent on the cell’s distance to the first responder cell, and consistent over time up to ∼24 h. When first responder cells were laser ablated, the first-phase [Ca2+] was slowed down, diminished, and discoordinated compared to random cell ablation. Cells that were next earliest to respond often took over the role of the first responder upon ablation. In summary, we discover and characterize a distinct first responder β-cell state, critical for the islet first-phase response to glucose.
Multiple Mechanisms of HIV-1 resistance to PGT135 in Chinese Subtype B’ Slow Progressor
Authors: Sun Shasha , Zou Sen , Hu Yuanyuan , Liu Ying , Ren Li , Hao Yanling , Hu Xintao , Ruan Yuhua , Ma Liying , Shao Yiming , Hong Kunxue 
Published: December 2020

ABSTRACTIn our study, we describe a slow progressor CBJC515 from whom we constructed pseudoviruses expressing autologous Env. We surprisingly found all the pseudoviruses were resistant to PGT135. By making site-directed mutations and chimeric Env constructs, we found the early 05 strains escaped from PGT135 by losing the N332 glycan site, while the later 06 and 08 strains may escape with the retention of key epitopes through the change of V1/V4/C2 region or by N398/N611 glycan, which was selected as unique N-glycosylation site of CBJC515 compared with CBJC437 whose viruses were also harboring key epitopes but sensitive to PGT135. These findings provide insights into how HIV-1 can escape from N332-directed broadly neutralizing antibody (bNAb) responses without changing the epitope itself, and these ways may be useful to prolong the exposures of bNAb epitopes and contribute to bNAb development. Furthermore, our chimeric experiments also allowed us to explore the co-evolution and retention of functionality among regions. We confirmed that the V1V2 region has a wide range of effectiveness in interfering with the function of envelope protein and the V3 region can promote protein function recovery and buffer the harmful polymorphisms in the other regions contributing to the Env antigenic diversity. These results may provide some clues for the design of vaccines against HIV-1 strains.IMPORTANCEOur findings of mechanisms escaping from PGT135 verified the extensive role of long V1 region in mediating escape from V3-bNAbs. In addition, we also found multiple additional ways suggested that extreme variation may be needed by HIV-1 to escape from PGT135 without changing the epitope itself. Although the V3-glycan bNAb responses are among the most promising vaccine targets, as they are commonly elicited during infection, our findings indicated there may be additional difficulties to be taken into account in immunogen design, such as the consideration of other regions and some glycosylation sites affecting the mask of key epitopes, as well as the selection pressure that may be required by other bNAbs. Our chimeric experiment also highlighted the key role of V3 region in contributing to the maintenance of Env diversity by buffering deleterious polymorphisms, which may be helpful for vaccine design.
Dissociated face- and word-selective intracerebral responses in the human ventral occipito-temporal cortex
Authors: Hagen Simen , Lochy Aliette , Jacques Corentin , Maillard Louis , Colnat-Coulbois Sophie , Jonas Jacques , Rossion Bruno 
Published: December 2020

