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Rxivist uses download data on preprints from bioRxiv to help you find the papers being discussed in your field. Currently indexing 101,433 bioRxiv papers from 428,488 authors.

Most tweeted bioRxiv papers, last 7 days

386 results found. For more information, click each entry to expand.

21: Gene regulation gravitates towards either addition or multiplication when combining the effects of two signals
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Posted to bioRxiv 27 May 2020

Gene regulation gravitates towards either addition or multiplication when combining the effects of two signals
10 tweets systems biology

Eric M Sanford, Benjamin L Emert, Allison Coté, Arjun Raj

Signals often ultimately affect the transcription of genes, and often, two different signals can affect the transcription of the same gene. In such cases, it is natural to ask how the combined transcriptional response compares to the individual responses. Mechanistic models can predict a range of combined responses, with the most commonly applied models predicting additive or multiplicative responses, but systematic genome-wide evaluation of these predictions are not available. Here, we performed a comprehensive analysis of the transcriptional response of human MCF-7 cells to two different signals (retinoic acid and TGF-β), applied individually and in combination. We found that the combined responses exhibited a range of behaviors, but clearly favored both additive and multiplicative combined transcriptional responses. We also performed paired chromatin accessibility measurements to measure putative transcription factor occupancy at regulatory elements near these genes. We found that increases in chromatin accessibility were largely additive, meaning that the combined accessibility response was the sum of the accessibility responses to each signal individually. We found some association between super-additivity of accessibility and multiplicative or super-multiplicative combined transcriptional responses, while sub-additivity of accessibility associated with additive transcriptional responses. Our findings suggest that mechanistic models of combined transcriptional regulation must be able to reproduce a range of behaviors. ### Competing Interest Statement AR receives royalties related to Stellaris RNA FISH probes. All other authors declare no competing interests.

22: Spatially-specific working memory activity in the human superior colliculus
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Posted to bioRxiv 18 Jun 2020

Spatially-specific working memory activity in the human superior colliculus
10 tweets neuroscience

Masih Rahmati, Kevin DeSimone, Clayton E. Curtis, Kartik K Sreenivasan

Theoretically, working memory (WM) representations are encoded by population activity of neurons with distributed tuning across the stored feature. Here, we leverage computational neuroimaging approaches to map the topographic organization of human superior colliculus (SC) and model how population activity in SC encodes WM representations. We first modeled receptive field properties of voxels in SC, deriving a detailed topographic organization resembling that of the primate SC. Neural activity within male and female human SC persisted throughout a retention interval of several types of modified memory-guided saccade tasks. Assuming an underlying neural architecture of the SC based on its retinotopic organization, we used an encoding model to show that the pattern of activity in human SC represents locations stored in WM. Our tasks and models allowed us to dissociate the locations of visual targets and the motor metrics of memory-guided saccades from the spatial locations stored in WM, thus confirming that human SC represents true WM information. These data have several important implications. They add the SC to a growing number of cortical and subcortical brain areas that form distributed networks supporting WM functions. Moreover, they specify a clear neural mechanism by which topographically organized SC encodes WM representations. Significance Statement Using computational neuroimaging approaches, we mapped the topographic organization of human superior colliculus (SC) and modeled how population activity in SC encodes working memory (WM) representations, rather than simpler visual or motor properties that have been traditionally associated with the laminar maps in the primate SC. Together, these data both position the human SC into a distributed network of brain areas supporting WM and elucidate the neural mechanisms by which the SC supports WM. ### Competing Interest Statement The authors have declared no competing interest.

23: A 'Naturalistic Neuroimaging Database' for understanding the brain using ecological stimuli
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Posted to bioRxiv 25 May 2020

A 'Naturalistic Neuroimaging Database' for understanding the brain using ecological stimuli
10 tweets neuroscience

Sarah Aliko, Jiawen Huang, Florin Gheorghiu, Stefanie Meliss, Jeremy I Skipper

Neuroimaging has advanced our understanding of human psychology using reductionist stimuli that often do not resemble information the brain naturally encounters. It has improved our understanding of the network organization of the brain mostly through analyses of 'resting-state' data for which the functions of networks cannot be verifiably labelled. We make a 'Naturalistic Neuroimaging Database' (NNDb v1.0) publically available to allow for a more complete understanding of the brain under more ecological conditions during which networks can be labelled. Eighty-six participants underwent behavioural testing and watched one of 10 full-length movies while functional magnetic resonance imaging was acquired. Resulting timeseries data are shown to be of high quality, with good signal-to-noise ratio, few outliers and low movement. Data-driven functional analyses provide further evidence of data quality. They also demonstrate accurate timeseries/movie alignment and how movie annotations might be used to label networks. The NNDb can be used to answer questions previously unaddressed with standard neuroimaging approaches, progressing our knowledge of how the brain works in the real world. ### Competing Interest Statement The authors have declared no competing interest.

