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

ABSTRACT: Analysis of gene expression in Pseudonocardia dioxanivorans strain CB1190 during growth with H2/bicarbonate or pyruvate

ORGANISM(S): Pseudonocardia dioxanivorans CB1190

PROVIDER: GSE41145 | GEO | 2013/04/24

SECONDARY ACCESSION(S): PRJNA175919

REPOSITORIES: GEO

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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

2013-04-24 | E-GEOD-41145 | biostudies-arrayexpress

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.

2012-02-21 | GSE33197 | GEO

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

Sphingomonas sp. H2 strain:H2 | isolate:H2

Project description:Sphingomonas sp. H2 strain:H2 | isolate:H2 Genome sequencing and assembly

| PRJNA732547 | ENA

Idiomarina sp. H2 strain:H2

Project description:Idiomarina sp. H2 strain:H2 Genome sequencing and assembly

| PRJNA456221 | ENA

Pseudomonas sp. H2 strain:H2

Project description:Pseudomonas sp. H2 strain:H2 Genome sequencing and assembly

| PRJNA261945 | ENA

Pseudonocardia dioxanivorans CB1190

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

| PRJNA175919 | ENA

Mycobacterium intracellulare H2 strain:H2

Project description:Mycobacterium intracellulare clinical strain, H2 Genome Sequencing

| PRJNA81227 | ENA

Pseudonocardia dioxanivorans strain CB1190 during growth on THF or succinate

Project description:Analysis of gene expression in Pseudonocardia dioxanivorans strain CB1190 during growth on THF (tetradhydrofuran) or succinate, and re-analysis of GSE33197 published expression data. Two new treatments, based on carbon/energy source used for growth: THF and succinate. Three previously published treatments (pyruvate, dioxane, and glycolate) from GEO Series GSE33197 were also reanalyzed. Triplicate microarrays (biological replicates) were prepared for each treatment. Gene expression changes were compared directly between the new treatments (THF vs. succinate) and to previously published data during growth on pyruvate (GEO accession numbers GSM821862-GSM821864) in order to yield THF vs. pyruvate and succinate vs. pyruvate contrasts. Included as part of the re-analysis of GSE33197 were data from dioxane and glycolate treatments (GSM821865-GSM821870). The complete dataset representing: (1) the THF- and succinate-treated CB1190 Samples and (2) the pyruvate-, dioxane- and glycolate-treated CB1190 Samples from Series GSE33197 (re-processed using RMA), is linked below as a supplementary file (GSE48814_complete_data.txt).

2013-07-12 | E-GEOD-48814 | biostudies-arrayexpress

Pyruvate fermentation vs Lactate-Sulfate

Project description:In order to obtain a global view of energy metabolism pathways of the sulfate-reducer Desulfovibrio vulgaris Hildenborough and the proteins involved therein whole-genome microarrays were used to compare the transcriptional response of cells grown with hydrogen/sulfate, pyruvate/sulfate, lactate/thiosulfate, and pyruvate with limiting sulfate, relative to growth in standard lactate/sulfate condition. Growth with hydrogen/sulfate showed the largest number of differently expressed genes and the largest changes in expression levels. The most up-regulated energy metabolism genes were those coding for the periplasmic [NiFeSe] hydrogenase, followed by the Ech hydrogenase, and the most down-regulated were genes coding for the Coo hydrogenase. The results point to the involvement of formate cycling and the ethanol pathway during growth on hydrogen, whereas there is evidence for CO cycling during growth on lactate and pyruvate, but not on H2. Growth with thiosulfate showed the hallmarks of a reduced energy status of the cells with down regulation of the ATP synthase and the Qmo and Dsr complexes., whereas growth with pyruvate showed the smallest differences but an increased role for the Ech hydrogenase.that in this case functions in reverse from the case of growth with H2. The multiple periplasmic hydrogenases and formate dehydrogenases, do not display the same regulation pattern showing that their metabolic roles are not totally interchangeable. This result together with the observation that several genes coding for proteins that have not been biochemically characterised were considerably affected in this study, reveals a more complex energy metabolism than previously considered and provides guidance for further studies. Keywords: Growth protocol

2008-05-31 | GSE8015 | GEO

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