bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pancreas patch-seq links physiologic dysfunction in diabetes to single-cell transcriptomic phenotypes
Authors: Camunas-Soler Joan , Dai Xiaoqing , Hang Yan , Bautista Austin , Lyon James , Suzuki Kunimasa , Kim Seung K , Quake Stephen R , MacDonald Patrick E 
Published: February 2019

SummaryPancreatic islet cells regulate glucose homeostasis through insulin and glucagon secretion; dysfunction of these cells leads to severe diseases like diabetes. Prior single-cell transcriptome studies have shown heterogeneous gene expression in major islet cell-types; however it remains challenging to reconcile this transcriptomic heterogeneity with observed islet cell functional variation. Here we achieved electrophysiological profiling and single-cell RNA sequencing in the same islet cell (pancreas patch-seq) thereby linking transcriptomic phenotypes to physiologic properties. We collected 1,369 cells from the pancreas of donors with or without diabetes and assessed function-gene expression networks. We identified a set of genes and pathways that drive functional heterogeneity in β-cells and used these to predict β-cell electrophysiology. We also report specific transcriptional programs that correlate with dysfunction in type 2 diabetes (T2D) and extend this approach to cryopreserved cells from donors with type 1 diabetes (T1D), generating a valuable resource for understanding islet cell heterogeneity in health and disease.Key findingsPancreas patch-seq provides a single-cell survey of function-transcriptome pairing in 1,369 islet cells from donors with and without diabetesExpression of a specific subset of genes predicts β-cell electrophysiology in transcriptome-function networks.Compromised β-cell function in T2D correlates with altered ETV1 expression and inflammatory pathwaysFunctional heterogeneity in α-cells maps to ER stress and islet lineage markersApplication of patch-seq to cells from rare cryopreserved islets from donors with T1D
Nucleic Acid Cleavage with a Hyperthermophilic Cas9 from an Unculturable Ignavibacterium
Authors: Schmidt Stephanie Tzouanas , Yu Feiqiao Brian , Blainey Paul C. , May Andrew P. , Quake Stephen R. 
Published: February 2019

AbstractCRISPR-Cas9 systems have been effectively harnessed to engineer the genomes of organisms from across the tree of life. Nearly all currently characterized Cas9 proteins are derived from mesophilic bacteria, and canonical Cas9 systems are challenged by applications requiring enhanced stability or elevated temperatures. We discovered IgnaviCas9, a Cas9 protein from a hyperthermophilic Ignavibacterium identified through mini-metagenomic sequencing of samples from a hot spring. IgnaviCas9 is active at temperatures up to 100 °C in vitro, which enables DNA cleavage beyond the 44 °C limit of Streptococcus pyogenes Cas9 (SpyCas9) and the 70 °C limit of both Geobacillus stearothermophilus Cas9 (GeoCas9) and Geobacillus thermodenitrificans T12 Cas9 (ThermoCas9). As a potential application of this enzyme, we demonstrated that IgnaviCas9 can be used in bacterial RNA-seq library preparation to remove unwanted cDNA from 16s ribosomal rRNA (rRNA) without increasing the number of steps, thus underscoring the benefits provided by its exceptional thermostability in improving molecular biology and genomic workflows. Taken together, IgnaviCas9 is an exciting addition to the CRISPR-Cas9 toolbox and expands its temperature range.
Disrupted Mechanobiology Links the Molecular and Cellular Phenotypes in Familial Dilated Cardiomyopathy
Authors: Clippinger Sarah R. , Cloonan Paige E. , Greenberg Lina , Ernst Melanie , Tom Stump W. , Greenberg Michael J. 
Published: February 2019

AbstractFamilial dilated cardiomyopathy (DCM) is a leading cause of sudden cardiac death and a major indicator for heart transplant. The disease is frequently caused by mutations of sarcomeric proteins; however, it is not well understood how these molecular mutations lead to alterations in cellular organization and contractility. To address this critical gap in our knowledge, we studied the molecular and cellular consequences of a DCM mutation in troponin-T, ΔK210. We determined the molecular mechanism of ΔK210 and used computational modeling to predict that the mutation should reduce the force per sarcomere. In mutant cardiomyocytes, we found that ΔK210 not only reduces contractility, but also causes cellular hypertrophy and impairs cardiomyocytes’ ability to adapt to changes in substrate stiffness (e.g., heart tissue fibrosis that occurs with aging and disease). These results link the molecular and cellular phenotypes and implicate alterations in mechanosensing as an important factor in the development of DCM.
Gene regulatory network of human GM-CSF secreting T helper cells
Authors: Éliás Szabolcs , Schmidt Angelika , Gomez-Cabrero David , Tegnér Jesper 
Published: February 2019

