Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Conditioning of uropathogenic Escherichia coli to nitrosative stress

ABSTRACT: While in transit within and between hosts, uropathogenic E. coli (UPEC) encounter multiple stresses, including substantial levels of nitric oxide and reactive nitrogen intermediates. Strains of UPEC become conditioned to high concentrations of acidified sodium nitrite (ASN), a model system used to generate nitrosative stress. We used microarrays to define the expression profile of UPEC that have been conditioned for growth in ASN.

ORGANISM(S): Escherichia coli Escherichia coli UTI89

PROVIDER: GSE15319 | GEO | 2009/03/21

SECONDARY ACCESSION(S): PRJNA115853

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Transcription profilung of E. coli known to be uropathogenic conditioning to nitrosative stress

Project description:While in transit within and between hosts, uropathogenic E. coli (UPEC) encounter multiple stresses, including substantial levels of nitric oxide and reactive nitrogen intermediates. Strains of UPEC become conditioned to high concentrations of acidified sodium nitrite (ASN), a model system used to generate nitrosative stress. We used microarrays to define the expression profile of UPEC that have been conditioned for growth in ASN. Experiment Overall Design: Separate colonies of the UPEC isolate UTI89 grown on LB agar plates from a -80Â°C freezer stock were used to start overnight shaking cultures in MES-buffered LB broth (MES-LB, pH 5.0). Each culture was then diluted 1:100 into 7 ml MES-LB with or without 3 mM ASN in loosely capped 20-by-150-mm borosilicate glass tubes and grown with shaking at 37Â°C. Growth was monitored by optical density until OD600 = 1.5, at which point cultures were spun down, and pellets frozen at -80Â°C for at least 12 h. RNA was extracted with hot phenol-chloroform and purified by CsCl centrifugation. cDNA was synthesized, fragmented, and labeled for hybridization to Affymetrix GeneChipÂ® E. coli Genome 2.0 Arrays.

2009-03-28 | E-GEOD-15319 | biostudies-arrayexpress

Nitrosative stress response in uropathogenic Escherichia coli (UPEC)

Project description:A strain of UPEC CFT073 lacking the three known NO detoxifiaction mechanisms, Hmp, FlRd and Nrf is used to study the global effect of NO on the pathogen Cultures were anaerobically grown in triplicates under two conditions: Without nitrosative stress or with nitrosative stress, induced by anaerobic growth on nitrate. RNA was extracted from the samples and following rRNA depletion, samples were analyzed by RNA-seq for genome wide transcriptional differences.

2015-06-15 | E-GEOD-69830 | biostudies-arrayexpress

Uropathogenic Escherichia coli biofilm proteomics

Project description:We previously determined that loss of respiratory quinol oxidase cytochrome bd disrupts biofilm formation in uropathogenic Escherichia coli (UPEC). In this study, we extracted and interrogated the outer membrane and extracellular matrix of colony biofilms formed by UPEC isolate UTI89 and an isogenic mutant lacking cytochrome bd (∆cydAB).

2021-04-01 | PXD023998 | Pride

sRNA-mediated regulation of P-fimbriae phase variation in intracellular uropathogenic Escherichia coli

Project description:The experiment design involves RNA-seq of Hfq bound RNA co-immunoprecipitation in the uropathogenic Escherichia coli (UPEC) strain UTI89.

2016-05-31 | E-MTAB-3498 | biostudies-arrayexpress

Nitrosative stress response in uropathogenic Escherichia coli (UPEC)

Project description:A strain of UPEC CFT073 lacking the three known NO detoxifiaction mechanisms, Hmp, FlRd and Nrf is used to study the global effect of NO on the pathogen

2015-06-15 | GSE69830 | GEO

Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol

Project description:The expression levels of uropathogenic E. coli (UPEC) UTI89 cells in YESCA broth with and without 4% dimehtyl sulfoxide (DMSO) and 2% ethanol (EtOH) were studied.

