bluuebunny/crossref_metadata_2025_split huggingface dataset:
A rigorous method for integrating multiple heterogeneous databases in genetic studies
Authors: Bukszár József , van den Oord Edwin JCG 
Published: September 2020

ABSTRACTThe large number of existing databases provides a freely available independent source of information with a considerable potential to increase the likelihood of identifying genes for complex diseases. We developed a flexible framework for integrating such heterogeneous databases into novel large scale genetic studies and implemented the methods in a freely-available, user-friendly R package called MIND. For each marker, MIND computes the posterior probability that the marker has effect in the novel data collection based on the information in all available data. MIND 1) relies on a very general model, 2) is based on the mathematical formulas that provide us with the exact value of the posterior probability, and 3) has good estimation properties because of its very efficient parameterization. For an existing data set, only the ranks of the markers are needed, where ties among the ranks are allowed. Through simulations, cross-validation analyses involving 18 GWAS, and an independent replication study of 6,544 SNPs in 6,298 samples we show that MIND 1) is accurate, 2) outperforms marker selection for follow up studies based onp-values, and 3) identifies effects that would otherwise require replication of over 20 times as many markers.AUTHOR SUMMARYThe large number of existing databases provides a freely available independent source of information with a considerable potential to increase the likelihood of identifying genes for complex diseases. We developed a flexible framework for integrating such heterogeneous databases into novel large scale genetic studies and implemented the methods in a freely-available, user-friendly R package called MIND. For each marker, MIND computes an estimate of the (posterior) probability that the marker has effect in the novel data collection based on the information in all available data. For an existing data set, only the ranks of the markers are needed to be known, where ties among the ranks are allowed. MIND 1) relies on a realistic model that takes confounding effects into account, 2) is based on the mathematical formulas that provide us with the exact value of the posterior probability, and 3) has good estimation properties because of its very efficient parameterization. Simulation, validation, and a replication study in independent samples show that MIND is accurate and greatly outperforms marker selection without using existing data sets.
Ubiquitylome Analysis Reveals a Central Role for the Ubiquitin-Proteasome System in Plant Innate Immunity
Authors: Ma Xiyu , Zhang Chao , Kim Do Young , Huang Yanyan , He Ping , Vierstra Richard D. , Shan Libo 
Published: September 2020

ABSTRACTProtein ubiquitylation profoundly expands proteome functionality and diversifies cellular signaling processes, with recent studies providing ample evidence for its importance to plant immunity. To gain a proteome-wide appreciation of ubiquitylome dynamics during immune recognition, we employed a two-step affinity enrichment protocol based on a 6His-tagged ubiquitin (Ub) variant coupled with high sensitivity mass spectrometry to identifyArabidopsisproteins rapidly ubiquitylated upon plant perception of the microbe-associated molecular pattern (MAMP) peptide flg22. The catalog from two-week-old seedlings treated for only 30 minutes with flg22 contained nearly 1,000 conjugates, 150 Ub footprints, and all seven types of Ub linkages, and included previously uncharacterized conjugates of immune components, such as RECEPTOR-LIKE KINASE 1 (RKL1) shown to negatively regulate plant immunity.In vivoubiquitylation assays confirmed modification of several candidates upon immune elicitation, and revealed distinct modification patterns and dynamics for key immune components, including poly- and monoubiquitylation, as well as induced or reduced levels of ubiquitylation. Gene ontology and network analyses of the collection also uncovered rapid modification of the Ub-proteasome system itself, suggesting a critical auto-regulatory loop necessary for an effective MAMP-triggered immune response and subsequent disease resistance. Included targets were UBIQUITIN-CONJUGATING ENZYME 13 (UBC13) and proteasome component REGULATORY PARTICLE NON-ATPASE SUBUNIT 8b (RPN8b), whose subsequent biochemical and genetic analyses implied negative roles in immune elicitation. Collectively, our proteomic analyses further strengthened the connection between ubiquitylation and flg22-based immune signaling, identified novel components and pathways regulating plant immunity, and increased the database of ubiquitylated substrates in plants.One-sentence summaryProteome-wide catalogs of ubiquitylated proteins revealed a rapid engagement of the ubiquitin-proteasome system in Arabidopsis innate immunity.
SARS-CoV-2 ribosomal frameshifting pseudoknot: Improved secondary structure prediction and detection of inter-viral structural similarity
Authors: Trinity Luke , Lansing Lance , Jabbari Hosna , Stege Ulrike 
Published: September 2020