24: SARS-CoV-2 Simulations Go Exascale to Capture Spike Opening and Reveal Cryptic Pockets Across the Proteome
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Posted to bioRxiv 30 Jun 2020

SARS-CoV-2 Simulations Go Exascale to Capture Spike Opening and Reveal Cryptic Pockets Across the Proteome
10 tweets biophysics

Maxwell I. Zimmerman, Justin R. Porter, Michael D Ward, Sukrit Singh, Neha Vithani, Artur Meller, Upasana L. Mallimadugula, Catherine E. Kuhn, Jonathan H. Borowsky, Rafal P. Wiewiora, Matthew F. D. Hurley, Aoife M Harbison, Carl A. Fogarty, Joseph E. Coffland, Elisa Fadda, Vincent A. Voelz, John D Chodera, Gregory R. Bowman

SARS-CoV-2 has intricate mechanisms for initiating infection, immune evasion/suppression, and replication, which depend on the structure and dynamics of its constituent proteins. Many protein structures have been solved, but far less is known about their relevant conformational changes. To address this challenge, over a million citizen scientists banded together through the Folding@home distributed computing project to create the first exascale computer and simulate an unprecedented 0.1 seconds of the viral proteome. Our simulations capture dramatic opening of the apo Spike complex, far beyond that seen experimentally, which explains and successfully predicts the existence of "cryptic" epitopes. Different Spike homologues modulate the probabilities of open versus closed structures, balancing receptor binding and immune evasion. We also observe dramatic conformational changes across the proteome, which reveal over 50 "cryptic" pockets that expand targeting options for the design of antivirals. All data and models are freely available online, providing a quantitative structural atlas. ### Competing Interest Statement The authors have declared no competing interest.

25: Quantitative PCR for cannabis flower containing SARs-CoV-2
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Posted to bioRxiv 11 Jun 2020

Quantitative PCR for cannabis flower containing SARs-CoV-2
9 tweets genomics

Douglas Smith, Liam T Kane, Yvonne Helbert

In January of 2020, COVID-19 became a worldwide pandemic. As many industries shutdown to comply with social distancing measures, the cannabis industry was deemed an essential business in most US jurisdictions. Cannabis is manually farmed, trimmed and packaged and as a result can be a potential inhaled SARs-CoV-2 fomite. Many of the comorbidities described in COVID-19 are also qualifying conditions for medical cannabis access. Bat Guano has been identified as a rich source for novel coronavirus discovery and bat guano is also a common fertilizer in the cannabis field. Employees of cannabis grows have been reported to test qPCR positive for SARs-CoV-2. To better assess cannabis fomite risk we developed a SARs-CoV-2 quantitative PCR assay optimized to operate with a hemp flower background matrix. ### Competing Interest Statement Authors of this paper are employed by Medicinal Genomics which sells pathogen detection kits into the Cannabis Industry

26: Projecting single-cell transcriptomics data onto a reference T cell atlas to interpret immune responses
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Posted to bioRxiv 24 Jun 2020

Projecting single-cell transcriptomics data onto a reference T cell atlas to interpret immune responses
8 tweets bioinformatics

Massimo Andreatta, Jesus Corria-Osorio, Sören Müller, Rafael Cubas, George Coukos, Santiago J. Carmona

Single-cell RNA-sequencing (scRNA-seq) has emerged as a revolutionary technology for characterizing the heterogeneity of cell populations. However, robust reference atlases that can be used to systematically interpret cellular states across studies and diseases are currently lacking. Here, we generated the first cross-study T cell atlases for cancer and viral infection and developed a novel algorithm, ProjecTILs, that enables the projection of new scRNA-seq data onto these reference atlases. ProjecTILs accurately predicted the effects of multiple perturbations, including the ablation of immunoregulatory targets controlling T cell differentiation, such as Tox , Ptpn2 , miR-155 and Regnase-1 , and suggested novel gene programs that were altered in these cells. Moving beyond mouse models, we used ProjecTILs to conduct a meta-analysis of human tumor-infiltrating T lymphocytes (TILs), revealing a remarkable conservation of TIL subtypes between human and mouse and across cancer types. Clonotype analysis supported a model in which rare human tumor-specific effector-memory (EM)-like CD8 TILs that resemble blood-circulating EM cells, differentiate into proliferative terminal exhausted/dysfunctional effector TILs through a progenitor subtype that upregulates the exhaustion master regulator TOX . Our novel computational method allows exploring the effect of human and murine T cell perturbations ( e.g. as the result of therapy or genetic engineering) in terms of reference cellular states, altered genetic programs and clonotype structure, revealing mechanisms of action behind immunotherapies and opening opportunities for their improvement. ### Competing Interest Statement MA, JCO and SJC declare no conflicts of interest. GC has received grants, research support or is coinvestigator in clinical trials by BMS, Celgene, Boehringer Ingelheim, Roche, Iovance and Kite; has received honoraria for consultations or presentations by Roche, Genentech, BMS, AstraZeneca, Sanofi-Aventis, Nextcure and GeneosTx; he has patents in the domain of antibodies and vaccines targeting the tumor vasculature as well as technologies related to T-cell expansion and engineering for T-cell therapy; and he receives royalties from the University of Pennsylvania for CAR-T technologies licensed to Novartis. SM and RC are employees of Genentech, Inc, a member of the Roche family and receive salary and stock from Roche.

