bluuebunny/crossref_metadata_2025_split huggingface dataset:
Parallel social information processing circuits are differentially impacted in autism
Authors: Lewis Eastman M. , Stein-O’Brien Genevieve L. , Patino Alejandra V. , Nardou Romain , Grossman Cooper D. , Brown Matthew , Bangamwabo Bidii , Ndiaye Ndeye , Giovinazzo Daniel , Dardani Ian , Jiang Connie , Goff Loyal A. , Dölen Gül 
Published: March 2020

AbstractParallel processing circuits are thought to dramatically expand the network capabilities of the nervous system. Magnocellular and parvocellular oxytocin neurons have been proposed to subserve two parallel streams of social information processing, which allow a single molecule to encode a diverse array of ethologically distinct behaviors, although to date direct evidence to support this hypothesis is lacking. Here we provide the first comprehensive characterization of magnocellular and parvocellular oxytocin neurons, validated across anatomical, projection target, electrophysiological, and transcriptional criteria. We next used novel multiple feature selection tools inFmr1KO mice to provide direct evidence that normal functioning of the parvocellular but not magnocellular oxytocin pathway is required for autism-relevant social reward behavior. Finally, we demonstrate that autism risk genes are uniquely enriched in parvocellular oxytocin neurons. Taken together these results provide the first evidence that oxytocin pathway specific pathogenic mechanisms account for social impairments across a broad range of autism etiologies.One Sentence SummaryPathoclisis of parvocellular oxytocin neurons plays an important role in the pathogenesis of social impairments in autism.
When Darkness Becomes a Ray of Light in the Dark Times: Understanding the COVID-19 via the Comparative Analysis of the Dark Proteomes of SARS-CoV-2, Human SARS and Bat SARS-Like Coronaviruses
Authors: Giri Rajanish , Bhardwaj Taniya , Shegane Meenakshi , Gehi Bhuvaneshwari R. , Kumar Prateek , Gadhave Kundlik , Oldfield Christopher J. , Uversky Vladimir N. 
Published: March 2020

AbstractRecently emerged coronavirus designated as SARS-CoV-2 (also known as 2019 novel coronavirus (2019-nCoV) or Wuhan coronavirus) is a causative agent of coronavirus disease 2019 (COVID-19), which is rapidly spreading throughout the world now. More than 9,00,000 cases of SARS-CoV-2 infection and more than 47,000 COVID-19-associated mortalities have been reported worldwide till the writing of this article, and these numbers are increasing every passing hour. World Health Organization (WHO) has declared the SARS-CoV-2 spread as a global public health emergency and admitted that the COVID-19 is a pandemic now. The multiple sequence alignment data correlated with the already published reports on the SARS-CoV-2 evolution and indicated that this virus is closely related to the bat Severe Acute Respiratory Syndrome-like coronavirus (bat SARS-like CoV) and the well-studied Human SARS coronavirus (SARS CoV). The disordered regions in viral proteins are associated with the viral infectivity and pathogenicity. Therefore, in this study, we have exploited a set of complementary computational approaches to examine the dark proteomes of SARS-CoV-2, bat SARS-like, and human SARS CoVs by analysing the prevalence of intrinsic disorder in their proteins. According to our findings, SARS-CoV-2 proteome contains very significant levels of structural order. In fact, except for Nucleocapsid, Nsp8, and ORF6, the vast majority of SARS-CoV-2 proteins are mostly ordered proteins containing less intrinsically disordered protein regions (IDPRs). However, IDPRs found in SARS-CoV-2 proteins are functionally important. For example, cleavage sites in its replicase 1ab polyprotein are found to be highly disordered, and almost all SARS-CoV-2 proteins were shown to contain molecular recognition features (MoRFs), which are intrinsic disorder-based protein-protein interaction sites that are commonly utilized by proteins for interaction with specific partners. The results of our extensive investigation of the dark side of the SARS-CoV-2 proteome will have important implications for the structural and non-structural biology of SARS or SARS-like coronaviruses.SignificanceThe infection caused by a novel coronavirus (SARS-CoV-2) that causes severe respiratory disease with pneumonia-like symptoms in humans is responsible for the current COVID-19 pandemic. No in-depth information on structures and functions of SARS-CoV-2 proteins is currently available in the public domain, and no effective anti-viral drugs and/or vaccines are designed for the treatment of this infection. Our study provides the first comparative analysis of the order- and disorder-based features of the SARS-CoV-2 proteome relative to human SARS and bat CoV that may be useful for structure-based drug discovery.
Arterial pulsations drive oscillatory flow of CSF but not directional pumping
Authors: Kedarasetti Ravi Teja , Drew Patrick J. , Costanzo Francesco 
Published: March 2020

