bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cardiac Cell Type-Specific Gene Regulatory Programs and Disease Risk Association
Authors: Hocker James D. , Poirion Olivier B. , Zhu Fugui , Buchanan Justin , Zhang Kai , Chiou Joshua , Wang Tsui-Min , Hou Xiaomeng , Li Yang E. , Zhang Yanxiao , Farah Elie N. , Wang Allen , McCulloch Andrew D. , Gaulton Kyle J. , Ren Bing , Chi Neil C. , Preissl Sebastian 
Published: September 2020

ABSTRACTBackgroundCis-regulatory elements such as enhancers and promoters are crucial for directing gene expression in the human heart. Dysregulation of these elements can result in many cardiovascular diseases that are major leading causes of morbidity and mortality worldwide. In addition, genetic variants associated with cardiovascular disease risk are enriched withincis-regulatory elements. However, the location and activity of thesecis-regulatory elements in individual cardiac cell types remains to be fully defined.MethodsWe performed single nucleus ATAC-seq and single nucleus RNA-seq to define a comprehensive catalogue of candidatecis-regulatory elements (cCREs) and gene expression patterns for the distinct cell types comprising each chamber of four non-failing human hearts. We used this catalogue to computationally deconvolute dynamic enhancers in failing hearts and to assign cardiovascular disease risk variants to cCREs in individual cardiac cell types. Finally, we applied reporter assays, genome editing and electrophysiogical measurements inin vitrodifferentiated human cardiomyocytes to validate the molecular mechanisms of cardiovascular disease risk variants.ResultsWe defined >287,000 candidatecis-regulatory elements (cCREs) in human hearts at single-cell resolution, which notably revealed gene regulatory programs controlling specific cell types in a cardiac region/structure-dependent manner and during heart failure. We further report enrichment of cardiovascular disease risk variants in cCREs of distinct cardiac cell types, including a strong enrichment of atrial fibrillation variants in cardiomyocyte cCREs, and reveal 38 candidate causal atrial fibrillation variants localized to cardiomyocyte cCREs. Two such risk variants residing within a cardiomyocyte-specific cCRE at theKCNH2/HERGlocus resulted in reduced enhancer activity compared to the non-risk allele. Finally, we found that deletion of the cCRE containing these variants decreasedKCNH2expression and prolonged action potential repolarization in an enhancer dosage-dependent manner.ConclusionsThis comprehensive atlas of human cardiac cCREs provides the foundation for not only illuminating cell type-specific gene regulatory programs controlling human hearts during health and disease, but also interpreting genetic risk loci for a wide spectrum of cardiovascular diseases.
Phylogeographic model selection using convolutional neural networks
Authors: da Fonseca Emanuel Masiero , Colli Guarino R. , Werneck Fernanda P. , Carstens Bryan C. 
Published: September 2020

AbstractThe field of phylogeography has evolved rapidly in terms of the analytical toolkit to analyze the ever-increasing amounts of genomic data. Despite substantial advances, researchers have not fully explored all potential analytical tools to tackle the challenge posed by the huge size of genomic datasets. For example, deep learning techniques, such as convolutional neural networks (CNNs), widely employed in image and video classification, are largely unexplored for phylogeographic model selection. In non-model organisms, the lack of information about their ecology, natural history, and evolution can lead to uncertainty about which set of demographic models should be considered. Here we investigate the utility of CNNs for assessing a large number of competing phylogeographic models using South American lizards as an example, and approximate Bayesian computation (ABC) to contrast the performance of CNNs. First, we evaluated three demographic scenarios (constant, expansion, and bottleneck) for each of four recovered lineages and found that the overall model accuracy was higher than 98% for all lineages. Next, we evaluated a set of 26 models that accounted for evolutionary relationships, gene flow, and changes in effective population size among these lineages and recovered an overall accuracy of 87%. In contrast, ABC was unable to single out a best fit model among 26 competing models. Finally, we used the CNN model to investigate the evolutionary history of two South American lizards. Our results indicate the presence of hidden genetic diversity, gene flow between non-sister populations, and changes in effective population sizes through time, likely in response to Pleistocene climatic oscillations. Our results demonstrate that CNNs can be easily and usefully incorporated into the phylogeographer’s toolkit.
Constitutively active TrkB kinase signalling reduces actin filopodia dynamics and cell migration
Authors: Gupta Rohini , Bauer Melanie , Wohlleben Gisela , Luzak Vanessa , Wegat Vanessa , Segebarth Dennis , Bady Elena , Langlhofer Georg , Wachter Britta , Havlicek Steven , Lüningschrör Patrick , Villmann Carmen , Polat Bülent , Monoranu Camelia M. , Kuper Jochen , Blum Robert 
Published: September 2020

