Project description:Comparisson of expression profiling of a etrA deletion mutant strain (experimental sample) with that of the wild type Shewanella oneidensis MR-1 strain to assess global direct/indirect genetic regulation EtrA in Shewanella oneidensis MR-1 shares 73.6% and 50.8% amino acid sequence identity with the oxygen-sensing regulator Fnr in E. coli and Anr in Pseudomonas aeruginosa, respectively; however, its regulatory role of anaerobic metabolism in Shewanella spp. is complex and not well understood. Whole-genome expression profiling using a etrA gene deletion mutant as the experimental sample and the wild type strain as the reference, determine that EtrA fine-tunes the expression of genes involved in various anaerobic metabolic pathways, including nitrate, fumarate and dimethyl sulfoxide reduction. Moreover, genes involved in prophage activation and and genes implicated in aerobic metabolism were also differentially expressed. In contrast to previous studies that attributed a minor regulatory role to EtrA in Shewanella spp., this study demonstrates that EtrA acts as a global transcriptional regulator and cofers physiological advantages to the strain under certain growth conditions.
Project description:To identify the transcriptional targets of the DNA-binding response regulator HnoC (SO_2540), mRNA transcript levels in Shewanella oneidensis were measured using whole genome microarray analysis. Transcript levels were compared between WT Shewanella oneidensis and a hnoC deletion strain.
Project description:We have shown that pre-incubation with Bifidobacterium bifidum (B. bifidum) strain BF-1, a probiotic strain known to improve H. pylori-associated gastritis, suppresses the induction of IL-8 by the pathogen. To investigate how BF-1 affects gene expression in H. pylori-infected cells, we performed microarray analysis to assess gene expression in epithelial cells, which had been pre-incubated with BF-1 and infected with H. pylori.
Project description:The adult mammalian brain is composed of distinct regions that have specialized roles. The BF/POA regions are thought to have an important role in the regulation of sleep/wake behavior. However, genetic markers of the responsible cells for the regulation of sleep/wake behavior are largely unknown. To identify the molecular markers of the BF/POA regions, we sampled the BF/POA regions and compared gene expression in the BF/POA regions with those of other brain regions which we previously reported in the BrainStars (B*) project, in which we sampled ~50 small brain regions, including sensory centers and centers for motion, time, memory, fear, and feeding. We sampled each region every 4 hours for 24 hours, and pooled the sample sets for DNA-microarray assays. We then used informatics to identify candidates for genes with high or low expression in the BF/POA regions. We used our findings to develop an integrated database (http://poabf.brainstars.org/) for exploring genome-wide expression in the adult mouse brain including the BF/POA regions.
Project description:To identify the transcriptional targets of the DNA-binding response regulator HnoC (SO_2540), mRNA transcript levels in Shewanella oneidensis were measured using whole genome microarray analysis. Transcript levels were compared between WT Shewanella oneidensis and a hnoC deletion strain. Transcript levels of a WT and hnoC deletion strain were measured after 15 hrs growth, 4 independent replicates were performed for each strain
Project description:We have shown that pre-incubation with Bifidobacterium bifidum (B. bifidum) strain BF-1, a probiotic strain known to improve H. pylori-associated gastritis, suppresses the induction of IL-8 by the pathogen. To investigate how BF-1 affects gene expression in H. pylori-infected cells, we performed microarray analysis to assess gene expression in epithelial cells, which had been pre-incubated with BF-1 and infected with H. pylori. Four-condition experiment. Biological replicates with a dye-exchange experiment. Biological replicates with a longer incubation time experiment.