ABSTRACTGM-CSF produced by autoreactive CD4 positive T helper cells is involved in the pathogenesis of autoimmune diseases, such as Multiple Sclerosis. However, the molecular regulators that establish and maintain the features of GM-CSF positive CD4 T cells are unknown. In order to identify these regulators, we isolated human GM-CSF producing CD4 T cells from human peripheral blood by using a cytokine capture assay. We compared these cells to the corresponding GM-CSF negative fraction, and furthermore, we studied naïve CD4 T cells, memory CD4 T cells and bulk CD4 T cells from the same individuals as additional control cell populations. As a result, we provide a rich resource of integrated chromatin accessibility (ATAC-seq) and transcriptome (RNA-seq) data from these primary human CD4 T cell subsets, and we show that the identified signatures are associated with human autoimmune disease, especially Multiple Sclerosis. By combining information about mRNA expression, DNA accessibility and predicted transcription factor binding, we reconstructed directed gene regulatory networks connecting transcription factors to their targets, which comprise putative key regulators of human GM-CSF positive CD4 T cells as well as memory CD4 T cells. Our results suggest potential therapeutic targets to be investigated in the future in human autoimmune disease.
In Situ Electrochemical Studies of the Terrestrial Deep Subsurface Biosphere at the Sanford Underground Research Facility, South Dakota, USA
Authors: Jangir Yamini , Karbelkar Amruta A. , Beedle Nicole M. , Zinke Laura A. , Wanger Greg , Anderson Cynthia M. , Reese Brandi Kiel , Amend Jan P. , El-Naggar Mohamed Y. 
Published: February 2019

ABSTRACTThe terrestrial deep subsurface is host to significant and diverse microbial populations. However, these microbial populations remain poorly characterized, partially due to the inherent difficulty of sampling,in situstudies, and isolating of thein situmicrobes. Motivated by the ability of microbes to gain energy from redox reactions at mineral interfaces, we here presentin situelectrochemical colonization (ISEC) as a method to directly study microbial electron transfer activity and to enable the capture and isolation of electrochemically active microbes. We installed a potentiostatically controlled ISEC reactor containing four working electrodes 1500 m below the surface at the Sanford Underground Research Facility. The working electrodes were poised at different redox potentials, spanning anodic to cathodic, to mimic energy-yielding mineral reducing and oxidizing reactions predicted to occur at this site. We present a 16S rRNA analysis of thein situelectrode-associated microbial communities, revealing the dominance of novel bacterial lineages under cathodic conditions. We also demonstrate that thein situelectrodes can be further used for downstream electrochemical laboratory enrichment and isolation of novel strains. Using this workflow, we isolatedBacillus,Anaerospora,Comamonas,Cupriavidus, andAzonexusstrains from the electrode-attached biomass. Finally, the extracellular electron transfer activity of the electrode-oxidizingComamonasstrain (isolated at −0.19 V vs. SHE and designated WE1-1D1) and the electrode-reducingBacillusstrain (isolated at +0.53 V vs. SHE and designated WE4-1A1-BC) were confirmed in electrochemical reactors. Our study highlights the utility ofin situelectrodes and electrochemical enrichment workflows to shed light on microbial activity in the deep terrestrial subsurface.SIGNIFICANCEA large section of microbial life resides in the deep subsurface, but an organized effort to explore this deep biosphere has only recently begun. A detailed characterization of the resident microbes remains scientifically and technologically challenging due to difficulty in access, sampling, and emulating the complex interactions and energetic landscapes of subsurface communities with standard laboratory techniques. Here we describe an in situ approach that exploits the ability of many microbes to perform extracellular electron transfer to/from solid surfaces such as mineral interfaces in the terrestrial subsurface. By deploying and controlling the potential of in situ electrodes 4850 ft below the surface at the Sanford Underground Research Facility (South Dakota, USA), we highlight the promise of electrochemical techniques for studying active terrestrial subsurface microbial communities and enabling the isolation of electrochemically active microbes.
The influence of sex on the urogenital microbiome of rhesus monkeys
Authors: Hallmaier-Wacker L. K. , Lueert S. , Roos C. , Knauf S. 
Published: February 2019

