ABSTRACT: Transcriptional profiling of the bacteria Paenibacillus vortex comparing control untreated cells with kanamycin treated cells after 18 hours of exposure. Goal was to determine the effect of the antibiotic kanamycin in concentration which affect the colony morphology on global bacteria gene expression. Two-condition experiment, control cells vs. kanamycin treated cells. Biological replicates: 2 control replicates, 2 treated replicates. Pooling of 5 technical replicates for each biological replicate.
Project description:Transcriptional profiling of H37Rv (WT), Mut1 and Comp1 bacteria under aerobic (Aer/0 day, i.e 0 D) and hypoxic conditions (Hyp/5 days standing culture, i.e 5 D). Mut1: H37Rv carrying devR gene disruption by in frame insertion of kanamycin resistance cassette and expressing DevRN-Kan fusion protein. Comp1: Mut1 complemented with low copy number plasmid carrying devR gene expressed from its native constitutive upstream promoter. (Reference: Majumdar et al., 2010, PLoS One 5:e9448). Goal is to compare transcriptional patterns of WT, Mut1 and Comp1 strains under aerobic (0 D) and hypoxic (5 D) conditions in vitro. Two color and One-color experiments,Organism: Mycobacterium tuberculosis, Genotypic Technology designed Custom Mycobacterium tuberculosis H37Rv Whole Genome 8x15k GE Microarray (AMADID-020181)
Project description:Amino acid racemases are enzymes that catalyze the conversion between L and D- forms of amino acids. While the role of alanine and glutamate raemases in bacteria (specifically Salmonella) are well-studied, relatively less is known about the function of other non-canonical racemases. This study focuses on delineating the role of two such putative aspartate raceases viz. YgeA and AspR in Salmonella Typhimurium. For this purpose, Salmonella strains engineered to lack either one or both of these genes were compared to the wild type strain under planktonic and biofilm-inducing conditions to identify the global changes in gene expression orchestrated by these genes. Organism : Salmonella Typhimurium , Agilent Custom Salmonella Typhimurium str. 14028S Gene Expression 8x15k Array (AMADID: 046639) designed by Genotypic Technology Private Limited.
Project description:We report the application of a high-throughput technique, RNA-seq, to study the transcriptomic response of P. putida DOT-T1E in the presence of antibiotics with different mechanisms of action with the aim to study in more detail the defense mechanisms that bacteria use to resist against toxic compounds. We find that P. putida DOT-T1E responde in a different way against each antimicrobial compound, what clearly shows that bacteria defense in different ways depending on the targets that compounds uses to attack. Our work is the first global transcriptomic analysis done in P. putida DOT-T1E in the presence of a considerable range of antibiotics. P. putida DOT-T1E mRNA profiles in the presence of control condition (LB) and 8 different antibiotics (ampicillin, chloramphenicol, kanamycin, ciprofloxacin, tetracycline, spectinomycin, gentamicin and rifampicin)
Project description:We show that treatment with HPUra (for S. pneumoniae) and trimethoprim (for E. coli) leads to a skewed gene dosage profile (increase around the origin of replication), which is also propagated to the transcriptome level. Kanamycin, however, does not have this effect. In case of S. pneumoniae this shift in gene dosage distribution leads to the population-wide activation of competence. Pairwise comparison of untreated to antibiotic-treated cells (either DNA-seq or RNA-seq). It was performed with deep sequencing, using an Illumina HiSeq 2000 machine with 100 bp read length. S. pneumoniae samples treated with kanamycin was analysed from a single sample, while all other conditions were from duplicate samples.
Project description:Transcriptional profiles of uropathogenic Escherichia coli CFT073 exposed to cranberry-derived proanthocyanidins (PACs) were determined. Our results indicate that bacteria grown on media supplemented with PACs were iron-deprived. To our knowledge, this is the first time that PACs have been shown to induce a state of iron-limitation in this bacterium. Cultures of E. coli CFT073 were streaked onto LB agar plates and incubated (37°C, 24 h). A single colony was inoculated into 150 mL of LB broth. Three inoculated flasks contained LB broth alone (controls), and three inoculated flasks were supplemented with cranberry PACs (100 µg/mL). After incubation (37°C, 5 h, 200 rpm to mid-log growth phase), bacteria were harvested for RNA extraction.
Project description:Transcriptional profiling of A. oleivorans DR1 treated Kanamycin 4µg/ml for 15min . To identify effect of kanamycin in A. oleivornas DR1, the cells were grown to exponential phase (OD600 ~0.4) and treated kanamycin 4µg/ml for 15 min.
Project description:We have employed a whole genome microarray for gene expression profilling to understand the global view of the cellular mechanism and metabolic response of B. cereus B3711 exposed to 1 mM silver nitrate. RNA was extracted from B. cereus grown under silver treated and untreated set of conditions in duplicates at two different time points (30 & 60 min). Comparing the transcript profile of the control and treated cells, several differentially expressed genes were identified. These includes genes involved in various metabolic pathways, such as arginine and alanine metabolism, membrane transport system and alternate respiratory proteins such as arsenate reductase, stress related proteins, proteins of transcriptional regulators, hypothetical proteins and protein of two-component systems. Agilent one-color experiment,Organism: Bacillus cereus ,Agilent-023971 Genotypic designed Custom Bacillus cereus 8x15k , Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)