bluuebunny/crossref_metadata_2025_split huggingface dataset:
FR-Match: Robust matching of cell type clusters from single cell RNA sequencing data using the Friedman-Rafsky non-parametric test
Authors: Zhang Yun , Aevermann Brian D. , Bakken Trygve E. , Miller Jeremy A. , Hodge Rebecca D. , Lein Ed S. , Scheuermann Richard H. 
Published: May 2020

AbstractSingle cell/nucleus RNA sequencing (scRNAseq) is emerging as an essential tool to unravel the phenotypic heterogeneity of cells in complex biological systems. While computational methods for scRNAseq cell type clustering have advanced, the ability to integrate datasets to identify common and novel cell types across experiments remains a challenge. Here, we introduce a cluster-to-cluster cell type matching method – FR-Match – that utilizes supervised feature selection for dimensionality reduction and incorporates shared information among cells to determine whether two cell type clusters share the same underlying multivariate gene expression distribution. FR-Match is benchmarked with existing cell-to-cell and cell-to-cluster cell type matching methods using both simulated and real scRNAseq data. FR-Match proved to be a stringent method that produced fewer erroneous matches of distinct cell subtypes and had the unique ability to identify novel cell phenotypes in new datasets.In silicovalidation demonstrated that the proposed workflow is the only self-contained algorithm that was robust to increasing numbers of true negatives (i.e. non-represented cell types). FR-Match was applied to two human brain scRNAseq datasets sampled from cortical layer 1 and full thickness middle temporal gyrus. When mapping cell types identified in specimens isolated from these overlapping human brain regions, FR-Match precisely recapitulated the laminar characteristics of matched cell type clusters, reflecting their distinct neuroanatomical distributions. An R package and Shiny application are provided athttps://github.com/JCVenterInstitute/FRmatchfor users to interactively explore and match scRNAseq cell type clusters with complementary visualization tools.
A novelhemAmutation is responsible for small colony variant phenotype inEscherichia coli
Authors: Hubbard Alasdair T. M. , Roberts Adam P. 
Published: May 2020

AbstractWe identified a small colony variant (SCV) of a clinical isolate ofEscherichia colifrom Malawi following sequentialin vitroselection in sub-inhibitory concentrations of amoxicillin-clavulanic acid and gentamicin. The SCV was auxotrophic for hemin and had impaired biofilm formation compared to the ancestral isolates. A single novel nucleotide polymorphism (SNP) inhemA, which encodes a glutamyl-tRNA reductase responsible for the initial step of porphyrin biosynthesis leading to the production of haem, was responsible for the SCV phenotype. We showed this phenotype was stable over multiple generations and the SNP inhemAresulted in a significant fitness cost to the isolate which persisted even in the presence of hemin. AshemAis not found in mammalian cells, and disruption of the gene results in impaired biofilm formation and a significant fitness cost, it represents a potential target for novel drug development specifically for the treatment of catheter-associated urinary tract infections caused by biofilm-producingE. coli.
Variants in ACE2 and TMPRSS2 genes are not major determinants of COVID-19 severity in UK Biobank subjects
Authors: Curtis David 
Published: May 2020

AbstractIt is plausible that variants in the ACE2 and TMPRSS2 genes might contribute to variation in COVID-19 severity and that these could explain why some people become very unwell whereas most do not. Exome sequence data was obtained for 49,953 UK Biobank subjects of whom 74 had tested positive for SARS-CoV-2 and could be presumed to have severe disease. A weighted burden analysis was carried out using SCOREASSOC to determine whether there were differences between these cases and the other sequenced subjects in the overall burden of rare, damaging variants in ACE2 or TMPRSS2. There were no statistically significant differences in weighted burden scores between cases and controls for either gene. There were no individual DNA sequence variants with a markedly different frequency between cases and controls. Whether there are small effects on severity, or whether there might be rare variants with major effect sizes, would require studies in much larger samples. Genetic variants affecting the structure and function of the ACE2 and TMPRSS2 proteins are not a major determinant of whether infection with SARS-CoV-2 results in severe symptoms. This research has been conducted using the UK Biobank Resource.
Sleep Deficits and Cannabis Use Behaviors: An Analysis of Shared Genetics Using Linkage Disequilibrium Score Regression and Polygenic Risk Prediction
Authors: Winiger Evan A. , Ellingson Jarrod M. , Morrison Claire L. , Corley Robin P. , Pasman Joëlle A. , Wall Tamara L. , Hopfer Christian J. , Hewitt John K. 
Published: May 2020