AbstractThe extent to which faces and written words share neural circuitry in the human brain is actively debated. Here we compared face-selective and word-selective responses in a large group of patients (N = 37) implanted with intracerebral depth electrodes in the ventral occipito-temporal cortex (VOTC). Both face-selective (i.e., significantly different responses to faces vs. nonface visual objects) and word-selective (i.e., significantly different responses to words vs. pseudofonts) neural activity is isolated through frequency-tagging. Critically, this sensitive approach allows to objectively quantify category-selective neural responses and disentangle them from general visual responses. About 70% of significant contacts show either only face-selectivity or only word-selectivity, with the expected right and left hemispheric dominance, respectively. Spatial dissociations are also found within core regions of face and word processing, with a medio-lateral dissociation in the fusiform gyrus (FG) and surrounding sulci, while a postero-anterior dissociation is found in the inferior occipital gyrus (IOG). Only 30% of the significant contacts show both face- and word-selective responses. Critically, in these contacts, across the VOTC or in the FG and surrounding sulci, between-category selective-amplitudes (faces vs. words) showed no-to-weak correlations, despite strong correlations in both the within-category selective amplitudes (face-face, word-word) and the general visual responses to words and faces. Overall, we conclude that category-selectivity for faces and written words is largely dissociated in the human VOTC.Significance StatementIn modern human societies, faces and written words have become arguably the most significant stimuli of the visual environment. Despite extensive research in neuropsychology, electroencephalography and neuroimaging over the past three decades, whether these two types of visual signals are recognized by similar or dissociated processes and neural networks remains unclear. Here we provide an original contribution to this outstanding scientific issue by directly comparing frequency-tagged face- and word-selective neural responses in a large group of epileptic patients implanted with intracerebral electrodes covering the ventral occipito-temporal cortex. While general visual responses to words and faces show significant overlap, the respective category-selective responses are neatly dissociated in spatial location and magnitude, pointing to largely dissociated processes and neural networks.
PET/CT targeted tissue sampling reveals virus specific dIgA can alter the distribution and localization of HIV after rectal exposure
Authors: Taylor Roslyn A. , Xiao Sixia , Carias Ann M. , McRaven Michael D. , Thakkar Divya N. , Araínga Mariluz , Allen Edward J. , Rogers Kenneth A. , Kumarapperuma Sidath C. , Gong Siqi , Fought Angela J , Anderson Meegan R. , Thomas Yanique , Schneider Jeffrey R. , Goins Beth , Fox Peter , Villinger Francois J , Ruprecht Ruth M. , Hope Thomas J. 
Published: December 2020

AbstractHIV vaccines have not been successful in clinical trials. Dimeric IgA (dIgA) is the most abundant antibody class in mucosal tissues, making dIgA a prime candidate for potential HIV vaccines. We coupled Positron Emission Tomography (PET) imaging and fluorescent microscopy of64Cu-labeled, photoactivatable-GFP HIV (PA-GFP-BaL) and fluorescently labeled dIgA to determine how dIgA antibodies influence virus interaction with mucosal barriers and viral penetration in colorectal tissue. Our results show that HIV virions rapidly disseminate throughout the colon two hours after exposure. The presence of dIgA resulted in an increase in virions and penetration depth in the transverse colon. Moreover, virions were found in the mesenteric lymph nodes two hours after viral exposure, and the presence of dIgA led to an increase in virions in mesenteric lymph nodes. Taken together, these technologies enablein vivoandin situvisualization of antibody-virus interactions and detailed investigations of early events in HIV infection.
Establishing defined daily doses (DDDs) for antimicrobial agents used for pigs, cattle and poultry in Japan and comparing them with European DDD values
Authors: Fujimoto Kyoko , Kawasaki Mai , Abe Reiko , Yokoyama Takashi , Haga Takeshi , Sugiura Katsuaki 
Published: December 2020

