bluuebunny/crossref_metadata_2025 huggingface dataset:
Modulation of microglial activity by salt load and SGK1
Authors: Inoue Koichi , Morimoto Hiroyuki , Ueki Takatoshi
Published: April 2020

Microglial cells are derived from myelogenous cells and their chronic activation elicits brain inflammation, which influences neurological activity. Comprehensive understanding of the regulation of microglial activation could therefore contribute to overcoming neuropsychiatric disorders. Recently, the importance of serum- and glucocorticoid-inducible kinases (SGKs) has been explored in immune cells such as T cells, dendritic cells and macrophages. We have already shown that SGK1 and SGK3 are expressed in microglial cells and associated with the regulation of lipopolysaccharide (LPS)-induced inflammatory molecules. Here we investigate whether salt load influences expression of SGK1 and inflammatory responses in murine primary microglia and an immortalized microglial cell line, BV-2. Additional amounts of NaCl were administrated and immunoblotting was carried out, and SGK1 was induced in dose- and time-dependent manners. Next, the dynamics of inflammatory mediators iNOS and TNFα were investigated by administration of LPS. iNOS mRNA was induced by LPS application and enhanced by NaCl preload. In support of these results, nitric oxide was produced by LPS and accelerated by NaCl preload. In contrast, however, NaCl preload reduced the release of TNFα, suggesting the modulation of immune responses by salt load. The effects of salt load on both cases were attenuated in SGK1-deleted cells. Taken together, these results indicate that salt load modulates inflammatory responses and that SGK1 assists salt load-induced inflammatory responses.
Optimization of SARS-CoV-2 detection by RT-QPCR without RNA extraction
Authors: Merindol Natacha , Pépin Geneviève , Marchand Caroline , Rheault Marylène , Peterson Christine , Poirier André , Germain Hugo , Danylo Alexis
Published: April 2020

Rapid and reliable screening of SARS-CoV-2 is fundamental to assess viral spread and limit the pandemic we are facing. In this study we evaluated the reliability and the efficiency of a direct RT-QPCR method (without RNA extraction) using SeeGene Allplex™ 2019-nCoV RT-QPCR and the influence of swab storage media composition on further viral detection.

We show that SeeGene’s assay provides similar efficiency as the RealStar®SARS-CoV-2 RT-PCR kit (Altona Diagnostics), and that RNA extraction is not necessary nor advantageous if samples are stored in UTM or molecular water but is recommended if samples are stored in saline solution and in Hanks medium.
Blind Uneven Proliferation of CD4+ T cells During Primary Infection Generates the Majority of the HIV Reservoir
Authors: Boshier Florencia A. T. , Reeves Daniel B. , Duke Elizabeth R. , Swan David A. , Prlic Martin , Cardozo-Ojeda E. Fabian , Schiffer Joshua T.
Published: April 2020

The HIV reservoir is a population of 1-10 million anatomically dispersed, latently infected memory CD4+ T cells in which an HIV DNA molecule is quiescently integrated into human chromosomal DNA. When antiretroviral therapy (ART) is stopped and HIV replication initiates in one of these cells, systemic viral spread resumes, rekindling progression to AIDS. Therefore, HIV latency prevents cure. The HIV reservoir contains clones: identical HIV sequences that are integrated within identical human chromosomal DNA locations. The presence of these clones demonstrates that proliferation of CD4+ T cells sustains infection despite ART. The reservoir has a precise structure consisting of a small number of large clones and a large number of small clones. However, the mechanisms leading to this structure have not been identified. We developed a mathematical model that recapitulates the profound depletion and brisk recovery of CD4+ T cells, reservoir creation, and viral load trajectory during primary HIV infection. We extended the model to simulate stochastically individual HIV reservoir clones and identified that uneven proliferation among clones during recovery from CD4+ lymphopaenia is sufficient to explain the observed clonal reservoir distribution. We project that within one month of infection 75-95% of reservoir cells are generated from cellular proliferation rather than denovo viral infection. Recent detection of HIV infected clones during the first 5 weeks of infection support our model’s predictions.
Analysis of the SARS-CoV-2 spike protein glycan shield: implications for immune recognition
Authors: Grant Oliver C. , Montgomery David , Ito Keigo , Woods Robert J.
Published: April 2020

Here we have generated 3D structures of glycoforms of the spike (S) glycoprotein from SARS-CoV-2, based on reported 3D structures and glycomics data for the protein produced in HEK293 cells. We also analyze structures for glycoforms representing those present in the nascent glycoproteins (prior to enzymatic modifications in the Golgi), as well as those that are commonly observed on antigens present in other viruses.

These models were subjected to molecular dynamics (MD) simulation to determine the extent to which glycan microheterogeneity impacts the antigenicity of the S glycoprotein. Lastly, we have identified peptides in the S glycoprotein that are likely to be presented in human leukocyte antigen (HLA) complexes, and discuss the role of S protein glycosylation in potentially modulating the adaptive immune response to the SARS-CoV-2 virus or to a related vaccine.