27: No evidence for increased transmissibility from recurrent mutations in SARS-CoV-2
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Posted to bioRxiv 21 May 2020

No evidence for increased transmissibility from recurrent mutations in SARS-CoV-2
8 tweets genomics

Lucy van Dorp, Damien Richard, Cedric C.S. Tan, Liam P. Shaw, Mislav Acman, Francois Balloux

The COVID-19 pandemic is caused by the coronavirus SARS-CoV-2, which jumped into the human population in late 2019 from a currently uncharacterised animal reservoir. Due to this extremely recent association with humans, SARS-CoV-2 may not yet be fully adapted to its human host. This has led to speculations that some lineages of SARS-CoV-2 may be evolving towards higher transmissibility. The most plausible candidate mutations under putative natural selection are those which have emerged repeatedly and independently (homoplasies). Here, we formally test whether any of the recurrent mutations that have been observed in SARS-CoV-2 are significantly associated with increased viral transmission. To do so, we develop a phylogenetic index to quantify the relative number of descendants in sister clades with and without a specific allele. We apply this index to a carefully curated set of recurrent mutations identified within a dataset of 46,723 SARS-CoV-2 genomes isolated from patients worldwide. We do not identify a single recurrent mutation in this set convincingly associated with increased viral transmission. Instead, recurrent SARS-CoV-2 mutations currently in circulation appear to be evolutionary neutral. Recurrent mutations also seem primarily induced by the human immune system via host RNA editing, rather than being signatures of adaptation to the novel human host. In conclusion, we find no evidence at this stage for the emergence of significantly more transmissible lineages of SARS-CoV-2 due to recurrent mutations. ### Competing Interest Statement The authors have declared no competing interest.

28: Computational 4D-OCM for label-free imaging of collective cell invasion and force-mediated deformations in collagen
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Posted to bioRxiv 11 Sep 2020

Computational 4D-OCM for label-free imaging of collective cell invasion and force-mediated deformations in collagen
8 tweets biophysics

Jeffrey A Mulligan, Lu Ling, Claudia Fischbach, Steven G Adie

Traction force microscopy (TFM) is an important family of techniques used to measure and study the role of cellular traction forces (CTFs) associated with many biological processes. However, current standard TFM methods rely on imaging techniques that do not provide the experimental capabilities necessary to study CTFs within 3D collective and dynamic systems embedded within optically scattering media. Traction force optical coherence microscopy (TF-OCM) was developed to address these needs, but has only been demonstrated for the study of isolated cells embedded within optically clear media. Here, we present computational 4D-OCM methods that enable the study of dynamic invasion behavior of large tumor spheroids embedded in collagen. Our multi-day, time-lapse imaging data provided detailed visualizations of evolving spheroid morphology, collagen degradation, and collagen deformation, all using label-free scattering contrast. These capabilities, which provided insights into how stromal cells affect cancer progression, significantly expand access to critical data about biophysical interactions of cells with their environment, and lay the foundation for future efforts toward volumetric, time-lapse reconstructions of collective CTFs with TF-OCM. ### Competing Interest Statement The authors have declared no competing interest.

