Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 88,970 bioRxiv papers from 381,395 authors.
Most downloaded bioRxiv papers, since beginning of last month
86,853 results found. For more information, click each entry to expand.
482 downloads microbiology
Jana Krüger, Rüdiger Groß, Carina Conzelmann, Janis A. Müller, Lennart Koepke, Konstantin M. J. Sparrer, Desiree Schütz, Thomas Seufferlein, Thomas F.E. Barth, Steffen Stenger, Sandra Heller, Alexander Kleger, Jan Münch
Gastrointestinal symptoms in COVID-19 are associated with prolonged symptoms and increased severity. We employed human intestinal organoids derived from pluripotent stem cells (PSC-HIOs) to analyze SARS-CoV-2 pathogenesis and to validate efficacy of specific drugs in the gut. Certain, but not all cell types in PSC-HIOs express SARS-CoV-2 entry factors ACE2 and TMPRSS2, rendering them susceptible to SARS-CoV-2 infection. Remdesivir, a promising drug to treat COVID-19, effectively suppressed SARS-CoV-2 infection of PSC-HIOs. In contrast, the histamine-2-blocker famotidine showed no effect. Thus, PSC-HIOs provide an interesting platform to study SARS-CoV-2 infection and to identify or validate drugs. ### Competing Interest Statement The authors have declared no competing interest.
481 downloads cell biology
Racha Chouaib, Adham Safieddine, Xavier Pichon, Arthur Imbert, Oh Sung Kwon, Aubin Samacoits, Abdel-Meneem Traboulsi, Marie-Cécile Robert, Nikolay Tsanov, Emeline Coleno, Ina Poser, Christophe Zimmer, Anthony Hyman, Hervé Le Hir, Kazem Zibara, Marion Peter, Florian Mueller, Thomas Walter, Edouard Bertrand
Local translation allows a spatial control of gene expression. Here, we performed a dual protein/mRNA localization screen, using smFISH on 523 human cell lines expressing GFP-tagged genes. A total of 32 mRNAs displayed specific cytoplasmic localizations, and we observed local translation at unexpected locations, including cytoplasmic protrusions, cell edges, endosomes, Golgi, the nuclear envelope and centrosomes, the latter being cell cycle dependent. Quantitation of mRNA distribution and automatic pattern classification revealed a high degree of localization heterogeneity between cells. Surprisingly, mRNA localization frequently required ongoing translation, indicating widespread co-translational RNA targeting. Interestingly, while P-body accumulation was frequent (15 mRNAs), four mRNAs accumulated in foci that were distinct structures. These foci lacked the mature protein, but nascent polypeptide imaging showed that they were specialized translation factories. For beta-catenin, foci formation was regulated by Wnt, relied on APC-dependent polysome aggregation, and led to nascent protein degradation. Thus, translation factories uniquely regulate nascent protein metabolism and create a fine granular compartmentalization of translation. ### Competing Interest Statement The authors have declared no competing interest.
480 downloads microbiology
William B. Klimstra, Natasha L Tilston-Lunel, Sham Nambulli, James Boslett, Cynthia M McMillen, Theron Gilliland, Matthew D Dunn, Chengqun Sun, Sarah E Wheeler, Alan Wells, Amy L. Hartman, Anita K McElroy, Douglas S. Reed, Linda J Rennick, W. Paul Duprex
SARS CoV 2, the causative agent of COVID 19, emerged at the end of 2019 and by mid-June 2020, the virus has spread to at least 215 countries, caused more than 8,000,000 confirmed infections and over 450,000 deaths, and overwhelmed healthcare systems worldwide. Like SARS CoV, which emerged in 2002 and caused a similar disease, SARS CoV 2 is a betacoronavirus. Both viruses use human angiotensin converting enzyme 2 (hACE2) as a receptor to enter cells. However, the SARS CoV 2 spike (S) glycoprotein has a novel insertion that generates a putative furin cleavage signal and this has been postulated to expand the host range. Two low passage (P) strains of SARS CoV 2 (Wash1: P4 and Munich: P1) were cultured twice in Vero E6 cells and characterized virologically. Sanger and MinION sequencing demonstrated significant deletions in the furin cleavage signal of Wash1: P6 and minor variants in the Munich: P3 strain. Cleavage of the S glycoprotein in SARS CoV 2 infected Vero E6 cell lysates was inefficient even when an intact furin cleavage signal was present. Indirect immunofluorescence demonstrated the S glycoprotein reached the cell surface. Since the S protein is a major antigenic target for the development of neutralizing antibodies we investigated the development of neutralizing antibody titers in serial serum samples obtained from COVID 19 human patients. These were comparable regardless of the presence of an intact or deleted furin cleavage signal. These studies illustrate the need to characterize virus stocks meticulously prior to performing either in vitro or in vivo pathogenesis studies. ### Competing Interest Statement The authors have declared no competing interest.