AbstractTrk receptors and gene fusions ofNTRKare targets in precision oncology. Classical Trk signalling concepts fail to explain ligand-independent signalling of intracellular TrkB orNTRKfusion proteins. Here, we show that abundance of the intracellular domain of TrkB is sufficient for ligand-independent autophosphorylation. This constitutive TrkB signalling reduced actin filopodia dynamics, could phosphorylate FAK, and changed cell morphology. Mutating Y705in the kinase domain of TrkB alone specifically blocked these pathways. Engineered intracellular kinase domain proteins and a cancer-related intracellularNTRK2-fusion protein (SQSTM1-NTRK2) also underwent constitutive activation. In migrating glioblastoma-like U87MG cells, self-active TrkB kinase reduced cell migration. Moreover, we found evidences for constitutively active, intracellular TrkB in tissue of human grade IV glioblastoma. Structural modelling of the kinase domain let us postulate that ‘release from cis-autoinhibition by abundance’ is sufficient for TrkB/FAK/Actin signalling via Y705. These constitutive signalling pathways could be fully blocked within minutes by clinically approved, anti-tumorigenic Trk inhibitors. In conclusion, our data provide an explanation and biological function for TrkB kinase domain signalling in the absence of a ligand.
The Novel PII-Interacting Regulator PirC (Sll0944) Identifies 3-Phosphoglycerate Mutase (PGAM) as Central Control Point of Carbon Storage Metabolism in Cyanobacteria
Authors: Orthwein Tim , Scholl Jörg , Spät Philipp , Lucius Stefan , Koch Moritz , Macek Boris , Hagemann Martin , Forchhammer Karl 
Published: September 2020

AbstractNitrogen limitation imposes a major transition in the life-style of non-diazotrophic cyanobacteria, which is regulated via a complex interplay of regulatory factors, involving, the nitrogen-specific transcription factor NtcA and the pervasive signal processor PII. Immediately upon nitrogen-limitation, newly fixed carbon is re-directed towards glycogen synthesis. How the metabolic switch for distributing fixed carbon to either glycogen or cellular building blocks is operated was poorly understood. Here we identify fromSynechocystissp. PCC 6803 a novel PII interactor, PirC, (Sll0944) that controls 3-phosphoglycerate mutase (PGAM), the enzyme that deviates newly fixed CO2towards lower glycolysis. PirC acts as competitive inhibitor of PGAM and this interaction is tuned by PII/2-oxoglutarate. High oxoglutarate release PirC from PII-complex to inhibit PGAM. Accordingly, PirC deficient mutant, as compared to the wild-type, shows strongly reduced glycogen levels upon nitrogen deprivation whereas polyhydroxybutyrate granules are over-accumulated. Metabolome analysis revealed an imbalance in 3-phosphoglycerate to pyruvate levels in the PirC mutant, conforming that PirC controls the carbon flux in cyanobacteria via mutually exclusive interaction with either PII or PGAM.
mTOR S-nitrosylation inhibits autophagy and lysosomal proteolysis
Authors: Tan Bryce W.Q. , Tan Sijie , Tan Byorn W.L. , Navakkode Sheeja , Ng Cheng Yang , Yuan Steven , Liang Mui Cheng , Liu Chao , Yin Shi , Chai Chou , Chew Katherine C.M. , Tai Yee Kit , Sajikumar Sreedharan , Lam Yulin , Liao Ping , Shen Han-Ming , Lim Kah-Leong , Wong Esther , Soong Tuck Wah 
Published: September 2020

