scholarly journals Mr.Vc: a database of microarray and RNA-seq of Vibrio cholerae

Database ◽  
2019 ◽  
Vol 2019 ◽  
Author(s):  
Zhiyuan Zhang ◽  
Guozhong Chen ◽  
Jun Hu ◽  
Wajid Hussain ◽  
Fenxia Fan ◽  
...  
Keyword(s):  
Vibrio Cholerae ◽  
Diarrheal Disease ◽  
Gene Annotation ◽  
Relevant Information ◽  
Differentially Expressed ◽  
Data Repository ◽  
Rna Seq ◽  
Experimental Conditions ◽  
Life Threatening ◽  
Infectious Cycle

AbstractGram-negative bacterium Vibrio cholerae is the causative agent of cholera, a life-threatening diarrheal disease. During its infectious cycle, V. cholerae routinely switches niches between aquatic environment and host gastrointestinal tract, in which V. cholerae modulates its transcriptome pattern accordingly for better survival and proliferation. A comprehensive resource for V. cholerae transcriptome will be helpful for cholera research, including prevention, diagnosis and intervention strategies. In this study, we constructed a microarray and RNA-seq database of V. cholerae (Mr.Vc), containing gene transcriptional expression data of 145 experimental conditions of V. cholerae from various sources, covering 25 937 entries of differentially expressed genes. In addition, we collected relevant information including gene annotation, operons they may belong to and possible interaction partners of their protein products. With Mr.Vc, users can easily find transcriptome data they are interested in, such as the experimental conditions in which a gene of interest was differentially expressed in, or all genes that were differentially expressed in an experimental condition. We believe that Mr.Vc database is a comprehensive data repository dedicated to V. cholerae and could be a useful resource for all researchers in related fields. Mr.Vc is available for free at http://bioinfo.life.hust.edu.cn/mrvc.

scholarly journals The Sodium-Driven Flagellar Motor Controls Exopolysaccharide Expression in Vibrio cholerae

2004 ◽  
Vol 186 (15) ◽  
pp. 4864-4874 ◽  
Author(s):  
Crystal M. Lauriano ◽  
Chandradipa Ghosh ◽  
Nidia E. Correa ◽  
Karl E. Klose
Keyword(s):  
Vibrio Cholerae ◽  
Gene Transcription ◽  
Biofilm Formation ◽  
Diarrheal Disease ◽  
Response Regulator ◽  
Gene Clusters ◽  
Signaling Cascade ◽  
Genes Encoding ◽  
Life Threatening

ABSTRACT Vibrio cholerae causes the life-threatening diarrheal disease cholera. This organism persists in aquatic environments in areas of endemicity, and it is believed that the ability of the bacteria to form biofilms in the environment contributes to their persistence. Expression of an exopolysaccharide (EPS), encoded by two vps gene clusters, is essential for biofilm formation and causes a rugose colonial phenotype. We previously reported that the lack of a flagellum induces V. cholerae EPS expression. To uncover the signaling pathway that links the lack of a flagellum to EPS expression, we introduced into a rugose flaA strain second-site mutations that would cause reversion back to the smooth phenotype. Interestingly, mutation of the genes encoding the sodium-driven motor (mot) in a nonflagellated strain reduces EPS expression, biofilm formation, and vps gene transcription, as does the addition of phenamil, which specifically inhibits the sodium-driven motor. Mutation of vpsR, which encodes a response regulator, also reduces EPS expression, biofilm formation, and vps gene transcription in nonflagellated cells. Complementation of a vpsR strain with a constitutive vpsR allele likely to mimic the phosphorylated state (D59E) restores EPS expression and biofilm formation, while complementation with an allele predicted to remain unphosphorylated (D59A) does not. Our results demonstrate the involvement of the sodium-driven motor and suggest the involvement of phospho-VpsR in the signaling cascade that induces EPS expression. A nonflagellated strain expressing EPS is defective for intestinal colonization in the suckling mouse model of cholera and expresses reduced amounts of cholera toxin and toxin-coregulated pili in vitro. Wild-type levels of virulence factor expression and colonization could be restored by a second mutation within the vps gene cluster that eliminated EPS biosynthesis. These results demonstrate a complex relationship between the flagellum-dependent EPS signaling cascade and virulence.