AbstractStudy ObjectivesEstimate the genetic relationship of cannabis use with sleep deficits and eveningness chronotype.MethodsWe used linkage disequilibrium score regression (LDSC) to analyze genetic correlations between sleep deficits and cannabis use behaviors. Secondly, we generated sleep deficit polygenic risk scores (PRSs) and estimated their ability to predict cannabis use behaviors using logistic regression. Summary statistics came from existing genome wide association studies (GWASs) of European ancestry that were focused on sleep duration, insomnia, chronotype, lifetime cannabis use, and cannabis use disorder (CUD). A target sample for PRS prediction consisted of high-risk participants and participants from twin/family community-based studies (n = 796, male = 66%; mean age = 26.81). Target data consisted of self-reported sleep (sleep duration, feeling tired, and taking naps) and cannabis use behaviors (lifetime use, number of lifetime uses, past 180-day use, age of first use, and lifetime CUD symptoms).ResultsSignificant genetic correlation between lifetime cannabis use and eveningness chronotype (rG = 0.24,p< 0.01), as well as between CUD and both short sleep duration (<7 h) (rG = 0.23,p= 0.02) and insomnia (rG = 0.20,p= 0.02). Insomnia PRS predicted earlier age of first cannabis use (β= −0.09,p= 0.02) and increased lifetime CUD symptom count use (β= 0.07,p= 0.03).ConclusionCannabis use is genetically associated with both sleep deficits and an eveningness chronotype, suggesting that there are genes that predispose individuals to both cannabis use and sleep deficits.
Clarithromycin Exerts an Antibiofilm Effect againstSalmonella typhimuriumrdar Biofilm Formation, and Transforms the Physiology towards an Apparent Oxygen-depleted Energy and Carbon Metabolism
Authors: Zafar Munira , Jahan Humera , Shafeeq Sulman , Nimtz Manfred , Jänsch Lothar , Römling Ute , Choudhary M. Iqbal 
Published: May 2020

ABSTRACTUpon biofilm formation, production of extracellular matrix components and alteration in physiology and metabolism allows bacteria to build up multicellular communities which can facilitate nutrient acquisition during unfavorable conditions and provide protection towards various forms of environmental stresses to individual cells. Thus, bacterial cells become tolerant against antimicrobials and the immune system within biofilms. In the current study, we evaluated the antibiofilm activity of the macrolides clarithromycin and azithromycin. Clarithromycin showed antibiofilm activity against rdar (red, dry and rough) biofilm formation of the gastrointestinal pathogenSalmonella typhimuriumATCC14028 Nalrat 1.56 μM subinhibitory concentration in standing culture and dissolved cell aggregates at 15 μM in a microaerophilic environment suggesting that the oxygen level affects the activity of the drug. Treatment with clarithromycin significantly decreased transcription and production of the rdar biofilm activator CsgD, with biofilm genes such ascsgBandadrAto be consistently downregulated. WhilefliAand other flagellar regulon genes were upregulated, apparent motility was downregulated. RNA sequencing showed a holistic cell response upon clarithromycin exposure, whereby not only genes involved in the biofilm-related regulatory pathways, but also genes that likely contribute to intrinsic antimicrobial resistance, and the heat shock stress response were differentially regulated. Most significantly, clarithromycin exposure shifts the cells towards an apparent oxygen- and energy-depleted status, whereby the metabolism that channels into oxidative phosphorylation is downregulated, and energy gain by degradation of propane 1,2-diol, ethanolamine and L-arginine catabolism is upregulated. This initial analysis will allow the subsequent identification of novel intrinsic antimicrobial resistance determinants.
Precise optical control of gene expression inC. elegansusing genetic code expansion and Cre recombinase
Authors: Davis Lloyd , Radman Inja , Goutou Angeliki , Tynan Ailish , Baxter Kieran , Xi Zhiyan , O’Shea Jack M. , Chin Jason W. , Greiss Sebastian 
Published: May 2020