479 downloads neuroscience
Morlet wavelets are frequently used for time-frequency analysis of non-stationary time series data, such as neuroelectrical signals recorded from the brain. The crucial parameter of Morlet wavelets is the width of the Gaussian that tapers the sine wave. This width parameter controls the trade-off between temporal precision and frequency precision. It is typically defined as the "number of cycles," but this parameter is opaque, and often leads to uncertainty and suboptimal analysis choices, as well as being difficult to interpret and evaluate. The purpose of this paper is to present alternative formulations of Morlet wavelets in time and in frequency that allow parameterizing the wavelets directly in terms of the desired temporal and spectral smoothing (as full-width at half-maximum). This formulation provides clarity on an important data analysis parameter, and should facilitate proper analyses, reporting, and interpretation of results. MATLAB code is provided.
478 downloads ecology
Greg R. Boyce, Emile Gluck-Thaler, Jason C. Slot, Jason E. Stajich, William J. Davis, Tim Y. James, John R. Cooley, Daniel G. Panaccione, Jørgen Eilenberg, Henrik H. De Fine Licht, Angie M. Macias, Matthew C. Berger, Kristen L. Wickert, Cameron M. Stauder, Ellie J. Spahr, Matthew D. Maust, Amy M. Metheny, Chris Simon, Gene Kritsky, Kathie T. Hodge, Richard A. Humber, Terry Gullion, Dylan P. G. Short, Teiya Kijimoto, Dan Mozgai, Nidia Arguedas, Matt T. Kasson
Entomopathogenic fungi routinely kill their hosts before releasing infectious spores, but select species keep insects alive while sporulating, which enhances dispersal. Transcriptomics and metabolomics studies of entomopathogens with post-mortem dissemination from their parasitized hosts have unraveled infection processes and host responses, yet mechanisms underlying active spore transmission by Entomophthoralean fungi in living insects remain elusive. Here we report the discovery, through metabolomics, of the plant-associated amphetamine, cathinone, in four Massospora cicadina-infected periodical cicada populations, and the mushroom-associated tryptamine, psilocybin, in annual cicadas infected with Massospora platypediae or Massospora levispora, which appear to represent a single fungal species. The absence of some fungal enzymes necessary for cathinone and psilocybin biosynthesis along with the inability to detect intermediate metabolites or gene orthologs are consistent with possibly novel biosynthesis pathways in Massospora. The neurogenic activities of these compounds suggest the extended phenotype of Massospora that modifies cicada behavior to maximize dissemination is chemically-induced.
476 downloads cancer biology
Invasive lobular breast carcinoma (ILC), one of the major breast cancer histological subtypes, exhibits unique clinical and molecular features compared to the other well-studied ductal cancer subtype (IDC). The pathognomonic feature of ILC is loss of E-cadherin, mainly caused by inactivating mutations within the CDH1 gene, but the extent of contribution of this genetic alteration to ILC-specific molecular characteristics remains largely understudied. To profile these features transcriptionally, we conducted single cell RNA sequencing on a panel of IDC and ILC cell lines, as well as an IDC cell line (T47D) with CRISPR-Cas9-mediated knock out (KO) of CDH1. Inspection of intra-cell line heterogeneity illustrated genetically and transcriptionally distinct subpopulations in multiple cell lines and highlighted rare populations of MCF7 cells highly expressing an apoptosis-related signature, positively correlated with a pre-adaptation signature to estrogen deprivation. Investigation of CDH1 KO-induced alterations showed transcriptomic membranous systems remodeling, elevated resemblance to ILCs in regulon activation, and suggests IRF1 as a potential mediator of reduced proliferation and increased cytokine-mediated immune-reactivity in ILCs.