AbstractMammalian Target of Rapamycin (mTOR) is a master regulator of autophagy and lysosomes, and its downstream kinase-dependent pathways have been extensively characterized. Here, we report an unexpected kinase-independent regulation of autophagy and lysosomes by S-nitrosylation at Cys423 position of mTOR that resulted in suppression of VPS34 and PIKfyve-dependent phosphoinositide synthesis. Physiologically, S-nitrosylation of mTOR reduced basal lysosomal proteolysis via nitric oxide synthase (NOS)-mediated synthesis of NO from lysosomal arginine precursor, a marker of cellular nutrition status. Significantly, we found increased lysosomal NOS-mTOR complexes in APP-PS1 Alzheimer’s disease (AD) murine model, and increased mTOR S-nitrosylation in AD patient-derived fibroblasts. Lastly, we demonstrated that pharmacological inhibition of NOS or overexpression of mTORCys423Alamutant reversed lysosomal and autophagic dysfunction in AD patient-derived fibroblasts, suggesting novel therapeutic strategies for autophagosome-lysosomal activation.
A key linear epitope for a potent neutralizing antibody to SARS-CoV-2 S-RBD
Authors: Li Tingting , Han Xiaojian , Wang Yingming , Gu Chenjian , Wang Jianwei , Hu Chao , Li Shenglong , Wang Kai , Luo Feiyang , Huang Jingjing , Long Yingyi , Song Shuyi , Wang Wang , Hu Jie , Wu Ruixin , Mu Song , Hao Yanan , Chen Qian , Gao Fengxia , Shen Meiying , Long Shunhua , Gong Fang , Li Luo , Wu Yang , Xu Wei , Cai Xia , Qu Di , Yuan Zhenghong , Gao Qingzhu , Zhang Guiji , He Changlong , Nai Yaru , Deng Kun , Du Li , Tang Ni , Xie Youhua , Huang Ailong , Jin Aishun 
Published: September 2020

AbstractThe spread of SARS-CoV-2 confers a serious threat to the public health without effective intervention strategies1–3. Its variant carrying mutated Spike (S) protein D614G (SD614G) has become the most prevalent form in the current global pandemic4,5. We have identified a large panel of potential neutralizing antibodies (NAbs) targeting the receptor-binding domain (RBD) of SARS-CoV-2 S6. Here, we focused on the top 20 potential NAbs for the mechanism study. Of them, the top 4 NAbs could individually neutralize both authentic SARS-CoV-2 and SD614Gpseudovirus efficiently. Our epitope mapping revealed that 16/20 potent NAbs overlapped the same steric epitope. Excitingly, we found that one of these potent NAbs (58G6) exclusively bound to a linear epitope on S-RBD (termed as 58G6e), and the interaction of 58G6e and the recombinant ACE2 could be blocked by 58G6. We confirmed that 58G6e represented a key site of vulnerability on S-RBD and it could positively react with COVID-19 convalescent patients’ plasma. We are the first, as far as we know, to provide direct evidences of a linear epitope that can be recognized by a potent NAb against SARS-CoV-2 S-RBD. This study paves the way for the applications of these NAbs and the potential safe and effective vaccine design.
A bootstrap approach is a superior statistical method for the comparison of cell-to-cell movement data
Authors: Johnston Matthew G. , Faulkner Christine 
Published: September 2020

SummaryPlasmodesmata are an increasing focus of plant research, and plant physiologists frequently aim to understand the dynamics of intercellular movement and plasmodesmal function. For this, experiments that measure the spread of GFP between cells are commonly performed to indicate whether plasmodesmata are more open or closed in different conditions or in different genotypes.We propose cell-to-cell movement data sets are better analysed by a bootstrap method that tests the null hypothesis that means (or medians) are the same between two conditions, instead of the commonly used Mann-Whitney-Wilcoxon test. We found that that with hypothetical distributions similar to cell-to-cell movement data, the Mann-Whitney-Wilcoxon produces a false positive rate of 17% while the bootstrap method maintains a false positive at the set rate of 5% under the same circumstances. Here we present this finding, as well as our rationale, an explanation of the bootstrap method and an R script for easy use. We have further demonstrated its use on published datasets from independent laboratories.
Changes in cellular signaling patterns before and after stroke in the middle cerebral arteries of stroke prone spontaneously hypertensive rats
Authors: Chokshi Killol , Warren Julie , Squires Krista , Kitselman Kayla A. , Doré Jules , Daneshtalab Noriko 
Published: September 2020