AbstractSynthetic strategies for optically controlling gene expression may enable the precise spatiotemporal control of genes in any combination of cells that cannot be targeted with specific promoters. We develop an efficient genetic code expansion system inC. elegansand use it to create a photo-activatable Cre recombinase. We laser-activate Cre in single neurons within a bilaterally symmetric pair to selectively switch on expression of a loxP controlled optogenetic channel in the targeted neuron. We use the system to dissect, in freely moving animals, the individual contributions of the mechanosensory neurons PLML/PLMR to theC. eleganstouch response circuit, revealing distinct and synergistic roles for these neurons. We thus demonstrate how genetic code expansion and optical targeting can be combined to break the symmetry of neuron pairs and dissect behavioural outputs of individual neurons that cannot be genetically targeted.
Release of potential pro-inflammatory peptides from SARS-CoV-2 spike glycoproteins in neutrophil-extracellular traps
Authors: Blanco-Míguez Aitor , Sánchez Borja 
Published: May 2020

AbstractCOVID-2019 has progressed in around 10-15% of patients to an acute respiratory distress syndrome characterized by extensive pulmonary inflammation and elevated production of pro-inflammatory cytokines. Neutrophil activation seems to be crucial in the initiation and perpetuation of this exacerbated lung inflammation. However, the precise mechanisms by which this activation occurs remain yet elusive. To this end, this in silico study tried to identify potential proinflammatory inducing peptides (PIPs) produced by the action of the elastase released in neutrophil-extracellular traps over SARS-CoV-2 particles. We found nine potential PIPs exclusive from the SARS-CoV-2, showing homology against T cell recognition epitopes. Moreover, 78 percent of these exclusive PIPs were found produced by the enzymatic cleavage on the spike glycoproteins, suggesting that high PIP concentrations might be released following SARS-CoV-2 huge replication rate. Therefore, these PIPs might play a role in the exacerbated inflammatory response observed in some patients.HighlightsNine potential PIPs were predicted exclusive from the SARS-CoV-2.SARS-CoV-2 PIPs showed homology against T cell recognition epitopes.Most of PIPs were produced by enzymatic cleavage of the spike glycoproteins.The release of these PIPs might be related to the increased inflammatory response observed in the patients.Graphical abstract
Formation of biomolecular condensates in bacteria by tuning protein electrostatics
Authors: Yeong Vivian , Werth Emily G. , Brown Lewis M. , Obermeyer Allie C. 
Published: May 2020

AbstractBiomolecular condensates provide a strategy for cellular organization without a physical membrane barrier while allowing for dynamic, responsive organization of the cell. To date, very few biomolecular condensates have been identified in prokaryotes, presenting an obstacle to engineering these compartments in bacteria. As a novel strategy for bacterial compartmentalization, protein supercharging and complex coacervation were employed to engineer liquid-like condensates inE. coli. A simple model for the phase separation of supercharged proteins was developed and used to predict intracellular condensate formation. Herein, we demonstrate that GFP-dense condensates formed by expressing GFP variants of sufficient charge in cells are dynamic and enrich specific nucleic acid and protein components. This study provides a fundamental characterization of intracellular phase separation inE. colidriven by protein supercharging and highlights future utility in designing functional synthetic membraneless organelles.
Identification of Drugs Blocking SARS-CoV-2 Infection using Human Pluripotent Stem Cell-derived Colonic Organoids
Authors: Duan Xiaohua , Han Yuling , Yang Liuliu , Nilsson-Payant Benjamin E. , Wang Pengfei , Zhang Tuo , Xiang Jenny , Xu Dong , Wang Xing , Uhl Skyler , Huang Yaoxing , Chen Huanhuan Joyce , Wang Hui , tenOever Benjamin , Schwartz Robert E. , Ho David. D. , Evans Todd , Pan Fong Cheng , Chen Shuibing 
Published: May 2020