AbstractThe vaginal microbiome of nonhuman primates (NHPs) differs substantially from humans in terms of Lactobacillus abundance, overall taxonomic diversity, and vaginal pH. Given these differences, it remains unclear in what way the NHP genital microbiome protects against pathogens, in particular sexually transmitted diseases. Considering the effect that microbiome variations can have on disease acquisition and outcome, we examined endogenous and exogenous factors that influence the urogenital microbiome of captive rhesus monkeys. The male urethral (n=37) and vaginal (n=194) microbiome of 11 breeding groups were examined in a cross-sectional study. During lactation and menstruation, the vaginal microbiome becomes significantly more diverse and more similar to the microbes observed in the male urethra. Group association and cage-mate (sexual partners) relationships were additionally associated with significant differences in the urogenital microbiome. Our results demonstrate that microbiome considerations are necessary in order to make informed selection of NHPs as translational animal models.
Brain gene expression in a novel mouse model of postpartum mood disorder
Authors: Humby Trevor , Davies William 
Published: February 2019

AbstractIntroductionSteroid sulfatase (STS) is an enzyme which cleaves sulfate groups from a variety of steroid hormones, thereby altering their activity and solubility. The expression and activity of STS is increased in female mammalian tissues (including brain) during late pregnancy and into the postpartum period. STS-deficient human and mouse mothers (as a consequence of genetic mutation or acute pharmacological manipulation) show evidence for elevated psychopathology and abnormal behaviour respectively in the postpartum period. In mice, these behavioural effects can be partially normalised through administration of the antipsychotic ziprasidone.MethodsTo explore the neurobiology underlying these postpartum behavioural effects, we compared whole brain gene expression by microarray in behaviourally-defined new mouse mothers acutely administered the STS inhibitor 667-Coumate (10mg/kg p.o.) or vehicle solution (n=12 per group); significant changes were followed-up with pathway analysis and quantitative polymerase chain reaction (qPCR). Finally, the effects of combined 667-Coumate and antipsychotic (ziprasidone) administration (0, 0.3 and 1.0mg/kg i.p.) on the brain expression of the most robustly differentially-expressed candidate genes was examined (n≥7 per group).ResultsSurprisingly, no significant gene expression changes were detected between vehicle and 667-Coumate-treated brains at a False Discovery Rate (FDR) corrected p<0.1. 1,081 unique expression changes were detected at a less-stringent cut-off of p<0.05, just two top hits were verified by qPCR, and pathway analysis indicated a significant enrichment of genes involved in olfactory transduction (corrected p-value=1.8×10−3). The expression of the two most robust differentially-expressed genes (Stoml3 and Cyp2g1) was not affected by ziprasidone administration.ConclusionsBehavioural abnormalities in new mothers in the postpartum period elicited as a result of STS deficiency are likely to be the culmination of many small gene expression changes. Our data are consistent with the idea that olfactory function is key to postpartum maternal behaviour in mice, and suggest that aberrant expression of olfactory system genes may partially underlie abnormal maternal behaviour in STS-deficient women.
The COMPARE Data Hubs
Authors: Amid Clara , Pakseresht Nima , Silvester Nicole , Jayathilaka Suran , Lund Ole , Dynovski Lukasz D. , Pataki Bálint Á. , Visontai Dávid , Cotten Matthew , Xavier Basil Britto , Alako Blaise , Belka Ariane , Cisneros Jose J. L. , Haringhuizen George B. , Harrison Peter W. , Höper Dirk , Holt Sam , Hundahl Camilla , Hussein Abdulrahman , Kaas Rolf S. , Malhotra-Kumar Surbhi , Leinonen Rasko , Nieuwenhuijse David F. , Rahman Nadim , Ribeiro Carolina dos S , Skiby Jeffrey E. , Stéger József , Szalai-Gindl János M. , Thomsen Martin C. F. , Csabai István , Koopmans Marion , Aarestrup Frank , Cochrane Guy 
Published: February 2019

