bluuebunny/crossref_metadata_2025_split huggingface dataset:
Suitability of Google Trends™ for digital surveillance during ongoing COVID-19 epidemic: a case study from India
Authors: Satpathy Parmeshwar , Kumar Sanjeev , Prasad Pankaj 
Published: August 2020

AbstractBackgroundIndia went into the largest population-level lockdown on 25th March 2020 in response to the declaration of COVID-19 pandemic by World Health Organization (WHO). Digital surveillance has been shown to be useful to supplement the traditional surveillance. Google Trends™ (GT) is one such platform reported to be useful during pandemics of H1N1, Ebola and MERS.ObjectiveWe used GT to correlate the information seeking behaviour regarding COVID-19 of Indians with curiosity and apprehensiveness generated through media coverage as well as status of the epidemic both at national and state levels.MethodsWe retrieved GT data between 1st January 2020 to 31st May 2020 for India using a comprehensive search strategy. We obtained data on daily tests and cases from WHO, ECDC and covid19india.org websites. We explored the trends of COVID-19 in the form of relative search volume (RSV) from GT platform and correlated them with media reports. We used time-lag correlation analysis to assess the temporal relationships between Google search terms and daily new COVID-19 cases and daily tests for 14 days.ResultsPeaks in RSV correlated with media coverage or government declarations suggestive of curiosity and apprehensiveness both at national level and high-burden states. High time-lag correlation was observed between both the daily reported number of tests and cases and RSV for the terms “COVID 19”, “COVID”, “social distancing”, “soap” and “lockdown” at national level. Similar high time-lag correlation was observed for the terms “COVID 19”, “COVID”, “Corona”, “social distancing”, “soap”, “lockdown” in five high-burden states.ConclusionThis study reveals the advantages of infodemiology using GT to monitor an emerging infectious disease like COVID-19 in India. Google searches in India during the ongoing COVID-19 pandemic reflects mostly curiosity and apprehension of citizens. GT can also complement traditional surveillance in India as well as high burden states.
Evaluation of the current therapeutic approaches for COVID-19: a meta-analysis
Authors: Abdelrahman Zeinab , Liu Qian , Jiang Shanmei , Li Mengyuan , Zhang Yue , Wang Xiaosheng 
Published: August 2020

AbstractBackground and rationaleLimited data on the efficacy and safety of currently applied COVID-19 therapeutics and their impact on COVID-19 outcomes have raised additional concern.Aim and MethodsWe estimated the impact of the current treatments on the efficacy and safety of COVID-19 by a meta-analysis. The comprehensive search included studies reporting clinical features and treatment strategies published from January 21, 2020, to May 15, 2020.ResultsWe included 52 studies that involved 13,966 COVID-19 patients. We found that the most prevalent treatments were antivirals (proportion: 0.74, 95% CI1: [0.65, 0.83]) and antibiotics (proportion: 0.73, 95% CI: [0.62, 0.83]). The COVID-19 severity increased among patients taking glucocorticoids (risk ratio (RR)2 = 1.71, 95% CI: [1.06, 2.76]) or immunoglobulins (RR = 3.83, 95% CI: [1.27, 11.53]), and renal replacement therapy (RRT) and glucocorticoids increased the length of ICU stay (RRT3: RR = 11.89, 95% CI: [3.26, 43.39]; glucocorticoids: RR = 3.10, 95% CI: [1.52, 6.29]). The COVID-19 severity and mortality increased among patients taking tocilizumab (severity: F = 25.53, P = 0.02; mortality: F4 = 19.37, P = 0.02). The most effective treatment was the combination of arbidol with lopinavir/ritonavir compared with placebo (mean difference = 0.5, 95% CI [-0.60, 1.66]), and the safest combination was remdesivir and lopinavir/ritonavir (RR = 0.78, 95% CI [0.32, 1.91]).Conclusionglucocorticoids, immunoglobulins, RRT, and tocilizumab might worsen COVID-19 outcomes, and themost effective and safest treatment strategy for COVID-19 is the combination of different antivirals.
FLOW CYTOMETRY MULTIPLEXED METHOD FOR THE DETECTION OF NEUTRALIZING HUMAN ANTIBODIES TO THE NATIVE SARS-CoV-2 SPIKE PROTEIN
Authors: Horndler Lydia , Delgado Pilar , Balabanov Ivaylo , Cornish Georgina , Llamas Miguel A. , Serrano-Villar Sergio , Fresno Manuel , van Santen Hisse M. , Alarcón Balbino 
Published: August 2020