The 3D structures show that the protein surface is extensively shielded from antibody recognition by glycans, with the exception of the ACE2 receptor binding domain, and also that the degree of shielding is largely insensitive to the specific glycoform. Despite the relatively modest contribution of the glycans to the total molecular weight (17% for the HEK293 glycoform) the level of surface shielding is disproportionately high at 42%.
Characterization of the oral microbiome of medically controlled type-2 diabetes patients
Authors: Almeida-Santos Ana , Martins-Mendes Daniela , Gayà-Vidal Magdalena , Pérez-Pardal Lucía , Beja-Pereira Albano
Published: April 2020

Type 2 diabetes mellitus (T2DM) is a chronic metabolic disease that is becoming a significant global health care problem. Several studies have shown that people with diabetes are more susceptible to oral problems, such as periodontitis and, although the causes are still inconclusive, the oral microbiota seems to be an important factor in this interaction. This study aimed to characterize the oral microbiome of a sample representing T2DM patients from Portugal and exploit potential associations between some microorganisms and variables like teeth brushing, smoking habits, and nutrient intake. By sequencing the hypervariable regions V3-V4 of the 16S rRNA gene in 50 individuals belonging to a group of diabetes patients and a control group, we found a total of 233 taxa, from which only 65% were shared between both groups. No differences were found in terms of alpha and beta diversity between groups or habits categories. Also, there were no significant differences in the oral microbiome profiles of control and diabetes patients. Only the classSynergistiaand the genusTG5, which are related to periodontitis, were statistically more frequent in the control group. This finding can be justified by the fact that these diabetic patients usually have their oral health under close medical control than an average healthy person, which in this study was represented by the control group.

IMPORTANCE

Diabetes has become a significant global health care issue as its incidence continues to increase exponentially, with type 2 diabetes being responsible for more than 90% of these cases. Portugal is one of the countries with a higher prevalence of diabetes in Europe. It has been reported that diabetic people have an increased risk of developing several health problems such as oral infections mostly caused by opportunistic pathogens. Some studies have pointed out a relationship between diabetes and oral microbiome. Therefore, the characterization of the microbial ecosystem of the mouth in reference groups is crucial to provide information to tackle oral health pathogen-borne conditions. In this study, we provide the first characterization of the oral microbiome of type 2 diabetes mellitus patients from Portugal, and therefore, contributing new data and knowledge to elucidate the relationship between diabetes and the oral microbiome.
Tasimelteon (HETLIOZ®) effective in the treatment of Jet Lag Disorder in an 8-hour phase advance; a multicenter, randomized, double-blind, placebo-controlled trial
Authors: Polymeropoulos Christos M , Mohrman Michael A , Keefe Madison S , Brzezynski Jennifer L , Wang Jingyuan , Prokosch Lydia S , Polymeropoulos Vasilios M , Xiao Changfu , Birznieks Gunther , Polymeropoulos Mihael H
Published: April 2020

Background

Travelers frequently experience Jet Lag Disorder (JLD) symptoms due to misalignment of the circadian rhythm with respect to the new time zone. In the JET8 Study, we assessed the efficacy and safety of tasimelteon (HETLIOZ®) in healthy participants using a laboratory model of JLD induced by an 8-h phase advance of the sleep-wake cycle. We hypothesized that tasimelteon treatment in participants experiencing JLD would cause increased sleep time, increased next-day alertness, and reduced next-day sleepiness.

Methods

We undertook a randomized, double-blind, placebo-controlled trial in 12 US clinical research sleep centers. We screened healthy adults ages 18-73 years, who were eligible for the randomization phase of JET8 if they typically went to bed between 21:00 and 01:00, slept between 7-9 hours each night, and slept at a consistent bedtime. We used block randomization stratified by site to assign participants (1:1) to receive a single oral dose of tasimelteon (20mg) or placebo 30 min before their 8-h phase-advanced bedtime. The primary endpoint was Total Sleep Time in the first 2/3 of the night (TST2/3), which was measured by polysomnography during the 8-h sleep episode, and assessed in the intent-to-treat population. The trial is completed and registered with ClinicalTrials.gov,NCT03373201.

Results

Between October 16, 2017 and January 17, 2018, we screened 607 healthy participants for JET8, of whom 320 (53%) were assigned to receive tasimelteon (n=160) or placebo (n=160). Tasimelteon treatment resulted in increased TST2/3by 60.3 min (95%CI 44.0 to 76.7,P<0.0001) compared to placebo and had a highly significant benefit in secondary endpoints including TST of the whole night, next day alertness, next day sleepiness, and latency to persistent sleep.

Conclusion

A single dose of tasimelteon improves symptoms, including sleep and next day functioning in participants, following an 8-h phase advance of the sleep-wake cycle in a laboratory model of JLD simulating eastward trans-meridian travel.
Polygenic associations and causal inferences between serum immunoglobulins and amyotrophic lateral sclerosis
Authors: Chen Xu , Shen Xiaojun , Zhang Xuzhuo , Zhan Yiqiang , Fang Fang
Published: April 2020

Chronic inflammation might contribute to the development of amyotrophic lateral sclerosis (ALS), the relationship between serum immunoglobulins and risk of ALS remains however unclear. In order to overcome limitations like reverse causation and residual confounding commonly seen in the observational studies, we applied molecular epidemiological analyses to examine the polygenic and causal associations between serum immunoglobulins and ALS. Summary statistics from the large-scale genome-wide association studies (GWAS) among European ancestry populations (∼15000 individuals for serum immunoglobulins, and more than 36000 individuals for ALS) were accessed from different consortia. The relationships between three types of serum immunoglobulins (IgA, IgM, and IgG) and ALS were investigated in a discovery phase and then in a replication phase. Polygenic risk score (PRS) analysis was performed with PRSice package to test the polygenic association, and Mendelian randomization (MR) analysis was performed with TwoSampleMR package to infer the causality. An inverse polygenic association was discovered between IgA and ALS as well as between IgM and ALS. Such associations were however not replicated using a larger GWAS of ALS, and no causal association was observed for either IgA-ALS or IgM-ALS. A positive polygenic association was both discovered [odds ratio (OR) = 1.18, 95% confidence interval (CI): 1.12-1.25, P=5.9×10−7] and replicated (OR=1.13, 95% CI: 1.06-1.20, P=0.001) between IgG and ALS. A causal association between IgG and ALS was also suggested in both the discovery (OR=1.06, 95%CI: 1.02-1.10, P=0.009) and replication (OR=1.07, 95%CI: 0.90-1.24, P=0.420) analyses, although the latter was not statistically significant. This study suggests a shared polygenic risk between serum IgG (as a biomarker for chronic inflammation) and ALS.
Effects of statins on lipid profile of kidney transplant recipients: a meta-analysis of randomized controlled trials
Authors: Huang Xiu , Jia Yong , Zhu Xiaoyu , Zhang Yangyang , Jiang Lili , Wei Xuejiao , Zhao Dan , Zhao Xiaoxia , Du Yujun
Published: April 2020

