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Basal in vitro transcriptomes of Mycobacterium tuberculosis complex (MTC) clinical isolates

ABSTRACT: This study uses microarray analyses to examine baseline gene expression profiles for Mycobacterium tuberculosis complex clinical isolates relative to reference strain CDC1551 during log phase growth in vitro in 7H9 broth. For this in vitro analyses, log-phase mycobacteria in starter cultures grown to mid-log from frozen stocks were inoculated into 7H9-OADC medium in 25-cm2 vented flasks at an OD of ~0.05 and grown without shaking for ~1 week to an OD of ~0.5-0.6.

ORGANISM(S): Mycobacterium tuberculosis

PROVIDER: GSE21111 | GEO | 2010/07/09

SECONDARY ACCESSION(S): PRJNA129701

REPOSITORIES: GEO

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Basal in vitro transcriptomes of Mycobacterium tuberculosis complex (MTC) clinical isolates

Project description:This study uses microarray analyses to examine baseline gene expression profiles for Mycobacterium tuberculosis complex clinical isolates relative to reference strain CDC1551 during log phase growth in vitro in 7H9 broth. For this in vitro analyses, log-phase mycobacteria in starter cultures grown to mid-log from frozen stocks were inoculated into 7H9-OADC medium in 25-cm2 vented flasks at an OD of ~0.05 and grown without shaking for ~1 week to an OD of ~0.5-0.6. Computed

2010-07-08 | E-GEOD-21111 | biostudies-arrayexpress

The carbonic anhydrase inhibitor ethoxzolamide inhibits the Mycobacterium tuberculosis PhoPR regulon and Esx-1 secretion and attenuates virulence

Project description:The purpose of this study was to examine how ethoxzolamide modulates gene M. tuberculosis gene expression at acidic pH. We observed that ethoxzolamide downregulates genes of the PhoPR regulon. Mtb strain CDC1551 was grown at 37C in T-25 vented, standing tissue culture flasks in 8 ml of buffered 7H9 medium seeded an initial OD of 0.2. Three conditions were examined with two biological replicates: 1) DMSO treated, pH 7.0, 2) DMSO treated, pH 5.7, 3) 40 µM ethoxzolamide treated, pH 5.7. The CDC1551(phoP::Tn) mutant was grown in a similar manner and treated with DMSO at pH 7.0 and 5.7. Following six days incubation, total bacterial RNA was extracted and analyzed as previously described.

2015-05-20 | E-GEOD-63917 | biostudies-arrayexpress

Transcriptional profiling of M. tuberculosis CDC1551 wild type vs aprABC null, aprBC null, aprC null and phoP transposon mutants.

Project description:Following phagocytosis by macrophages, Mycobacterium tuberculosis (Mtb) senses the intracellular environment and remodels its gene expression for growth in the phagosome. Abramovitch et.al. in this current study identified an Acid and Phagosome Regulated (aprABC) locus that is unique to the Mtb complex and whose gene expression is induced during growth in acidic environments in vitro and in macrophages. The authors propose a model where phoP senses the acidic pH of the phagosome and induces aprABC expression to fine-tune processes unique for intracellular adaptation of Mtb complex bacteria. This study uses microarray analyses to compare transcriptional responses of wild type Mycobacterium tuberculosis (CDC1551) to aprABC locus deletion mutants and the phoP transposon mutant. The bacteria were grown to early log phase in vented T-75 standing flasks containing 12 mL of pH 7.0 7H9 OADC medium. Transcript levels of the wild type bacteria were compared to the following mutants: aprABC null, aprBC null, aprC null, phoP::Tn mutant.

