bluuebunny/crossref_metadata_2025 huggingface dataset:
A distinct fingerprint of inflammatory mediators and miRNAs inPlasmodium vivaxsevere thrombocytopenia
Authors: Santos Marina L. S. , Coimbra Roney S. , Sousa Tais N. , Guimarães Luiz F. F. , Gomes Matheus S. , Amaral Laurence R. , Pereira Dhelio B. , Fontes Cor J. F. , Hawwari Ibrahim , Franklin Bernardo S. , Carvalho Luzia H.
Published: August 2020

Background

Severe thrombocytopenia can be a determinant factor in the morbidity ofPlasmodium vivax(Pv), the most widespread human malaria. Although immune mechanisms may drivePv-induced severe thrombocytopenia (PvST), the current data on the cytokine landscape in PvST is scarce, and often conflicting. The analysis of the bidirectional circuit of inflammatory mediators and miRNAs would lead to a better understanding of the mechanisms underlying PvST.

Methods

We combined Luminex proteomics, NanoString miRNA quantification, and machine learning, to evaluate an extensive array of plasma mediators in uncomplicatedPvpatients, whose blood platelet counts varied from reference values to PvST.

Results

Unsupervised clustering analysis identified PvST-linked signatures comprised of both inflammatory (CXCL10, CCL4, and IL-18) and regulatory (IL-10, IL-1Ra, HGF) mediators. As part of PvST signatures, IL-6 and IL-8 were critical to discriminatePvsubgroups, while CCL2 and IFN-γ from healthy controls. Supervised machine learning spotlighted IL-10 inPv-mediated thrombocytopenia, and provided evidence for a potential signaling route involving IL-8 and HGF. Finally, we identified a set of miRNAs capable of modulating these signaling pathways.

Conclusions

The results place IL-10 and IL-8/HGF in the center of PvST and propose investigating these signaling pathways across the spectrum of malaria infections.
Impressions of Vibrotactile Signals in Older Adults With and Without History of Stroke
Authors: Seim Caitlyn E. , Ritter Brandon , Flavin Kara E. , Lansberg Maarten G. , Okamura Allison M.
Published: August 2020

Vibrotactile feedback is mechanical stimulation produced using actuators in contact with the body. The stimulation parameters (frequency, amplitude, location, duration) can be adjusted to produce a variety of sensations. By characterizing how users respond to different settings, interaction designers can create more usable and enjoyable haptic interfaces. This form of haptic feedback is being used widely for alerts, gaming, and simulation; however, emerging technologies in the fields of brain health and physical therapy are introducing new users to this stimulation. For applications using vibrotactile stimulation to advance, researchers are studying perceived sensations and affective response. However, these studies often focus on healthy, younger users. It is well known that older adults and those with acquired brain injury have different physiology and different perception than young adults. Here we present a set of vibrotactile signals to adults over 40 years old with and without history of stroke and query affective impression and experienced sensations. Signals on the palm and those with a changing stimulus location were associated with higher valence ratings, while low-amplitude signals showed lowest arousal. Users preferred stimulation that they could perceive, and they could not perceive most signals applied to the forearm. Reported sensations include tickle, tingling, and numbness.

CCS Concepts

Human-centered computing → User studies; Haptic devices; Ubiquitous and mobile devices.
Insulin-like growth factor 1 signaling in the placenta requires endothelial nitric oxide synthase to support trophoblast function and normal fetal growth
Authors: Wilson Rebecca L , Troja Weston , Sumser Emily K , Maupin Alec , Lampe Kristin , Jones Helen N
Published: August 2020