AbstractThe brain lacks a traditional lymphatic system for metabolite clearance. The existence a “glymphatic system” where metabolites are removed from the brain’s extracellular space by convective exchange between interstitial fluid (ISF) and cerebrospinal fluid (CSF) along the paravascular spaces (PVS) around cerebral blood vessels has been controversial for nearly a decade. While recent work has shown clear evidence of directional flow of CSF in the PVS in anesthetized mice, the driving force for the observed fluid flow remains elusive. The heartbeat-driven peristaltic pulsation of arteries has been proposed as a probable driver of directed CSF flow. In this study, we use rigorous fluid dynamic simulations to provide a physical interpretation for peristaltic pumping of fluids. Our simulations match the experimental results and show that arterial pulsations only drive oscillatory motion of CSF in the PVS. The observed directional CSF flow can be explained by naturally occurring and/or experimenter-generated pressure differences.
Encoding Fear of Heights by Basolateral Amygdala Neurons
Authors: Liu Jun , Lin Longnian , Wang Dong V 
Published: March 2020

SUMMARYFear of heights is evolutionarily important for survival, yet it is unclear how and which brain regions encode such height threats. Given the importance of the basolateral amygdala (BLA) in processing both learned and innate fear, we investigated how BLA neurons may respond to high place exposure in freely behaving mice. We found that a discrete set of BLA neurons exhibited robust firing increases when the mouse was either exploring or placed on a high place, accompanied by increased heart rate and freezing. Importantly, these high-place fear neurons were only activated under height threats but not mild anxiogenic conditions. Furthermore, after a fear conditioning procedure, these high-place fear neurons developed conditioned responses to the context, but not the cue, indicating a convergence in encoding of dangerous/risky contextual information. Our results provide insights into the neural representation of the fear of heights and may have implications for treatment of excessive fear disorders.
Adaptive FDR thresholding of Fourier shell correlation for resolution estimation of cryo-EM maps
Authors: Beckers Maximilian , Sachse Carsten 
Published: March 2020

AbstractFourier shell correlation (FSC) has become a standard quantity for resolution estimation in electron cryo-microscopy. However, the resolution determination step is still subjective and not fully automated as it involves a series of map interventions before FSC computation and includes the selection of a common threshold. Here, we apply the statistical methods of permutation sampling and false discovery rate (FDR) control to the resolution-dependent correlation measure. The approach allows fully automated and mask-free resolution determination based on adaptive thresholding of FSC curves. We demonstrate the applicability for global, local and directional resolution estimation and show that the developed criterion termed FDR-FSC gives realistic resolution estimates based on a statistical significance criterion while eliminating the need of any map manipulations. The algorithms are implemented in a user-friendly GUI based software tool termed SPoC (https://github.com/MaximilianBeckers/SPOC).
Establishing cell-intrinsic limitations in cell cycle progression controls graft growth and promotes differentiation of pancreatic endocrine cells
Authors: Sui Lina , Xin Yurong , Georgieva Daniela , Diedenhofen Giacomo , Haataja Leena , Su Qi , Wang Yong , Zuccaro Michael , Kim Jinrang , Fu Jiayu , Xing Yuan , Baum Danielle , Goland Robin S. , Oberholzer Jose , Barbetti Fabrizio , Arvan Peter , Kleiner Sandra , Egli Dieter 
Published: March 2020