Objective

To assess the benefits of statins on lipid profile in kidney transplant recipients via a meta-analysis.

Methods

We systematically identified peer-reviewed clinical trials, review articles, and treatment guidelines from PubMed, Embase, the Cochrane Library, Wanfang, Chinese National Knowledge Infrastructure (CNKI), SinoMed (CBM), and Chongqing VIP databases from inception to April 2019. In the analysis, only randomized controlled clinical trials performed in human were included.

Results

Eight articles were included in the analysis, involving 335 kidney transplant recipients who received statins and 350 kidney transplant patients as the control group. Results revealed that statins improved the lipid profile of kidney transplant recipients. Specifically, statin therapy significantly reduced total cholesterol and low-density lipoprotein cholesterol. However, it had no effects on high-density lipoprotein cholesterol and triglycerides levels.

Conclusions

The present study provides valuable knowledge on the potential benefits of statins in kidney transplant recipients. This meta-analysis shows that statin therapy modifies the lipid profile in this patient population.
Robust neutralization assay based on SARS-CoV-2 S-bearing vesicular stomatitis virus (VSV) pseudovirus and ACE2-overexpressed BHK21 cells
Authors: Xiong Hua-Long , Wu Yang-Tao , Cao Jia-Li , Yang Ren , Ma Jian , Qiao Xiao-Yang , Yao Xiang-Yang , Zhang Bao-Hui , Zhang Ya-Li , Hou Wang-Heng , Yang-Shi  , Xu Jing-Jing , Liang-Zhang  , Wang Shao-Juan , Fu Bao-Rong , Yang Ting , Ge Sheng-Xiang , Zhang Jun , Yuan Quan , Huang Bao-Ying , Li Zhi-Yong , Zhang Tian-Ying , Xia Ning-Shao
Published: April 2020

The global pandemic of Coronavirus disease 2019 (COVID-19) is a disaster for human society. A convenient and reliablein vitroneutralization assay is very important for the development of neutralizing antibodies, vaccines and other inhibitors. In this study, G protein-deficient vesicular stomatitis virus (VSVdG) bearing full-length and truncated spike (S) protein of SARS-CoV-2 were evaluated. The virus packaging efficiency of VSV-SARS-CoV-2-Sdel18 (S with C-terminal 18 amino acid truncation) is much higher than VSV-SARS-CoV-2-S. A neutralization assay for antibody screening and serum neutralizing titer quantification was established based on VSV-SARS-CoV-2-Sdel18 pseudovirus and human angiotensin-converting enzyme 2 (ACE2) overexpressed BHK21 cell (BHK21-hACE2). The experimental results can be obtained by automatically counting EGFP positive cell number at 12 hours after infection, making the assay convenient and high-throughput. The serum neutralizing titer of COVID-19 convalescent patients measured by VSV-SARS-CoV-2-Sdel18 pseudovirus assay has a good correlation with live SARS-CoV-2 assay. Seven neutralizing monoclonal antibodies targeting receptor binding domain (RBD) of SARS-CoV-2-S were obtained. This efficient and reliable pseudovirus assay model could facilitate the development of new drugs and vaccines.
Single-cell analysis of severe COVID-19 patients reveals a monocyte-driven inflammatory storm attenuated by Tocilizumab
Authors: Guo Chuang , Li Bin , Ma Huan , Wang Xiaofang , Cai Pengfei , Yu Qiaoni , Zhu Lin , Jin Liying , Jiang Chen , Fang Jingwen , Liu Qian , Zong Dandan , Zhang Wen , Lu Yichen , Li Kun , Gao Xuyuan , Fu Binqing , Liu Lianxin , Ma Xiaoling , Weng Jianping , Wei Haiming , Jin Tengchuan , Lin Jun , Qu Kun
Published: April 2020

Despite the current devastation of the COVID-19 pandemic, several recent studies have suggested that the immunosuppressive drug Tocilizumab can powerfully treating inflammatory responses that occur in this disease. Here, by employing single-cell analysis of the immune cell composition of severe-stage COVID-19 patients and these same patients in post Tocilizumab-treatment remission, we have identified a monocyte subpopulation specific to severe disease that contributes to inflammatory storms in COVID-19 patients. Although Tocilizumab treatment attenuated the strong inflammatory immune response, we found that immune cells including plasma B cells and CD8+T cells still exhibited an intense humoral and cell-mediated anti-virus immune response in COVID-19 patients after Tocilizumab treatment. Thus, in addition to providing a rich, very high-resolution data resource about the immune cell distribution at multiple stages of the COVID-19 disease, our work both helps explain Tocilizumab’s powerful therapeutic effects and defines a large number of potential new drug targets related to inflammatory storms.
Structure dynamics of ApoA-I amyloidogenic variants in small HDL increase their ability to mediate cholesterol efflux
Authors: Nilsson Oktawia , Lindvall Mikaela , Obici Laura , Ekström Simon , Lagerstedt Jens O. , Del Giudice Rita
Published: April 2020