ABSTRACTA correct identification of seropositive individuals for the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) infection is of paramount relevance to assess the degree of protection of a human population to present and future outbreaks of the COVID-19 pandemic. We describe here a sensitive and quantitative flow cytometry method using the cytometer-friendly non-adherent Jurkat T cell line that stably expresses the full-length native spike “S” protein of SARS-CoV-2 and a truncated form of the human EGFR that serves a normalizing role. S protein and huEGFRt coding sequences are separated by a T2A self-cleaving sequence, allowing to accurately quantify the presence of anti-S immunoglobulins by calculating a ratio of the mean fluorescence intensities obtained by double-staining with the sera and a monoclonal antibody specific for EGFR. We show that the method allows to detect immune individuals regardless of the result of other serological tests or even repeated PCR monitoring. It can also be employed to detect neutralizing activity in the sera of individuals. Finally, the method can be used in a multiplexed format to simultaneously measure all anti-S human immunoglobulin isotypes in blood and mucosal fluids including total saliva.
The SARS-CoV-2 Envelope and Membrane proteins modulate maturation and retention of the Spike protein, allowing optimal formation of VLPs in presence of Nucleoprotein
Authors: Boson Bertrand , Legros Vincent , Zhou Bingjie , Mathieu Cyrille , Cosset François-Loïc , Lavillette Dimitri , Denolly Solène 
Published: August 2020

AbstractThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a β-coronavirus, is the causative agent of the COVID-19 pandemic. Like for other coronaviruses, its particles are composed of four structural proteins, namely Spike S, Envelope E, Membrane M and Nucleoprotein N proteins. The involvement of each of these proteins and their interplays during the assembly process of this new virus are poorly-defined and are likely β-coronavirus-type different. Therefore, we sought to investigate how SARS-CoV-2 behaves for its assembly by expression assays of S, in combination with E, M and/or N. By combining biochemical and imaging assays, we showed that E and M regulate intracellular trafficking of S and hence its furin-mediated processing. Indeed, our imaging data revealed that S remains at ERGIC or Golgi compartments upon expression of E or M, like for SARS-CoV-2 infected cells. By studying a mutant of S, we showed that its cytoplasmic tail, and more specifically, its C-terminal retrieval motif, is required for the M-mediated retention in the ERGIC, whereas E induces S retention by modulating the cell secretory pathway. We also highlighted that E and M induce a specific maturation of S N-glycosylation, which is observed on particles and lysates from infected cells independently of its mechanisms of intracellular retention. Finally, we showed that both M, E and N are required for optimal production of virus-like-proteins. Altogether, our results indicated that E and M proteins influence the properties of S proteins to promote assembly of viral particles. Our results therefore highlight both similarities and dissimilarities in these events, as compared to other β-coronaviruses.Author SummaryThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the COVID-19 pandemic. Its viral particles are composed of four structural proteins, namely Spike S, Envelope E, Membrane M and Nucleoprotein N proteins, though their involvement in the virion assembly remain unknown for this particular coronavirus. Here we showed that presence of E and M influence the localization and maturation of S protein, in term of cleavage and N-glycosylation maturation. Indeed, E protein is able to slow down the cell secretory pathway whereas M-induced retention of S requires the retrieval motif in S C-terminus. We also highlighted that E and M might regulate the N glycosylation maturation of S independently of its intracellular retention mechanism. Finally, we showed that the four structural proteins are required for optimal formation of virus-like particles, highlighting the involvement of N, E and M in assembly of infectious particles. Altogether, our results highlight both similarities and dissimilarities in these events, as compared to other β-coronaviruses.
Two Piwis with Ago-like functions silence somatic genes at the chromatin level
Authors: Drews Franziska , Karunanithi Sivarajan , Götz Ulrike , Marker Simone , deWijn Raphael , Pirritano Marcello , Rodrigues-Viana Angela M. , Jung Martin , Gasparoni Gilles , Schulz Marcel H. , Simon Martin 
Published: August 2020