29: Computationally efficient whole genome regression for quantitative and binary traits
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Posted to bioRxiv 20 Jun 2020

Computationally efficient whole genome regression for quantitative and binary traits
7 tweets genetics

Joelle Mbatchou, Leland Barnard, Joshua Backman, Anthony Marcketta, Jack A. Kosmicki, Andrey Ziyatdinov, Christian Benner, Colm O’Dushlaine, Mathew Barber, Boris Boutkov, Lukas Habegger, Manuel Ferreira, Aris Baras, Jeffrey Reid, Gonçalo R. Abecasis, Evan K. Maxwell, Jonathan Marchini

Genome-wide association analysis of cohorts with thousands of phenotypes is computationally expensive, particularly when accounting for sample relatedness or population structure. Here we present a novel machine learning method called REGENIE for fitting a whole genome regression model that is orders of magnitude faster than alternatives, while maintaining statistical efficiency. The method naturally accommodates parallel analysis of multiple phenotypes, and only requires local segments of the genotype matrix to be loaded in memory, in contrast to existing alternatives which much load genomewide matrices into memory. This results in substantial savings in compute time and memory usage. The method is applicable to both quantitative and binary phenotypes, including rare variant analysis of binary traits with unbalanced case-control ratios where we introduce a fast, approximate Firth logistic regression test. The method is ideally suited to take advantage of distributed computing frameworks. We demonstrate the accuracy and computational benefits of this approach compared to several existing methods using quantitative and binary traits from the UK Biobank dataset with up to 407,746 individuals. ### Competing Interest Statement All of the authors are current employees and/or stockholders of Regeneron Pharmaceuticals

30: Examining sex-differentiated genetic effects across neuropsychiatric and behavioral traits
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Posted to bioRxiv 05 May 2020

Examining sex-differentiated genetic effects across neuropsychiatric and behavioral traits
7 tweets genetics

Joanna Martin, Ekaterina A. Khramtsova, Slavina B Goleva, Gabriëlla A. M. Blokland, Michela Traglia, Raymond K Walters, Christopher Hübel, Jonathan R. I. Coleman, Gerome Breen, Anders D. Borglum, Ditte Demontis, Jakob Grove, Thomas Werge, Janita Bralten, Cynthia M. Bulik, Phil H. Lee, Carol A. Mathews, Roseann E. Peterson, Stacey J Winham, Naomi R Wray, Howard J Edenberg, Wei Guo, Yin Yao, Benjamin M. Neale, Stephen V Faraone, Tracey L. Petryshen, Lauren A. Weiss, Laramie E Duncan, Sex Differences Cross-Disorder Analysis Group of the Psychiatric Genomics Consortium, Jill M Goldstein, Jordan W. Smoller, Barbara E. Stranger, Lea K Davis

Background: The origin of sex differences in prevalence and presentation of neuropsychiatric and behavioral traits is largely unknown. Given established genetic contributions and correlations across these traits, we tested for a sex-differentiated genetic architecture within and between traits. Methods: Using genome-wide association study (GWAS) summary statistics for 20 neuropsychiatric and behavioral traits, we tested for differences in SNP-based heritability (h2) and genetic correlation (rg<1) between sexes. For each trait, we computed z-scores from sex-stratified GWAS regression coefficients and identified genes with sex-differentiated effects. We calculated Pearson correlation coefficients between z-scores for each trait pair, to assess whether specific pairs share variants with sex-differentiated effects. Finally, we tested for sex differences in between-trait genetic correlations. Results: With current sample sizes (and power), we found no significant, consistent sex differences in SNP-based h2. Between-sex, within-trait genetic correlations were consistently high, although significantly less than 1 for educational attainment and risk-taking behavior. We identified genome-wide significant genes with sex-differentiated effects for eight traits. Several trait pairs shared sex-differentiated effects. The top 0.1% of genes with sex-differentiated effects across traits overlapped with neuron- and synapse-related gene sets. Most between-trait genetic correlation estimates were similar across sex, with several exceptions (e.g. educational attainment & risk-taking behavior). Conclusions: Sex differences in the common autosomal genetic architecture of neuropsychiatric and behavioral phenotypes are small and polygenic, requiring large sample sizes. Genes with sex-differentiated effects are enriched for neuron-related gene sets. This work motivates further investigation of genetic, as well as environmental, influences on sex differences. ### Competing Interest Statement CM Bulik reports: Shire (grant recipient, Scientific Advisory Board member); Idorsia (consultant); Pearson (author, royalty recipient). EA Khramtsova is employed by Janssen Pharmaceutical Companies of Johnson and Johnson.