476 downloads neuroscience
Humans and other animals can identify objects by active touch, requiring the coordination of exploratory motion and tactile sensation. The brain integrates movements with the resulting tactile signals to form a holistic representation of object identity. We developed a shape discrimination task that challenged head-fixed mice to discriminate concave from convex shapes. Behavioral decoding revealed that mice did this by comparing contacts across whiskers. In contrast, mice performing a shape detection task simply summed up contacts over whiskers. We recorded populations of neurons in the barrel cortex, which processes whisker input, to identify how it encoded the corresponding sensorimotor variables. Neurons across the cortical layers encoded touch, whisker motion, and task-related signals. Sensory representations were task-specific: during shape discrimination, neurons responded most robustly to behaviorally relevant whiskers, overriding somatotopy. We suggest a similar dynamic modulation may underlie object recognition in other brain areas and species. ### Competing Interest Statement The authors have declared no competing interest.
476 downloads neuroscience
When people are forced to be isolated from one another, do they crave social interactions in the same way a hungry person craves food? To address this question, we used functional magnetic resonance imaging (fMRI) to measure neural responses in participants (n=40) evoked by food and social cues after ten hours of mandated fasting or total social isolation. After isolation, people felt lonely and craved social interaction. Midbrain regions showed increased activation to food cues after fasting and to social cues after isolation; these responses were correlated with self-reported craving. Neural patterns in response to food cues when participants were hungry generalized to social cues after isolation. Our results support the intuitive idea that acute isolation causes social craving, similar to hunger.
475 downloads bioinformatics
Many biological applications require the segmentation of cell bodies, membranes and nuclei from microscopy images. Deep learning has enabled great progress on this problem, but current methods are specialized for images that have large training datasets. Here we introduce a generalist, deep learning-based segmentation method called Cellpose, which can precisely segment cells from a wide range of image types and does not require model retraining or parameter adjustments. We trained Cellpose on a new dataset of highly-varied images of cells, containing over 70,000 segmented objects. We also demonstrate a 3D extension of Cellpose which reuses the 2D model and does not require 3D-labelled data. To support community contributions to the training data, we developed software for manual labelling and for curation of the automated results, with optional direct upload to our data repository. Periodically retraining the model on the community-contributed data will ensure that Cellpose improves constantly.
473 downloads neuroscience
Yang Eric Li, Sebastian Preissl, Xiaomeng Hou, Ziyang Zhang, Kai Zhang, Rongxin Fang, Yunjiang Qiu, Olivier Poirion, Bin Li, Hanqing Liu, Xinxin Wang, Jee Yun Han, Jacinta Lucero, Yiming Yan, Samantha Kuan, David Gorkin, Michael Nunn, Eran A. Mukamel, M. Margarita Behrens, Joseph Ecker, Bing Ren
The mammalian cerebrum performs high level sensory, motor control and cognitive functions through highly specialized cortical networks and subcortical nuclei. Recent surveys of mouse and human brains with single cell transcriptomics– and high-throughput imaging technologies, have uncovered hundreds of neuronal cell types and a variety of non-neuronal cell types distributed in different brain regions, but the cell-type-specific transcriptional regulatory programs responsible for the unique identity and function of each brain cell type have yet to be elucidated. Here, we probe the accessible chromatin in >800,000 individual nuclei from 45 regions spanning the adult mouse isocortex, olfactory bulb, hippocampus and cerebral nuclei, and use the resulting data to define 491,818 candidate cis regulatory DNA elements in 160 distinct sub-types. We link