Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comparative transcriptomics of Burkholderia pseudomallei from soil media and infected host

ABSTRACT: Burkholderia pseudomallei can adapt to and thrive in a variety of environments, including soil and water, and also can infect different hosts, including humans, leading to the tropical disease melioidosis. Modulation of gene and protein expression is one of this pathogen's adaptive survival mechanisms, which could lead to changes in the bacteria's cell membrane, metabolism, and virulence. To better understand bacterial adaptation and host-pathogen interactions, this study compared the expression profiles of B. pseudomallei from infected mice to B. pseudomallei cultivated in soil extract media. B. pseudomallei in vivo was created by infecting mice through the intraperitoneal route and harvesting the spleens on day 5 post infection. Total RNA was isolated and sequenced from the harvested spleen. Sequence reads were mapped to the B. pseudomallei UKMD286 strain genome sequence.

INSTRUMENT(S): Illumina HiSeq 4000

ORGANISM(S): Burkholderia pseudomallei

SUBMITTER: Ahmad Kamal Ghazali

PROVIDER: E-MTAB-11200 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Infection with Burkholderia pseudomallei – immune correlates of survival in acute melioidosis

Project description:Melioidosis is a neglected tropical disease caused by the Gram-negative bacterium Burkholderia pseudomallei. It is widespread in Southeast Asia and under-reported across tropical regions worldwide. Patients present with a range of clinical syndromes including sepsis, pneumonia and focal abscesses, with a mortality rate of 40% in hospitalized patients in Thailand. Up to two-thirds of patients with melioidosis have diabetes mellitus. In this experiment we sought to characterize pathways activated by whole killed B. pseudomallei bacteria and by three vaccine candidate proteins from B. pseudomallei, BPSL2520 (uncharacterized protein), BPSS1525 (BopE) and BPSL2096 (AhpC) in patients with diabetes and acute melioidosis.

2017-09-22 | E-MTAB-6093 | biostudies-arrayexpress

Identification of Novel Virulence-related Genes in Burkholderia pseudomallei by Comparing Gene Expression Profiles in Two Mice Model Through Microarray

Project description:The gene expression profiles were investigated and compared in spleen, lungs and liver of susceptible (BALB/c) and resistant (C57BL/6) hosts to identify genes participated in survival and virulence functions encoded in the B. pseudomallei genome. Subsequently, genes with unknown function and located with virulence gene clusters or suspected to be transcription regulator were selected for a novel virulence gene investigation DNA microarray was used to compare gene expression profiles of B. pseudomallei 1909a in spleen, lung and liver of infection-susceptible BALB/c mice (Th2 prototype) and infection-resistant C57BL/6 mice, (Th1 prototype) during an acute infection. The gene expression profile of B. pseudomallei in culture medium at mid-log phase was used to identify genes that expressed higher or lower in vivo when compared to the in vitro gene profile KEYWORDS: Gene expression

2014-09-12 | E-GEOD-51369 | biostudies-arrayexpress

The Condition-Dependent Transcriptional Landscape of Burkholderia pseudomallei

Project description:Bacterial transcriptomes are dynamic, context-specific and condition-dependent. Infection by the soil bacterium, Burkholderia pseudomallei, causes melioidosis, an often fatal infectious disease of humans and animals. Possessing a large multi-chromosomal genome, B. pseudomallei is able to persist and survive in a multitude of environments. To obtain a comprehensive overview of B. pseudomallei expressed transcripts, we initiated whole-genome transcriptome profiling covering a broad spectrum of conditions and exposures M-bM-^@M-^S a so-called M-bM-^@M-^\condition compendiumM-bM-^@M-^]. Using the compendium, we confirmed many previously-annotated genes and operons, and also identified hundreds of novel transcripts including anti-sense transcripts and non-coding RNAs. By systematically examining genes exhibiting highly similar expression patterns, we ascribed putative functions to previously uncharacterized genes, and identified novel regulatory elements controlling these expression patterns. We also used the compendium to elucidate candidate virulence pathways associated with quorum-sensing and infection in mice. Our study showcases the power of a B. pseudomallei condition compendium as a valuable resource for understanding microbial physiology and the pathogenesis of melioidosis. The transcriptome profiles of Bp exposed to 82 conditions were captured using a custom-designed tiling microarray and compiled into a compendium revealing novel genomic features and co-expression network.

2013-09-12 | E-GEOD-43205 | biostudies-arrayexpress

Transcription profiling of human cell line THP-1 cells exposed to Daboiatoxin and cytokines involved in melioidosis caused by B. pseudomalli

Project description:Gene expression profiles of human cell (THP-1) lines exposed to a novel Daboiatoxin (DbTx) isolated from Daboia russelli russelli, and specific cytokines and inflammatory pathways involved in acute infection caused by Burkholderia pseudomallei. Experiment Overall Design: 1. Group I:- Human monocytic macrophage (THP-1) cell lines grown in the culture medium without any bacterial infection served as untreated control group (Three Biological Replicates). Experiment Overall Design: 2. Group II:- THP-1 cells were infected with Burkholderia pseudomallei (A600 nm = OD 0.6, ~5 x 107 cfu/ml) for 24h served as a disease control group (Three Biological Replicates). Experiment Overall Design: 3. Group III:- THP-1 cells were infected with B. pseudomallei and treated with Daboiatoxin (0.5 mM) isolated from Daboia russelli russelli venom served as a treatment group (Three Biological Replicates). Experiment Overall Design: 4. Group IV:- THP-1 cells were infected with B. pseudomallei (A600 nm = OD 0.6, ~5 x 107 cfu/ml) treated with standard antimicrobial drug ceftazidime (10mg/ml) served as a drug control (Three Biological Replicates). Experiment Overall Design: 5. Group V:- THP-1 cells were exposed to Daboiatoxin (0.5 mM) without bacterial infection (Three Biological Replicates).

