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Transcriptomic analysis of Clostridium acetobutylicum biofilm cells adsorbed onto fibrous matrix in biobutanol production

ABSTRACT: This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

ORGANISM(S): Clostridium acetobutylicum

SUBMITTER: Dong Liu

PROVIDER: E-GEOD-68901 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Transcriptomic analysis of Clostridium acetobutylicum biofilm cells adsorbed onto fibrous matrix in biobutanol production [I]

Project description:Immobilization of Clostridium acetobutylicum B3 onto fibrous matrix by surface-adsorption was developed and applied to biobutanol production. The immobilized C. acetobutylicum B3 cells formed biofilm and showed dramatically improved butanol tolerance and production rate. DNA array-based transcriptional analysis of C.acetobutylicum B3 biofilm cells was conducted to elucidate the gene expression profile of the biofilm cells. Results showed that about 16% of the whole genome was differentially expressed. The most apparently differentially expressed genes were involved in amino acid transport and metabolism, inorganic ion transport and metabolism, energy production and conversion, and coenzyme transport and metabolism. Samples for biofilm cells and planktonic cells were withdrawn at four diffierent fermentation phases. The gene expression pattern of biofilm cells were investigated relative to that of planktonic cells from the same phase. The experiment was carried out twice independently. Cotton fibrous matrix (60 g/L) was used as biofilm carrier.

2015-05-15 | E-GEOD-68899 | biostudies-arrayexpress

Transcriptomic analysis of Clostridium acetobutylicum biofilm cells adsorbed onto fibrous matrix in biobutanol production [II]

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Transcriptomic analysis of Clostridium acetobutylicum biofilm cells in repeated-batch fermentation

Project description:Previously, we performed DNA array-based transcriptomic analysis of Clostridium acetobutylicum biofilm adsorbed onto fibrous matrix in batch fermentation. Here, to further shed light on the transcriptomic modulation of maturing Clostridium acetobutylicum biofilm, we performed the DNA array-based transcriptomic analysis in repeated-batch fermentation. Significant time course changes in expression levels were observed for the genes involved in amino acid metabolism, oligopeptide ABC transporter, nitrogen fixation, and various other processes. Repeated-batch fermentation was carried out in 2-L stainless steel columns packed with 40 g of cotton towel ?cut into pieces?approximately 3 cm × 5 cm) containing 1.5 L of P2 medium. Medium circulation rate was maintained at 35 mL/min via a peristaltic pump and the temperature was controlled at 37°C. Fermentation broth was replaced with fresh P2 medium every 12 h. Samples were withdrawn at 6 h after the medium replacement at predetermined interval, except for the last 3 samples. The last 3 samples were withdrawn at 12 h, 15 h, and 17 h after the medium replacement, respectively, to study the transcriptomic response to the adverse condition at the end of fermentation. A total of 8 samples were withdrawn over a period of 7 days, and time course gene expression profiles were studied.

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The Diagnostic Value of Salivary microRNA in Esophageal Cancer

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To detect change of gene expression after knock-down of hormone receptor in hepatocellular carcinoma cell line

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-01-19 | E-GEOD-65081 | biostudies-arrayexpress

Study the function of miR-195 and miR-30d in prostate cancer cell (LNCap and DU145)

Project description:miRNAs are related with the initiation and development of prostate cancer. We discover the miR-195 and miR-30 can be as a biomarker of prognosis of prostate cancer in clinical patients. miRNA functions through affecting the mRNA degradation by binding the mRNA 3âUTR. So we test the change of transcriptional profile of miR-195 and miR-30d cell line respectively to further study the function of miR-195 and miR-30d. To study the function of miR-195 and miR-30d in prostate cancer, we setup the over-expression cell line of the miR-195 and miR-30d respectively in prostate cancer cell(LNCap and DU145), then study the change of transcriptional profile in cell line by microarray experiment (Affymetrix PrimeView human gene expression). We order the over-expression plasmid of vector, miR-195 and miR-30d from System Biosciences company (Cat No: Scramble Vector PMIRH000PA-1 as Control, miR-195 PMIRH195PA-1, miR-30d PMIRH30dPA-1), and packaged the virus and construct the stable cell line (LNCaP_Control, LNCaP_mir195, LNCaP_mir30d,DU145_Control, DU145_mir195, DU145_mir30d,). We test the transcriptional profile in cell line by microarray experiment (Affymetrix PrimeView human gene expression).

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