Project description:This series represents the work described in the publication Bacillus subtilis Genome Diversity by Earl et al. (Journal of Bacteriology, accepted) Keywords: comparative genomic hybridization Overall design: The aim of this study was to examine genome diversity among Bacillus subtilis species members. Strains were chosen from within both recognized subspecies and one close relative, Bacillus vallismortis.
Project description:Investigation of whole genome expression level changes in Bacillus anthracis Sterne deltaClpX mutant compared to the wild-type strain after growth in nutrient rich media. The deltaClpX mutant used in this study is described in McGillivray et al. 2009. ClpX Protease Contributes to Antimicrobial Peptide Resistance and Virulence Phenotypes of Bacillus anthracis. Journal of Innate Immunity 1(5): 494-506. Overall design: A six chip study using total RNA recovered from three separate cultures of the wild-type Bacillus anthracis Sterne strain and three separate cultures of the deltaClpX mutant strain. Each chip measures the expression level of 5287 chromosomal genes from Bacillus anthracis Sterne.
Project description:hole Genome Expression Profile of Human Peripheral Blood Mononuclear cells Exposed to Bacillus anthracis in vitro. Peripheral blood mononuclear cells exposed to a 1 MOI (multiplicity of infection pathogenic) of the B. anhracis spores. Overall design: Human Peripheral Blood Mononuclear cells Exposed to Bacillus anthracis in vitro
Project description:hole Genome Expression Profile of Human Peripheral Blood Mononuclear cells Exposed to Bacillus anthracis in vitro. Peripheral blood mononuclear cells exposed to a 1 MOI (multiplicity of infection pathogenic) of the B. anhracis spores. Human Peripheral Blood Mononuclear cells Exposed to Bacillus anthracis in vitro
Project description:The goal of this study is to obtain a genomic view of the Fur regulatory network under both iron replete and iron deficient conditions in Bacillus subtilis using ChIP-seq. Besides the known Fur target sites, 70 putative DNA binding sites were identified, and the vast majority had higher occupancy under iron sufficient conditions. In addition,we discovered a role for catechol degradation in bacillibactin metabolism, and provided evidence that catechol 2,3-dioxygenase can detoxify endogenously produced catechol substrates in addition to its more widely studied role in biodegradation of environmental aromatic compounds and pollutants. Overall design: To modulate intracellular iron levels, we employed a high-affinity Fe2+ exporter FrvA from L. monocytogenes to impose iron starvation. Bacillus wild-type cells (with C-terminal FLAG-tagged Fur at its native locus and an IPTG-inducible ectopic copy of frvA integrated at amyE locus) were harvested at 0 and 30 min after IPTG induction to study Fur-dependent regulation under iron sufficient and deficient conditions, respectively.
Project description:Investigation of whole genome gene expression level changes in sporulating Bacillus subtilis 168 delta-prpE mutant, compared to the wild-type strain. The mutation engineered into this strain results in impaired germination of spores. A six chip study using total RNA extracted from three separate wild-type cultures of sporulating Bacillus subtilis 168 and three separate cultures of sporulating mutant strain, Bacillus subtilis 168 delta-prpE, in which prpE (yjbP BSU11630) gene coding for a protein phosphatase is deleted entirely. Each chip consists of four fields able to measure the expression level of 4,104 genes from Bacillus subtilis subsp. subtilis strain 168 NC_000964 with eight 60-mer probe pairs (PM/MM) per gene, with two-fold technical redundancy.
Project description:Comparison of the Bacillus cereus with overexpressed Bacillus subtilis ComK (Bacillus cereus pNWcomKBsu) vs Bacillus cereus carrying empty plasmid (Bacillus cereus pNW33N) One condition design comparision of (IPTG induced overexpression construct vs IPTG induced empty plasmid) including a dye swap, 3 biological replicate
Project description:"Bacillus subtilis is an aerobic, endospore forming, rod-shaped Gram-positive bacterium. It has a relatively small genome of 4,215,606 bp with 4,197 protein coding genes. It is considered a model organism to study natural phenomena, such as chromosome replication, sporulation or swarming motility. Furthermore, many bacterial pathogens are closely related to B. subtilis, making it a highly significant system for research on potential targets for drug therapeutics. Although B. subtilis is among the best characterised bacterial systems, many of its gene products are still non-annotated, completely uncharacterised and/or their post-translational landscape is unknown. In the current study we aim at broadening the available information on Bacillus subtilis by providing a comprehensive resource for the microbial community encompassing a wide array of information at the genome, proteome, phosphoproteome and acetylome level."
Project description:Plant growth-promoting rhizobacteria (PGPR) are soil beneficial microorganisms that colonize plant roots for nutritional purposes and accordingly benefit plants by increasing plant growth or reducing disease. But it still remains unclear which mechanisms or pathways are involved in the interactions between PGPR and plants. To understand the complex plant-PGPR interactions, the changes in the transcriptome of typical PGPR standard Bacillus subtilis in responding to rice seedlings were analyzed. We compared and anylyzed the transcriptome changes of the bacteria Bacillus subtilis OKB105 in response to rice seedings for 2 h. Total RNA was extracted and Random priming cDNA synthesis, cDNA fragmentation and terminal labeling with biotinylated GeneChip DNA labeling reagent, and hybridization to the Affymetrix GeneChip Bacillus subtilis Genome Array.