Project description:Bacillus strains grown in LB media. Metabolite extraction from the cells was performed using 100% methanol at different growth stages.
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.
Project description:Cappable-seq was used to map transcription start sites globally in wild type Bacillus subtilis. Total RNA was isolated from cells grown in LB media until exponential phase. RNA corresponding to transcription start sites was capped with a 5' biotin tag, which was used for enrichment via a pull down with streptavidin beads. Enriched RNA was converted to cDNA and then subjected to illumina sequencing.
Project description:A total gene expression approach was applied to study the methylotrophic nature of B. methanolicus by comparing the gene expression in bacteria grown methylotropic compared to non-methylotrophic. Genes of interest with different gene expression were quantified in the same RNA samples by real-time PCR, confirming the results found in the microarray experiment. Genes of special interest that are expressed higher when grown methylotrophic, were the RuMP pathway genes located on the pBM19. Bacillus methanolicus was grown in minimal media with either methanol or mannitol as carbon source. The experiment was preformed in triplicate, with bacterial cultures grown on 3 different days.
Project description:Bacillus methanolicus MGA3, which has a low tolerance for 5-aminovalerate. To investigate the transcriptional response of Bacillus methanolicus to 5-aminovalerate transcriptomic analysis by differential RNA-Seq in the presence and absence of 5AVA was perfromed. In detail: B. methanolicus cultures were grown in MVcM or MVcMY media containing 200 mM methanol supplemented with and without 50 mM 5AVA, respectively. Cells were harvested in the mid log phase at an OD600 of 0.6 and isolation of total RNA isolation was performed individually for each cultivation condition. Isolated RNA samples from B. methanolicus MGA3 were used in biological triplicates for the cDNA library preparation prior to sequencing. Ribo-Zero rRNA Removal Kit (Bacteria) from Illumina (San Diego, CA, USA) was used to remove the ribosomal RNA molecules from the isolated total RNA. Removal of rRNA was checked by Agilent RNA Pico 6000 kit on Agilent 2100 Bioanalyzer (Agilent Technologies, Böblingen, Germany). RNA was free of detectable rRNA. Preparation of cDNA libraries were performed according to the manufacturer’s instructions of TruSeq stranded mRNA Kit (Illumina, San Diego, USA). Subsequently, each cDNA library was sequenced on a HiSeq1500 (2 x 75nt PE rapid v2) Sequencer system (Illumina, San Diego, USA).
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
Project description:First whole transcriptome assessment of a Bacillus megaterium strain. The B. megaterium DegU regulon was assessed for LB batch cultures with artificially induced degU expression. DegU is a pleiotropic regulator in B. subtilis governing adaptive responses such as secretory enzyme production.
Project description:To uncover the effects of KrrA regulation on gene transcription and define the bacterial response imposed by this regulation, a transcriptomic study was carried out in which Bacillus anthracis krrA was compared to WT in two growth conditions: LB in the presence or absence of ‘205.