2009-04-04 | E-GEOD-7577 | biostudies-arrayexpress

Mouse Macrophage Cells: Control vs. Burkholderia pseudomallei infected cells

Project description:Transcriptional profiling of mouse macrophage cells comparing control untreated cells with macrophage cells infected with Burkeholderia pseudomallei. Goal was to determine the effects of bacterial infection on global macrophage gene expression. Two-condition experiment, macrophage vs. infected macrophage cells.

2011-07-14 | E-GEOD-30642 | biostudies-arrayexpress

B. pseudomallei K96243 genome: Control vs. B. pseudomallei environmental or clinical isolates

Project description:To use whole genome microarrays to compare the differences in genome contents of 5 B. pseudomallei isolated from clinical specimens and environmental sample with B. pseudomallei K96243 reference strain and reveals variable patterns of Genomic Islands (GIs) Keywords: Comparative genomic hybridization DNA microarrays were used to compare genome of clinical and environmental B. pseudomallei isolates with B. pseudomallei K96243 reference strain (B. pseudomallei K96243 vs. B. pseudmallei isolates). Each hybridization was used for comparison between B. pseudomallei K96243 as a reference strain with environmental isolate BP45s, environmental isolate BP28L, clinical isolate H307, clinical isolate P54, clinical isolate P82. Two replicate per array. Multiple hits with 90-99.99 % identity correspond to other locus are replicate of their genes were averaged and analyzed.

2012-07-30 | E-GEOD-19558 | biostudies-arrayexpress

The Condition-Dependent Transcriptional Landscape of Burkholderia pseudomallei

Project description:Bacterial transcriptomes are dynamic, context-specific and condition-dependent. Infection by the soil bacterium, Burkholderia pseudomallei, causes melioidosis, an often fatal infectious disease of humans and animals. Possessing a large multi-chromosomal genome, B. pseudomallei is able to persist and survive in a multitude of environments. To obtain a comprehensive overview of B. pseudomallei expressed transcripts, we initiated whole-genome transcriptome profiling covering a broad spectrum of conditions and exposures – a so-called “condition compendium”. Using the compendium, we confirmed many previously-annotated genes and operons, and also identified hundreds of novel transcripts including anti-sense transcripts and non-coding RNAs. By systematically examining genes exhibiting highly similar expression patterns, we ascribed putative functions to previously uncharacterized genes, and identified novel regulatory elements controlling these expression patterns. We also used the compendium to elucidate candidate virulence pathways associated with quorum-sensing and infection in mice. Our study showcases the power of a B. pseudomallei condition compendium as a valuable resource for understanding microbial physiology and the pathogenesis of melioidosis.

2013-09-12 | GSE43205 | GEO

Toxicogenomic Effect of Burkholderia pseudomallei in a Human Macrophage Cell (THP-1) Model of Acute Melioidosis Using Whole-genome Microarray

2010-05-31 | GSE7577 | GEO

Quantitative proteomic analysis of Burkholderia pseudomallei Bsa Type III secretion system effectors using hyper-secreting mutants

Project description:Burkholderia pseudomallei is an intracellular pathogen and the causative agent of melioidosis, a severe disease of humans and animals. One of the virulence factors critical for early stages of infection is the Burkholderia secretion apparatus (Bsa) Type 3 Secretion System (T3SS), a molecular syringe that injects bacterial proteins, called effectors, into eukaryotic cells where they subvert cellular functions to the benefit of the bacteria. While the Bsa T3SS itself is known to be important for invasion, intracellular replication, and virulence, only a few genuine effector proteins have been identified and the complete repertoire of proteins secreted by the system has not yet been fully characterised. We constructed a mutant lacking bsaP, a homologue of the T3SS gatekeeper family of proteins that exert control over the timing and magnitude of effector protein secretion. Mutants lacking BsaP, or the T3SS translocon protein BipD, were observed to hyper-secrete the known Bsa effector protein BopE, providing evidence of their role in post-translational control of the Bsa T3SS and representing key reagents for the identification of its secreted substrates. Isobaric Tags for Relative and Absolute Quantification (iTRAQ), a gel-free quantitative proteomics technique, was used to compare the secreted protein profiles of the Bsa T3SS hyper-secreting mutants of B. pseudomallei with the isogenic parent strain and a bsaZ mutant incapable of effector protein secretion. Our study provides one of the most comprehensive core secretomes of B. pseudomallei described to date and identified 26 putative Bsa-dependent secreted proteins that may be considered candidate effectors. Two of these proteins, BprD and BapA, were validated as novel effector proteins secreted by the Bsa T3SS of B. pseudomallei.

2015-01-28 | PXD001656 | Pride

The expression of virulence and antimicrobial related proteins in different Burkholderia mallei and Burkholderia pseudomallei isolates

Project description:Burkholderia mallei and Burkholderia pseudomallei are both potential biological threats agents. Melioidosis caused by B. pseudomallei is endemic in Southeast Asia and Northern Australia, while glanders caused by B. mallei infections are rare. Here we studied the proteomes of different B. mallei and B. pseudomallei isolates to determine species specific characteristics. Analyzing the expressed proteomes of B. mallei and B. pseudomallei revealed differences between B. mallei and B. pseudomallei but also between isolates from the same species. Expression of multiple virulence factors and proteins of several PKS/NRPS clusters was demonstrated. Proteome analysis can be used not only to identify bacteria but also to characterize the expression of important factors that putatively contribute to pathogenesis of B. mallei and B. pseudomallei.

2022-12-15 | PXD028126 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data