a significant fraction of them to putative target genes expressed in diverse cerebral cell types and uncover transcriptional regulators involved in a broad spectrum of molecular and cellular pathways in different neuronal and glial cell populations. Our results provide a foundation for comprehensive analysis of gene regulatory programs of the mammalian brain and assist in the interpretation of non-coding risk variants associated with various neurological disease and traits in humans. To facilitate the dissemination of information, we have set up a web portal (<http://catlas.org/mousebrain>). ### Competing Interest Statement B.R. is a co-founder and consultant of Arima Genomics, Inc.. J.R.E is on the scientific advisory board of Zymo Research, Inc : #ref-1 : #ref-3 : #ref-4 : #ref-5
471 downloads microbiology
Rebecca L. Brocato, Lucia M. Principe, Robert K. Kim, Xiankun Zeng, Janice A. Williams, Yanan Liu, Rong Li, Jeffrey M. Smith, Joseph W. Golden, Dave Gangemi, Sawsan Youssef, Zhongde Wang, Jacob Glanville, Jay W. Hooper
Animal models recapitulating human COVID-19 disease, especially with severe disease, are urgently needed to understand pathogenesis and evaluate candidate vaccines and therapeutics. Here, we develop novel severe disease animal models for COVID-19 involving disruption of adaptive immunity in Syrian hamsters. Cyclophosphamide (CyP) immunosuppressed or RAG2 knockout (KO) hamsters were exposed to SARS-CoV-2 by the respiratory route. Both the CyP-treated and RAG2 KO hamsters developed clinical signs of disease that were more severe than in immunocompetent hamsters, notably weight loss, viral loads, and fatality (RAG2 KO only). Disease was prolonged in transiently immunosuppressed hamsters and uniformly lethal in RAG2 KO hamsters. We evaluated the protective efficacy of a neutralizing monoclonal antibody and found that pretreatment, even in immunosuppressed animals, limited infection. Our results suggest that functional B and/or T cells are not only important for the clearance of SARS-CoV-2, but also play an early role in protection from acute disease. ### Competing Interest Statement The authors have declared no competing interest.
469 downloads biochemistry
Xiaodi Tang, Shenghai Chang, Wen Qiao, Qinghua Luo, Yuejia Chen, Zhiying Jia, James Coleman, Ke Zhang, Ting Wang, Zhibo Zhang, Changbin Zhang, Xiaofeng Zhu, Xiawei Wei, Changjiang Dong, Xing Zhang, Haohao Dong
The asymmetric outer membrane (OM) of Gram-negative bacteria serves as the first line of defense against cytotoxic substances such as antibiotics. The Mla pathway is known to maintain the lipid asymmetry of the OM by transporting phospholipids between the inner and outer membranes. Six Mla proteins MlaFEDBCA are involved, with the ABC transporter MlaFEDB acts through a mechanism yet to be elucidated. Here we determine cryo-EM structures of MlaFEDB in apo, phospholipid-, ADP- or AMP-PNP-bound state to 3.3-3.75 Angstrom resolution and establish a proteoliposome-based transport system containing MlaFEDB, MlaC and MlaA/OmpF to reveal the transport direction of phospholipids. Mutagenetic in vitro transport assays and in vivo sensitivity assays reveal functional residues which recognize and transport phospholipids as well as regulate the activity and structural stability of the MlaFEDB complex. Our work provides molecular basis for understanding the mechanism of the Mla pathway which could be targeted for antimicrobial drug development. ### Competing Interest Statement The authors have declared no competing interest.
468 downloads microbiology
Hongjing Gu, Qi Chen, Guan Yang, Lei He, Hang Fan, Yong-Qiang Deng, Yanxiao Wang, Yue Teng, Zhongpeng Zhao, Yujun Cui, Yuchang Li, Xiao-Feng Li, Jiangfan Li, Nana Zhang, Xiaolan Yang, Shaolong Chen, Guangyu Zhao, Xiliang Wang, Deyan Luo, Hui Wang, Xiao Yang, Yan Li, Gencheng Han, Yuxian He, Xiaojun Zhou, Shusheng Geng, Xiaoli Sheng, Shibo Jiang, Shihui Sun, Cheng-Feng Qin, Yusen Zhou
Coronavirus 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 receptor-binding 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 the in vivo protective efficacy of SARS-CoV-2 vaccine. ### Competing Interest Statement The authors have declared no competing interest.