AbstractBackgroundHemorrhagic stroke is associated with loss of middle cerebral artery (MCA) autoregulation in the stroke-prone spontaneously hypertensive rat (SHRsp). The signaling mechanism associated with the functional loss has yet to be defined. We hypothesize that physiological alterations coincide with changes to cerebrovascular inflammatory and contractile signaling and altered calcium signaling. METHODS: SHRsp rats were fed a high salt (4% NaCl) diet and sacrificed at 9 weeks of age for pre-stroke and after evidence of stroke for post-stroke samples. The MCAs were isolated for measuring protein levels using immunofluorescence (IF) & western blot (WB) for inflammatory signaling and contractile proteins. Tissues surrounding the MCA were analyzed for neuro-inflammation, neuronal damage, total and activated inflammatory proteins (ERK1/2 and p38MAPK), cerebrovascular contraction (PKC and MLC), and transient receptor potential V4 (TRPV4) expression. RESULTS: Our data show increase in activated inflammatory proteins after stroke with an associated decrease in expression of activated contractile proteins and TRPV4 channel expression compared to pre-stroke MCA. The post-stroke samples also show significant increase in neuro-inflammation and neuronal damage compared to pre-stroke samples.CONCLUSIONAn increase in activated/total (p38 MAPK &ERK1/2) is accompanied by a decrease in activated/total PKC & TRPV4 channel expression in post-stroke SHRsps. The decrease in vessel structural integrity and altered vascular tone of the MCAs may affect its ability to contract in response to pressure. Significant neuro-inflammation and neuronal damage in the brain tissues surrounding the MCA in post-stroke samples suggest MCA dysfunction is accompanied with neuronal and neural damage during stroke.
Experimental-based Computational Modeling Distinguishes Early Cardiac Outflow Tract Compensation Mechanisms
Authors: Lindsey Stephanie E. , Vignon-Clementel Irene E. , Butcher Jonathan T. 
Published: September 2020

AbstractMechanical forces are essential for proper growth and remodeling of the primitive pharyngeal arch arteries (PAAs) into the great vessels of the heart. Despite general acknowledgement of a link between abnormal hemodynamics and cardiac malformations, the direct correlation between hemodynamics and pharyngeal arch artery morphogenesis remains poorly understood. The elusiveness behind understanding hemodynamic-malformation links is largely due to the difficulty of performing isolated hemodynamic perturbations and quantifying key hemodynamic indices in-vivo. To overcome this issue, minimally invasive occlusion experiments were combined with three-dimensional anatomical models of development and in-silico testing of experimental phenomenon. This combined experimental-computational approach led to a mechanistic understanding of physiological compensation mechanisms in abnormal cardiac morphogenesis. Using our experimental-based framework, we detail morphological and hemodynamic changes twenty-four hours post vessel occlusion. To gain mechanistic insights into the dynamic vessel adaptation process, we perform in-silico occlusions which allow for quantification of instantaneous changes in mechanical loading. We follow the propagation of small defects in a single embryo Hamburger Hamilton (HH) Stage 18 embryo to a more serious defect in an HH29 embryo. Results demonstrate that abnormal PAA hemodynamics can precipitate abnormal cardiac function given the correct timing and location of injury. Following vessel occlusion, morphology changes along the arches are no longer a simple flow-mediated response but rather work to maintain a range of wall shear stress values. Occlusion of the presumptive aortic arch overrides natural growth mechanisms and prevents it from becoming the dominant arch of the aorta.Author SummaryThe developing great vessels transport flow from the heart to the rest of the body. Proper spatial temporal morphogenesis of the primitive paired vessels into the definitive outflow tract of the heart is critical for normal cardiac function. Malpatterning of the great vessels is highly prevalent in congenital heart defects and occurs in conjunction with other intracardiac malformations, such as impaired ventricle and valve development. In this work, we combine experimental-based computational modeling with theoretical adaptation principles. Our combined experimental-computational framework allows for the delineation of immediate and longer-term vascular remodeling as well as the physical mechanisms behind such changes. We show that a small flow obstruction originating within the developing vessels can propagate into structurally serious malformations with impaired functionality.
In silico prediction of COVID-19 test efficiency with DinoKnot
Authors: Newman Tara , Chang Hiu Fung Kevin , Jabbari Hosna 
Published: September 2020

AbstractThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel coronavirus spreading across the world causing the disease COVID-19. The diagnosis of COVID-19 is done by quantitative reverse-transcription polymer chain reaction (qRT-PCR) testing which utilizes different primer-probe sets depending on the assay used. Using in silico analysis we aimed to determine how the secondary structure of the SARS-CoV-2 RNA genome affects the interaction between the reverse primer during qRT-PCR and how it relates to the experimental primer-probe test efficiencies. We introduce the program DinoKnot (Duplex Interaction of Nucleic acids with pseudoKnots) that follows the hierarchical folding hypothesis to predict the secondary structure of two interacting nucleic acid strands (DNA/RNA) of similar or different type. DinoKnot is the first program that utilizes stable stems in both strands as a guide to find the structure of their interaction. Using DinoKnot we predicted the interaction of the reverse primers used in four common COVID-19 qRT-PCR tests with the SARS-CoV-2 RNA genome. In addition, we predicted how 12 mutations in the primer/probe binding region may affect the primer/probe ability and subsequent SARS-CoV-2 detection. While we found all reverse primers are capable of interacting with their target area, we identified partial mismatching between the SARS-CoV-2 genome and some reverse primers. We predicted three mutations that may prevent primer binding, reducing the ability for SARS-CoV-2 detection. We believe our contributions can aid in the design of a more sensitive SARS-CoV-2 test.Author summaryThe current testing for the disease COVID-19 that is caused by the novel cornonavirus SARS-CoV-2 uses oligonucleotides called primers that bind to specific target regions on the SARS-CoV-2 genome to detect the virus. Our goal was to use computational tools to predict how the structure of the SARS-CoV-2 RNA genome affects the ability of the primers to bind to their target region. We introduce the program DinoKnot (Duplex interaction of nucleic acids with pseudoknots) that is able to predict the interactions between two DNA or RNA molecules. We used DinoKnot to predict the efficiency of four common COVID-19 tests, and the effect of mutations in the SARS-CoV-2 virus on ability of the COVID-19 tests in detecting those strains. We predict partial mismatching between some primers and the SARS-CoV-2 genome but that all primers are capable of interacting with their target areas. We also predict three mutations that prevent primer binding and thus SARS-CoV-2 detection. We discuss the limitations of the current COVID-19 testing and suggest the design of a more sensitive COVID-19 test that can be aided by our findings.
Monsters with a shortened vertebral column: A population phenomenon in radiating fishLabeobarbus(Cyprinidae)
Authors: Golubtsov Alexander S. , Korostelev Nikolai B. , Levin Boris A. 
Published: September 2020

ABSTRACTThe phenomenon of a massive vertebral deformity was recorded in the radiatingLabeobarbusassemblage from the middle reaches of the Genale River (south-eastern Ethiopia, East Africa). Within this sympatric assemblage, five trophic morphs – generalized, lipped, piscivorous and two scraping feeders – were reported between 1993 and 2019. In 2009, a new morph with prevalence of ∼10% was discovered. The new morph, termed ‘short’, had an abnormally shortened vertebral column and a significantly heightened body. This type of deformity is common in farmed Atlantic salmon and other artificially reared fish, but is rare in nature. In the GenaleLabeobarbusassemblage, the deformity was present exclusively within the generalized and lipped morphs. The short morph had between seven and 36 deformed (compressed and/or fused) vertebrae. Their body height was positively correlated with number of deformed vertebrae. In another collection in 2019, the short morph was still present at a frequency of 11%. Various environmental and genetic factors could contribute to the development of this deformity in the GenaleLabeobarbus, but based on the available data, it is impossible to confidently identify the key factor(s). Whether the result of genetics, the environment, or both, this high-bodied phenotype is assumed to be an anti-predator adaptation, as there is evidence of its selective advantage in the generalized morph. The Genale “monstrosity” is the first reported case of a massive deformity of the vertebral column in a natural population of African fishes.“We have also what are called monstrosities; but they graduate into varieties. By a monstrosity I presume is meant some considerable deviation of structure in one part, either injurious to or not useful to the species, and not generally propagated. If it could be shown that monstrosities were even propagated for a succession of generations in a state of nature, modifications might be effected (with the aid of natural selection) more abruptly than I am inclined to believe they are.” Darwin (1860, pp. 46, 426).