scholarly journals Characterization of the Immune Response to Vibrio cholerae Infection in a Natural Host Model

2021 ◽  
Vol 11 ◽  
Author(s):  
Dustin A. Farr ◽  
Dhrubajyoti Nag ◽  
Jeffrey H. Withey
Keyword(s):  
Immune Response ◽  
Vibrio Cholerae ◽  
Diarrheal Disease ◽  
Natural Host ◽  
Zebrafish Model ◽  
Mucin Production ◽  
Immunological Markers ◽  
Contaminated Food ◽  
Life Threatening ◽  
El Tor

The gram-negative bacterium Vibrio cholerae causes the life-threatening diarrheal disease cholera, which is spread through the ingestion of contaminated food or water. Cholera epidemics occur largely in developing countries that lack proper infrastructure to treat sewage and provide clean water. Numerous vertebrate fish species have been found to be natural V. cholerae hosts. Based on these findings, zebrafish (Danio rerio) have been developed as a natural host model for V. cholerae. Diarrheal symptoms similar to those seen in humans are seen in zebrafish as early as 6 hours after exposure. Our understanding of basic zebrafish immunology is currently rudimentary, and no research has been done to date exploring the immune response of zebrafish to V. cholerae infection. In the present study, zebrafish were infected with either pandemic El Tor or non-pandemic, environmental V. cholerae strains and select immunological markers were assessed to determine cellular immunity and humoral immunity. Significant increases in the gene expression of two transcription factors, T-bet and GATA3, were observed in response to infection with both V. cholerae strains, as were levels of mucosal related antibodies. Additionally, the cytokine IL-13 was shown to be significantly elevated and paralleled the mucin output in zebrafish excretions, strengthening our knowledge of IL-13 induced mucin production in cholera. The data presented here further solidify the relevancy of the zebrafish model in studying V. cholerae, as well as expanding its utility in the field of cholera immunology.

scholarly journals FINDER: An automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences

2021 ◽  
Author(s):  
Sagnik Banerjee ◽  
Priyanka Bhandary ◽  
Margaret Woodhouse ◽  
Taner Z. Sen ◽  
Roger P. Wise ◽  
...  
Keyword(s):  
Gene Annotation ◽  
Gene Prediction ◽  
Active Regions ◽  
Expression Data ◽  
Rna Seq ◽  
Experimental Conditions ◽  
Eukaryotic Genes ◽  
Associated Proteins ◽  
Gene Structures ◽  
Automated Software

AbstractBackgroundGene annotation in eukaryotes is a non-trivial task that requires meticulous analysis of accumulated transcript data. Challenges include transcriptionally active regions of the genome that contain overlapping genes, genes that produce numerous transcripts, transposable elements and numerous diverse sequence repeats. Currently available gene annotation software applications depend on pre-constructed full-length gene sequence assemblies which are not guaranteed to be error-free. The origins of these sequences are often uncertain, making it difficult to identify and rectify errors in them. This hinders the creation of an accurate and holistic representation of the transcriptomic landscape across multiple tissue types and experimental conditions. Therefore, to gauge the extent of diversity in gene structures, a comprehensive analysis of genome-wide expression data is imperative.ResultsWe present FINDER, a fully automated computational tool that optimizes the entire process of annotating genes and transcript structures. Unlike current state-of-the-art pipelines, FINDER automates the RNA-Seq pre-processing step by working directly with raw sequence reads and optimizes gene prediction from BRAKER2 by supplementing these reads with associated proteins. The FINDER pipeline (1) reports transcripts and recognizes genes that are expressed under specific conditions, (2) generates all possible alternatively spliced transcripts from expressed RNA-Seq data, (3) analyzes read coverage patterns to modify existing transcript models and create new ones, and (4) scores genes as high- or low-confidence based on the available evidence across multiple datasets. We demonstrate the ability of FINDER to automatically annotate a diverse pool of genomes from eight species.ConclusionsFINDER takes a completely automated approach to annotate genes directly from raw expression data. It is capable of processing eukaryotic genomes of all sizes and requires no manual supervision – ideal for bench researchers with limited experience in handling computational tools.