Specific mutations in Apolipoprotein A-I (ApoA-I) of high-density lipoprotein (HDL) are responsible for a late-onset systemic amyloidosis. Carriers do not exhibit increased cardiovascular disease risk despite reduced levels of ApoA-I/ HDL-cholesterol. To explain this paradox, we show that the HDL particle profile of L75P and L174S patients presents a higher relative abundance of the 8.4 nm vs 9.6 nm particles, and that serum from patients, as well as reconstituted 8.4 and 9.6 nm HDL particles (rHDL), possess increased capacity to catalyze cholesterol efflux from macrophages. Synchrotron radiation circular dichroism and hydrogen-deuterium exchange revealed that the variants in 8.4 nm rHDL have altered secondary structure composition and display a more flexible binding to lipids compared to their native counterpart. The reduced HDL-cholesterol levels of patients carrying ApoA-I amyloidogenic variants are thus balanced by higher proportion of small, dense HDL particles and better cholesterol efflux due to altered, region-specific protein structure dynamics.
Measuring the quality of scientific references in Wikipedia: an analysis of more than 115M citations to over 800,000 scientific articles
Authors: Nicholson Joshua M. , Uppala Ashish , Sieber Matthias , Grabitz Peter , Mordaunt Milo , Rife Sean
Published: April 2020

Wikipedia is a widely used online reference work which cites hundreds of thousands of scientific articles across its entries. The quality of these citations has not been previously measured, and such measurements have a bearing on the reliability and quality of the scientific portions of this reference work. Using a novel technique, a massive database of qualitatively described citations, and machine learning algorithms, we analyzed 1,923,575 Wikipedia articles which cited a total of 824,298 scientific articles, and found that most scientific articles (57%) are uncited or untested by subsequent studies, while the remainder show a wide variability in contradicting or supporting evidence (2-41%). Additionally, we analyzed 51,804,643 scientific articles from journals indexed in the Web of Science and found that most (85%) were uncited or untested by subsequent studies, while the remainder show a wide variability in contradicting or supporting evidence (1-14%).
Computational search of hybrid human/ SARS-CoV-2 dsRNA reveals unique viral sequences that diverge from those of other coronavirus strains
Authors: Pasquier Claude , Robichon Alain
Published: April 2020

The role of the RNAi/Dicer/Ago system to degrade RNA viruses has been elusive in mammals, which prompted authors to think that interferon (IFN) synthesis is essential in this clade relegating the RNAi defense strategy against viral infection as accessory function. We explore the theoretical possibilities that RNAi triggered by SARS-CoV-2 might degrade some host transcripts in the opposite direction although this hypothesis seems counter intuitive. SARS-CoV-2 genome was therefore computational searched for exact intra pairing within the viral RNA and also hybrid exact pairing with human transcriptome over a minimum 20 bases length. Minimal segments of 20 bases length of SARS-CoV-2 RNA were found based on the theoretical matching with existing complementary strands in the human host transcriptome. Few human genes potentially annealing with SARS-CoV-2 RNA, among them mitochondrial deubiquitinase USP30, a subunit of ubiquitin protein ligase complex FBXO21 along with two long coding RNAs were retrieved. The hypothesis that viral originated RNAi might mediate degradation of messengers of the host transcriptome was corroborated by clinical observation and phylogenetic comparative analysis indicating a strong specificity of these hybrid pairing sequences for both SARS-CoV-2 and human genomes.
A new model for vertebrate mineralization via stabilized amorphous calcium carbonate for avian eggshell formation
Authors: Stapane Lilian , Le Roy Nathalie , Ezagal Jacky , Rodriguez-Navarro Alejandro B. , Labas Valérie , Combes-Soia Lucie , Hincke Maxwell T. , Gautron Joël
Published: April 2020

Amorphous calcium carbonate (ACC) is an unstable mineral phase, which is progressively transformed into aragonite or calcite in biomineralization of marine invertebrate shells or avian eggshells, respectively. We have previously proposed a model of vesicular transport to provide stabilized ACC in chicken uterine fluid where mineralization takes place. Herein, we report further experimental evidence for this model. We confirmed the presence of extracellular vesicles (EVs) that contain ACC in uterine fluid using transmission electron microscopy and elemental analysis. We also demonstrate high levels of expression of vesicular markers in the oviduct segments where eggshell is formed. Moreover, proteomics and immunofluorescence confirmed the presence of major vesicular, mineralization-specific and eggshell matrix proteins in the uterus and in purified EVs. We propose a comprehensive role for EVs in eggshell mineralization, in which annexins transfer calcium into vesicles and carbonic anhydrase 4 catalyzes the formation of HCO3−, for accumulation of ACC in vesicles. We hypothesize that ACC is stabilized by ovalbumin and/or lysozyme or additional vesicle proteins identified in this study. Finally, EDIL3 and MFGE8 are proposed to serve as guidance molecules to target EVs to the mineralization site. We therefore report for the first time experimental evidence for the components of vesicular transport to supply ACC in vertebrate biomineralization. These results could give insight to understand the mineralization of otoconia, which are calcium carbonate biomineralized structures present in all vertebrates and necessary for balance and sensing linear acceleration.
M2 Cortex-Dorsolateral striatum stimulation reverses motor symptoms and synaptic deficits in Huntington’s Disease
Authors: Fernández-García Sara , Conde-Berriozabal Sara , García-García Esther , Gort-Paniello Clara , Bernal-Casas David , Barriga Gerardo García-Díaz , López-Gil Javier , Muñoz-Moreno Emma , Sòria Guadalupe , Campa Leticia , Artigas Francesc , Rodriguez Manuel J , Alberch Jordi , Masana Mercè
Published: April 2020

