ABSTRACT: This SuperSeries is composed of the following subset Series: GSE36341: mRNA degradation in Mycobacterium tuberculosis under aerobic conditions GSE36342: mRNA degradation in Mycobacterium smegmatis under aerobic conditions GSE36343: mRNA degradation in Mycobacterium tuberculosis during cold and hypoxic stress GSE36344: mRNA degradation in Mycobacterium tuberculosis with DosR ectopically induced Refer to individual Series
Project description:Transcription was arrested using 50 ug/ul of rifampin leaving RNA degradation as the sole vector responsible for mRNA abundance. mRNA half-lives were calculated from the decay of signal intensity from T0. Three replicates were sampled before transcription arrest, and after 5 and 10 minutes of mRNA decay for a total of 9 arrays. Five minutes of RNA degradation occurred during the processing of these samples, therefore sample times, indicated in the sample name, represent 0, five, and ten minutes of RNA degradation.
Project description:Transcription was arrested using 50 ug/ul of rifampin leaving RNA degradation as the sole vector responsible for mRNA abundance. mRNA half-lives were calculated from the decay of signal intensity from T0. Four replicates were sampled after 0, 5 10, 15, 20, and 30 minutes of mRNA decay for a total of 24 arrays.
Project description:Transcription was arrested using 50 ug/ul of rifampin leaving RNA degradation as the sole vector responsible for mRNA abundance at 20C (cold) or in 0.2%O2 (hypoxia). mRNA half-lives were calculated from the decay of signal intensity from T0. Three replicates were sampled after 0, 1, 2, and 5 hours of mRNA decay in both cold and hypoxia for a total of 24 arrays.
Project description:After induction of DosR from a tet regulated promoter (uninduced controls were treated with an equivalent ammount of the solvent, DMSO), transcription was arrested using 50 ug/ul of rifampin leaving RNA degradation as the sole vector responsible for mRNA abundance. mRNA half-lives were calculated from the decay of signal intensity from T0. Three replicates for each condition (DosR induced and uninduced) were sampled after 0, 10, 20, 30, and 60 minutes of mRNA decay for a total of 30 arrays.
Project description:The bacteriostatic and bactericidal effects and the corresponding expression profiles of Mycobacterium tuberculosis to representative oxidative and nitrosative stresses were investigated by growth and survival studies and whole genome expression analysis. The response of M. tuberculosis to a range of hydrogen peroxide (H2O2) concentrations tended to fall into three distinct categories: (1) low level exposure resulted in induction of few H2O2 sensitive genes, (2) intermediate exposure resulted in massive transcriptional changes without an effect on growth or survival, and (3) high exposure resulted in a muted transcriptional response and eventual death. Nitric oxide (NO) exposure initiated much of the same transcriptional response as H2O2. However, unlike H2O2 exposure, NO exposure affected a dose-dependent bacteriostatic activity without killing and induction of dormancy-related genes. Included in the shared response to H2O2 and NO was the induction of genes encoding oxidative stress detoxification and iron-sulfur cluster repair functions. Expression of several key oxidative stress defense genes was constitutive, or increased moderately from an already elevated level, suggesting bacilli that are continually primed for oxidative stress defense. Deletion of the known oxidative stress responsive regulator, FurA, resulted in the constitutive expression of furA, katG, and Rv1907c; while other genes do not appear to be solely controlled by FurA. In contrast to Escherichia coli, M. tuberculosis appears highly resistant to DNA damage-dependent killing caused by low mill molar levels of H2O2. Furthermore, instead of limiting access to iron to prevent hydroxyl radical formation from H2O2 and thus DNA damage, M. tuberculosis induced iron uptake genes in response to H2O2 and NO. Set of arrays that are part of repeated experiments Compound Based Treatment: H2O2 or DETA/NO treatment
Project description:We used DNA microarrays to detect differentially expresses genes in a spontaneous mutant of Mycobacterium tuberculosis H37Rv resistant to azoles. We identified three adjacent upregulated genes encoding a transcription regulatory protein and two membrane proteins belonging to the family of RND efflux transporters. Hybridization were performed using RNA extracted from three different biological samples coming from cultures grown in mid-exponential phase.
Project description:Transcriptional profile of chemically generated Mycobacterium tuberculosis cell wall deficient forms, comparing untreated control cells (bacillary forms) and cell wall deficient cells. Two-condition experiment, MTB-K vs. MTB-Sph cells. Biological replicates: 3 controls, 3 spheroplasts, independently grown and harvested. In controls and spheroplasts, good quality RNA samples obtained from each pellet were pooled together and used for microarray experiments to get an average of three separate experiments, five replicates per array.
Project description:This study uses microarray analyses to examine baseline gene expression profiles for Mycobacterium tuberculosis complex clinical isolates relative to reference strain CDC1551 during log phase growth in vitro in 7H9 broth. For this in vitro analyses, log-phase mycobacteria in starter cultures grown to mid-log from frozen stocks were inoculated into 7H9-OADC medium in 25-cm2 vented flasks at an OD of ~0.05 and grown without shaking for ~1 week to an OD of ~0.5-0.6. Computed