2012-02-15 | GSE35797 | GEO

Response of Porphyromonas gingivalis to nitrosative stress

Project description:Transcriptional profiling of P. gingivalis cells comparing cells grown in anaerobic conditions to cells grown in anaerobic conditions and exposed to nitrite and to GSNO. Two-condition experiment, anaerobically vs. anaerobically exposed to nitrosative stress cells. Biological replicates: 1 independently grown and harvested bacterial cells for each nitrosative exposure tested. Four technical replicates for each experiment.

2012-10-05 | E-GEOD-38220 | biostudies-arrayexpress

DamX controls reversible cell morphology-switching in uropathogenic Escherichia coli.

Project description:Transcriptional analysis of UTI89 - uropathogenic E.coli (UPEC) strain grown in urine/Luria bertani medium culture in vitro as well as during three distinct phases of UPEC bladder infection: intracellular growth, filament formation and filament reversal. UTI89 was used to infect a bladder epithelial cell line cultured within a dynamic flow chamber system and harvested at particular stages of its pathogenecity cascade. Total RNA was processed and cy3 labeled for microarray analysis using Agilent custom Escherichia coli UTI89 arrays designed using E-Array.

2017-05-28 | E-MTAB-3611 | biostudies-arrayexpress

Cell wall-deficient Mycoplasma hominis represses biofilm formation of uropathogenic Escherichia coli.

Project description:The features of Mycoplasma in human organ such lung and urinary tract are enigmatic. Here, the role of M. hominis in regard to biofilm formation of uropathogenic Escherichia coli (UPEC) strain CFT073 was investigated. Although M. hominis were inferred to not impact on UPEC bacterial fitness including growth and productions of signaling molecules as autoinducer-2 (AI-2) and indole, we found that the presence of M. hominis dramatically decreased biofilm formation of UPEC CFT073 as well as slightly repressed attachment and cytotoxicity of that. Importantly, this activity was observed on UPEC strain specifically, not enterohemorrhagic E. coli (EHEC) strain that exists on intestine. Whole-transcriptome profiling and quantitative real-time polymerase chain reaction (qRT-PCR) analysis revealed PhoPQ system and anti-termination protein (encoded by ybcQ) participates on the reduction of biofilm formation by M. hominis (corroborated by qRT-PCR). Furthermore, collaborating with previous report that toxin-antitoxin (TA) system involved in biofilm formation, M. hominis increased on the transcriptions of toxin genes including hha (toxin gene in Hha-TomB TA system) and pasT (toxin part in PasT-PasI TA system). Hence, we propose that one possible role of M. hominis is to influence bacterial biofilm formation in urinary tract. Only fourteen genes were induced (2.5-fold) by the presence of M. hominis in Uropathogenic Escherichia coli (UPEC) biofilm cells. Among upregulated genes, ybcQ (encodes anti-termination protein Q homolog) and phoP/phoQ (encode DNA-binding response regulators in two-component regulatory system), were induced by the presence of M. hominis. Two-condition experiment, UPEC CFT073 alone vs. UPEC CFT073 with Mycoplasma hominis PG21 (10^5 ccu/ml). For preparing the total RNA, UPEC CFT073 cells were grown at 37Â°C in biofilm cells on glass wool with or without M. hominis for 24 h.

2016-01-08 | E-GEOD-43376 | biostudies-arrayexpress

Uropathogenic E. coli UTI89 cells in the presence of dimethyl sulfoxide or ethanol

Project description:The expression levels of uropathogenic E. coli (UPEC) UTI89 cells in YESCA broth with and without 4% dimehtyl sulfoxide (DMSO) and 2% ethanol (EtOH) were studied. To determine the up- or down-regulated expression profile in the presence of dimethyl sulfoxide (DMSO) and ethanol (EtOH), UPEC UTI89 were grown in YESCA broth with 4% dimethyl sulfoxide (DMSO) or 2% ethanol (EtOH) or no comound at 26°C with 200 rpm shaking for 24 hours were used for RNA extraction and hybridization on Affymetrix microarrays.

2012-02-15 | E-GEOD-35797 | biostudies-arrayexpress

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