468 downloads systems biology
SARS-CoV-2 infections are rapidly spreading around the globe. The rapid development of therapies is of major importance. However, our lack of understanding of the molecular processes and host cell signaling events underlying SARS-CoV-2 infection hinder therapy development. We employed a SARS-CoV-2 infection system in permissible human cells to study signaling changes by phospho-proteomics. We identified viral protein phosphorylation and defined phosphorylation-driven host cell signaling changes upon infection. Growth factor receptor (GFR) signaling and downstream pathways were activated. Drug-protein network analyses revealed GFR signaling as key pathway targetable by approved drugs. Inhibition of GFR downstream signaling by five compounds prevented SARS-CoV-2 replication in cells, assessed by cytopathic effect, viral dsRNA production, and viral RNA release into the supernatant. This study describes host cell signaling events upon SARS-CoV-2 infection and reveals GFR signaling as central pathway essential for SARS-CoV-2 replication. It provides with novel strategies for COVID-19 treatment. ### Competing Interest Statement The authors filed a patent application on the use of GFR signaling inhibitors for the treatment of COVID-19.
468 downloads genomics
Drew Neavin, Quan Nguyen, Maciej S. Daniszewski, Helena H Liang, Han Sheng Chiu, Anne Senabouth, Samuel W. Lukowski, Duncan E Crombie, Grace E Lidgerwood, Damián Hernández, James C. Vickers, Anthony L Cook, Nathan J. Palpant, Alice Pébay, Alex W. Hewitt, Joseph E. Powell
The discovery that somatic cells can be reprogrammed to induced pluripotent stem cells (iPSCs) - cells that can be differentiated into any cell type of the three germ layers - has provided a foundation for in vitro human disease modelling, drug development, and population genetics studies. In the majority of instances, the expression levels of genes, plays a critical role in contributing to disease risk, or the ability to identify therapeutic targets. However, while the effect of the genetic background of cell lines has been shown to strongly influence gene expression, the effect has not been evaluated at the level of individual cells. Differences in the effect of genetic variation on the gene expression of different cell-types, would provide significant resolution for in vitro research using preprogramed cells. By bringing together single cell RNA sequencing and population genetics, we now have a framework in which to evaluate the cell-types specific effects of genetic variation on gene expression. Here, we performed single cell RNA-sequencing on 64,018 fibroblasts from 79 donors and we mapped expression quantitative trait loci (eQTL) at the level of individual cell types. We demonstrate that the large majority of eQTL detected in fibroblasts are specific to an individual sub-type of cells. To address if the allelic effects on gene expression are dynamic across cell re-programming, we generated scRNA-seq data in 19,967 iPSCs from 31 reprogramed donor lines. We again identify highly cell type specific eQTL in iPSCs, and show that that the eQTL in fibroblasts are almost entirely disappear during reprogramming. This work provides an atlas of how genetic variation influences gene expression across cell subtypes, and provided evidence for patterns of genetic architecture that lead to cell-types specific eQTL effects. ### Competing Interest Statement The authors have declared no competing interest.
467 downloads animal behavior and cognition
Despite the ecological importance of long-distance dispersal in insects, its underlying mechanistic basis is poorly understood. One critical question is how insects interact with the wind to increase their travel distance as they disperse. To gain insight into dispersal using a species amenable to further investigation using genetic tools, we conducted release-and-recapture experiments in the Mojave Desert using the fruit fly, Drosophila melanogaster . We deployed chemically-baited traps in a 1 km-radius ring around the release site, equipped with machine vision systems that captured the arrival times of flies as they landed. In each experiment, we released between 30,000 and 200,000 flies. By repeating the experiments under a variety of conditions, we were able to quantify the influence of wind on flies' dispersal behavior. Our results confirm that even tiny fruit flies could disperse ~15 km in a single flight in still air, and might travel many times that distance in a moderate wind. The dispersal behavior of the flies is well explained by a model in which animals maintain a fixed body orientation relative to celestial cues, actively regulate groundspeed along their body axis, and allow the wind to advect them sideways. The model accounts for the observation that flies actively fan out in all directions in still air, but are increasingly advected downwind as winds intensify. In contrast, our field data do not support a Lévy flight model of dispersal, despite the fact that our experimental conditions almost perfectly match the core assumptions of that theory. ### Competing Interest Statement The authors have declared no competing interest.