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to the COVID-19 pandemic; a pandemic of a scale that has not been seen in the modern era. Despite over 29 million reported cases and over 900, 000 deaths worldwide as of September 2020, herd immunity and widespread vaccination efforts by many experts are expected to be insufficient in addressing this crisis for the foreseeable future. Thus, there is an urgent need for treatments that can lessen the effects of SARS-CoV-2 in patients who become seriously affected. Many viruses including HIV, the common cold, SARS-CoV and SARS-CoV-2 use a unique mechanism known as −1 programmed ribosomal frameshifting (−1 PRF) to successfully replicate and infect cells in the human host. SARS-CoV (the coronavirus responsible for SARS) and SARS-CoV-2 possess a unique RNA structure, a three-stemmed pseudoknot, that stimulates −1 PRF. Recent experiments identified that small molecules can be introduced as antiviral agents to bind with the pseudoknot and disrupt its stimulation of −1 PRF. If successfully developed, small molecule therapy that targets −1 PRF in SARS-CoV-2 is an excellent strategy to improve patients’ prognoses. Crucial to developing these successful therapies is modeling the structure of the SARS-CoV-2 −1 PRF pseudoknot. Following a structural alignment approach, we identify similarities in the −1 PRF pseudoknots of the novel coronavirus SARS-CoV-2, the original SARS-CoV, as well as a third coronavirus: MERS-CoV, the coronavirus responsible for Middle East Respiratory Syndrome (MERS). In addition, we provide a better understanding of the SARS-CoV-2 −1 PRF pseudoknot by comprehensively investigating the structural landscape using a hierarchical folding approach. Since understanding the impact of mutations is vital to long-term success of treatments that are based on predicted RNA functional structures, we provide insight on SARS-CoV-2 −1 PRF pseudoknot sequence mutations and their effect on the resulting structure and its function.
Single individual structural variant detection uncovers widespread hemizygosity in molluscs
Authors: Calcino Andrew D , Kenny Nathan J , Gerdol Marco 
Published: September 2020

AbstractThe advent of complete genomic sequencing has opened a window into genomic phenomena obscured by fragmented assemblies. A good example of these is the existence of hemizygous regions of autosomal chromosomes, which can result in marked differences in gene content between individuals within species. While these hemizygous regions, and presence/absence variation of genes that can result, are well known in plants, firm evidence has only recently emerged for their existence in metazoans.Here we use recently published, complete genomes from wild-caught molluscs to investigate the prevalence of hemizygosity and pan-genomes across a well-known and ecologically important clade. We show that hemizygous regions are widespread in mollusc genomes, not clustered in individual chromosomes, and often contain genes linked to transposition, DNA repair and stress response. With targeted investigations of HSP70-12 and C1qDC, we also show how individual gene families are distributed within pan-genomes.This work suggests that pan-genomes are widespread across the conchiferan Mollusca, and represent useful tools for genomic evolution, allowing the maintenance of additional genetic diversity within the population. As genomic sequencing and re-sequencing becomes more routine, the prevalence of hemizygosity, and its impact on selection and adaptation, are key targets for research across the tree of life.
A homologue of the mammalian tumour suppressor protein PTEN is a functional lipid phosphatase and required for chemotaxis in filamentous fungi
Authors: Hassing Berit , Candy Alyesha , Eaton Carla J. , Fernandes Tania R. , Mesarich Carl H. , Di Pietro Antonio , Scott Barry 
Published: September 2020