31: Targeting androgen regulation of TMPRSS2 and ACE2 as a therapeutic strategy to combat COVID-19
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Posted to bioRxiv 16 Oct 2020

Targeting androgen regulation of TMPRSS2 and ACE2 as a therapeutic strategy to combat COVID-19
7 tweets molecular biology

Qu Deng, Reyaz ur Rasool, Ronnie M Russell, Ramakrishnan Natesan, Irfan A Asangani

The COVID-19 pandemic is expected to have an adverse effect on the progression of multiple cancers, including prostate cancer, due to the ensuing cytokine storm and associated oncogenic signaling. Epidemiological data showing increased severity and mortality of COVID-19 in men suggests a potential role for androgen in SARS-CoV-2 infection. Here, we present evidence for the transcriptional regulation of SARS-CoV-2 host cell receptor ACE2 and co-receptor TMPRSS2 by androgen in mouse tissues and human prostate and lung cell lines. Additionally, we demonstrate the endogenous interaction between TMPRSS2 and ACE2 in human cells and validate ACE2 as a TMPRSS2 substrate. In an overexpression model, and the prostate and lung cells, Camostat – a TMPRSS2 inhibitor, blocked the cleavage of pseudotype SARS-CoV-2 surface Spike without disrupting TMPRSS2-ACE2 interaction. Thus providing evidence for the first time a direct role of TMPRSS2 in priming the SARS-CoV-2 Spike protein, required for viral fusion to the host cell. Importantly, androgen-deprivation, anti-androgens such as enzalutamide/AR-PROTAC, or Camostat treatment attenuated the SARS-CoV-2 S-mediated entry in lung and prostate cells. Together, our preclinical data provide a strong rationale for clinical evaluations of the TMPRSS2 inhibitors, androgen-deprivation therapy and androgen receptor antagonists alone or in combination with anti-viral drugs as early as clinically possible to prevent inflammation driven COVID-19 progression. ### Competing Interest Statement The authors have declared no competing interest.

32: ACE2 and TMPRSS2 are expressed on the human ocular surface, suggesting susceptibility to SARS-CoV-2 infection
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Posted to bioRxiv 09 May 2020

ACE2 and TMPRSS2 are expressed on the human ocular surface, suggesting susceptibility to SARS-CoV-2 infection
7 tweets pathology

Lingli Zhou, Zhenhua Xu, Gianni M. Castiglione, Uri S Soiberman, Charles G. Eberhart, Elia J Duh

Purpose: Conjunctival signs and symptoms are observed in a subset of patients with COVID-19, and SARS-CoV-2 has been detected in tears, raising concerns regarding the eye both as a portal of entry and carrier of the virus. The purpose of this study was to determine whether ocular surface cells possess the key factors required for cellular susceptibility to SARS-CoV-2 entry/infection. Methods: We analyzed human post-mortem eyes as well as surgical specimens for the expression of ACE2 (the receptor for SARS-CoV-2) and TMPRSS2, a cell surface-associated protease that facilitates viral entry following binding of the viral spike protein to ACE2. Results: Across all eye specimens, immunohistochemical analysis revealed expression of ACE2 in the conjunctiva, limbus, and cornea, with especially prominent staining in the superficial conjunctival and corneal epithelial surface. Surgical conjunctival specimens also showed expression of ACE2 in the conjunctival epithelium, especially prominent in the superficial epithelium, as well as the substantia propria. All eye and conjunctival specimens also expressed TMPRSS2. Finally, western blot analysis of protein lysates from human corneal epithelium obtained during refractive surgery confirmed expression of ACE2 and TMPRSS2. Conclusions: Together, these results indicate that ocular surface cells including conjunctiva are susceptible to infection by SARS-CoV-2, and could therefore serve as a portal of entry as well as a reservoir for person-to-person transmission of this virus. This highlights the importance of safety practices including face masks and ocular contact precautions in preventing the spread of COVID-19 disease. ### Competing Interest Statement The authors have declared no competing interest.

33: Hidden genomic diversity of SARS-CoV-2: implications for qRT-PCR diagnostics and transmission
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Posted to bioRxiv 02 Jul 2020

Hidden genomic diversity of SARS-CoV-2: implications for qRT-PCR diagnostics and transmission
6 tweets genomics

Nicolae Sapoval, Medhat Mahmoud, Michael D. Jochum, Yunxi Liu, R. A. Leo Elworth, Qi Wang, Dreycey Albin, Huw Ogilvie, Michael D. Lee, Sonia Villapol, Kyle M. Hernandez, Irina Maljkovic Berry, Jonathan Foox, Afshin Beheshti, Krista Ternus, Kjersti M Aagaard, David Posada, Christopher E. Mason, Fritz J. Sedlazeck, Adam M. Phillippy

