bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficacy and Safety of Polyherbal formulation as an add-on to the standard of care in mild to moderate COVID-19: A randomized, double-blind, placebo-controlled trial
Authors: Patankar Suresh B. , Rangnekar Hrishikesh , Joshi Kalpana , Suryawanshi Kishor , Soni Pravin , Gorde Anupama , Shah Tejas , Patankar Sagar , Jha Diwakar , Raje Rajesh 
Published: May 2021

ABSTRACTObjectiveTo assess the efficacy and safety of polyherbal formulation (designated as IP) in comparison to placebo as add on to the standard of care (SoC) among patients with mild to moderate novel corona virus disease 2019 (COVID-19)MethodsLaboratory proved patients of mild to moderate COVID-19 disease were randomized to either placebo or IP as an add-on to SoC. Using quantitative reverse transcription-polymerase chain reaction (qRTPCR), we assessed the effect on viral load (VL). Change in immunological parameters such as blood lymphocyte subset, serum immunoglobulin was determined. The clinical improvement was assessed using a numerical rating scale (NRS) and WHO ordinal scale. Patients were followed for 30 days after randomization.ResultsIn total, 72 patients were randomized to either placebo (n=33) and IP (n=39). Fifty-two patients (n=21 in placebo and n=31 in IP arm) had qRT-PCR on day 0 and day 4. There was significant reduction in VL in IP arm (from 662081 copies/mL on day 0 to 48963 copies/mL on day 4; p=0.002)) but not in the placebo arm (from 385670 copies/mL on day 0 to 66845 copies/mL on day 4, p=0.106). Change in the NRS score and WHO ordinal scale score was significant in both treatment arms. However, the difference between the two groups was statistically significant in favour of drug group,. The increase in Th1 response was significant in the IP arm (p=0.023) but not in the placebo arm (p=0.098), thus implying immunomodulatory activity in the drug. No safety concerns were observed in any of the trial participants.ConclusionThis study finds that polyherbal formulation reduces viral load and contributes to immunomodulation and improvement in clinical conditions when used as add-on to the standard care in patients with mild to moderate COVID-19 without any side effects. These findings need to be further confirmed in a large, prospective, randomized study.
A chemotactic sensor controlsSalmonella-host cell interaction
Authors: Hoffmann Stefanie , Gendera Kathrin , Schmidt Christiane , Kirchweger Peter , Imhof Axel , Bogdan Christian , Muller Yves A. , Hensel Michael , Gerlach Roman G. 
Published: May 2021

AbstractIntimate cell contact and subsequent type three secretion system-dependent cell invasion are key steps in host colonization ofSalmonella. Adhesion to complex glycostructures at the apical membrane of polarized cells is mediated by the giant adhesin SiiE. This protein is secreted by a type 1 secretion system (T1SS) and needs to be retained at the bacterial surface to exert its adhesive function. Here, we show that SiiE surface expression was linked to the presence of L-aspartate sensed by theSalmonella-specific methyl-accepting chemotaxis protein CheM. Bacteria lacking CheM were attenuated for invasion of polarized cells, whereas increased invasion was seen withSalmonellaexposed to the non-metabolizable aspartate analog α-methyl-D, L-aspartate (MeAsp). While components of the chemotaxis phosphorelay or functional flagella were dispensable for the increased invasion, CheM directly interacted with proteins associated with the SiiE T1SS arguing for a novel non-canonical signaling mechanism. As a result, CheM attractant signaling caused a shift from secreted to surface-retained and adhesion-competent SiiE. Thus, CheM controls the virulence function of SiiE in a precise spatio-temporal fashion depending on the host micro-milieu.
High-throughput analysis of single human cells reveals the complex nature of DNA replication timing control
Authors: Massey Dashiell J. , Koren Amnon 
Published: May 2021

AbstractDNA replication initiates from replication origins firing throughout S phase. Debate remains about whether origins are a fixed set of loci, or a loose agglomeration of potential sites used stochastically in individual cells, and about how consistent their firing time is. We developed an approach to profile DNA replication from whole-genome sequencing of thousands of single cells, which includes “in silico flow cytometry”, a method for discriminating replicating and non-replicating cells. Using two microfluidic platforms, we analyzed up to 2,437 replicating cells from a single sample. The resolution and scale of the data allow focused analysis of replication initiation sites, demonstrating that most occur in confined genomic regions. While initiation order is remarkably similar across cells, we unexpectedly identify several subtypes of initiation regions in late-replicating regions. Taken together, high throughput, high resolution sequencing of individual cells reveals previously underappreciated variability in replication initiation and progression.
S-Palmitoylation-Dependent Regulation of Cardiomyocyte Rac1 Signaling Activity and Cardiac Hypertrophy
Authors: Brody Matthew J. , Baldwin Tanya A. , Subramani Arasakumar , Kanisicak Onur , Vagnozzi Ronald J. , Molkentin Jeffery D. 
Published: May 2021