Summary ParagraphThe current COVID-19 pandemic is caused by SARS-coronavirus 2 (SARS-CoV-2). There are currently no therapeutic options for mitigating this disease due to lack of a vaccine and limited knowledge of SARS-CoV-2 biology. As a result, there is an urgent need to create new disease models to study SARS-CoV-2 biology and to screen for therapeutics using human disease-relevant tissues. COVID-19 patients typically present with respiratory symptoms including cough, dyspnea, and respiratory distress, but nearly 25% of patients have gastrointestinal indications including anorexia, diarrhea, vomiting, and abdominal pain. Moreover, these symptoms are associated with worse COVID-19 outcomes1. Here, we report using human pluripotent stem cell-derived colonic organoids (hPSC-COs) to explore the permissiveness of colonic cell types to SARS-CoV-2 infection. Single cell RNA-seq and immunostaining showed that the putative viral entry receptor ACE2 is expressed in multiple hESC-derived colonic cell types, but highly enriched in enterocytes. Multiple cell types in the COs can be infected by a SARS-CoV-2 pseudo-entry virus, which was further validatedin vivousing a humanized mouse model. We used hPSC-derived COs in a high throughput platform to screen 1280 FDA-approved drugs against viral infection. Mycophenolic acid and quinacrine dihydrochloride were found to block the infection of SARS-CoV-2 pseudo-entry virus in COs bothin vitroandin vivo, and confirmed to block infection of SARS-CoV-2 virus. This study established bothin vitroandin vivoorganoid models to investigate infection of SARS-CoV-2 disease-relevant human colonic cell types and identified drugs that blocks SARS-CoV-2 infection, suitable for rapid clinical testing.
Rapid adaptation of SARS-CoV-2 in BALB/c mice: Novel mouse model for vaccine efficacy
Authors: Gu Hongjing , Chen Qi , Yang Guan , He Lei , Fan Hang , Deng Yong-Qiang , Wang Yanxiao , Teng Yue , Zhao Zhongpeng , Cui Yujun , Li Yuchang , Li Xiao-Feng , Li Jiangfan , Zhang Nana , Yang Xiaolan , Chen Shaolong , Zhao Guangyu , Wang Xiliang , Luo Deyan , Wang Hui , Yang Xiao , Li Yan , Han Gencheng , He Yuxian , Zhou Xiaojun , Geng Shusheng , Sheng Xiaoli , Jiang Shibo , Sun Shihui , Qin Cheng-Feng , Zhou Yusen 
Published: May 2020

AbstractCoronavirus disease 2019 (COVID-19) threatens global public health and economy. In order to develop safe and effective vaccines, suitable animal models must be established. Here we report the rapid adaption of SARS-CoV-2 in BALB/c mice, based on which a convenient, economical and effective animal model was developed. Specifically, we found that mouse-adapted SARS-CoV-2 at passage 6 (MACSp6) efficiently infected both aged and young wild-type BALB/c mice, resulting in moderate pneumonia as well as inflammatory responses. The elevated infectivity of MACSp6 in mice could be attributed to the substitution of a key residue (N501Y) in the receptorbinding domain (RBD). Using this novel animal model, we further evaluated the in vivo protective efficacy of an RBD-based SARS-CoV-2 subunit vaccine, which elicited highly potent neutralizing antibodies and conferred full protection against SARS-CoV-2 MACSp6 challenge. This novel mouse model is convenient and effective in evaluating thein vivoprotective efficacy of SARS-CoV-2 vaccine.SummaryThis study describes a unique mouse model for SARS-CoV-2 infection and confirms protective efficacy of a SARS-CoV-2 RBD subunit vaccine.
Reproductive tissues-specific meta-QTLs and candidate genes for development of heat-tolerant rice cultivars
Authors: Raza Qasim , Riaz Awais , Bashir Khurram , Sabar Muhammad 
Published: May 2020

