Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11638767.fastq.gz | Fastqsanger.gz | |||
| SRR11638768.fastq.gz | Fastqsanger.gz | |||
| SRR11638769.fastq.gz | Fastqsanger.gz |
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Project description:The gene expression profile of wild-type Desulfovibrio vulgaris grown on cathodic hydrogen, generated at an iron electrode surface with an imposed negative potential of -1.1 V (cathodic protection conditions). The gene expression profile of cells grown on cathodic hydrogen was compared to that of cells grown with gaseous hydrogen bubbling through the culture. Relative to the latter, the electrode-grown cells over-expressed two hydrogenases, the hyn1 genes for [NiFe] hydrogenase-1, and the hyd genes, encoding [Fe] hydrogenase. The hmc genes for the high molecular weight cytochrome (Hmc) complex, which allows electron flow from the hydrogenases across the cytoplasmic membrane, were also over-expressed. In contrast, cells grown on gaseous hydrogen over-expressed the hys genes for [NiFeSe] hydrogenase. Cells growing on the electrode also over-expressed genes encoding proteins which promote biofilm formation. Although the gene expression profiles for these two modes of growth were distinct, they were more closely related to each other than to that for cells grown in a lactate- and sulfate-containing medium. Electrochemically measured corrosion rates were lower for iron electrodes covered with hyn1-, hyd-, and hmc-mutant biofilms, as compared to wild-type biofilms. This confirms the importance, suggested by the gene expression studies, of the corresponding gene products in D. vulgaris-mediated iron corrosion. Keywords: Growth on Iron Electrode and Biofilm formation For each condition 2 unique biological samples were hybridized to 4 arrays that each contained duplicate spots. Genomic DNA was used as universal reference.
2010-05-26 | E-GEOD-10388 | biostudies-arrayexpress
Project description:The gene expression profile of wild-type Desulfovibrio vulgaris grown on cathodic hydrogen, generated at an iron electrode surface with an imposed negative potential of -1.1 V (cathodic protection conditions). The gene expression profile of cells grown on cathodic hydrogen was compared to that of cells grown with gaseous hydrogen bubbling through the culture. Relative to the latter, the electrode-grown cells over-expressed two hydrogenases, the hyn1 genes for [NiFe] hydrogenase-1, and the hyd genes, encoding [Fe] hydrogenase. The hmc genes for the high molecular weight cytochrome (Hmc) complex, which allows electron flow from the hydrogenases across the cytoplasmic membrane, were also over-expressed. In contrast, cells grown on gaseous hydrogen over-expressed the hys genes for [NiFeSe] hydrogenase. Cells growing on the electrode also over-expressed genes encoding proteins which promote biofilm formation. Although the gene expression profiles for these two modes of growth were distinct, they were more closely related to each other than to that for cells grown in a lactate- and sulfate-containing medium. Electrochemically measured corrosion rates were lower for iron electrodes covered with hyn1-, hyd-, and hmc-mutant biofilms, as compared to wild-type biofilms. This confirms the importance, suggested by the gene expression studies, of the corresponding gene products in D. vulgaris-mediated iron corrosion. Keywords: Growth on Iron Electrode and Biofilm formation
2008-02-13 | GSE10388 | GEO
Project description:cathodic biofilm in microbial electrolysis cell Raw sequence reads
| PRJNA481657 | ENA
Project description:Identification of putative proteins of interest that are involved in cathodic electron uptake by the novel iron-corroding strain D. ferrophilus IS5
2020-09-28 | PXD020803 | Pride
Project description:To identify novel genes modulating Candida albicans biofilm formation, a screen of 2451 overexpression strains allowed us to identify 16 genes whose overexpression significantly reduced biofilm formation. Genome-wide expression and binding analyses were conducted upon overexpression of ZCF15 and ZCF26 and wild type planktonic and biofilm cells were performed. A ChIP assays was performed. Briefly, untagged strain (CEC4665) and two replicates each of ZCF15 (CEC5929 and CEC5930) and ZCF26 (CEC5931 and CEC5932) strain were grown in biofilm condition for 18 h and cells were cross-linked with 1% final concentration of formaldehyde for 25 min at 30°C.The DNA was immunoprecipitated with anti-protein A antibodies (Sigma Aldrich Cat. No. P3775). The immunoprecipitated (IP) DNA were used to determine the binding of Zcf15 and Zcf26 across the genome by ChIP-sequencing
2023-01-11 | E-MTAB-11384 | biostudies-arrayexpress
Project description:Enterococcus faecalis is a common commensal organism and a prolific nosocomial pathogen that causes biofilm-associated infections. Numerous E. faecalis OG1RF genes required for biofilm formation have been identified, but few studies have compared genetic determinants of biofilm formation and biofilm morphology across multiple conditions. Here, we cultured transposon (Tn) libraries in CDC biofilm reactors in two different media and used Tn sequencing (TnSeq) to identify core and accessory biofilm determinants, including many genes that are poorly characterized or annotated as hypothetical. Multiple secondary assays (96-well plates, submerged Aclar, and MultiRep biofilm reactors) were used to validate phenotypes of new biofilm determinants.
2021-04-03 | GSE171419 | GEO