Currently, there is no effective treatment for placenta dysfunctionin utero. In a ligated mouse model of fetal growth restriction (FGR), nanoparticle-mediatedhuman insulin-like 1 growth factor(hIGF1) gene delivery (NP-Plac1-hIGF1) increasedhIGF1expression and maintained fetal growth. However, whether it can restore fetal growth remains to be determined. Using the endothelial nitric oxide synthase knockout (eNOS−/−) mouse model, a genetic model of FGR, we found that despite inducing expression ofhIGF1in the placentas treated with NP-Plac1-hIGF1 (P=0.0425), FGR did not resolve. This was associated with no change to the number of fetal capillaries in the placenta labyrinth; an outcome increased with NP-Plac1-hIGF1 treatment in the ligated mouse model, despite increased expression of angiopoietin 1 (P=0.05) and suggestedIGF1signaling in the placenta requires eNOS to modulate placenta angiogenesis. To further assess this hypothesis, we used the BeWo Choriocarcinoma cell line and human placenta explant cultures that were treated with NP-Plac1-hIGF1, oxidative stress was induced with hydrogen peroxide (H2O2) and NOS activity inhibited using the inhibitor L-NMMA. In both BeWo and explants, the protective effect of NP-Plac1-hIGF1 treatment against H2O2induced cell death/lactate dehydrogenase release was prevented by eNOS inhibition (P=0.003 and P<0.0001, respectively). This was associated with an increase in mRNA expression of oxidative stress markersHIF1α(P<0.0001) andADAM10(P=0.0002) in the NP-Plac1-hIGF1+H2O2+L-NMMA treated BeWo cells. These findings show for the first time the requirement of eNOS/NOS in IGF1 signaling in placenta cells that may have implications for placental angiogenesis and fetal growth.
Teamwork in the manufacturing workplace may hinder social distance
Authors: Kokubun Keisuke
Published: August 2020

The spread of new coronavirus (COVID-19) infections show no signs of stopping. Therefore, if the era of With-Colona will continue for a while, we must consider how to deal with this disaster well. The practice of social distance is one of the powerful tools for that purpose. In previous research, analysis of the factors that influence social distance has also been carried out using information from the US occupation information site O*NET. However, they targeted all industries, not specific industries. Therefore, in this paper, we analyzed the factors that influence Physical Proximity in the manufacturing industry, which has a large impact on the economy given the scale of employment. As the method, first, exploratory factor analysis is performed using O*NET information, and the extracted 7 variables, Sitting Work, Adverse Conditions, Information Processing, Bridging Work, Teamwork, Response to Aggression, and Intelligent Work, are used in the regression analysis. As a result, it was shown that Teamwork is the biggest factor that influences Physical Proximity. Also, Adverse Conditions and Response to Aggression showed a positive correlation and Sitting Work showed a negative correlation. By job type, Maintenance, Installation & Repair tended to have higher Physical Proximity than Manufacturing Production Process Development, Production & Quality Assurance. Keywords: New Coronavirus (COVID-19), social distance, physical proximity, teamwork, explanatory factor analysis, O*NET
Declining SARS-CoV-2 PCR sensitivity with time and dependence on clinical features: consequences for control
Authors: Bergmans B.J.M. , Reusken C.B.E.M. , van Oudheusden A.J.G. , Godeke G.J. , Marinović A.A. Bonačić , de Vries E. , Kluiters-de Hingh Y.C.M. , Vingerhoets R. , Berrevoets M.A.H. , Verweij J.J. , Nieman A.E. , Reimerink J. , Murk J.L. , Swart A.N.
Published: August 2020

Real-time reverse transcription-polymerase chain reaction (RT-PCR) on upper respiratory tract (URT) samples is the primary method to diagnose SARS-CoV-2 infections and guide public health measures, with a supportive role for serology. However, the clinical sensitivity of RT-PCR remains uncertain. In the present study, Bayesian statistical modeling was used to retrospectively determine the sensitivity of RT-PCR using SARS-CoV-2 serology in 644 COVID-19-suspected patients with varying degrees of disease severity and duration. The sensitivity of RTPCR ranged between 79–95%; while increasing with disease severity, it decreased rapidly over time in mild COVID-19 cases. Negative URT RT-PCR results should therefore be interpreted in the context of clinical characteristics, especially with regard to containment of viral transmission based on the ‘test, trace and isolate’ principle.
Knowledge and Risk Perception of the Novel Coronavirus Disease among Adult Population in Nigeria: A cross-sectional study
Authors: Hedima Erick Wesley , Michael Samuel Adeyemi , David Emmanuel Agada
Published: August 2020

COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly infectious disease declared a pandemic by the World Health Organization. The risks of getting infected with the novel coronavirus in Nigeria is high as evident by the increase in the daily number of confirmed cases.

Objective

The objectives of this study were to assess the knowledge and risk perception of adult Nigerian population regarding the novel coronavirus pandemic.

Methods

We conducted an online cross-sectional survey in which five hundred and ten (510) adult participants consented and filled the questionnaire. The questionnaire is divided in to four sections: the first part was directed at the socio-demographic characteristics of the participants, the second was dedicated to the assessment of knowledge, the third part assessed risk perception and the fourth section assessed preventive measures.