Huntington’s disease (HD) is a neurological disorder characterized by motor disturbances. HD pathology is most prominent in the striatum, the central hub of basal ganglia. The cortex is the main striatal afference and progressive cortico-striatal disconnection characterizes HD. We mapped cortico-striatal dysfunction in HD mice to ultimately modulate the activity of selected cortico-striatal circuits to ameliorate motor symptoms and recover synaptic plasticity. Multimodal MRIin vivosuggested prominent functional network deficits in fronto-striatal compared to motor-striatal pathways, which were accompanied by reduced glutamate levels in the striatum of HD mice. Moreover, optogenetically-stimulated glutamate release from fronto-striatal terminals was reduced in HD mice and electrophysiological responses in striatal neurons were blunted. Remarkably, repeated M2 Cortex-dorsolateral striatum optogenetic stimulation normalized motor behavior in HD mice and evoked a sustained increase of synaptic plasticity. Overall, these results reveal that the selective stimulation of fronto-striatal pathways can become an effective therapeutic strategy in HD.
Structural Basis for the Inhibition of the RNA-Dependent RNA Polymerase from SARS-CoV-2 by Remdesivir
Authors: Yin Wanchao , Mao Chunyou , Luan Xiaodong , Shen Dan-Dan , Shen Qingya , Su Haixia , Wang Xiaoxi , Zhou Fulai , Zhao Wenfeng , Gao Minqi , Chang Shenghai , Xie Yuan-Chao , Tian Guanghui , Jiang He-Wei , Tao Sheng-Ce , Shen Jingshan , Jiang Yi , Jiang Hualiang , Xu Yechun , Zhang Shuyang , Zhang Yan , Xu H. Eric
Published: April 2020

The pandemic of Corona Virus Disease 2019 (COVID-19) caused by SARS-CoV-2 has become a global crisis. The replication of SARS-CoV-2 requires the viral RNA-dependent RNA polymerase (RdRp), a direct target of the antiviral drug, Remdesivir. Here we report the structure of the SARS-CoV-2 RdRp either in the apo form or in complex with a 50-base template-primer RNA and Remdesivir at a resolution range of 2.5-2.8 Å. The complex structure reveals that the partial double-stranded RNA template is inserted into the central channel of the RdRp where Remdesivir is incorporated into the first replicated base pair and terminates the chain elongation. Our structures provide critical insights into the working mechanism of viral RNA replication and a rational template for drug design to combat the viral infection.
Relative Abundance of SARS-CoV-2 Entry Genes in the Enterocytes of the Lower Gastrointestinal Tract
Authors: Lee Jaewon J. , Kopetz Scott , Vilar Eduardo , Shen John Paul , Chen Ken , Maitra Anirban
Published: April 2020

COVID-19, the disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has rapidly spread throughout the world and was declared a pandemic by the World Health Organization, thus leading to a rapid surge in the efforts to understand the mechanisms of transmission, methods of prevention, and potential therapies. While COVID-19 frequently manifests as a respiratory infection,1there is evidence for infection of the gastrointestinal (GI) tract1–4with documented viral RNA shedding in the stool of infected patients.2,4In this study, we aimed to investigate the expression ofACE2andTMPRSS2, which are required for SARS-CoV-2 entry into mammalian cells,5from single-cell RNA sequencing (scRNA-seq) datasets of five different parts of the GI tract: esophagus, stomach, pancreas, small intestine, and colon/rectum.
Lipidomic and Ultrastructural Characterization of Cell Envelope ofStaphylococcus aureusGrown in the Presence of Human Serum
Authors: Hines Kelly M. , Alvarado Gloria , Chen Xi , Gatto Craig , Pokorny Antje , Alonzo Francis , Wilkinson Brian J. , Xu Libin
Published: April 2020

Staphylococcus aureuscan incorporate exogenous straight-chain unsaturated and saturated fatty acids (SCUFAs and SCFAs, respectively) to replace some of the normally biosynthesized branched-chain fatty acids and SCFAs. In this study, the impact of human serum on theS. aureuslipidome and cell envelope structure was comprehensively characterized. When grown in the presence of 20% human serum, typical human serum lipids, such as cholesterol, sphingomyelin, phosphatidylethanolamines, and phosphatidylcholines, were present in the total lipid extracts. Mass spectrometry showed that SCUFAs were incorporated into all majorS. aureuslipid classes,i.e., phosphatidylglycerols, lysyl-phosphatidylglycerols, cardiolipins, and diglucosyldiacylglycerols. Heat-killedS. aureusretained much fewer serum lipids and failed to incorporate SCUFAs, suggesting that association and incorporation of serum lipids withS. aureusrequires a living or non-denatured cell. Cytoplasmic membranes isolated from lysostaphin-produced protoplasts of serum-grown cells retained serum lipids, but washing cells with Triton X-100 removed most of them. Furthermore, electron microscopy studies showed that serum-grown cells had thicker cell envelopes and associated material on the surface, which was partially removed by Triton X-100 washing. To investigate which serum lipids were preferentially hydrolyzed byS. aureuslipases for incorporation, we incubated individual serum lipid classes withS. aureusand found that cholesteryl esters (CEs) and triglycerides (TGs) are the major donors of the incorporated fatty acids. Further experiments using purified Geh lipase confirmed CEs and TGs being the substrates of this enzyme. Thus, growth in the presence of serum altered the nature of the cell surface with implications for interactions with the host.