The COVID-19 pandemic has sparked an urgent need to uncover the underlying biology of this devastating disease. Though RNA viruses mutate more rapidly than DNA viruses, there are a relatively small number of single nucleotide polymorphisms (SNPs) that differentiate the main SARS-CoV-2 clades that have spread throughout the world. In this study, we investigated over 7,000 SARS-CoV-2 datasets to unveil both intrahost and interhost diversity. Our intrahost and interhost diversity analyses yielded three major observations. First, the mutational profile of SARS-CoV-2 highlights iSNV and SNP similarity, albeit with high variability in C>T changes. Second, iSNV and SNP patterns in SARS-CoV-2 are more similar to MERS-CoV than SARS-CoV-1. Third, a significant fraction of small indels fuel the genetic diversity of SARS-CoV-2. Altogether, our findings provide insight into SARS-CoV-2 genomic diversity, inform the design of detection tests, and highlight the potential of iSNVs for tracking the transmission of SARS-CoV-2. ### Competing Interest Statement The authors have declared no competing interest.

34: Somatic CAG expansion in Huntington's disease is dependent on the MLH3 endonuclease domain, which can be excluded via MLH3 splice redirection to suppress expansion
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Posted to bioRxiv 27 Oct 2020

Somatic CAG expansion in Huntington's disease is dependent on the MLH3 endonuclease domain, which can be excluded via MLH3 splice redirection to suppress expansion
6 tweets genetics

Jennie C. L. Roy, Antonia Vitalo, Marissa A. Andrew, Eduarda Mota-Silva, Marina Kovalenko, Zoe Burch, Anh M. Nhu, Paula E. Cohen, Ed Grabczyk, Vanessa C Wheeler, Ricardo Mouro Pinto

Somatic expansion of the CAG repeat tract that causes Huntington's disease (HD) is thought to contribute to the rate of disease pathogenesis. Therefore, factors influencing repeat expansion are potential therapeutic targets. Genes in the DNA mismatch repair pathway are critical drivers of somatic expansion in HD mouse models. Here, we have tested, using genetic and pharmacological approaches, the role of the endonuclease domain of the mismatch repair protein MLH3 in somatic CAG expansion in HD mice and patient cells. A point mutation in the MLH3 endonuclease domain completely eliminated CAG expansion in the brain and peripheral tissues of a HD knock-in mouse model ( Htt Q111). To test whether the MLH3 endonuclease could be manipulated pharmacologically, we delivered splice switching oligonucleotides in mice to redirect Mlh3 splicing to exclude the endonuclease domain. Splice redirection to an isoform lacking the endonuclease domain was associated with reduced CAG expansion. Finally, CAG expansion in HD patient-derived primary fibroblasts was also significantly reduced by redirecting MLH3 splicing to the endogenous endonuclease domain-lacking isoform. These data indicate the potential of targeting the MLH3 endonuclease domain to slow somatic CAG repeat expansion in HD, a therapeutic strategy that may be applicable across multiple repeat expansion disorders. ### Competing Interest Statement V.C.W. is a scientific advisory board member of Triplet Therapeutics, a company developing new therapeutic approaches to address triplet repeat disorders such Huntington's disease and Myotonic Dystrophy, and of LoQus23 Therapeutics, and has provided paid consulting services to Alnylam and Acadia Pharmaceuticals. Her financial interests in Triplet Therapeutics were reviewed and are managed by Massachusetts General Hospital and Partners HealthCare in accordance with their conflict of interest policies. R.M.P. and V.C.W have received sponsored research funding from Pfizer unrelated to the content of this manuscript. E.G. is a named inventor on a patent related to this work (US10669542B2).

35: Emergent robustness of bacterial quorum sensing in fluid flow
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Posted to bioRxiv 24 Oct 2020

Emergent robustness of bacterial quorum sensing in fluid flow
6 tweets biophysics

Mohit P Dalwadi, Philip Pearce

Bacteria use intercellular signaling, or quorum sensing (QS), to share information and respond collectively to aspects of their surroundings. The autoinducers that carry this information are exposed to the external environment; consequently, they are affected by factors such as removal through fluid flow, a ubiquitous feature of bacterial habitats ranging from the gut and lungs to lakes and oceans. To understand how QS genetic architectures in cells promote appropriate population-level phenotypes throughout the bacterial life cycle requires knowledge of how these architectures determine the QS response in realistic spatiotemporally varying flow conditions. Here, we develop and apply a general theory that identifies and quantifies the conditions required for QS activation in fluid flow by systematically linking cell- and population-level genetic and physical processes. We predict that, when a subset of the population meets these conditions, cell-level positive feedback promotes a robust collective response by overcoming flow-induced autoinducer concentration gradients. By accounting for a dynamic flow in our theory, we predict that positive feedback in cells acts as a low-pass filter at the population level in oscillatory flow, allowing a population to respond only to changes in flow that occur over slow enough timescales. Our theory is readily extendable, and provides a framework for assessing the functional roles of diverse QS network architectures in realistic flow conditions. ### Competing Interest Statement The authors have declared no competing interest.