SummaryPhosphoinositides (PI) are essential components of eukaryotic membranes and function in a large number of signalling processes. While lipid second messengers are well studied in mammals and yeast, their role in filamentous fungi is poorly understood. We used fluorescent PI-binding molecular probes to localise the phosphorylated phosphatidylinositol species PI[3]P, PI[3,5]P2, PI[4]P and PI[4,5]P2 in hyphae of the endophyte Epichloë festucae in axenic culture and during interaction with its grass host Lolium perenne. We also analysed the roles of the phosphatidylinositol-4-phosphate 5-kinase MssD and the predicted phosphatidylinositol-3,4,5-triphosphate 3-phosphatase TepA, a homologue of the mammalian tumour suppressor protein PTEN. Deletion of tepA in E. festucae and in the root-infecting tomato pathogen Fusarium oxysporum had no impact on growth in culture or the host interaction phenotype. However, this mutation did uncover the presence of PI[3,4,5]P3 in septa of E. festucae and showed that TepA is required for chemotropism in F. oxysporum. The identification of PI[3,4,5]P3 in septa of ΔtepA strains suggests that filamentous fungi are able to generate PI[3,4,5]P3 using an alternative biosynthetic pathway and that fungal PTEN homologues are functional lipid phosphatases. The F. oxysporum chemotropism defect demonstrates a conserved role of PTEN homologues in chemotaxis across protists, fungi and mammals.
Latency and amplitude of the stop-signal P3 event-related potential are related to inhibitory GABAaactivity in primary motor cortex
Authors: Hynd Megan , Soh Cheol , Rangel Benjamin O. , Wessel Jan R. 
Published: September 2020

AbstractBy stopping actions even after their initiation, humans can adapt their ongoing behavior rapidly to changing environmental circumstances. The neural processes underlying the implementation of rapid action-stopping are still controversially discussed. In the early 1990s, a fronto-central P3 event-related potential (ERP) was identified in the human EEG response following stop-signals in the classic stop-signal task, accompanied by the proposal that this ERP reflects the “inhibitory” side of the purported horse-race underlying successful action-stopping. Later studies have lent support to this interpretation by finding that the amplitude and onset of the stop-signal P3 relate to both overt behavior and to movement-related EEG activity in ways predicted by the race model. However, such studies are limited by the ability of EEG to allow direct inferences about the presence (or absence) of true, physiologically inhibitory signaling at the neuronal level. To address this, we here present a cross-modal individual differences investigation of the relationship between the features stop-signal P3 ERP and GABAergic neurotransmission in primary motor cortex (M1, as measured by paired-pulse transcranial magnetic stimulation). Following recent work, we measured short-interval intracortical inhibition (SICI), a marker of inhibitory GABAaactivity in M1, in a group of 41 human participants who also performed the stop-signal task while undergoing EEG recordings. In line with the P3-inhibition hypothesis, we found that subjects with stronger inhibitory GABA activity in M1 also showed both faster onsets and larger amplitudes of the stop-signal P3. This provides direct evidence linking the properties of this ERP to a true physiological index of motor system inhibition. We discuss these findings in the context of recent theoretical developments and empirical findings regarding the neural implementation of inhibitory control during action-stopping.
Proteomic analysis of metabolic pathways supports chloroplast-mitochondria cross-talk in a Cu-limited diatom
Authors: Hippmann Anna A. , Schuback Nina , Moon Kyung-Mee , McCrow John P. , Allen Andrew E. , Foster Leonard F. , Green Beverley R. , Maldonado Maria T. 
Published: September 2020

AbstractDiatoms are one of the most successful phytoplankton groups in our oceans, being responsible for over 20% of the Earth’s photosynthetic productivity. Their chimeric genomes have genes derived from red algae, green algae, bacteria and heterotrophs, resulting in multiple isoenzymes targeted to different cellular compartments with the potential for differential regulation under nutrient limitation. The resulting interactions between metabolic pathways are not yet fully understood.We previously showed how acclimation to Cu limitation enhanced susceptibility to overreduction of the photosynthetic electron transport chain and its reorganization to favor photoprotection over light-harvesting in the oceanic diatomThalassiosira oceanica(Hippmann et al., 2017). In order to gain a better understanding of the overall metabolic changes that help alleviate the stress of Cu limitation, we have further analyzed the comprehensive proteomic datasets generated in that study to identify differentially expressed proteins involved in carbon, nitrogen and oxidative stress-related metabolic pathways.Metabolic pathway analysis showed integrated responses to Cu limitation. The up-regulation of ferredoxin (Fdx) was correlated with up-regulation of plastidial Fdx-dependent isoenzymes involved in nitrogen assimilation as well as enzymes involved in glutathione synthesis, thus integrating nitrogen uptake and metabolism with photosynthesis and oxidative stress resistance. The differential expression of glycolytic isoenzymes located in the chloroplast and mitochondria may enable them to channel both excess electrons and/or ATP between these compartments. Additional evidence for chloroplast-mitochondrial cross-talk is the increased expression of chloroplast and mitochondrial proteins involved in the proposed malate shunt under Cu limitation.One sentence summaryDiatoms adapt to Cu limitation by regulating their large repertoire of isoenzymes to channel electrons away from the chloroplast, enhance nitrogen uptake, and integrate the oxidative stress response.123
Impact of temporal pH fluctuations on the coexistence of nasal bacteria
Authors: Dedrick Sandra , Akbari M. Javad , Dyckman Samantha , Zhao Nannan , Liu Yang-Yu , Momeni Babak 
Published: September 2020