AbstractMonitoring of antimicrobial use is essential to manage the development and selection of antimicrobial resistance. A variety of indicators has become available to monitor antimicrobial use in human and animal medicine. One of them is an indicator based on defined daily dose (DDD). By using the number of DDDs used and normalizing it by the population at risk of being treated in a defined period, one can estimate the number of treatment days with antimicrobial agents in a population. For veterinary medicine, the European Medicines Agency (EMA) has published the European values of DDD (DDDvet) for food-producing animals. In this study, we defined Japanese defined daily doses for antimicrobial agents (DDDjp) using DDD values that we previously assigned for antimicrobial products approved for use in pigs, cattle and poultry in Japan and compared them with DDDvet values. For the comparison, the quotient of Japanese and European values (QDDD) was calculated and the effect of the administration route and the number of active substances contained in the preparation was investigated. A total of 59, 51 and 27 DDDjp values were defined for 43, 32 and 25 antimicrobial agents using the data of 269, 195 and 131 products approved for use in pigs, cattle and poultry respectively. A comparison was possible for 44, 27 and 17 pairs of DDDjp and DDDvet values for antimicrobial agents used for pigs, cattle and poultry respectively. The comparison showed median QDDD value of 0.66 and 0.63 for antimicrobial agents used for pigs and cattle respectively (P<0.01), indicating that the Japanese daily doses are significantly lower than the corresponding EMA values in these species. For the antimicrobial agents used for poultry, no siginificant difference was observed between DDDjp and DDDvet values with median QDDD value of 1.17. The difference between DDDvet and DDDjp values and absence of DDDvet values for some antimicrobial agents marketed in Japan indicate that DDDjp rather than DDDvet should be used as the basis for the calculation of antimicrobial use monitoring in farm animals in Japan.
mRNA vaccine CVnCoV protects non-human primates from SARS-CoV-2 challenge infection
Authors: Rauch Susanne , Gooch Karen , Hall Yper , Salguero Francisco J. , Dennis Mike J. , Gleeson Fergus V. , Harris Debbie , Ho Catherine , Humphries Holly E. , Longet Stephanie , Ngabo Didier , Paterson Jemma , Rayner Emma L. , Ryan Kathryn A. , Sharpe Sally , Watson Robert J. , Mueller Stefan O. , Petsch Benjamin , Carroll Miles W. 
Published: December 2020

AbstractThe ongoing severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic necessitates the fast development of vaccines to meet a worldwide need. mRNA-based vaccines are the most promising technology for rapid and safe SARS-CoV-2 vaccine development and production. We have designed CVnCoV, a lipid-nanoparticle (LNP) encapsulated, sequence optimised mRNA-based SARS-CoV-2 vaccine that encodes for full length, pre-fusion stabilised Spike protein. Unlike other mRNA-based approaches, CVnCoV exclusively consists of non-chemically modified nucleotides and can be applied at comparatively low doses. Here we demonstrate that CVnCoV induces robust humoral and cellular responses in non-human primates (NHPs). Animals vaccinated with 8 μg of CVnCoV were protected from challenge infection with SARS-CoV-2. Comprehensive analyses of pathological changes in challenged animals via lung histopathology and Computed Tomography (CT) scans gave no indication of enhanced disease upon CVnCoV vaccination. These results demonstrate safety, immunogenicity, and protective efficacy of CVnCoV in NHPs that extend our previously published preclinical data and provide strong support for further clinical testing in ongoing phase 2b/3 efficacy studies.
EKLF/KLF1 expression defines a unique macrophage subset during mouse erythropoiesis
Authors: Mukherjee Kaustav , Xue Li , Planutis Antanas , Gnanapragasam Merlin Nithya , Chess Andrew , Bieker James J. 
Published: December 2020

ABSTRACTErythroblastic islands are a specialized niche that contain a central macrophage surrounded by erythroid cells at various stages of maturation. However, identifying the precise genetic and transcriptional control mechanisms in the island macrophage remains difficult due to macrophage heterogeneity. Using unbiased global sequencing and directed genetic approaches focused on early mammalian development, we find that fetal liver macrophage exhibit a unique expression signature that differentiates them from erythroid and adult macrophage cells. The importance of EKLF/KLF1 in this identity is shown by expression analyses in EKLF-/- and in EKLF-marked macrophage cells. Single cell sequence analysis simplifies heterogeneity and identifies clusters of genes important for EKLF-dependent macrophage function and novel cell surface biomarkers. Remarkably, this singular set of macrophage island cells appears transiently during embryogenesis. Together these studies provide a detailed perspective on the importance of EKLF in establishment of the dynamic gene expression network within erythroblastic islands in the developing embryo and provide the means for their efficient isolation.
Transgelin: A New Gene Involved in LDL Endocytosis Identified by a Genome-wide CRISPR-Cas9 Screen
Authors: Lucero Diego , Dikilitas Ozan , Mendelson Michael M. , Islam Promotto , Neufeld Edward B. , Bansal Aruna T. , Freeman Lita A. , Vaisman Boris , Tang Jingrong , Combs Christian A. , Li Yuesheng , Voros Szilard , Kullo Iftikhar J. , Remaley Alan T. 
Published: December 2020