36: Analysis of the Immune Response to Sciatic Nerve Injury Identifies Efferocytosis as a Key Mechanism of Nerve Debridement
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Posted to bioRxiv 24 Oct 2020

Analysis of the Immune Response to Sciatic Nerve Injury Identifies Efferocytosis as a Key Mechanism of Nerve Debridement
6 tweets neuroscience

Ashley L Kalinski, Choya Yoon, Lucas D Huffman, Patrick C Duncker, Rafi Kohen, Ryan Passino, Hannah Hafner, Craig Johnson, Riki Kawaguchi, Kevin S Carbajal, Juan Sebastian Jara, Edmund Hollis, Daniel Geschwind, Benjamin Segal, Roman J Giger

Sciatic nerve crush injury triggers sterile inflammation within the distal nerve and axotomized dorsal root ganglia (DRGs). Granulocytes and pro-inflammatory Ly6C high monocytes infiltrate the nerve first, and rapidly give way to Ly6C negative inflammation-resolving macrophages. In axotomized DRGs, few hematogenous leukocytes are detected and resident macrophages acquire a ramified morphology. Single-cell RNA-sequencing of injured sciatic nerve identifies five macrophage subpopulations, repair Schwann cells, and mesenchymal precursor cells. Macrophages at the nerve crush site are molecularly distinct from macrophages associated with Wallerian degeneration. In the injured nerve, macrophages "eat" apoptotic leukocytes, a process called efferocytosis, and thereby promote an anti-inflammatory milieu. Myeloid cells in the injured nerve, but not axotomized DRGs, strongly express receptors for the cytokine GM-CSF. In GM-CSF deficient ( Csf2-/- ) mice, inflammation resolution is delayed and conditioning-lesion induced regeneration of DRG neuron central axons is abolished. Thus, carefully orchestrated inflammation resolution in the nerve is required for conditioning-lesion induced neurorepair. ### Competing Interest Statement The authors have declared no competing interest.

37: Cell-type, single-cell, and spatial signatures of brain-region specific splicing in postnatal development
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Posted to bioRxiv 27 Aug 2020

Cell-type, single-cell, and spatial signatures of brain-region specific splicing in postnatal development
6 tweets neuroscience

Anoushka Joglekar, Andrey D Przhibelskiy, Ahmed Mahfouz, Paul Collier, Susan Lin, Anna K Schlusche, Jordan Marrocco, Stephen R. Williams, Bettina Haase, Ashley Hayes, Jennifer G Chew, Neil I Weisenfeld, Man Ying Wong, Alexander N Stein, Simon Hardwick, Toby Hunt, Zachary Bent, Olivier Fedrigo, Steven A. Sloan, Davide Risso, Erich D. Jarvis, Paul Flicek, Wenjie Luo, Geoffrey S. Pitt, Adam Frankish, August B Smit, Margaret Elizabeth Ross, Hagen U Tilgner

Alternative RNA splicing varies across brain regions, but the single-cell resolution of such regional variation is unknown. Here we present the first single-cell investigation of differential isoform expression (DIE) between brain regions, by performing single cell long-read transcriptome sequencing in the mouse hippocampus and prefrontal cortex in 45 cell types at postnatal day 7. Using isoform tests for brain-region specific DIE, which outperform exon-based tests, we detect hundreds of brain-region specific DIE events traceable to specific cell-types. Many DIE events correspond to functionally distinct protein isoforms, some with just a 6-nucleotide exon variant. In most instances, one cell type is responsible for brain-region specific DIE. Cell types indigenous to only one anatomic structure display distinctive DIE, where for example, the choroid plexus epithelium manifest unique transcription start sites. However, for some genes, multiple cell-types are responsible for DIE in bulk data, indicating that regional identity can, although less frequently, override cell-type specificity. We validated our findings with spatial transcriptomics and long-read sequencing, yielding the first spatially resolved splicing map in the postnatal mouse brain. Our methods are highly generalizable. They provide a robust means of quantifying isoform expression with cell-type and spatial resolution, and reveal how the brain integrates molecular and cellular complexity to serve function. ### Competing Interest Statement The authors have declared no competing interest.