AbstractMost sRNA biogenesis mechanisms involve either RNAseIII cleavage or ping-pong amplification by different Piwi proteins harboring slicer activity. Here, we follow the question why the mechanism of transgene-induced silencing in the ciliate Paramecium needs both Dicer activity and two Ptiwi proteins. This pathway involves primary siRNAs produced from non-translatable transgenes and secondary siRNAs from endogenous remote loci. Our data does not indicate any signatures from ping-pong amplification but Dicer cleavage of long dsRNA. We show that Ptiwi13 and 14 have different preferences for primary and secondary siRNAs but do not load them mutually exclusive. Both Piwis enrich for antisense RNAs and Ptiwi14 loaded siRNAs show a 5′-U signature. Both Ptiwis show in addition a general preference for Uridine-rich sRNAs along the entire sRNA length. Our data indicates both Ptiwis and 2’-O-methylation to contribute to strand selection of Dicer cleaved siRNAs. This unexpected function of two distinct vegetative Piwis extends the increasing knowledge of the diversity of Piwi functions in diverse silencing pathways. As both Ptiwis show differential subcellular localisation, Ptiwi13 in the cytoplasm and Ptiwi14 in the vegetative macronucleus, we conclude that cytosolic and nuclear silencing factors are necessary for efficient chromatin silencing.
Pathogenicity, immunogenicity, and protective ability of an attenuated SARS-CoV-2 variant with a deletion at the S1/S2 junction of the spike protein
Authors: Wang Pui , Lau Siu-Ying , Deng Shaofeng , Chen Pin , Mok Bobo Wing-Yee , Zhang Anna Jinxia , Lee Andrew Chak-Yiu , Chan Kwok-Hung , Song Wenjun , To Kelvin Kai-Wang , Chan Jasper Fuk-Woo , Yuen Kwok-Yung , Chen Honglin 
Published: August 2020

AbstractSARS-CoV-2 contains a PRRA polybasic cleavage motif considered critical for efficient infection and transmission in humans. We previously reported that virus variants with spike protein S1/S2 junction deletions spanning this motif are attenuated. Here we characterize a further cell-adapted SARS-CoV-2 variant, Ca-DelMut. Ca-DelMut replicates more efficiently than wild type or parental virus in cells, but causes no apparent disease in hamsters, despite replicating in respiratory tissues. Unlike wild type virus, Ca-DelMut does not induce proinflammatory cytokines in hamster infections, but still triggers a strong neutralizing antibody response. Ca-DelMut-immunized hamsters challenged with wild type SARS-CoV-2 are fully protected, demonstrating sterilizing immunity.
A non-human primate model of familial Alzheimer’s disease
Authors: Sato Kenya , Sasaguri Hiroki , Kumita Wakako , Inoue Takashi , Kurotaki Yoko , Nagata Kenichi , Mihira Naomi , Sato Kaori , Sakuma Tetsushi , Yamamoto Takashi , Tagami Michihira , Manabe Riichiroh , Ozaki Kokoro , Okazaki Yasushi , Saido Takaomi C. , Sasaki Erika 
Published: August 2020

SummaryAlzheimer’s disease (AD) is a major cause of dementia, with the number of patients with this condition anticipated to exceed 50 million worldwide in the near future. Despite extensive research efforts, no effective measures are available to facilitate the prevention or treatment of AD, which is due in part to a lack of animal models able to closely replicate a human-like disease state. Here, we describe the generation of three mutant marmoset individuals in which exon 9 ofPSEN1gene product has been deleted (PSEN1-ΔE9). Such ΔE9 mutations have been reported to cause early on-set familial AD (references1–5). We used Transcription Activator-Like Effector Nuclease (TALEN) to destroy the 3’ splice site of exon 9 in the marmosetPSEN1gene. To this end, TALEN exhibits high genome-editing efficacy, generates few off-target effects, and produces minimal mosaicism. Indeed, whole genome sequencing and other analyses illustrated an absence of off-target effects and an apparent absence of mosaicism. Fibroblasts obtained from newborn marmosets exhibited uncleaved full-length presenilin 1 protein (PS1) caused by the perturbation of PS1 endoproteolysis as well as an increased ratio of Aβ42/Aβ40production, a signature of familial AD pathogenesis. To our knowledge, this is the first non-human primate model of familial AD. We intend to make our marmoset model available to the research community to facilitate the global fight against AD.
Gradual evolution of allopolyploidy inArabidopsis suecica
Authors: Burns Robin , Mandáková Terezie , Gunis Joanna , Soto-Jiménez Luz Mayela , Liu Chang , Lysak Martin A. , Novikova Polina Yu. , Nordborg Magnus 
Published: August 2020