AbstractTo manipulate nasal microbiota for respiratory health, we need to better understand how this microbial community is assembled and maintained. Previous work has demonstrated that the pH in the nasal passage experiences temporal fluctuations. Yet, the impact of such pH fluctuations on nasal microbiota is not fully understood. Here, we examine how temporal fluctuations in pH might affect the coexistence of nasal bacteria. We take advantage of the cultivability of nasal bacteria to experimentally assess their responses to pH. Based on experimentally observed responses, we formulate a mathematical model to numerically investigate the impact of temporal pH fluctuations on species coexistence. Through extensive numerical simulations, we find that the composition of nasal communities is robust against pH fluctuations. Our results suggest that nasal microbiota could be more robust than expected against environmental fluctuations.
Single-Cell RNA Sequencing of Batch Chlamydomonas Cultures Reveals Heterogeneity in their Diurnal Cycle Phase
Authors: Ma Feiyang , Salomé Patrice A. , Merchant Sabeeha S. , Pellegrini Matteo 
Published: September 2020

ABSTRACTThe photosynthetic unicellular alga Chlamydomonas (Chlamydomonas reinhardtii) is a versatile reference for algal biology because of the facility with which it can be cultured in the laboratory. Genomic and systems biology approaches have previously been used to describe how the transcriptome responds to environmental changes, but this analysis has been limited to bulk data, representing the average behavior from pools of cells. Here, we apply single-cell RNA sequencing (scRNA-seq) to probe the heterogeneity of Chlamydomonas cell populations under three environments and in two genotypes differing in the presence of a cell wall. First, we determined that RNA can be extracted from single algal cells with or without a cell wall, offering the possibility to sample algae communities in the wild. Second, scRNA-seq successfully separated single cells into non-overlapping cell clusters according to their growth conditions. Cells exposed to iron or nitrogen deficiency were easily distinguished despite a shared tendency to arrest cell division to economize resources. Notably, these groups of cells recapitulated known patterns observed with bulk RNA-seq, but also revealed their inherent heterogeneity. A substantial source of variation between cells originated from their endogenous diurnal phase, although cultures were grown in constant light. We exploited this result to show that circadian iron responses may be conserved from algae to land plants. We propose that bulk RNA-seq data represent an average of varied cell states that hides underappreciated heterogeneity.One-sentence summaryWe show that single-cell RNA-seq (scRNA-seq) can be applied to Chlamydomonas cultures to reveal the that heterogenity in bulk cultures is largely driven by diurnal cycle phasesThe author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantcell.org) is: Matteo Pellegrini (matteop@mcdb.ucla.edu)
Calcium imaging and the curse of negativity
Authors: Vanwalleghem Gilles , Constantin Lena , Scott Ethan K. 
Published: September 2020