AbstractLimitations in cell proliferation are a key barrier to reprogramming differentiated cells to pluripotent stem cells, and conversely, acquiring these limitations may be important to establish the differentiated state. The pancreas, and beta cells in particular have a low proliferative potential, which limits regeneration, but how these limitations are established is largely unknown. Understanding proliferation potential is important for the safty of cell replacement therapy with cell products made from pluripotent stem cell which have unlimited proliferative potential. Here we test a novel hypothesis, that these limitations are established through limitations in S-phase progression. We used a stem cell-based system to expose differentiating stem cells to small molecules that interfere with cell cycle progression either by inducing G1 arrest, impairing S-phase entry, or S-phase completion. Upon release from these molecules, we determined growth potential, differentiation and function of insulin-producing endocrine cells bothin vitroand after graftingin vivo. We found that the combination of G1 arrest with a compromised ability to complete DNA replication promoted the differentiation of pancreatic progenitor cells towards insulin-producing cells, improved the stability of the differentiated state, and protected mice from diabetes without the formation of cystic growths. Therefore, a compromised ability to enter S-phase and replicate the genome is a functionally important property of pancreatic endocrine differentiation, and can be exploited to generate insulin-producing organoids with predictable growth potential after transplantation.
Notch effector Hes1 marks an early perichondrial population of skeletal progenitor cells at the onset of endochondral bone development
Authors: Matsushita Yuki , Nagata Mizuki , Welch Joshua D. , Wong Sunny Y. , Ono Wanida , Ono Noriaki 
Published: March 2020

SummaryThe perichondrium, a fibrous tissue surrounding the fetal cartilage, is an essential component of developing endochondral bones that provides a source of skeletal progenitor cells. However, perichondrial cells remain poorly characterized due to lack of knowledge on their cellular diversity and subset-specific mouse genetics tools. Single cell RNA-seq analyses reveal a contiguous nature of the fetal chondrocyte-perichondrial cell lineage that shares an overlapping set of marker genes. Subsequent cell-lineage analyses using multiplecreERlines active in fetal perichondrial cells –Hes1-creER,Dlx5-creER– and chondrocytes –Fgfr3-creER– illustrate their distinctive contribution to endochondral bone development; postnatally, these cells contribute to the functionally distinct bone marrow stromal compartments. Particularly, Notch effectorHes1-creERmarks an early skeletal progenitor cell population in the primordium that robustly populates multiple skeletal compartments. These findings support the concept that perichondrial cells participate in endochondral bone development through a distinct route, by providing a complementary source of skeletal progenitor cells.
Endothelial mTOR maintains hematopoiesis during aging
Authors: Ramalingam Pradeep , Poulos Michael G. , Gutkin Michael C. , Katsnelson Lizabeth , Freire Ana G. , Lazzari Elisa , Butler Jason M. 
Published: March 2020

AbstractAging leads to a decline in hematopoietic stem and progenitor cell (HSPC) function. We recently discovered that aging of bone marrow endothelial cells (BMECs) leads to an altered crosstalk between the BMEC niche and HSPCs, that instructs young HSPCs to behave as aged HSPCs. Here, we demonstrate aging leads to a decrease in mTOR signaling within BMECs that potentially underlies the age-related impairment of their niche activity. Our findings reveal that pharmacological inhibition of mTOR using Rapamycin has deleterious effects on hematopoiesis. To formally determine whether endothelial-specific inhibition of mTOR can influence hematopoietic aging, we conditionally deleted mTOR in ECs (mTOR(ECKO)) of young mice and observed that their HSPCs displayed attributes of an aged hematopoietic system. Transcriptional profiling of HSPCs from mTOR(ECKO)mice revealed that their transcriptome resembled aged HSPCs. Notably, during serial transplantations, exposure of wild type HSPCs to an mTOR(ECKO)microenvironment was sufficient to recapitulate aging-associated phenotypes, confirming the instructive role of EC-derived signals in governing HSPC aging.SummaryRamalingam et al. demonstrate that pharmacological inhibition of mTOR adversely impacts aging hematopoiesis. The authors demonstrate that aging results in decreased mTOR signaling within the bone marrow endothelium and endothelial-specific inhibition of mTOR causes hematopoietic defects observed during physiological aging.
ER-Mitochondria Contacts Promote Mitochondrial-Derived Compartment Biogenesis
Authors: English Alyssa M. , Kornmann Benoît , Shaw Janet M. , Hughes Adam L. 
Published: March 2020