Results

Almost all of the participants (95.9%) claimed to be aware of COVID-19 with majority through the traditional media (55.3%), and social media (41%) while only a small percentage (3.7%) gained the awareness through health officials. Knowledge of COVID-19 was significantly poor among participants with lower level of formal education, (p = 0.0001). participants with higher income were found to have a good knowledge of the disease (p< 0.00001). being a health worker was not associated with good knowledge of COVID-19 (p = 0.00001). Risk perception was significantly high among the females (p = 0.044), young adult participants (p = 0.039) and healthcare workers (p = 0.001). Preventive measures like avoiding eating out (p = 0.001) and traveling to high risk areas (p = 0.017), wearing face mask (p = 0.01) and eating balanced diet (p = 0.014) were statistically significant across gender.

Conclusion

In general, participants were aware of COVID-19 with a low proportion having a good knowledge about the disease and preventive measures. The findings from this online survey could guide information campaigns by public health authorities, clinicians, and the media.
The health sector cost of different policy responses to COVID-19 in low- and middle- income countries
Authors: Torres Rueda Sergio , Sweeney Sedona , Bozzani Fiammetta , Vassall Anna
Published: August 2020

Much attention has focussed in recent months on the impact that COVID-19 has on health sector capacity, including critical care bed capacity and resources such as personal protective equipment. However, much less attention has focussed on the overall cost to health sectors, including the full human resource costs and the health system costs to address the pandemic. Here we present estimates of the total costs of COVID-19 response in low- and middle-income countries for different scenarios of COVID-19 mitigation over a one year period. We find costs vary substantially by setting, but in some settings even mitigation scenarios place a substantial fiscal impact on the health system. We conclude that the choices facing many low- and middle- income countries, without further rapid emergency financial support, are stark, between fully funding an effective COVID-19 reponse or other core essential health services.
COVID-19: Estimation of the Actual Onset of Local Epidemic Cycles, Determination of Total Number of Infective, and Duration of the Incubation Period
Authors: de Carvalho Rogerio Atem , de Carvalho Eduardo Atem
Published: August 2020

Background

Most studies of the epidemic cycles of the pandemic of Sars-CoV-2, or COVID-19 as it became known, define the beginning of specific cycles in countries from the laboratory identification of the first cases of infection, however, there is the awareness that cycles may have started earlier, without proper identification. This influences all the parameters that govern the statistical models used for controlling the infection.

Purpose

This work proposes two models based on experimental data. The Logistic Model it is used to obtain three parameters of the epidemic cycle of COVID-19, namely: the final count for the total infected, the daily infection rate and the lag time. Complimentary, a novel inventory model is proposed to calculate the number of infective persons, as well as to determine the incubation period.

Methods

The data on epidemic cycles of Germany, Italy, and Sweden are treated previously by the Moving Average Method with Initial value (MAMI), then a variation of the Logistic Model, obtained through curve-fitting, is used to obtain the three parameters. The inventory model is introduced to calculate the actual number of infected persons and the behavior of the incubation period is analyzed.

Results

After comparing data from the three countries it is possible to determine the actual probable dates of the beginning of the epidemic cycles for each one, determine the size of the incubation period, as well as to determine the total number of infective persons during the cycle.

Conclusions

The actual probable dates of the beginning of the epidemic cycles in the countries analyzed are determined, the total number of infected is determined, and it is statistically proven that the incubation cycle for Sars-CoV-2 is five days.
Clinical Impact of Panel Based Error Corrected Next Generation Sequencing versus Flow Cytometry to Detect Measurable Residual Disease (MRD) in Acute Myeloid Leukemia (AML)
Authors: Patkar Nikhil , Kakirde Chinmayee , Shaikh Anam Fatima , Salve Rakhi , Bhanshe Prasanna , Chatterjee Gaurav , Rajpal Sweta , Joshi Swapnali , Chaudhary Shruti , Kodgule Rohan , Ghoghale Sitaram , Deshpande Nilesh , Shetty Dhanalaxmi , Khizer Syed Hasan , Jain Hasmukh , Bagal Bhausaheb , Menon Hari , Khattry Navin , Sengar Manju , Tembhare Prashant , Subramanian Papagudi , Gujral Sumeet
Published: August 2020