AbstractTo identify new genes involved in the cellular uptake of low-density lipoprotein (LDL), we applied a novel whole genome CRISPR/Cas9 knockout-screen on HepG2 cell lines. We identifiedTAGLN(transgelin), an actin-binding protein, as a new gene involved in LDL endocytosis.In silicovalidation demonstrated that genetically predicted differences in expression ofTAGLNin human populations were associated with plasma lipids (triglycerides, total cholesterol, HDL, and LDL cholesterol) in the Global Lipids Genetics Consortium and lipid-related phenotypes in the UK Biobank. Decreased cellular LDL uptake observed inTAGLN-knockout cells due to decreased LDL receptor internalization, led to alterations in cellular cholesterol content and compensatory changes in cholesterol biosynthesis. Transgelin was also shown to be involved in the actin-dependent phase of clathrin-mediated endocytosis of other cargo besides LDL. The identification of novel genes involved in LDL uptake may improve the diagnosis of hypercholesterolemia and provide future therapeutic targets for the prevention of cardiovascular disease.
Orchard Management and Landscape Context Mediate the Floral Microbiome of Pear
Authors: Schaeffer Robert N. , Pfeiffer Vera W. , Basu Saumik , Brousil Matthew , Strohm Christopher , DuPont S. Tianna , Vannette Rachel L. , Crowder David W. 
Published: December 2020

ABSTRACTCrop-associated microbiota are key factors affecting host health and productivity. Most crops are grown within heterogeneous landscapes, and interactions between management practices and landscape context often affect plant and animal biodiversity in agroecosystems. However, whether these same factors typically affect crop-associated microbiota is less clear. Here, we assessed whether orchard management strategies and landscape context affected bacterial and fungal communities in pear (Pyrus communis) flowers. We found that bacteria and fungi responded differently to management schemes. Organically-certified orchards had higher fungal diversity in flowers than conventional or bio-based integrated pest management (IPM) orchards, but organic orchards had the lowest bacterial diversity. Orchard management scheme also best predicted the distribution of several important bacterial and fungal genera that either cause or suppress disease, with organic and bio-based IPM best explaining the distributions of bacterial and fungal genera, respectively. Moreover, patterns of bacterial and fungal diversity were affected by interactions between management, landscape context, and climate. When examining the similarity of bacterial and fungal communities across sites, both abundance- and taxa-related turnover were mediated primarily by orchard management scheme and landscape context, and specifically the amount of land in cultivation. Our study reveals local- and landscape-level drivers of floral microbiome structure in a major fruit crop, providing insights that can inform microbiome management to promote host health and high-yielding quality fruit.IMPORTANCEIn tree fruits, proper crop management during bloom is essential for producing disease-free fruit. Tree fruits are often grown in heterogeneous landscapes; however, few studies have assessed whether landscape context and crop management affect the floral microbiome, which plays a critical role in shaping plant health and disease tolerance. Such work is key for identification of tactics and/or contexts where beneficial microbes proliferate, and pathogenic microbes are limited. Here, we characterize the floral microbiome of pear crops in Washington State, USA, where major production occurs in inter-mountain valleys and basins with variable elevation and microclimates. Our results show that both local (crop management) and landscape (habitat types and climate) level factors affect floral microbiota, but in disparate ways for each kingdom, suggesting a need for unique management strategies for each group. More broadly, these findings can potentially inform microbiome management in orchards for promotion of host health and high-quality yields.