scholarly journals A Combination of Metagenomic and Cultivation Approaches Reveals Hypermutator Phenotypes within Vibrio cholerae-Infected Patients

mSystems ◽  
2021 ◽  
Author(s):  
Inès Levade ◽  
Ashraful I. Khan ◽  
Fahima Chowdhury ◽  
Stephen B. Calderwood ◽  
Edward T. Ryan ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Whole Genome Sequencing ◽  
Vibrio Cholerae ◽  
Genome Sequencing ◽  
Diarrheal Disease ◽  
Asymptomatic Infection ◽  
Whole Genome ◽  
Metagenomic Sequencing ◽  
Content Type ◽  
Life Threatening

Pathogen evolution within patients can impact phenotypes such as drug resistance and virulence, potentially affecting clinical outcomes. V. cholerae infection can result in life-threatening diarrheal disease or asymptomatic infection. Here, we describe whole-genome sequencing of V. cholerae isolates and culture-free metagenomic sequencing from stool of symptomatic cholera patients and asymptomatic carriers.

scholarly journals Role of Zooplankton Diversity in Vibrio cholerae Population Dynamics and in the Incidence of Cholera in the Bangladesh Sundarbans

2011 ◽  
Vol 77 (17) ◽  
pp. 6125-6132 ◽  
Author(s):  
Guillaume Constantin de Magny ◽  
Pronob K. Mozumder ◽  
Christopher J. Grim ◽  
Nur A. Hasan ◽  
M. Niamul Naser ◽  
...  
Keyword(s):  
Population Dynamics ◽  
Vibrio Cholerae ◽  
Diarrheal Disease ◽  
Ecological Factors ◽  
Crustacean Zooplankton ◽  
Content Type ◽  
Life Threatening ◽  
Bodies Of Water ◽  
Zooplankton Communities

ABSTRACTVibrio cholerae, a bacterium autochthonous to the aquatic environment, is the causative agent of cholera, a severe watery, life-threatening diarrheal disease occurring predominantly in developing countries.V. cholerae, including both serogroups O1 and O139, is found in association with crustacean zooplankton, mainly copepods, and notably in ponds, rivers, and estuarine systems globally. The incidence of cholera and occurrence of pathogenicV. choleraestrains with zooplankton were studied in two areas of Bangladesh: Bakerganj and Mathbaria. Chitinous zooplankton communities of several bodies of water were analyzed in order to understand the interaction of the zooplankton population composition with the population dynamics of pathogenicV. choleraeand incidence of cholera. Two dominant zooplankton groups were found to be consistently associated with detection ofV. choleraeand/or occurrence of cholera cases, namely, rotifers and cladocerans, in addition to copepods. Local differences indicate there are subtle ecological factors that can influence interactions betweenV. cholerae, its plankton hosts, and the incidence of cholera.

scholarly journals VCGIDB: A Database and Web Resource for the Genomic Islands from Vibrio cholerae

Pathogens ◽  
2019 ◽  
Vol 8 (4) ◽  
pp. 261
Author(s):  
YoungJae Hur ◽  
Mauricio Chalita ◽  
Sung-min Ha ◽  
Inwoo Baek ◽  
Jongsik Chun
Keyword(s):  
Vibrio Cholerae ◽  
Genomic Island ◽  
Diarrheal Disease ◽  
Prediction Method ◽  
Genomic Islands ◽  
Large Genome ◽  
Web Resource ◽  
Comprehensive Information ◽  
The World ◽  
Life Threatening

Vibrio cholerae is the causative agent of cholera, which is a severe, life-threatening diarrheal disease. The current seventh pandemic has not been eradicated and the outbreak is still ongoing around the world. The evolution of the pandemic-causing strain has been greatly influenced by lateral gene transfer, and the mechanisms of acquisition of pathogenicity in V. cholerae are mainly involved with genomic islands (GIs). Thus, detecting GIs and their comprehensive information is necessary to understand the continuing resurgence and newly emerging pathogenic V. cholerae strains. In this study, 798 V. cholerae strains were tested using the GI-Scanner algorithm, which was developed to detect candidate GIs and identify them in a comparative genomics approach. The algorithm predicted 435 highly possible genomic islands, and we built a database, called Vibrio cholerae Genomic Island Database (VCGIDB). This database shows advanced results that were acquired from a large genome set using phylogeny-based predictions. Moreover, VCGIDB is a highly expendable database that does not require intensive computation, which enables us to update it with a greater number of genomes using a novel genomic island prediction method. The VCGIDB website allows the user to browse the data and presents the results in a visual manner.