We accrued 201 patients of adult AML treated with conventional therapy, in morphological remission and evaluated MRD using sensitive error corrected next generation sequencing (NGS-MRD) and multiparameter flow cytometry (FCM-MRD) at the end of induction (PI) and consolidation (PC). Nearly 71% of patients harbored PI NGS-MRD and 40.9% harbored PC NGS-MRD (median VAF 0.76%). Patients harboring NGS-MRD had a significantly higher cumulative incidence of relapse (p=0.003), inferior overall survival (p=0.001) and relapse free survival (p<0.001) as compared to NGS-MRD negative patients. NGS-MRD was predictive of inferior outcome in intermediate cytogenetic risk and demonstrated potential in favorable cytogenetic risk AML. Patients who cleared PI NGS-MRD had a significantly improved survival as compared to patients who became negative subsequently indicating that kinetics of NGS-MRD clearance was of paramount importance. NGS-MRD identified over 80% of cases identified by flow cytometry at PI time point whereas FCM identified 49.3% identified by NGS. Only a fraction of cases were truly missed by NGS as compared to FCM-MRD. NGS-MRD emerged as the most important independent prognostic factor predictive of inferior outcome (p<0.001). We demonstrate a widely applicable, scalable NGS-MRD approach that is clinically informative and advantageous when compared to FCM-MRD in AML treated with conventional therapies.
3D Printed N95 Equivalent for PPE Shortages: The Kansas City Mask
Authors: Dalla Shiv , Bacon Brandon , Ayres Jack , Holmstead Stephen , Elliot Alan J. Ahlberg
Published: August 2020

Introduction

During the COVID-19 pandemic, the shortage of personal protective equipment (PPE) was well-reported and discussed, not only in the healthcare sector but across all of society as the demands for PPE skyrocketed. As hospitalizations for COVID-19-related illness continue to increase, many recent reports indicate the supply of PPE is persistently and significantly less than the demand. These PPE shortages encouraged communities of 3D printing experts and hobbyists to design and distribute homemade, 3D-printed PPE, including N95 mask substitutes. The mask presented, the Kansas City Mask (KC Mask), is one such product which was created from the maker community in partnership with local physicians and hospitals. This report discusses the design, manufacturing, and validation of the KC Mask design and its usage in the COVID-19 pandemic as well as future use as stopgap PPE.

Methods

The KC Mask was adapted from a similar design called the Montana Mask. Mask components were 3D printed and assembled then fit tested by qualitative fit testing (QLFT) at Truman Medical Center in Kansas City, MO as a proof of concept.

Results

The QLFT was successful and the KC Mask was approved for use by pandemic response administration staff at the hospital. Fortunately, the KC Mask has not required wide utilization, however, because supply chains for Kansas City area hospitals have, at the time of this publication, not yet been exhausted by the pandemic.

Conclusion

The results of Truman Medical Center’s approval of the KC Mask are promising for this N95 stop-gap substitute. Although further analysis and study is needed for this design, persistently increasing caseloads and PPE shortages necessitate an urgent dissemination of these preliminary results. The authors do not advocate for the KC Mask as a replacement of traditional N95 masks or other PPE but do endorse the KC Mask as a stopgap measure, proven to be effective in situations of dire PPE shortage based on CDC guidelines.
A negative feedback model to explain regulation of SARS-CoV-2 replication and transcription
Authors: Gao Shan , Cheng Zhi , Jin Xiufeng , Wang Fang , Xuan Yibo , Zhou Hao , Liu Chang , Ruan Jishou , Duan Guangyou , Li Xin
Published: August 2020

Background

Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although a preliminary understanding of the replication and transcription mechanisms of SARS-CoV-2 has recently emerged, their regulation remains unclear.

Results

Based on reanalysis of public data, we propose a negative feedback model to explain the regulation of replication and transcription in—but not limited to—SARS-CoV-2. The key step leading to new discoveries was the identification of the cleavage sites of nsp15—an RNA uridylate-specific endoribonuclease, encoded by CoVs. According to this model, nsp15 regulates the synthesis of subgenomic RNAs (sgRNAs) and genomic RNAs (gRNAs) by cleaving transcription regulatory sequences in the body. The expression level of nsp15 determines the relative proportions of sgRNAs and gRNAs, which in turn change the expression level of nps15 to reach equilibrium between the replication and transcription of CoVs.