AbstractThe majority of diploid organisms have polyploid ancestors. The evolutionary process of polyploidization (and subsequent re-diploidization) is poorly understood, but has frequently been conjectured to involve some form of “genome shock” — partly inspired by studies in crops, where polyploidy has been linked to major genomic changes such as genome reorganization and subgenome expression dominance. It is unclear, however, whether such dramatic changes would be characteristic of natural polyploidization, or whether they are a product of domestication. Here, we study polyploidization inArabidopsis suecica(n = 13), a post-glacial allopolyploid species formed via hybridization ofA. thaliana(n = 5) andA. arenosa(n = 8). We generated a chromosome-level genome assembly ofA. suecicaand complemented it with polymorphism and transcriptome data from multiple individuals of all species. Despite a divergence of ∼6 Mya between the two ancestral species and appreciable differences in their genome composition, we see no evidence of a genome shock: theA. suecicagenome is highly colinear with the ancestral genomes, there is no subgenome dominance in expression, and transposable element dynamics appear to be stable. We do, however, find strong evidence for changes suggesting gradual adaptation to polyploidy. In particular, theA. thalianasubgenome shows upregulation of meiosis-related genes, possibly in order to prevent aneuploidy and undesirable homeologous exchanges that are frequently observed in experimentally generatedA. suecica, and theA. arenosasubgenome shows upregulation of cyto-nuclear related processes, possibly in response to the new cytoplasmic environment ofA. suecica,with plastids maternally inherited fromA. thaliana.
Dynamics of the N-terminal domain of SARS-CoV-2 nucleocapsid protein drives dsRNA melting in a counterintuitive tweezer-like mechanism
Authors: Caruso Ícaro P. , Sanches Karoline , Da Poian Andrea T. , Pinheiro Anderson S. , Almeida Fabio C. L. 
Published: August 2020

ABSTRACTThe N protein of betacoronaviruses is responsible for nucleocapsid assembly and other essential regulatory functions. Its N-terminal domain (NTD) interacts and melts the double-stranded transcriptional regulatory sequences (dsTRS), regulating the discontinuous subgenome transcription process. Here, we used molecular dynamics (MD) simulations to study the binding of SARS-CoV-2 N-NTD to non-specific (NS) and TRS dsRNAs. We probed dsRNAs’ Watson and Crick (WC) base-pairing over 25 replicas of 100 ns MD simulations, showing that only one N-NTD of dimeric N is enough to destabilize dsRNAs, initiating melting. N-NTD dsRNA destabilizing activity was more efficient for dsTRS than dsNS. N-NTD dynamics, especially a tweezer-like motion of β2-β3 and 2-β5 loops, played a key role in WC base-pairing destabilization. Based on experimental information available in the literature, we constructed kinetics models for N-NTD-mediated dsRNA melting. Our results support a 1:1 stoichiometry (N-NTD:dsRNA), matching MD simulations and raising different possibilities for N-NTD action: (i) two N-NTDs of dimeric N would act independently, increasing efficiency; (ii) two N-NTDs of dimeric N would bind to two different RNA sites, bridging distant regions of the genome; and (iii) monomeric N would be active, opening up the possibility of a regulatory dissociation event.IMPORTANCECoronaviruses are among the largest positive-sense RNA viruses. They display a unique discontinous transcription mechanism, involving N protein as a major player. The N-NTD promote the dsRNA melting releasing the nascent sense negative strand via a poorly known mechanism of action. It specifically recognizes the body TRS conserved RNA motif located at the 5’ end of each ORF. N protein has the ability to transfer the nascent RNA strand to the leader TRS. The mechanism is essential and one single mutation at the RNA binding site of the N-NTD impairs the viral replication. Here, we describe a counterintuitive mechanism of action of N-NTD based on molecular dynamics simulation and kinetic modelling of the experimental melting activity of N-NTD. This data impacts directly in the understanding of the way N protein acts in the cell and will guide future experiments.
The nucleoid-associated protein IHF acts as a “domainin” protein coordinating the bacterial virulence traits with global transcription
Authors: Reverchon Sylvie , Meyer Sam , Forquet Raphaël , Hommais Florence , Muskhelishvili Georgi , Nasser William 
Published: August 2020