AbstractData sharing enables research communities to exchange findings and build upon the knowledge that arises from their discoveries. Areas of public and animal health as well as food safety would benefit from rapid data sharing when it comes to emergencies. However, ethical, regulatory, and institutional challenges, as well as lack of suitable platforms which provide an infrastructure for data sharing in structured formats often lead to data not being shared, or at most shared in form of supplementary materials in journal publications. Here, we describe an informatics platform that includes workflows for structured data storage, managing and pre-publication sharing of pathogen sequencing data and its analysis interpretations with relevant stakeholders.
Direct Effects of Cigarette Smoke in Pulmonary Arterial Cells alter Vascular Tone through Arterial Remodeling and Kv7.4 Channel Dysregulation
Authors: Sevilla-Montero J , Labrousse-Arias D , Fernández-Pérez C , Barreira B , Mondejar-Parreño G , Cogolludo A , Calzada MJ 
Published: February 2019

AbstractChronic obstructive pulmonary disease (COPD) is a widespread disease, with no curative therapies nowadays. Exposure to cigarette smoking is considered the chief leading cause of COPD. Current drugs therapies improve patient quality of life, however they do not revert the progression of the disease. Therefore, a deeper study of the cellular and molecular mechanisms that underlie this pathology is required to be able to carry out targeted and effective treatments. Although the effects of cigarette smoke in the progressive deterioration of the airway have been extensively studied in COPD patients, its effects on pulmonary vasculature have been unexplored, due to the classic conception that vascular damage is a consequence of alveolar hypoxia and loss of capillary bed. In this paper, we aimed to study the effects of cigarette smoke extract (CSE) in regulating pulmonary arterial cells phenotypic modulation, in particular the effects in fibroblasts (hPAFib) and smooth muscle cells (hPASMC), and in murine pulmonary arteries. Our results demonstrated that CSE exposure had direct effects on hPAFib and hPASMC, promoting a senescent phenotype that in turn contributed, through the secretion of inflammatory molecules, to increase the proliferative potential of non-exposed cells. CSE also increased total ROS levels in hPAFib and hPASMC, and upregulated NADPH oxidase subunits NOX1 and p22phox. Most importantly, CSE affected cell contractility and dysregulated the expression and activity of voltage-gated K+ channel Kv7.4. This contributed to limit vascular responses impairing vasoconstriction and endothelium-dependent and independent relaxation.
Genetic and shared couple environmental contributions to smoking and alcohol use in the UK population
Authors: Clarke Toni-Kim , Adams Mark J. , Howard David M. , Xia Charley , Davies Gail , Hayward Caroline , Campbell Archie , Padmanabhan Sandosh , Smith Blair H. , Murray Alison , Porteous David , Deary Ian J. , McIntosh Andrew M. 
Published: February 2019

AbstractAlcohol use and smoking are leading causes of death and disability worldwide. Both genetic and environmental factors have been shown to influence individual differences in the use of these substances. In the present study we tested whether genetic factors, modelled alongside common family environment, explained phenotypic variance in alcohol use and smoking behaviour in the Generation Scotland (GS) family sample of up to 19,377 individuals. SNP and pedigree-associated effects combined explained between 18% and 41% of the variance in substance use. Shared couple effects explained a significant amount of variance across all substance use traits, particularly alcohol intake, for which 38% of the phenotypic variance was explained. We tested whether the within-couple substance use correlations were due to assortative mating by testing the association between partner polygenic risk scores in 34,987 couple pairs from the UK Biobank (UKB). Only couples’ smoking status PRSs were significantly associated (b=0.01, S.E=0.005, p=0.02). However, an individual’s alcohol PRS was associated with their partner’s phenotype (b=0.04, S.E=0.007, p < 2 x 10-7). In support of this, G carriers of a functional ADH1B polymorphism (rs1229984), known to be associated with greater alcohol intake, were found to consume less alcohol if they had a partner who carried an A allele at this SNP. Together these results show that the shared couple environment contributes significantly to patterns of substance use. It is unclear whether this is due to shared environmental factors, assortative mating, or indirect genetic effects. Future studies would benefit from longitudinal data and larger sample sizes to assess this further.
Defined neuronal populations drive fatal phenotype in Leigh Syndrome
Authors: Bolea Irene , Gella Alejandro , Sanz Elisenda , Prada-Dacasa Patricia , Menardy Fabien , Machuca-Márquez Pablo , Bard Angela Michelle , Kalume Franck , Quintana Albert 
Published: February 2019