ABSTRACTS-palmitoylation is a reversible lipid modification that regulates trafficking, localization, activity, and/or stability of protein substrates by serving as a fatty acid anchor to cell membranes. However, S-palmitoylation-dependent control of signal transduction in cardiomyocytes and its effects on cardiac physiology are not well understood. We performed an in vivo gain-of-function screen of zinc finger Asp-His-His-Cys (zDHHC) family S-acyl transferases that catalyze S-palmitoylation and identified the Golgi-localized enzyme zDHHC3 as a critical regulator of cardiac maladaptation. The closely-related enzyme, zDHHC7, also induced severe cardiomyopathy but this effect was not observed with overexpression of plasma membrane enzyme zDHHC5, endoplasmic reticulum enzyme zDHHC6, or Golgi enzyme zDHHC13. To identify effectors that may underlie zDHHC3-induced cardiomyopathy we performed quantitative site-specific S-acyl proteomics in zDHHC3-overexpressing cells that revealed the small GTPase Rac1 as a novel substrate. We generated cardiomyocyte-specific transgenic mice overexpressing zDHHC3, which develop severe cardiac disease. Cardiomyopathy and congestive heart failure in zDHHC3 transgenic mice are preceded by enhanced S-palmitoylation of Rac1 and induction of additional Rho family small GTPases including RhoA, Cdc42, and the Rho family-specific chaperone RhoGDI. In contrast, transgenic mice overexpressing an enzymatically-dead mutant of zDHHC3 do not exhibit this profound induction of RhoGTPase signaling or develop cardiac disease. Rac1 S-palmitoylation, plasma membrane localization, activity, and downstream hypertrophic signaling were substantially increased in zDHHC3 overexpressing hearts. Taken together, these data suggest inhibition of zDHHC3/7 S-acyl transferase activity at the cardiomyocyte Golgi or disruption of Rac1 S-palmitoylation as novel therapeutic strategies to treat cardiac disease or other diseases associated with enhanced RhoGTPase signaling.
CD147 antibody specifically and effectively inhibits infection and cytokine storm of SARS-CoV-2 variants
Authors: Geng Jiejie , Chen Liang , Yuan Yufeng , Chen Ruo , Wang Ke , Deng Yongqiang , Du Peng , Liu Jiangning , Wu Guizhen , Wang Youchun , Xu Ke , Sun Xiuxuan , Guo Ting , Yang Xu , Wu Jiao , Jiang Jianli , Li Ling , Zhang Jun , Zhang Kui , Zhu Hua , Zheng Zhaohui , Fu Xianghui , Yang Fengfan , Chen Xiaochun , Tang Hao , Zhang Zheng , Wei Ding , Zhang Yang , Shi Ying , Zhu Yumeng , Pei Zhuo , Huo Fei , Chen Shirui , Wang Qingyi , Xie Wen , Li Yirong , Shi Mingyan , Bian Huijie , Zhu Ping , Chen Zhi-Nan 
Published: May 2021