scholarly journals Joint between-sample normalization and differential expression detection through ℓ0-regularized regression

2019 ◽  
Vol 20 (S16) ◽  
Author(s):  
Kefei Liu ◽  
Li Shen ◽  
Hui Jiang
Keyword(s):  
Differential Expression ◽  
Fundamental Problem ◽  
Large Fraction ◽  
Differential Expression Analysis ◽  
Specific Antigen ◽  
Differentially Expressed ◽  
Detection Accuracy ◽  
Continuous Variables ◽  
Rna Seq ◽  
Experimental Conditions

Abstract Background A fundamental problem in RNA-seq data analysis is to identify genes or exons that are differentially expressed with varying experimental conditions based on the read counts. The relativeness of RNA-seq measurements makes the between-sample normalization of read counts an essential step in differential expression (DE) analysis. In most existing methods, the normalization step is performed prior to the DE analysis. Recently, Jiang and Zhan proposed a statistical method which introduces sample-specific normalization parameters into a joint model, which allows for simultaneous normalization and differential expression analysis from log-transformed RNA-seq data. Furthermore, an ℓ0 penalty is used to yield a sparse solution which selects a subset of DE genes. The experimental conditions are restricted to be categorical in their work. Results In this paper, we generalize Jiang and Zhan’s method to handle experimental conditions that are measured in continuous variables. As a result, genes with expression levels associated with a single or multiple covariates can be detected. As the problem being high-dimensional, non-differentiable and non-convex, we develop an efficient algorithm for model fitting. Conclusions Experiments on synthetic data demonstrate that the proposed method outperforms existing methods in terms of detection accuracy when a large fraction of genes are differentially expressed in an asymmetric manner, and the performance gain becomes more substantial for larger sample sizes. We also apply our method to a real prostate cancer RNA-seq dataset to identify genes associated with pre-operative prostate-specific antigen (PSA) levels in patients.

scholarly journals FINDER: an automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Sagnik Banerjee ◽  
Priyanka Bhandary ◽  
Margaret Woodhouse ◽  
Taner Z. Sen ◽  
Roger P. Wise ◽  
...  
Keyword(s):  
Gene Annotation ◽  
Gene Prediction ◽  
Active Regions ◽  
Expression Data ◽  
Rna Seq ◽  
Experimental Conditions ◽  
Eukaryotic Genes ◽  
Associated Proteins ◽  
Gene Structures ◽  
Automated Software

Abstract Background Gene annotation in eukaryotes is a non-trivial task that requires meticulous analysis of accumulated transcript data. Challenges include transcriptionally active regions of the genome that contain overlapping genes, genes that produce numerous transcripts, transposable elements and numerous diverse sequence repeats. Currently available gene annotation software applications depend on pre-constructed full-length gene sequence assemblies which are not guaranteed to be error-free. The origins of these sequences are often uncertain, making it difficult to identify and rectify errors in them. This hinders the creation of an accurate and holistic representation of the transcriptomic landscape across multiple tissue types and experimental conditions. Therefore, to gauge the extent of diversity in gene structures, a comprehensive analysis of genome-wide expression data is imperative. Results We present FINDER, a fully automated computational tool that optimizes the entire process of annotating genes and transcript structures. Unlike current state-of-the-art pipelines, FINDER automates the RNA-Seq pre-processing step by working directly with raw sequence reads and optimizes gene prediction from BRAKER2 by supplementing these reads with associated proteins. The FINDER pipeline (1) reports transcripts and recognizes genes that are expressed under specific conditions, (2) generates all possible alternatively spliced transcripts from expressed RNA-Seq data, (3) analyzes read coverage patterns to modify existing transcript models and create new ones, and (4) scores genes as high- or low-confidence based on the available evidence across multiple datasets. We demonstrate the ability of FINDER to automatically annotate a diverse pool of genomes from eight species. Conclusions FINDER takes a completely automated approach to annotate genes directly from raw expression data. It is capable of processing eukaryotic genomes of all sizes and requires no manual supervision—ideal for bench researchers with limited experience in handling computational tools.