AbstractDysfunctions of the mitochondrial energy-generating machinery cause a series of progressive, untreatable and usually fatal diseases collectively known as mitochondrial disease. High energy-requiring organs such as the brain are especially affected, leading to developmental delay, ataxia, respiratory failure, hypotonia, seizures and premature death. While neural affectation is a critical component of the pathology, only discrete neuronal populations are susceptible. However, their molecular identity and their contribution to the disease remain unknown. Mice lacking the mitochondrial Complex I subunit NDUFS4 (Ndufs4KO mice) recapitulate the classical signs of Leigh Syndrome (LS), the most common presentation of mitochondrial disease with predominant CNS affectation. Here, we identify the critical role of two genetically-defined neuronal populations driving the fatal phenotype in Ndufs4KO mice. Selective inactivation of Ndufs4 in Vglut2-expressing glutamatergic neurons causes brainstem inflammation, motor and respiratory deficits, and early death. On the other hand, Ndufs4 deletion in GABAergic neurons leads to basal ganglia inflammation without motor or respiratory involvement, but accompanied by severe refractory epileptic seizures preceding premature death. These results provide novel insight in the cell type-specific contribution to LS pathology and open new avenues to understand the underlying cellular mechanisms of mitochondrial disease.
Considerations for clinical curation, classification and reporting of low-penetrance and low effect size variants associated with disease risk
Authors: Senol-Cosar Ozlem , Schmidt Ryan J. , Qian Emily , Hoskinson Derick , Mason-Suares Heather , Funke Birgit , Lebo Matthew S. 
Published: February 2019

ABSTRACTPurposeClinically relevant variants exhibit a wide range of penetrance. Medical practice has traditionally focused on highly penetrant variants with large effect sizes and, consequently, classification and clinical reporting frameworks are tailored to that variant type. At the other end of the penetrance spectrum, where variants are often referred to as “risk alleles”, traditional frameworks are no longer appropriate. This has led to inconsistency in how such variants are interpreted and classified. Here, we describe a conceptual framework to begin addressing this gap.MethodsWe used a set of risk alleles to define data elements that can characterize the validity of reported disease associations. We assigned weight to these data elements and established classification categories expressing confidence levels. This framework was then expanded to develop criteria for inclusion of risk alleles on clinical reports.ResultsFoundational data elements include cohort size, quality of phenotyping, statistical significance, and replication of results. Criteria for determining inclusion of risk alleles on clinical reports include presence of clinical management guidelines, effect size, severity of the associated phenotype, and effectiveness of intervention.ConclusionsThis framework represents an approach for classifying risk alleles and can serve as a foundation to catalyze community efforts for refinement.
Adrenergic signaling in muscularis macrophages limits neuronal death following enteric infection
Authors: Matheis Fanny , Muller Paul A. , Graves Christina , Gabanyi Ilana , Kerner Zachary J. , Costa-Borges Diego , Mucida Daniel 
Published: February 2019

SummaryEnteric–associated neurons (EANs) are closely associated with immune cells and continuously monitor and modulate homeostatic intestinal functions, including motility. Bidirectional interactions between immune and neuronal cells are altered during disease processes such as neurodegeneration or irritable bowel syndrome. We investigated how infection-induced inflammation affects intrinsic EANs and the role of intestinalmuscularismacrophages (MMs) in this process. Using murine model of bacterial infection, we observed long-term gastrointestinal symptoms including reduced motility and subtype-specific neuronal loss. Neuronal-specific translational–profiling uncovered a caspase 11–dependent EAN cell–death mechanism induced by enteric infections. MMs responded to luminal infection by upregulating a neuroprotective program; gain– and loss–of-function experiments indicated that β2-adrenergic receptor (β2-AR) signaling in MMs mediates neuronal protection during infection via an arginase 1-polyamine axis. Our results identify a mechanism of neuronal cell death post–infection and point to a role for tissue–resident MMs in limiting neuronal damage.