AbstractBacterial pathogenic growth requires a swift coordination of pathogenicity functions with various kinds of environmental stresses encountered in the course of host infection. Among the factors critical for bacterial adaptation are changes of DNA topology and binding effects of nucleoid-associated proteins transducing the environmental signals to the chromosome and coordinating the global transcriptional response to stress. In this study we use the model phytopathogenDickeya dadantiito analyse the organisation of transcription by the nucleoid-associated protein IHF. We determine both phenotypic effects ofihfAmutation onD. dadantiivirulence and the transcriptional response under various conditions of growth. For the first time in enterobacteria, we examine the transcriptome of an IHF-depleted mutant under conditions of DNA relaxation, revealing a subtle interplay between IHF and DNA topology. We show that this mutation reorganises the genomic expression by altering the distribution of DNA supercoils along the chromosome at different length scales, thus affecting many virulence genes involved in both symptomatic and asymptomatic phases of infection, including those required for pectin catabolism. Altogether, we propose that IHF is a “domainin” protein, the inactivation of which impairs the coordination of chromosomal stress-response domains harbouring various virulence traits, thus abrogating the pathogenicity ofD. dadantii.
Flagellin fromPseudomonas aeruginosamodulates SARS-CoV-2 infectivity in CF airway epithelial cells by increasing TMPRSS2 expression
Authors: Ruffin Manon , Bigot Jeanne , Calmel Claire , Mercier Julia , Pizzorno Andrés , Rosa-Calatrava Manuel , Corvol Harriet , Balloy Viviane , Terrier Olivier , Guillot Loïc 
Published: August 2020

AbstractThe major challenge of the COVID-19 health crisis is to identify the factors of susceptibility to SARS-Cov2 in order to adapt the recommendations to the populations and to reduce the risk of getting COVID-19 to the most vulnerable people especially those having chronic respiratory diseases including cystic fibrosis (CF). Airway epithelial cells (AEC) are playing a critical role in the immune response and in COVID-19 severity. SARS-CoV-2 infects the airways through ACE2 receptor and the host protease TMPRSS2 was shown to play a major role in SARS-CoV-2 infectivity. Here, we show that the main component ofP. aeruginosaflagella, ie. flagellin is able to increase TMPRSS2 expression in AEC, and even more in those deficient for CFTR. Importantly, this increased TMPRSS2 expression is associated with an increase in the level of SARS-CoV-2 infection. Considering the urgency of the health situation, this result is of major significance for patients with CF which are frequently infected and colonized byP. aeruginosaduring the course of the disease.
Deletion of an enhancer in FGF5 is associated with ectopic expression in goat hair follicles and the cashmere growth phenotype
Authors: Li Yefang , Song Shen , Liu Xuexue , Zhang Yanli , Wang Dandan , He Xiaohong , Zhao Qianjun , Pu Yabin , Guan Weijun , Ma Yuehui , Jiang Lin 
Published: August 2020

AbstractResearch on cashmere growth has a significant effect on the production of cashmere and a profound influence on cashmere goat breeding. Whole-genome sequencing is a powerful platform to rapidly gain novel insights into the identification of genetic mechanisms underlying cashmere fiber growth. Here, we generated whole-genome sequences of 115 domestic goats from China, Nepal and Pakistan, including 51 cashmere goats and 64 non-cashmere goats. We found genetically distinct clusters according to their geographic locations but genetic admixture or introgression may have occurred between the Chinese and Nepalese goats. We identified that the fibroblast growth factor 5 gene (FGF5) shows a strong signature for positive selection in the cashmere goat. The 505-bp indel variant at the FGF5 gene locus appeared to be strongly associated with cashmere growth. Functional validation showed that the insertion variant may serve as an enhancer for transcription factor binding, resulting in increased transcription of the upstream FGF5 gene in non-cashmere goats. Our study provides useful information for the sustainable utilization and improved conservation of goat genetic resources and demonstrates that the indel mutation in the FGF5 gene could potentially serve as a molecular marker of cashmere growth in cashmere goat breeding.Author summaryCashmere goats have been selected for thousands of years and have become economically significant livestock in China and other central Asian countries. The mechanism of cashmere growth is not well understood because most studies have focused on the investigation of candidate genes. Here, we conducted a comprehensive whole-genome analysis for selection signatures in a total of 115 goats from 15 genetically diverse goat breeds. The results revealed a strong selection signature at the FGF5 gene locus associated with the cashmere growth phenotype. A 505-bp indel was located in the downstream region of FGF5 and significantly separated in the cashmere goats versus non-cashmere goats. Functional effect analysis of the indel revealed that it may act as an enhancer by specifically binding transcription factors to mediate quantitative changes in FGF5 mRNA expression. Our study illustrates how a structural mutation of the FGF5 gene has contributed to the cashmere growth phenotype in domestic goats.