IMPORTANCE

Comprehensive lipidomics ofS. aureusgrown in the presence of human serum suggests human serum lipids can associate with the cell envelope without being truly integrated into the lipid membrane. However, fatty acids-derived from human serum lipids, including unsaturated fatty acids, can be incorporated into lipid classes that can be biosynthesized byS. aureusitself. Cholesteryl esters and triglycerides are found to be the major source of incorporated fatty acids upon hydrolysis by lipases. These findings have significant implications for the nature of theS. aureuscell surface when grownin vivo. Changes in phospholipid and glycolipid abundances and fatty acid composition could affect membrane biophysics and function and the activity of membrane-targeting antimicrobials. Finally, the association of serum lipids with the cell envelope has implications for the physicochemical nature of the cell surface and its interaction with host defense systems.
Spatial modeling cannot currently differentiate SARS-CoV-2 coronavirus and human distributions on the basis of climate in the United States
Authors: Harbert Robert , Cunningham Seth W. , Tessler Michael
Published: April 2020

The SARS-CoV-2 coronavirus is wreaking havoc globally, yet knowledge of its biology is limited. Climate and seasonality influence the distributions of many diseases, and studies suggest a link between SARS-CoV-2 and cool weather. One such study, building species distribution models (SDMs), predicted SARS-CoV-2 risk may remain concentrated in the Northern Hemisphere, shifting northward in summer months. Others have highlighted issues with SARS-CoV-2 SDMs, notably: the primary niche of the virus is the host it infects, climate may be a weak distributional predictor, global prevalence data have issues, and the virus is not in a population equilibrium. While these issues should be considered, climate still may be important for predicting the future distribution of SARS-CoV-2. To further examine if there is a link, we model with raw cases and population scaled cases for SARS-CoV-2 county-level data from the United States. We show that SDMs built from population scaled cases data cannot be distinguished from control models built from raw human population data, while SDMs built on raw data fail to predict the current known distribution of cases in the US. The population scaled analyses indicate that climate may not play a central role in current US viral distribution and that human population density is likely a primary driver. Still, we do find slightly more population scaled viral cases in cooler areas. This coupled with our geographically constrained focus make it so we cannot rule out climate as a partial driver of the US SARS-CoV-2 distribution. Climate’s role on SARS-CoV-2 should continue to be cautiously examined, but at this time we should assume that SARS-CoV-2 can spread anywhere in the US.
Protocol for a multicentre study of nosocomial SARS-CoV2 transmission The NOSO-COR Project
Authors: Saadatian-Elahi Mitra , Picot-Sanchez Valentina , Henaff Laetitia , Pradel Florence , Escuret Vanessa , Dananché Cédric , Elias Christelle , Endtz Hubert , Vanhems Philippe
Published: April 2020

Introduction

The newly identified SARS-CoV2 can cause serious acute respiratory infections such as pneumonia with a mortality rate of approximately 2% to 4%. In the current context of high incidence rates of SARS-CoV2 in the community, a significant increase in the rate of nosocomial transmission is expected. The risk of nosocomial transmission could even be higher in low-income countries that have fragile healthcare systems. This protocol is intended to study and document suspected or confirmed cases of nosocomial SARS-CoV2 infection, the clinical spectrum and the determinants (risk factors/protective) at participating hospitals.

Methods and analysis

This will be an international multicentre prospective, observational, hospital-based study in adults and children. It will include volunteer patients, care givers and healthcare professionals in France and hospitals affiliated with the GABRIEL network.

Demographic and clinical data will be collected using case-report forms designed especially for the purpose of the project. A nasopharyngeal swab will be collected and tested for SARS-CoV2 by RT-PCR. Characteristics of the study participants, the proportion of confirmed nosocomial SARS-CoV2 infections relative to all patients with syndromes suggestive of 2019-nCoV infection will be analysed. Appropriate multivariate modelling will be used to identify the determinants associated with nosocomial onset.

Ethics and dissemination

This study was approved by the clinical research and committee of Ile de France V on March 8, 2020.

Registration details

The trial was registered in ClinicalTrials (NCT04290780).

Strengths and limitations of the study

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This prospective study will generate and evaluate original data on nosocomial SARS-CoV2 infection in France and in the low-income countries of the GABRIEL network using the same protocol and standardised CRF.

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The results will provide the opportunity to compare the management of nosocomial Covid-19 infection in different settings for mutual exchanges and optimisation.

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The results will make it possible to refine the definition of nosocomial SARS-CoV2 infection, strengthen preventive campaigns for in-hospital transmission of SARS-CoV2 and pave the way for new recommendations in terms of preventive measures.

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Selection bias owing to access to care in different populations and bias owing to the extent of access to personal protective equipment, in particular, in low-income countries may occur.

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The non-exhaustivity of the confounders to be collected should be considered for interpretation of the results.
Robust Estimation of Infection Fatality Rates during the Early Phase of a Pandemic
Authors: Simon Perikles
Published: April 2020

During a pandemic, robust estimation of case fatality rates (CFRs) is essential to plan and control suppression and mitigation strategies. At present, estimates for the CFR of COVID-19 caused by SARS-CoV-2 infection vary considerably. Expert consensus of 0.1–1% covers in practical terms a range from normal seasonable Influenza to Spanish Influenza. In the following, I deduce a formula for an adjusted Infection Fatality Rate (IFR) to assess mortality in a period following a positive test adjusted for selection bias.