38: Hydroxychloroquine-mediated inhibition of SARS-CoV-2 entry is attenuated by TMPRSS2
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Posted to bioRxiv 22 Jul 2020

Hydroxychloroquine-mediated inhibition of SARS-CoV-2 entry is attenuated by TMPRSS2
6 tweets microbiology

Tianling Ou, Huihui Mou, Lizhou Zhang, Amrita Ojha, Hyeryun Choe, Michael Farzan

Hydroxychloroquine, used to treat malaria and some autoimmune disorders, potently inhibits viral infection of SARS coronavirus (SARS-CoV-1) and SARS-CoV-2 in cell-culture studies. However, human clinical trials of hydroxychloroquine failed to establish its usefulness as treatment for COVID-19. This compound is known to interfere with endosomal acidification necessary to the proteolytic activity of cathepsins. Following receptor binding and endocytosis, cathepsin L can cleave the SARS-CoV-1 and SARS-CoV-2 spike (S) proteins, thereby activating membrane fusion for cell entry. The plasma membrane-associated protease TMPRSS2 can similarly cleave these S proteins and activate viral entry at the cell surface. Here we show that the SARS-CoV-2 entry process is more dependent than that of SARS-CoV-1 on TMPRSS2 expression. This difference can be reversed when the furin-cleavage site of the SARS-CoV-2 S protein is ablated. We also show that hydroxychloroquine efficiently blocks viral entry mediated by cathepsin L, but not by TMPRSS2, and that a combination of hydroxychloroquine and a clinically-tested TMPRSS2 inhibitor prevents SARS-CoV-2 infection more potently than either drug alone. These studies identify functional differences between SARS-CoV-1 and -2 entry processes, and provide a mechanistic explanation for the limited in vivo utility of hydroxychloroquine as a treatment for COVID-19. ### Competing Interest Statement The authors have declared no competing interest.

39: Adhesion-mediated heterogeneous actin organization governs apoptotic cell extrusion
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Posted to bioRxiv 26 Aug 2020

Adhesion-mediated heterogeneous actin organization governs apoptotic cell extrusion
6 tweets cell biology

Anh Phuong Le, Jean-Francois Rupprecht, Rene-Marc Mege, Yusuke Toyama, Chwee Teck Lim, Benoit Ladoux

Apoptotic extrusion is crucial in maintaining epithelial homeostasis and has implications in diseases of epithelial tissues. Current literature supports that epithelia respond to extrusion to maintain their integrity by the formation of a supracellular actomyosin ring (purse-string) in the neighbors that encompasses the dying cells. However, little is known about whether other types of actin structures could contribute to extrusion as well as how forces generated by mechanosensitive proteins in the cells are integrated. Here, we found that during extrusion, a heterogeneous actin network composed of lamellipodia protrusions and discontinuous actomyosin cables, was reorganized in the neighboring cells and was the main factor driving extrusion forwards. The early presence of basal lamellipodia protrusion participated both in basal sealing of the extrusion site and in orienting the actomyosin purse-string at the later stage of extrusion. These sequential events are essential in ensuring a successful extrusion in apicobasal direction. The co-existence of these two mechanisms is determined by the interplay between the cell-cell and cell-substrate adhesions. A theoretical model integrates the role of these cellular mechanosensitive components to explain why a dual-mode mechanism, which combined lamellipodia protrusion and purse-string contractility, leads to more efficient extrusion than a single-mode mechanism. We anticipate that our approach will be useful to provide mechanistic insight into epithelial homeostasis, morphogenetic events and tumorigenesis. ### Competing Interest Statement The authors have declared no competing interest.

40: The tiny Cretaceous stem-bird Oculudentavis revealed as a bizarre lizard
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Posted to bioRxiv 10 Aug 2020

The tiny Cretaceous stem-bird Oculudentavis revealed as a bizarre lizard
6 tweets paleontology

Arnau Bolet, Edward L. Stanley, Juan D. Daza, J. Salvador Arias, Andrej Čerňanský, Marta Vidal-García, Aaron M. Bauer, Joseph J. Bevitt, Adolf Peretti, Susan E. Evans

Oculudentavis khaungraae was described based on a tiny skull trapped in amber. The slender tapering rostrum with retracted osseous nares, large eyes, and short vaulted braincase led to its identification as the smallest avian dinosaur on record, comparable to the smallest living hummingbirds. Despite its bird-like appearance, Oculudentavis showed several features inconsistent with its original phylogenetic placement. Here we describe a more complete, specimen that demonstrates Oculudentavis is actually a bizarre lizard of uncertain position. The new interpretation and phylogenetic placement highlights a rare case of convergent evolution rarely seen among reptiles. Our results re-affirm the importance of Myanmar amber in yielding unusual taxa from a forest ecosystem rarely represented in the fossil record. ### Competing Interest Statement The authors have declared no competing interest.

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