AbstractRice holds the key to future food security. In rice-growing areas, temperature has already reached an optimum level for growth, hence, any further increase due to global climate change could significantly reduce rice yield. Several mapping studies have identified a plethora of reproductive tissue-specific and heat stress associated inconsistent quantitative trait loci (QTL), which could be exploited for improvement of heat tolerance. In this study, we performed a meta-analysis on previously reported QTLs and identified 35 most consistent meta-QTLs (MQTLs) across diverse genetic backgrounds and environments. Genetic and physical intervals of nearly 66% MQTLs were narrower than 5 cM and 2 Mb respectively, indicating hotspot genomic regions for heat tolerance. Comparative analyses of MQTLs underlying genes with microarray and RNA-seq based transcriptomic data sets revealed a core set of 45 heat-responsive genes, among which 24 were reproductive tissue-specific and have not been studied in detail before. Remarkably, all these genes corresponded to various stress associated functions, ranging from abiotic stress sensing to regulating plant stress responses, and included heat-shock genes (OsBiP2, OsMed37_1), transcription factors (OsNAS3, OsTEF1, OsWRKY10, OsWRKY21), transmembrane transporters (OsAAP7A, OsAMT2;1), sugar metabolizing (OsSUS4, α-Gal III) and abiotic stress (OsRCI2-7, SRWD1) genes. Functional data evidences fromArabidopsisheat-shock genes also suggest thatOsBIP2may be associated with thermotolerance of pollen tubes under heat stress conditions. Furthermore, promoters of identified genes were enriched with heat, dehydration, pollen and sugar responsive cis-acting regulatory elements, proposing a common regulatory mechanism might exist in rice for mitigsating reproductive stage heat stress. These findings strongly support our results and provide new candidate genes for fast-track development of heat-tolerant rice cultivars.Key MessageBy integrating genetics and genomics data, reproductive tissues-specific and heat stress responsive 35 meta-QTLs and 45 candidate genes were identified, which could be exploited through marker-assisted breeding for fast-track development of heat-tolerant rice cultivars.
LINE-1 DNA methylation in response to aging and vitamin D
Authors: Ong Lawrence T. C. , Schibeci Stephen D , Fewings Nicole L , Booth David R , Parnell Grant P 
Published: May 2020

AbstractRetrotransposons are genetic elements capable of their own propagation and insertion into the human genome. Because of their mutagenic potential, retrotransposons are heavily suppressed by mechanisms including DNA methylation. Increased age is associated with decreasing DNA methylation of the LINE-1 retrotransposon and may partially explain the predisposition towards malignancy with advancing age. Vitamin D has been investigated for its effects on DNA methylation at LINE-1 elements with mixed results. This study hypothesised that LINE-1 DNA methylation is altered by vitamin D exposure and age. Using whole genome bisulfite sequencing of adult and newborn haematopoietic progenitors, DNA methylation at LINE-1 elements was not found to vary between cells cultured with or without calcitriol, both in adults and newborns. In contrast, several LINE-1 regions were found to be differentially methylated between adults and children, but these were not uniformly hypermethylated in paediatric cells. The results of this study suggest that at least in haematopoietic cells, vitamin D does not appear to affect LINE-1 methylation.
Drosophilainsulin-like peptide 8 (DILP8) in ovarian follicle cells regulates ovulation and metabolism
Authors: Liao Sifang , Nässel Dick R. 
Published: May 2020

AbstractInDrosophilaeight insulin-like peptides (DILP1-8) are encoded on separate genes. These DILPs are characterized by unique spatial and temporal expression patterns during the lifecycle. Whereas functions of several of the DILPs have been extensively investigated at different developmental stages, the role of DILP8 signaling is primarily known from larvae and pupae where it couples organ growth and developmental transitions. In adult female flies, a study showed that a specific set of neurons that express the DILP8 receptor, Lgr3, is involved in regulation of reproductive behavior. Here, we further investigated the expression ofdilp8/DILP8 andLgr3in adult female flies and the functional role of DILP8 signaling. The only site where we found bothdilp8expression and DILP8 immunolabeling was in follicle cells of mature ovaries.Lgr3expression was detected in numerous neurons in the brain and ventral nerve cord, a small set of peripheral neurons innervating the abdominal heart, as well as in a set of follicle cells close to the oviduct. Ovulation was affected indilp8mutants as well as afterdilp8-RNAi usingdilp8and follicle cell Gal4 drivers. More eggs were retained in the ovaries and fewer were laid, indicating that DILP8 is important for ovulation. Our data suggest that DILP8 signals locally toLgr3expressing follicle cells as well as systemically toLgr3expressing efferent neurons in abdominal ganglia that innervate oviduct muscle. Thus, DILP8 may act at two targets to regulate ovulation: follicle cell rupture and oviduct contractions. Furthermore, we could show that manipulations ofdilp8expression affect food intake and starvation resistance. Possibly this reflects a feedback signaling between ovaries and the CNS that ensures nutrients for ovary development. In summary, it seems that DILP8 signaling in regulation of reproduction is an ancient function, conserved in relaxin signaling in mammals.