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A. borkumensis cells: pyruvate vs. cells grown on hexadecane, canola and diesel

ABSTRACT: Transcriptional profiling of Alcanivorax borkumensis cells, grown on either pyruvate or hexadecane, canola and diesel as carbon source.

ORGANISM(S): Alcanivorax borkumensis SK2

PROVIDER: GSE50528 | GEO | 2014/07/01

SECONDARY ACCESSION(S): PRJNA217898

REPOSITORIES: GEO

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A. borkumensis cells: pyruvate vs. cells grown on hexadecane, canola and diesel

Project description:Transcriptional profiling of Alcanivorax borkumensis cells, grown on either pyruvate or hexadecane, canola and diesel as carbon source. Two-condition experiment, cells grown on pyruvate vs. cells grown on hexadecane, canola or diesel. For each condition 4 replicates were used, as for the control condition also 4 replicates were used for analysis.

2014-07-01 | E-GEOD-50528 | biostudies-arrayexpress

A. borkumensis cells: control vs. 1-octanol-stressed cells

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Alcanivorax borkumensis SK2

Project description:A. borkumensis cells: pyruvate vs. cells grown on hexadecane, canola and diesel

| PRJNA217898 | ENA

A. borkumensis cells: control vs. 1-octanol-stressed cells

Project description:Transcriptional profiling of Alcanivorax borkumensis cells, grown on either pyruvate or hexadecane as carbon source, that were stressed with 1- octanol. The gene expression was measured 15 min, 30 min, 60 min and 90 min after 1-octanol addition. Two-condition experiment, 1-octanol-stressed vs. unstressed cells; different time points were investigated after 1-octanol was spiked in (15 min, 30 min, 60 min, 90 min); for each condition 3 replicates were used, for the control condition 4 replicates (pyruvate cultures) and 3 replicates (hexadecane cultures) were used for analysis

2013-02-27 | E-GEOD-44687 | biostudies-arrayexpress

Transcriptome analysis of Beijerinckiaceae bacterium RH AL1 grown with pyruvate as the carbon source in response to lanthanum supplementation

Project description:The increased fitness when grown with pyruvate as carbon source in response to lanthanum supplementation was used as starting point to study genes induced in Beijerinckiaceae bacterium RH AL1 upon exposure to lanthanum.

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Comparative transcriptomic analysis of Rhodococcus erythropolis PR4 under hydrocarbon degrading conditions

Project description:The marine bacterium Rhodococcus erythropolis PR4 was demonstrated to be able for assimilation/biodegradation of hydrocarbons. Not just the chromosome but two large plasmids provide versatile enzyme sets involved in many metabolic pathways. In order to identify the key elements involved in biodegradation of the model compound, hexadecane, and diesel oil, we performed whole transcriptome analysis on cells grown in the presence of n-hexadecane and diesel oil. Sodium acetate grown cells were used as control. The final goal of the project is a comparative transcriptomic analysis of Rhodococcus erythropolis PR4 cells grown on acetate, on the model compound: hexadecane and the real substrate: diesel oil. Comparative transcriptomics of Rhodococcus erythropolis PR4 grown on n-hexadecane, diesel oil, and sodium acetate.

2014-04-21 | E-GEOD-56474 | biostudies-arrayexpress

Pseudonocardia dioxanivorans strain CB1190 during growth with H2/bicarbonate or pyruvate

Project description:Analysis of gene expression in Pseudonocardia dioxanivorans strain CB1190 during growth with H2/bicarbonate or pyruvate Two treatments, based on carbon/energy source used for growth: pyruvate and H2/bicarbonate. Triplicate microarrays (biological replicates) were prepared for each treatment. Pyruvate was used as the reference treatment for subsequent analysis. Gene expression changes were compared pair-wise: H2/bicarbonate vs. pyruvate

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Comparative transcriptomic analysis of Rhodococcus erythropolis PR4 under hydrocarbon degrading conditions

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Analysis of gene expression in Pseudonocardia dioxanivorans strain CB1190 during growth with dioxane, glycolate or pyruvate

Project description:Analysis of gene expression in Pseudonocardia dioxanivorans strain CB1190 during growth with dioxane, glycolate or pyruvate. Three treatments, based on carbon source used for growth: pyruvate, dioxane and glycolate. Triplicate microarrays (biological replicates) were prepared for each treatment. Pyruvate was used as the reference treatment for subsequent analysis. Gene expression changes were compared pair-wise: dioxane vs. pyruvate, and glycolate vs. pyruvate

2012-02-21 | E-GEOD-33197 | biostudies-arrayexpress

Pyruvate carboxylase and carbon metabolism in Listeria monocytogenes

Project description:Transcriptional profile of wild type L. monocytogenes (EGDe) and a pycA mutant strain was compared on growth in BHI. The human pathogen L. monocytogenes is a facultatively intracellular bacterium that survives and replicates in the cytosol of many mammalian cells. The listerial metabolism, especially under intracellular conditions , is still poorly understood. Recent studies analyzed the carbon metabolism of L. monocytogenes by the 13C-isotopologue perturbation method in a defined minimal medium containing [U-13C6]glucose. It was shown that these bacteria produce oxaloacetate mainly by carboxylation of pyruvate due to an incomplete tricarboxylic acid cycle. Here we report that a pycA insertion mutant defective in pyruvate carboxylase (PYC) still grows, albeit at a reduced rate, in BHI medium, but is unable to multiply in a defined minimal medium with glucose or glycerol 36 as carbon source. Transcriptional profiling was performed on the pycA mutant and the wild type strain grown in BHI to get a closer insight into the effect of the pycA mutation in Listeria monocytogenes.

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