AbstractSARS-CoV-2 and its variants are raging worldwide. Unfortunately, the global vaccination is not efficient enough to attain a vaccine-based herd-immunity and yet no special and effective drug is developed to contain the spread of the disease. Previously we have identified CD147 as a novel receptor for SARS-CoV-2 infection. Here, we demonstrated that CD147 antibody effectively inhibits infection and cytokine storm caused by SARS-CoV-2 variants. In CD147KOVeroE6 cells, infections of SARS-CoV-2, its variants (B.1.1.7, B.1.351) and pseudovirus mutants (B.1.1.7, B.1.351, B.1.525, B.1.526 (S477N), B.1.526 (E484K), P.1, P.2, B.1.617.1, B.1.617.2) were decreased. Meanwhile, CD147 antibody effectively blocked the entry of variants and pseudomutants in VeroE6 cells, and inhibited the expression of cytokines. A model of SARS-CoV-2-infected hCD147 transgenic mice was constructed, which recapitulated the features of exudative diffuse alveolar damage and dynamic immune responses of COVID-19. CD147 antibody could effectively clear the virus and alveolar exudation, resolving the pneumonia. We found the elevated level of cyclophilin A (CyPA) in plasma of severe/critical cases, and identified CyPA as the most important proinflammatory intermediate causing cytokine storm. Mechanistically, spike protein of SARS-CoV-2 bound to CD147 and initiated the JAK-STAT pathway, which induced expression of CyPA. CyPA reciprocally bound to CD147, triggered MAPK pathway and consequently mediated the expression of cytokine and chemokine. In conclusion, CD147 is a critical target for SARS-CoV-2 variants and CD147 antibody is a promising drug to control the new wave of COVID-19 epidemic.
Yin Yang 1 sets up the stage for cerebellar astrocyte maturation
Authors: Mockenhaupt Karli , Tyc Katarzyna M. , McQuiston Adam , Hariprashad Avani , Biswas Debolina D. , Gupta Angela S. , Olex Amy L. , Singh Sandeep K. , Waters Michael R. , Dupree Jeff L. , Dozmorov Mikhail G. , Kordula Tomasz 
Published: May 2021

AbstractDiverse subpopulations of astrocytes tile different brain regions to accommodate local requirements of neurons and associated neuronal circuits. Nevertheless, molecular mechanisms governing astrocyte diversity remain mostly unknown. We explored the role of a zinc finger transcription factor Yin Yang 1 (YY1) that is expressed in astrocytes. We found that specific deletion of YY1 from astrocytes causes severe motor deficits in mice, induces Bergmann gliosis, and results in simultaneous loss of GFAP expression in velate and fibrous cerebellar astrocytes. Single cell RNA-seq analysis showed that YY1 exerts specific effects on gene expression in subpopulations of cerebellar astrocytes. We found that although YY1 is dispensable for the initial stages of astrocyte development, it regulates subtype-specific gene expression during astrocyte maturation. Moreover, YY1 is continuously needed to maintain mature astrocytes in the adult cerebellum. Our findings suggest that YY1 plays critical roles regulating cerebellar astrocyte maturation during development and maintaining a mature phenotype of astrocytes in the adult cerebellum.
Mad1’s ability to interact with Mad2 is essential to regulate and monitor meiotic synapsis in C. elegans
Authors: Devigne Alice , Bhalla Needhi 
Published: May 2021

ABSTRACTMeiotic homolog synapsis is essential to ensure accurate segregation of chromosomes during meiosis. In C. elegans, synapsis and a checkpoint that monitors synapsis relies on the spindle checkpoint components, Mad1 and Mad2, and Pairing Centers (PCs), cis-acting loci that interact with the nuclear envelope to mobilize chromosomes within the nucleus. Here, we show that mutations in some spindle checkpoint mutants affect PC movement early in meiotic prophase, consistent with a link between PC mobility and the regulation of synapsis. Further, we test what specific functions of Mad1 and Mad2 are required to regulate and monitor synapsis. We find that a mutation that abrogates Mad1’s localization to the nuclear periphery abolishes the synapsis checkpoint but has no effect on Mad2’s localization to the nuclear periphery or synapsis. By contrast, a mutation that prevents Mad1’s interaction with Mad2 abolishes the synapsis checkpoint, delays synapsis and fails to localize Mad2 to the nuclear periphery. These data indicate that Mad1’s primary role in regulating synapsis is through control of Mad2 and that Mad2 can bind other factors at the nuclear periphery. We also tested whether Mad2’s ability to adopt a specific conformation associated with its activity during spindle checkpoint function is required for its role in meiosis. A mutation that prevents Mad2 from adopting its active conformer fails to localize to the nuclear periphery, abolishes the synapsis checkpoint and exhibits substantial defects in meiotic synapsis. Thus, Mad2, and its regulation by Mad1, is a major regulator of meiotic synapsis in C. elegans.AUTHOR SUMMARYSexual reproduction relies on production of gametes, such as eggs and sperm, which are produced during meiosis. During this specialized cell division, chromosomes replicate, pair with their homologs, undergo synapsis and finally undergo recombination, all of which are required for correct meiotic chromosome segregation. Chromosomes are highly mobile during these steps in meiosis but the specific role of this mobility is unclear. Here, we show that spindle assembly checkpoint proteins, Mad1 and Bub3, that regulate and monitor meiotic synapsis are implicated in chromosome movement, solidifying the functional link between chromosome mobility and synapsis. Moreover, we provide additional data that another spindle checkpoint effector, Mad2, and its regulation by Mad1, plays an important role in regulating meiotic synapsis.
Two microbiota subtypes identified in Irritable Bowel Syndrome with distinct responses to the low-FODMAP diet
Authors: Vervier Kevin , Moss Stephen , Kumar Nitin , Adoum Anne , Barne Meg , Browne Hilary , Kaser Arthur , Kiely Chris , Neville Anne , Powell Nina , Raine Tim , Stares Mark D. , Zhu Ana , De La Revilla Negro Juan , Lawley Trevor , Parkes Miles 
Published: May 2021