467 downloads synthetic biology
The self-organization of proteins into specific assemblies is a hallmark of biological systems. Principles governing protein-protein interactions have long been known. However, principles by which such nanoscale interactions generate diverse phenotypes of mesoscale assemblies, including phase-separated compartments, remains challenging to characterize and understand. To illuminate such principles, we create a system of two proteins designed to interact and form mesh-like assemblies in living cells. We devise a novel strategy to map high-resolution phase diagrams in vivo, which provide mesoscale self-assembly signatures of our system. The structural modularity of the two protein components allows straightforward modification of their molecular properties, enabling us to characterize how point mutations that change their interaction affinity impact the phase diagram and material state of the assemblies in vivo. Both, the phase diagrams and their dependence on interaction affinity were captured by theory and simulations, including out-of-equilibrium effects seen in growing cells. Applying our system to interrogate biological mechanisms of self-assembly, we find that co-translational protein binding suffices to recruit an mRNA to the designed micron-scale structures. ### Competing Interest Statement The authors have declared no competing interest.
466 downloads bioinformatics
Cryo-electron microscopy (cryo-EM) maps are among the most valuable sources of information for protein structure modeling. However, due to the loss of contrast at high frequencies, they generally need to be post-processed before modeling in order to improve their interpretability. To that end, approaches based on B-factor correction are the most popular choices, yet they suffer from some limitations such as the fact that the correction is applied globally, ignoring the presence of heterogeneity in the map local quality that cryo-EM reconstructions tend to exhibit. With the aim of overcoming these limitations, here we present DeepEMhancer, a deep learning approach designed to perform automatic post-processing of cryo-EM maps. Trained on a dataset of pairs of experimental cryo-EM maps and maps sharpened by LocScape using their respective atomic models, DeepEMhancer has automatically learned how to post-process experimental maps performing masking-like and sharpening-like operations in a single step. DeepEMhancer has been evaluated on a testing set of 20 different experimental maps, showing its ability to obtain much cleaner and detailed versions of the experimental maps, thus, improving their interpretability. Additionally, we have illustrated the benefits of DeepEMhancer with a use case in which the structure of the SARS-CoV 2 RNA polymerase is improved. ### Competing Interest Statement The authors have declared no competing interest.
463 downloads biochemistry
The maintenance of lipid asymmetry (MLA) system is involved in lipid transport from/to the outer membrane in gram-negative bacteria, and contributes to broad-range antibiotic resistance. Here, we report the cryo-EM structure of the A. baumannii MlaBDEF core complex, in the apo, ADP- and AppNHp-bound states. This reveals multiple lipid binding sites, and suggests a mechanism for their transport. ### Competing Interest Statement The authors have declared no competing interest.
463 downloads neuroscience
Microglia are now considered drivers of Alzheimer's disease (AD) pathology. However, single-cell RNA-sequencing (scRNA-seq) of microglia in mice, a key preclinical model organism, have shown mixed results regarding translatability to human studies. To address this, scRNA-seq of microglia from C57BL/6J (B6) and wild-derived strains WSB/EiJ, CAST/EiJ and PWK/PhJ carrying APP/PS1 was performed and demonstrated that genetic diversity significantly altered features and dynamics of microglia in baseline neuroimmune functions and in response to amyloidosis. There was significant variation in abundance of microglial subpopulations, including numbers of disease-associated microglia and interferon-responding microglia across the strains. Further, for each subpopulation, significant gene expression differences were observed between strains, and relative to B6 that included nineteen genes previously associated with human AD including Apoe, Trem2, Bin1, Sorl1. This resource will be critical in the development of appropriately targeted therapeutics for AD and a range of other neurological diseases. ### Competing Interest Statement The authors have declared no competing interest.
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