Official datasets on cases and deaths were combined with data sets on number of tests. After data curation and quality control, a total of IFR (n=819) was calculated for 21 countries for periods of up to 26 days between registration of a case and death.

Estimates for IRFs increased with length of period, but levelled off at >9days with a median for all 21 countries of 0.11 (95%-CI: 0.073–0.15). An epidemiologically derived IFR of 0.040 % (95%-CI: 0.029%– 0.055%) was determined for Iceland and was very close to the calculated IFR of 0.057% (95%-CI: 0.042– 0.078), but 2.7–6-fold lower than CFRs. IFRs, but not CFRs, were positively associated with increased proportions of elderly in age-cohorts (n=21, spearman’s ρ=.73, p =.02).

Real-time data on molecular and serological testing may further displace classical diagnosis of disease and its related death. I will critically discuss, why, how and under which conditions the IFR, provides a more solid early estimate of the global burden of a pandemic than the CFR.
Innovation, conservation and repurposing of gene function in plant root cell type development
Authors: Kajala Kaisa , Shaar-Moshe Lidor , Mason G. Alex , Gouran Mona , Rodriguez-Medina Joel , Kawa Dorota , Pauluzzi Germain , Reynoso Mauricio , Canto-Pastor Alex , Lau Vincent , Artur Mariana A. S. , West Donnelly A. , Manzano Concepcion , Gray Sharon B. , Yao Andrew I. , Bajic Marko , Formentin Elide , Nirmal Niba , Rodriguez Alan , Pasha Asher , Borowsky Alexander T. , Deal Roger B. , Kliebenstein Daniel , Hvidsten Torgeir R. , Provart Nicholas J. , Sinha Neelima , Runcie Daniel E. , Bailey-Serres Julia , Brady Siobhan M.
Published: April 2020

Plant species have evolved myriads of solutions to adapt to dynamic environments, including complex cell type development and regulation. To understand this diversity, we profiled tomato root cell type translatomes and chromatin accessibility. Using xylem differentiation in tomato, relative to Arabidopsis, examples of functional innovation, repurposing and conservation of transcription factors are described. Repurposing and innovation of genes are further observed within an exodermis regulatory network and illustrate its function. Translatome analyses of rice, tomato and Arabidopsis tissues suggest that root meristems are more conserved, and that the functions of constitutively expressed genes are more conserved than those of cell type/tissue-enriched genes. These observations suggest that higher-order properties of cell type and pan-cell type regulation are conserved between plants and animals.

One Sentence Summary

Pan-species cell type translatome and chromatin accessibility data reveal novelty, conservation and repurposing of gene function.
NUDT21 links mitochondrial IPS-1 to RLR-containing stress granules and activates host antiviral defense
Authors: Aoyama-Ishiwatari Saeko , Okazaki Tomohiko , Iemura Shun-ichiro , Natsume Tohru , Okada Yasushi , Gotoh Yukiko
Published: April 2020

Viral RNA in the cytoplasm of mammalian host cells is recognized by retinoic acid– inducible protein–I (RIG-I)–like receptors (RLRs), which localize to cytoplasmic stress granules (SGs). Activated RLRs associate with the mitochondrial adaptor protein IPS-1, which activates antiviral host defense mechanisms including type I interferon (IFN) induction. It has remained unclear, however, how RLRs in SGs and IPS-1 in the mitochondrial outer membrane associate physically and engage in information transfer. Here we show that NUDT21, an RNA binding protein that regulates alternative transcript polyadenylation, physically associates with IPS-1 and mediates its localization to SGs in response to transfection with poly(I:C), a mimic of viral double-stranded RNA. We found that, despite its well-established function in the nucleus, a fraction of NUDT21 localizes to mitochondria in resting cells and becomes localized to SGs in response to poly(I:C) transfection. NUDT21 was also found to be required for efficient type I IFN induction in response to viral infection. Our results together indicate that NUDT21 links RLRs in SGs to mitochondrial IPS-1 and thereby activates host defense responses to viral infection.
In silicoAPC/C substrate discovery reveals cell cycle degradation of chromatin regulators including UHRF1
Authors: Kernan Jennifer L. , Martinez-Chacin Raquel C. , Wang Xianxi , Tiedemann Rochelle L. , Bonacci Thomas , Choudhury Rajarshi , Bolhuis Derek L. , Damrauer Jeffrey S. , Yan Feng , Harrison Joseph S. , Major Michael Ben , Hoadley Katherine , Suzuki Aussie , Rothbart Scott B. , Brown Nicholas G. , Emanuele Michael J.
Published: April 2020

The Anaphase-Promoting Complex/Cyclosome (APC/C) is an E3 ubiquitin ligase and critical regulator of cell cycle progression. Despite its vital role, it has remained challenging to globally map APC/C substrates. By combining orthogonal features of known substrates, we predicted APC/C substratesin silico. This analysis identified many known substrates and suggested numerous candidates. Unexpectedly, chromatin regulatory proteins are enriched among putative substrates and we show that several chromatin proteins bind APC/C, oscillate during the cell cycle and are degraded following APC/C activation, consistent with being direct APC/C substrates. Additional analysis revealed detailed mechanisms of ubiquitylation for UHRF1, a key chromatin regulator involved in histone ubiquitylation and DNA methylation maintenance. Disrupting UHRF1 degradation at mitotic exit accelerates G1-phase cell cycle progression and perturbs global DNA methylation patterning in the genome. We conclude that APC/C coordinates crosstalk between cell cycle and chromatin regulatory proteins. This has potential consequences in normal cell physiology, where the chromatin environment changes depending on proliferative state, as well as in disease.
Echocardiographic evaluation of normal adult left Ventricular geometry in a Nigerian population.
Authors: ugwuanyi Daniel chimuanya , Eze Joseph chukwuemeka , Uche Chiegwu Hyacienth , Thaddeus Nwagbara Chukwudi , Eze Charles Ugwoke
Published: April 2020