2011-07-09 | E-GEOD-22854 | biostudies-arrayexpress

Shotgun proteomic profiling of Yersinia ruckeri strains

Project description:Project goal is to identify proteomic profiles of Yersinia ruckeri, the causative agent of enteric redmouth disease in fish. Four strains (SP-05, CSF007-82, 7959-11 and YRNC-10) of Y. ruckeri were isolated from disease rainbow trout, Oncorhynchus mykiss. Strains, SP-05 and CSF007-82, belong to serotype 1 and biotype 1 (motile and lipase positive), while strains 7959-11 and YRNC-10 belong to serotype 1 and biotype 2 (non-motile and lipase negative) and belong to serotype 1. A single colony of each strain was inoculated into tryptic soy broth (Casein peptone, dipotassium hydrogen phosphate, glucose, sodium chloride, soya peptone, Sigma) and grown at 22 °C with shaking (150 rpm). These starter cultures were then diluted with fresh sterile tryptic soy broth to an optical density (OD 600) of 0.10 ± 0.05. Five hundred microlitres of the diluted starter cultures were inoculated in duplicates, into 25 ml of tryptic soy broth. Cultures were grown overnight at 22 °C with shaking (150 rpm) until the late log phase. Cells were harvested by centrifugation, then washed three times with PBS.

2017-09-22 | PXD005439 | Pride

Copra β-mannooligosaccharide utilization by Bifidobacterium adolescentis ATCC 15703

Project description:In order to understand gene expression profile of Bifidobacterium adolescentis ATCC 15703, it was grown in minimal media upto late log phase in the presence of β-mannooligosaccharide from copra till OD A600 = 0.800

2022-07-20 | GSE180349 | GEO

Ribosome profiling of E. coli K-12 MG1655 MOPS rich media with 0.2% glucose

Project description:Ribosome profiling was performed on E. coli wild type cells. All replicates were grown to an OD of ~0.4 in MOPS rich Media with 0.2% glucose supplemented, aerobically in shake flasks. Cultures were treated with chloramphenicol 2 min prior to harvest.

2015-06-09 | GSE63858 | GEO

Yeast translation

Project description:Red channel: 3 independent polysome preparations from BY4741 cells, grown in YPD to mid-log phase (OD 0.6-0.9). In each experiment 14 fractions were collected. In-vitro transcribed B.subtilis controls were added to each fraction and used for normalization. Green channel: Total RNA prepared from S288c cells. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set

2005-12-03 | GSE3732 | GEO

Cryptococcus neoformans wild type and sir2delta

Project description:Wild type strain H99 compared to independent sir2 deletion mutants grown to mid-log (0.6 OD600) in rich medium (YPD) shaking at 250rpm in baffled flasks.

2022-04-01 | GSE173209 | GEO

Global transcriptomic response of modified Bacillus anthracis over expressing protective antigen

Project description:In this study we focused on understanding the effect of over expression of recombinant protective antigen (rPA) on the Bacillus anthracis metabolism and genes expression with the purpose of improving the production of this recombinant toxin in particular and recombinant proteins in general. To achieve this goal controlled growth of the B. anthracis ames strain transformed with pYS5 (PA producer) plasmid encoding protective antigen and the corresponding empty vector pSW4 (non-producer) were performed and protein production, bacterial growth characteristics and gene transcription pattern were analyzed. Controlled condition batch runs were performed for both strains and samples from early log (OD 3), log (OD 10) and late log (OD 16) phase were used for gene expression profiling. We found that most of the genes belonging to transport, TCA, glycolysis, PPP and amino acid biosynthesis were up-regulated in the lag phase samples which help the cell coping with the increased requirements of nutrient and energy for rPA expression. These pathways are down-regulated in the log and latelog phase as cellular stress response onsets, which is reflected in the decreased specific growth rate.

2018-11-06 | GSE108973 | GEO

Impact of mutations in rv2887, putative transcriptional repressor, on gene expression in Mycobacterium tuberculosis.

Project description:This study was aimed towards understanding the consequences of mutating rv2887, a putative transcriptional repressor, on gene expression in Mycobacterium tuberculosis. Since clones carrying mutations in this gene were found to be highly resistant to a potent mycobactericidal compound, 14, we also tested the impact of short-term exposure to this compound on gene expression in Mycobacterium tuberculosis. Three different strains, wild type H37Rv and the two clones resistant to compound 14, named 1A and 8A, were grown to log phase in 7H9 complete medium. The cells were diluted to an OD of 0.5 and split in to two equal parts, 1 arm received the vehicle (DMSO) and the other arm received compound 14 at a final concentration of 3.9 Î¼M. The exposure lasted 4 hours, at which point the bacterial pellet was collected and processed for RNA extraction using protocols described previously.

2016-07-01 | E-GEOD-77556 | biostudies-arrayexpress

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