ABSTRACTObjectiveReducing FODMAPs can be clinically beneficial in IBS but the mechanism is poorly understood. We aimed to detect microbial signatures that might predict response to the low FODMAP diet and assess whether microbiota compositional and functional shifts could provide insights into its mode of action.DesignWe used metagenomics to determine high-resolution taxonomic and functional profiles of the stool microbiota from IBS cases and household controls (n=56 pairs) on their usual diet. Clinical response and microbiota changes were studied in 41 pairs after 4 weeks on a low FODMAP diet.ResultsUnsupervised analysis of baseline IBS cases pre-diet identified two distinct microbiota profiles, which we refer to as IBSP(pathogenic-like) and IBSH(health-like) subtypes. IBSPmicrobiomes were enriched in Firmicutes and genes for amino acid and carbohydrate metabolism, but depleted in Bacteroidetes species. IBSHmicrobiomes were similar to controls. On the low FODMAP diet IBSHand control microbiota were unaffected, but the IBSPsignature shifted towards a health-associated microbiome with an increase in Bacteroidetes (p=0.009), a decrease in Firmicutes species (p=0.004) and normalization of primary metabolic genes. The clinical response to the low FODMAP diet was greater in IBSPsubjects compared to IBSH(p = 0.02).Conclusion50% of IBS cases manifested a ‘pathogenic’ gut microbial signature. This shifted towards the healthy profile on the low FODMAP diet; and IBSPcases showed an enhanced clinical responsiveness to the dietary therapy. The effectiveness of FODMAP exclusion in IBSPmay result from the alterations in gut microbiota and metabolites produced. Microbiota signatures could be useful as biomarkers to guide IBS treatment; and investigating IBSPspecies and metabolic pathways might yield insights regarding IBS pathogenic mechanisms.Significance of this studyWhat is already known on this subject?IBS subjects often respond to a low FODMAP diet.The gut microbiota has been implicated in IBS.The microbiota in IBS subjects may change with diet.What are the new findings?We were able to stratify patients with IBS according to their gut microbiota species and metabolic gene signatures.We identified a distinct gut microbiota subtype with an enhanced clinical response to a low FODMAP diet compared to other IBS subjects.How might it impact on clinical practice in the foreseeable future?The potential development of a microbiota signature as a biomarker to manage IBS cases with a low FODMAP diet recommendation.If the bacteria represented in the IBSPsubtype are shown to play a pathogenic role in IBS, perhaps through the metabolic activity this provides a target for new therapies and an intermediate phenotype by which to assess them.
Elucidating the correlation between the number of TTTTGAT heptamer repeats and cholera toxin promoter activity in Vibrio cholerae O1 pandemic strains
Authors: Naha Arindam , Withey Jeffrey H. , Mukherjee Piyali , Saha Rudra Narayan , Samanta Prosenjit , Ghosh Amit , Miyoshi Shin-ichi , Dutta Shanta , Mukhopadhyay Asish K. 
Published: May 2021