AbstractMitochondria are dynamic organelles with essential roles in signaling and metabolism. We recently identified a new cellular structure called the mitochondrial-derived compartment (MDC) that is generated from mitochondria in response to amino acid elevation. MDCs protect cells from amino acid toxicity, but how cells form MDCs is unclear. Here, we show that MDCs are micron-sized, lumen-containing organelles that form at sites of contact between the ER and mitochondria. Upon formation, MDCs stably persist at ER-mitochondria contacts for extended periods of time. MDC formation requires the ER-mitochondria encounter structure (ERMES) and GTP hydrolysis by the conserved GTPase Gem1. Unexpectedly, MDC formation is not linked to the role of ERMES/Gem1 in the maintenance of mitochondrial phospholipid homeostasis. Our results identify an important role for ER-mitochondria contacts in the biogenesis of MDCs.Abbreviations used in this paper: ERMES, ER-mitochondria encounter structure; IMM, inner mitochondrial membrane; MDC, mitochondrial-derived compartment; OMM, outer mitochondrial membrane.SummaryEnglish et al. use super-resolution imaging to show that mitochondrial-derived compartments are lumen-containing organelles that form at sites of contact between the ER and mitochondria. Mitochondrial-derived compartment biogenesis requires a noncanonical function of the ERMES complex and the conserved GTPase Gem1.
Automated curation of CNMF-E-extracted ROI spatial footprints and calcium traces using open-source AutoML tools
Authors: Tran LM , Mocle AJ , Ramsaran AI , Jacob AD , Frankland PW , Josselyn SA 
Published: March 2020

AbstractIn vivo 1-photon calcium imaging is an increasingly prevalent method in behavioural neuroscience. Numerous analysis pipelines have been developed to improve the reliability and scalability of pre-processing and ROI extraction for these large calcium imaging datasets. Despite these advancements in pre-processing methods, manual curation of the extracted spatial footprints and calcium traces of neurons remains important for quality control. Here, we propose an additional semi-automated curation step for sorting spatial footprints and calcium traces from putative neurons extracted using the popular CNMF-E algorithm. We used the automated machine learning tools TPOT and AutoSklearn to generate classifiers to curate the extracted ROIs trained on a subset of human-labeled data. AutoSklearn produced the best performing classifier, achieving an F1 score > 92% on the ground truth test dataset. This automated approach is a useful strategy for filtering ROIs with relatively few labeled data points, and can be easily added to pre-existing pipelines currently using CNMF-E for ROI extraction.
CRISPR-TRAPSeq identifies the QKI RNA binding protein as important for astrocytic maturation and control of thalamocortical synapses
Authors: Sakers Kristina , Liu Yating , Llaci Lorida , Vasek Michael J. , Rieger Michael A. , Brophy Sean , Tycksen Eric , Lewis Renate , Maloney Susan E. , Dougherty Joseph D. 
Published: March 2020

AbstractQuaking RNA binding protein(QKI) is essential for oligodendrocyte development as myelination requires MBP mRNA regulation and localization by the cytoplasmic isoforms(e.g. QKI-6). QKI-6 is also highly expressed in astrocytes, which were recently demonstrated to have regulated mRNA localization. Here, we show via CLIPseq that QKI-6 binds 3’ UTRs of a subset of astrocytic mRNAs, including many enriched in peripheral processes. Binding is enriched near stop codons, which is mediated partially by QKI binding motifs(QBMs) yet spreads to adjacent sequences. We developed CRISPR TRAPseq: a viral approach for mosaic, cell-type specific gene mutation with simultaneous translational profiling. This enabled study of QKI-deleted astrocytes in an otherwise normal brain. Astrocyte-targeted QKI deletion altered translation and maturation, while also increasing synaptic density within the astrocyte’s territory. Overall, our data indicate QKI is required for astrocyte maturation and demonstrate an approach for a highly targeted translational assessment of gene knockout in specific cell-typesin vivo.
Development of CRISPR as a prophylactic strategy to combat novel coronavirus and influenza
Authors: Abbott Timothy R. , Dhamdhere Girija , Liu Yanxia , Lin Xueqiu , Goudy Laine , Zeng Leiping , Chemparathy Augustine , Chmura Stephen , Heaton Nicholas S. , Debs Robert , Pande Tara , Endy Drew , La Russa Marie , Lewis David B. , Qi Lei S. 
Published: March 2020