Abstract Background: Differences have shown to exist in some echocardiographic measurements that were attributed to racial, ethnic and gender. This study determined echocardiographic baseline data of normal adult left ventricular (LV) geometry in our locality. Methods: The study was performed on 1,192 apparently healthy adults. Participants below the age of 18 years or those with congenital or acquired cardiac abnormalities and history of long-term regular physical training were excluded. Trans-thoracic echocardiography was performed with Vivid T8 GE dedicated echocardiography machine with probe frequency of 1.7 to 3.2 MHz with integrated electrocardiography (ECG) recording electrodes. The study determined normal dimensions of interventricular diamensions. All measurements were indexed to body surface area (BSA) to obtain echocardiographic baseline normal reference values. Results: The mean + SD values of LV parameters for male and female participants were: LVIDd (44.80 ± 5.71 mm vs 42.75 ± 5.21 mm), LVIDs (33.54 ± 5.37 mm vs 30.38 ± 4.81 mm), and LVPWd (8.32 ± 1.26 mm vs 7.51 ± 1.22 mm). Females had more statistically significant interventricular septum in diastole (IVSd) (8.20 ± 1.38 mm vs 7.05 ± 1.27 mm) and interventricular septum in systole (IVSs) (9.08 ± 1.42 mm vs 8.99 ± 1.33 mm) (P < 0.05). Conclusion: This research established echocardiographic baseline normal adult left ventricular geometry in the study population because in order to detect abnormalities, accurate definition of normal values of echocardiographic measurements is of utmost importance for a reliable clinical decision making. KEYWORDS: Echocardiography, normal values, ventricular geometry, Nnewi Nigeria
Subcellular structure segmentation from cryo-electron tomograms via machine learning
Authors: Zhou Li , Yang Chao , Gao Weiguo , Perciano Talita , Davies Karen M. , Sauter Nicholas K.
Published: April 2020

We describe how to use several machine learning techniques organized in a learning pipeline to segment and identify subcellular structures from cryo electron tomograms. These tomograms are difficult to analyze with traditional segmentation tools. The learning pipeline in our approach starts from supervised learning via a special convolutional neural network trained with simulated data. It continues with semi-supervised reinforcement learning and/or a region merging techniques that try to piece together disconnected components that should belong to the same subcellular structure. A parametric or non-parametric fitting procedure is then used to enhance the segmentation results and quantify uncertainties in the fitting. Domain knowledge is used in generating the training data for the neural network and in guiding the fitting procedure through the use of appropriately chosen priors and constraints. We demonstrate that the approach proposed here work well for extracting membrane surfaces of protein reconstituted liposomes in a cellular environment that contains other artifacts.
Robust survival-based RNAi using in tandem silencing of adenine phosphoribosyltransferase
Authors: Orr Robert G. , Foley Stephen J. , Galotto Giulia , Liu Boyuan , Vidali Luis
Published: April 2020

RNA interference (RNAi) enables flexible and dynamic interrogation of entire gene families or essential genes without the need for exogenous proteins, unlike CRISPR-Cas technology. Unfortunately, isolation of plants undergoing potent gene silencing requires laborious design, visual screening, and physical separation for downstream characterization. Here, we developed a novel APT-based RNAi technology (APTi) inPhyscomitrella patensthat simultaneously improves upon the multiple limitations of current RNAi techniques. APTi exploits the pro-survival output of transiently silencing the APT gene in the presence of 2-fluoradenine, thereby establishing survival itself as a reporter of RNAi. To maximize silencing efficacy of gene targets we created vectors that facilitate insertion of any gene target sequence in tandem with the APT silencing motif. The APTi approach resulted in a homogenous population ofP. patensmutants specific for our gene target, with zero surviving background plants within 8 days. The observed mutants directly corresponded to a maximal 93% reduction of the tested target protein, substantially exceeding previous dsRNA methods. The positive selection nature of APTi represents a fundamental improvement in RNAi technology and will contribute to the growing demand for technologies amenable to high-throughput phenotyping.

One-sentence summary

Generation of dsRNA targeting theAPTgene in tandem with a target gene enables positive selection of strongly silencing plants.
The coordinated localization of mRNA to centrosomes facilitates error-free mitosis
Authors: Ryder Pearl V. , Fang Junnan , Lerit Dorothy A.
Published: April 2020

Centrosomes are microtubule-organizing centers required for error-free mitosis and embryonic development. The microtubule-nucleating activity of centrosomes is conferred by the pericentriolar material (PCM), a composite of numerous proteins subject to cell cycle-dependent oscillations in levels and organization. In diverse cell types, mRNAs localize to centrosomes and may contribute to changes in PCM abundance. Here, we investigate the regulation of mRNA localization to centrosomes in the rapidly cyclingDrosophila melanogasterembryo. We find that RNA localization to centrosomes is regulated during the cell cycle and developmentally. We identify a novel role for the fragile-X mental retardation protein (FMRP), which localizes to pericentrosomal RNA granules, in the post-transcriptional regulation of centrosomal RNA. Further, the mis-targeting of a model centrosomal mRNA,centrocortin(cen), is sufficient to alter cognate protein localization to centrosomes and impair spindle morphogenesis and genome stability.