ABSTRACTA complex regulatory cascade controls expression of the cholera toxin genes (ctxAB) in Vibrio cholerae; which eventually leads to choleragen (CT) production and secretion, resulting in rice watery diarrhoea. The cholera toxin promoter (PctxAB) contains a series of heptad repeats (5’-TTTTGAT-3’); which have been previously shown to play crucial role in ctxAB transcriptional regulation by recruiting the transcriptional activators ToxT, ToxR, and the nucleoid-associated protein H-NS along the ctx promoter. The numbers of these repeats vary between the two biotypes of V. cholerae O1 strains, and even among strains of the same biotype. In this study, we examined PctxAB activation of V. cholerae O1 pandemic strains to understand the significance of the distal heptad repeats in regulating ctx expression. Interestingly, we found that ctx activation may depend on the number of TTTTGAT heptad repeats within PctxAB, and we posit that the occupation of the distal repeats by H-NS could further prevent transcriptional activation of ctx genes in V. cholerae. We hypothesize that ToxT-dependent transcriptional activation may not require entire displacement of H-NS and propose a revision in the currently accepted model of ToxT dependent PctxAB transcriptional activation.IMPORTANCECT production by pathogenic V. cholerae O1 strains is regulated through the transcriptional silencing of CTX promoter by H-NS and counter repression by ToxT. The highly AT rich PctxAB is composed of the tandem repeats 5□ TTTTGAT 3□; the numbers of which differ among the classical and El Tor biotypes. However, it is still not very clear whether the numbers of these repeats could be correlated with promoter activation of the ctx operon. Here we report the role of the distal repeats in ctxAB expression levels. We demonstrate that PctxAB activation changes with the number of the heptad repats within the core promoter element, thereby suggesting a model for ctx regulation in the toxigenic strains of V. cholerae.
Elimination Of Aberrantly Specified Cell Clones Is Independent Of Interfacial Myosin II Accumulation
Authors: Klipa Olga , Hamaratoglu Fisun 
Published: May 2021

ABSTRACTSpatial organization of differently fated cells within an organ is essential and needs to be maintained during development. This is largely implemented via compartment boundaries that serve as barriers between distinct cell types. Biased accumulation of junctional non-muscle Myosin II along the interface between differently fated groups of cells contributes to boundary integrity and maintains its shape via increased tension [1-4]. Here we test whether interfacial Myosin driven tension is responsible for the elimination of aberrantly specified cells that would otherwise compromise compartment organization. To this end, we genetically reduce Myosin II levels in three different patterns: in both wild-type and misspecified cells, only in misspecified cells and specifically at the interface between wild-type and aberrantly specified cells. We find that recognition and elimination of aberrantly specified cells do not rely on tensile forces driven by interfacial Myosin cables. Moreover, apical constriction of misspecified cells and their separation from wild type neighbors occurs even when Myosin level is greatly reduced. Thus, we conclude that the forces that drive elimination of aberrantly specified cells are largely independent of Myosin II.
Human cytomegalovirus protein RL1 degrades the antiviral factor SLFN11 via recruitment of the CRL4 E3 ubiquitin ligase complex
Authors: Nightingale Katie , Fielding Ceri A. , Zerbe Cassie , Hunter Leah , Potts Martin , Fletcher-Etherington Alice , Nobre Luis , Wang Eddie C.Y. , Strang Blair L. , Houghton Jack , Antrobus Robin , Suarez Nicolas M. , Nichols Jenna , Davison Andrew J. , Stanton Richard J. , Weekes Michael P. 
Published: May 2021

AbstractHuman cytomegalovirus (HCMV) is an important human pathogen and a paradigm of viral immune evasion, targeting intrinsic, innate and adaptive immunity. We have employed two novel, orthogonal multiplexed tandem mass tag-based proteomic screens to identify host proteins downregulated by viral factors expressed during the latest phases of viral infection. This approach revealed that the HIV-1 restriction factor Schlafen-11 (SLFN11) was degraded by the poorly characterised, late-expressed HCMV protein RL1, via recruitment of the Cullin4-RING E3 Ubiquitin Ligase (CRL4) complex. SLFN11 potently restricted HCMV infection, inhibiting the formation and spread of viral plaques. Overall, we show that a restriction factor previously thought only to inhibit RNA viruses additionally restricts HCMV. We define the mechanism of viral antagonism and also describe an important resource for revealing additional molecules of importance in antiviral innate immunity and viral immune evasion.Significance StatementPrevious proteomic analyses of host factors targeted for downregulation by HCMV have focused on early or intermediate stages of infection. Using multiplexed proteomics, we have systematically identified viral factors that target each host protein downregulated during the latest stage of infection, after the onset of viral DNA replication. Schlafen-11 (SLFN11), an interferon-stimulated gene and restriction factor for retroviruses and certain RNA viruses, potently restricted HCMV infection. Our discovery that the late-expressed HCMV protein RL1 targets SLFN11 for proteasomal degradation provides the first evidence for a viral antagonist of this critical cellular protein. We therefore redefine SLFN11 as an important factor that targets DNA viruses as well as RNA viruses, offering novel therapeutic potential via molecules that inhibit RL1-mediated SLFN11 degradation.