scholarly journals A Review on Diagnostic Methods for the Identification of Vibrio cholerae

2020 ◽  
pp. 136-164
Author(s):  
Tarh, Jacqueline Ebob
Keyword(s):  
Vibrio Cholerae ◽  
Diarrheal Disease ◽  
Variable Number Tandem Repeat ◽  
Simultaneous Detection ◽  
Diagnostic Methods ◽  
Cholerae Strain ◽  
Low Resource Settings ◽  
Remote Areas ◽  
Low Resource ◽  
Life Threatening

The severe diarrheal disease Cholera, has gained public health importance because of its life-threatening effect. The detection of the causative agent of this disease (Vibrio cholerae (V.  Cholerae) O1 or O139) from a specimen (stool, vomitus of food sample) remains a major concern in the world today. Phenotypic finger printing (the conventional methods) of the toxigenic V. cholerae strain, remains the gold standard for the laboratory diagnosis of cholera; especially during cholera epidemic outbreaks. Detection around the remote areas which are usually rampaged by these outbreaks is usually difficult due to lack of required diagnostic facilities in small laboratories. However, the use of phenotypic approaches have some major setbacks as they are usually labor-intensive and time consuming. This delays treatment commencement especially in life threatening cases.To alleviate these setbacks, rapid molecular typing techniques involving the Polymerase chain reaction (PCR) amplification, hybridization methods, Pulsed Field Gel Electrophoresis (PFGE), Multilocus Sequence Typing (MLST), Multiple-Locus Variable Number Tandem Repeat Analysis (MVLA), Fluorescent Amplified Fragment Length Polymorphism (FAFLP),  Whole Genome Sequencing (WGS) etc. represent promising tools for early detection of the pathogen V. cholerae O1/O139 even in remote areas where laboratory resources are poor. Immunoassay-based techniques like enzyme-linked immune-sorbent assay (ELISA), coagglutination, immunofluorescence, and quartz crystal microbalance (QCM), are capital/labour intensive and expensive for low resource settings. Rapid diagnostic tests based on immune-chromatography principle have also been developed for simultaneous detection of V. choleraesero groups O1 and O139. These test kits are easy to use, transport, and fast. All these methods enable the subtyping of unrelated bacterial strains and they all operate with different accuracies, discriminatory ability, and reproducibility. This review sought to address some of the methods used in diagnosing the disease cholera, with the objective of identifying the best and easiest of the methods that can help to curb the cholera problem (deaths) often encountered, especially in low resource settings in the developing countries (Nigeria inclusive).

In vivo Production of Soluble Inorganic Pyrophosphatases in Two Strains of Vibrio cholerae

1970 ◽  
Vol 24 (1) ◽  
pp. 38-41
Author(s):  
Taslima Taher Lina ◽  
Mohammad Ilias
Keyword(s):  
Vibrio Cholerae ◽  
Specific Activity ◽  
Experimental Conditions ◽  
Environmental Strain ◽  
Cell Extracts ◽  
Atcc Strain ◽  
The Family ◽  
Effects Of Ph ◽  
Vibrio Cholerae O1

The in vivo production of soluble inorganic pyrophosphatases (PPases) was investigated in two strains, namely, Vibrio cholerae EM 004 (environmental strain) and Vibrio cholerae O1 757 (ATCC strain). V. cholerae is known to contain both family I and family II PPase coding sequences. The production of family I and family II PPases were determined by measuring the enzyme activity in cell extracts. The effects of pH, temperature, salinity of the growth medium on the production of soluble PPases were studied. In case of family I PPase, V. cholerae EM 004 gave the highest specific activity at pH 9.0, with 2% NaCl + 0.011% NaF and at 37°C. The strain V. cholerae O1 757 gave the highest specific activity at pH 9.0, with media containing 0% NaCl and at 37°C. On the other hand, under all the conditions family II PPase did not give any significant specific activity, suggesting that the family II PPase was not produced in vivo in either strains of V. cholerae under different experimental conditions. Keywords: Vibrio cholerae, Pyrophosphatases (PPases), Specific activityDOI: http://dx.doi.org/10.3329/bjm.v24i1.1235 Bangladesh J Microbiol, Volume 24, Number 1, June 2007, pp 38-41

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