ABSTRACTThe outbreak of the coronavirus disease 2019 (COVID-19), caused by the Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2), has infected more than 100,000 people worldwide with over 3,000 deaths since December 2019. There is no cure for COVID-19 and the vaccine development is estimated to require 12-18 months. Here we demonstrate a CRISPR-Cas13-based strategy, PAC-MAN (ProphylacticAntiviralCRISPR in huMAN cells), for viral inhibition that can effectively degrade SARS-CoV-2 sequences and live influenza A virus (IAV) genome in human lung epithelial cells. We designed and screened a group of CRISPR RNAs (crRNAs) targeting conserved viral regions and identified functional crRNAs for cleaving SARS-CoV-2. The approach is effective in reducing respiratory cell viral replication for H1N1 IAV. Our bioinformatic analysis showed a group of only six crRNAs can target more than 90% of all coronaviruses. The PAC-MAN approach is potentially a rapidly implementable pan-coronavirus strategy to deal with emerging pandemic strains.
The Mitochondrial Permeability Transition Phenomenon Elucidated by Cryo-EM Reveals the Genuine Impact of Calcium Overload on Mitochondrial Structure and Function
Authors: Strubbe-Rivera Jasiel O. , Schrad Jason R. , Pavlov Evgeny V. , Conway James F. , Parent Kristin N. , Bazil Jason N. 
Published: March 2020

AbstractMitochondria have a remarkable ability to uptake and store massive amounts of calcium. However, the consequences of massive calcium accumulation remain enigmatic. In the present study, we analyzed a series of time-course experiments to identify the sequence of events that occur in a population of guinea pig cardiac mitochondria exposed to excessive calcium overload that cause mitochondrial permeability transition (MPT). By analyzing coincident structural and functional data, we determined that excessive calcium overload is associated with large calcium phosphate granules and inner membrane fragmentation, which explains the extent of mitochondrial dysfunction. This data also reveals a novel mechanism for cyclosporin A, an inhibitor of MPT, in which it preserves inner membrane architecture despite the presence of massive calcium phosphate granules in the matrix. Overall, these findings establish a mechanism of calcium-induced mitochondrial dysfunction and the impact of calcium regulation on mitochondrial structure and function.
SARS-CoV-2 receptor ACE2 and TMPRSS2 are predominantly expressed in a transient secretory cell type in subsegmental bronchial branches
Authors: Lukassen Soeren , Chua Robert Lorenz , Trefzer Timo , Kahn Nicolas C. , Schneider Marc A. , Muley Thomas , Winter Hauke , Meister Michael , Veith Carmen , Boots Agnes W. , Hennig Bianca P. , Kreuter Michael , Conrad Christian , Eils Roland 
Published: March 2020

SUMMARYThe SARS-CoV-2 pandemic affecting the human respiratory system severely challenges public health and urgently demands for increasing our understanding of COVID-19 pathogenesis, especially host factors facilitating virus infection and replication. SARS-CoV-2 was reported to enter cells via binding to ACE2, followed by its priming by TMPRSS2. Here, we investigateACE2andTMPRSS2expression levels and their distribution across cell types in lung tissue (twelve donors, 39,778 cells) and in cells derived from subsegmental bronchial branches (four donors, 17,521 cells) by single nuclei and single cell RNA sequencing, respectively. WhileTMPRSS2is expressed in both tissues, in the subsegmental bronchial branchesACE2is predominantly expressed in a transient secretory cell type. Interestingly, these transiently differentiating cells show an enrichment for pathways related to RHO GTPase function and viral processes suggesting increased vulnerability for SARS-CoV-2 infection. Our data provide a rich resource for future investigations of COVID-19 infection and pathogenesis.
A Self-Supervised Workflow for Particle Picking in Cryo-EM
Authors: McSweeney Donal M. , McSweeney Sean M. , Liu Qun 
Published: March 2020

AbstractHigh-resolution single-particle cryo-EM data analysis relies on accurate particle picking. To facilitate the particle picking process, we have developed a self-supervised workflow. Our workflow includes an iterative strategy to use the 2D class average to improve training particles and a progressively improved convolutional neural network (CNN) for particle picking. To automate the selection of particles, we define a threshold (%/Res) using the ratio of percentage class distribution and resolution as a cutoff. Our workflow has been tested using six publicly available data sets with different particle sizes and shapes, and is able to automatically pick particles with minimal user input. The picked particles support high-resolution reconstructions at 3.0 Å or better. Our workflow offers a way toward automated single-particle Cryo-EM data analysis at the stage of particle picking. The workflow may be used in conjunction with commonly used single-particle analysis packages such as Relion, cryoSPARC, cisTEM, SPHIRE, and EMAN2.