Conclusions

The replication and transcription of CoVs are regulated by a negative feedback mechanism that influences the persistence of CoVs in hosts. Our findings enrich fundamental knowledge in the field of gene expression and its regulation, and provide new clues for future studies. One important clue is that nsp15 may be an important and ideal target for the development of drugs (e.g. uridine derivatives) against CoVs.
TimTrack: A drift-free algorithm for estimating geometric muscle features from ultrasound images
Authors: van der Zee Tim J. , Kuo Arthur D.
Published: August 2020

Ultrasound imaging is valuable for non-invasively estimating fascicle lengths and other features of pennate muscle, especially when performed computationally. Effective analysis techniques to date typically use optic flow to track displacements from image sequences, but are sensitive to integration drift for longer sequences. We here present an alternative algorithm that objectively estimates geometric features of pennate muscle from ultrasound images, without drift sensitivity. The algorithm identifies aponeuroses and estimates fascicle angles to derive fascicle lengths. Length estimates of human vastus lateralis and lateral gastrocnemius in healthy subjects (N = 9 and N = 1 respectively) compared well (root-mean-square error, RMSE < 0.80 cm) to manual estimates by independent observers (n = 3). The coefficient of multiple correlation (CMC) with manual estimates of fascicle length was comparable to previously reported for state-of-the-art optic flow algorithm (0.93-0.99), suggesting similar accuracy. The algorithm requires minimal manual intervention and can optionally extrapolate fascicle lengths that extend beyond the image frame. It facilitates automated analysis of ultrasound images without drift.
Dataset of the construction and characterization of stable biological nanoparticles
Authors: Gisonno Romina A. , Tricerri M. Alejandra , Gonzalez Marina C. , Garda Horacio A. , Ramella Nahuel A. , Ludovico Ivo Díaz
Published: August 2020

We suggest that the structural flexibility is key for certain proteins in order to fulfill functions that are required to interact with biological membranes, and that intra-chain chemical crosslinking may result in a different arrangement of protein with lipids. As interaction with biological membranes and lipids is a function attributed to many proteins in circulation, we intended to characterize an experimental design that helps in the study of many biological protein structures and their function. But in addition, by introducing intra-chain crosslinking, we obtained discoidal nano platforms that are stable under different conditions of temperate and time incubation. These platforms might be an excellent model to employ as biological carriers of intrinsic or external molecules. Thus, data shown here clearly strengthen the usefulness of an easy, accessible and inexpensive tool not only to study protein-lipid interactions, but to be used in different biological fields that require the transport of organic compounds.
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

Background

India 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.

Objective

We 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.

Methods

We 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.

Results

Peaks 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.

Conclusion

This 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

Background and rationale

Limited 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 Methods

We 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.

Results

We 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]).

Conclusion

glucocorticoids, 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

A 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

The 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 Summary

The 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

Most 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

SARS-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

Alzheimer’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

The 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

The 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.

IMPORTANCE

Coronaviruses 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

Bacterial 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

The 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

Research 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 summary

Cashmere 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.
Development of a reverse transcription polymerase chain reaction for the detection of severe fever with thrombocytopenia syndrome virus from suspected infected animals
Authors: Park Eun-sil , Fujita Osamu , Kimura Masanobu , Hotta Akitoyo , Imaoka Koichi , Shimojima Masayuki , Saijo Masayuki , Maeda Ken , Morikawa Shigeru
Published: August 2020

Background

Severe fever with thrombocytopenia syndrome virus (SFTSV) causes severe hemorrhagic fever in humans and cats. Clinical symptoms of SFTS-infected cats resemble to those of SFTS patients and SFTS-contracted cats shows high levels of viral RNA loads in the serum and body fluids. Due to the risk of direct infection from SFTS-infected cats to human, it is important to diagnose SFTS-suspected animals.

Methodology/Principle findings

Four primer sets were newly designed from consensus sequences constructed by 108 strains of SFTSV. A reverse transcription polymerase chain reaction (RT-PCR) with these four primer sets were successfully and specifically detected several clades of SFTSV. Their limits of detection are 1-10 copies/reaction. By this RT-PCR, 5 cat cases among 56 SFTS-suspected animal cases were diagnosed as SFTS. From these cats, IgM or IgG against SFTSV were detected by enzyme-linked immunosorbent assay (ELISA), but not neutralizing antibodies by plaque reduction neutralization titer (PRNT) test. This phenomenon is similar to those of fatal SFTS patients.

Conclusion/Significance

This newly developed RT-PCR could detect SFTSV RNA of several clades from SFTS-suspected animals. In addition to ELISA and PRNT test, the useful laboratory diagnosis systems of SFTS-suspected animals has been made in this study.

Author summary

This study developed RT-PCR to detect SFTS animal cases. This assay could detect SFTSV RNA belonging to different clades. Cats diagnosed as SFTS had IgM or IgG, but not neutralizing antibodies. SFTS cat cases were distributed in the area where SFTS patients have been reported highly, indicating the establishment of the circulation of SFTSV in the environment. These diagnostic assays could be helpful tools to detect and not to miss SFTS animal cases.