AbstractThe imaging of neuronal activity using calcium indicators has become a staple of modern neuroscience. However, without ground truths, there is a real risk of missing a significant portion of the real responses. Here, we show that a common assumption, the non-negativity of the neuronal responses as detected by calcium indicators, biases all levels of the frequently used analytical methods for these data. From the extraction of meaningful fluorescence changes to spike inference and the analysis of inferred spikes, each step risks missing real responses because of the assumption of non-negativity. We first show that negative deviations from baseline can exist in calcium imaging of neuronal activity. Then, we use simulated data to test three popular algorithms for image analysis, finding that suite2p may be the best suited to large datasets. Spike inference algorithms also showed their limitations in dealing with inhibited neurons, and new approaches may be needed to address this problem. We further suggest avoiding data analysis approaches that may ignore inhibited responses in favor of a first exploratory step to ensure that none are present. Taking these steps will ensure that inhibition, as well as excitation, is detected in calcium imaging datasets.
Cenote-Taker 2 Democratizes Virus Discovery and Sequence Annotation
Authors: Tisza Michael J. , Belford Anna K. , Dominguez-Huerta Guillermo , Bolduc Benjamin , Sullivan Matthew B. , Buck Christopher B. 
Published: September 2020

AbstractViruses, despite their great abundance and significance in biological systems, remain largely mysterious. Indeed, the vast majority of the perhaps hundreds of millions of viral species on the planet remain undiscovered. Additionally, many viruses deposited in central databases like GenBank and RefSeq are littered with genes annotated as “hypothetical protein” or the equivalent. Cenote-Taker2, a virus discovery and annotation tool available on command line and with a graphical user interface with free high-performance computation access, utilizes highly sensitive models of hallmark virus genes to discover familiar or divergent viral sequences from user-input contigs. Additionally, Cenote-Taker2 uses a flexible set of modules to automatically annotate the sequence features of contigs, providing more gene information than comparable tools. The outputs include readable and interactive genome maps, virome summary tables, and files that can be directly submitted to GenBank. We expect Cenote-Taker2 to facilitate virus discovery, annotation, and expansion of the known virome.
Molecular basis for cysteine oxidation by Plant Cysteine Oxidases fromArabidopsis thaliana
Authors: Guo Qiong , Chen Zhenzhen , Wu Gao , Wen Jie , Liao Shanhui , Xu Chao 
Published: September 2020

AbstractPlant Cysteine Oxidases (PCOs) play important roles in controlling the stability of Group VII ethylene response factors (ERF-VIIs) via N-Arg/degron pathway through catalyzing the oxidation of their N-Cys for subsequent Arginyl-tRNA--protein transferase 1 (ATE1) mediated arginine installation. Here we presented structures of PCO2, PCO4, and PCO5 fromArabidopsis thaliana(AtPCOs) and examined theirin vitroactivity by MS. On the basis of Tris-boundAtPCO2, we modelled the Cys-boundAtPCO2 structure and identified key residues involved in N-Cys oxidation. Alanine substitution of potential N-Cys interaction residues impaired the activity ofAtPCO5 remarkably. The structural research, complemented by mutagenesis and mass spectrometry experiments, not only uncovers the substrate recognition and catalytic mode byAtPCOs, but also sheds light on the future design of potent inhibitors for plant cysteine oxidases.
Comprehensive characterization of tissue-specific chromatin accessibility in L2Caenorhabditis elegansnematodes
Authors: Durham Timothy J. , Daza Riza M. , Gevirtzman Louis , Cusanovich Darren A. , Noble William Stafford , Shendure Jay , Waterston Robert H. 
Published: September 2020

AbstractRecently developed single cell technologies allow researchers to characterize cell states at ever greater resolution and scale.C. elegansis a particularly tractable system for studying development, and recent single cell RNA-seq studies characterized the gene expression patterns for nearly every cell type in the embryo and at the second larval stage (L2). Gene expression patterns are useful for learning about gene function and give insight into the biochemical state of different cell types; however, in order to understand these cell types, we must also determine how these gene expression levels are regulated. We present the first single cell ATAC-seq study inC. elegans. We collected data in L2 larvae to match the available single cell RNA-seq data set, and we identify tissue-specific chromatin accessibility patterns that align well with existing data, including the L2 single cell RNA-seq results. Using a novel implementation of the latent Dirichlet allocation algorithm, we leverage the single-cell resolution of the sci-ATAC-seq data to identify accessible loci at the level of individual cell types, providing new maps of putative cell type-specific gene regulatory sites, with promise for better understanding of cellular differentiation and gene regulation in the worm.