RNA-seq of Acinetobacter oleivorans DR1: on hydrogen peroxide
ABSTRACT: Transcriptional profiling of A. oleivorans DR1 treated low and high level of hydrogen peroxide for 15min . Overall design: To identify effect of hydrogen peroxide in A. oleivornas DR1, the cells were grown to exponential phase (OD600 ~0.4) and treated 0.1mM/1mM hydrogen peroxide for 15 min.
Project description:Adaptation to hydrogen peroxide in Saccharomyces cerevisiae is profiled with expression arrays. Adaptation describes the process in which a mild dose of toxin (in this case, hydrogen peroxide) is able to protect against a later acute dose. Here, we study two adaptive protocols (0.1 mM H2O2 and 0.1 + 0.4 mM H2O2) and one acute protocol (0.4 mM H2O2) to identify processes uniquely involved in adaptation. Predictions from these studies are validated in expression profiling of deletion mutants of the transcription factors Yap1, Mga2, and Rox1. Overall design: Three different treatment protocols were studied. Pretreatment - 0.1 mM H2O2 for 45 minutes. Adapted - 0.1 mM H2O2 for 45 minutes, followed by 0.4 mM H2O2 for 1 hour. Acute - 0.4 mM H2O2 for 1 hour. Each treatment protocol was examined with 4x biological replicates, with the dye orientation reversed in two of the replicates (no technical replicates). The effect of the pretreatment protocol (0.1 mM H2O2) was also studied in three transcription factor deletion mutants (Yap1, Mga2, and Rox1) with the same number/orientation of biological replicates.
Project description:Reactive oxygen species such as hydrogen peroxide occur in all aerobically living organisms. Oxidative stress during fermentation can impair the fitness of the production host and the quality of the product. B. pumilus has been described as highly resistant to hydrogen peroxide. The response of exponentially growing B. pumilus cells to hydrogen peroxide was studied. Two-condition experiment, unstressed versus hydrogen peroxide stressed cells, 3 biological replicates
Project description:Oxidative stress caused by Menadione or Hydrogen peroxide in synchronized Saccharomyces cerevisiae cultures. Alpha factor synchronized cultures (0.2-0.4 OD), treated at the beginning of S phase (25 min after release from G1 arrest) with either 2 mM Menadione (MD) or 0.24 mM Hydrogen peroxide (HP), show cell cycle effects. Cells treated with MD arrested at G1. Cells treated with HP delayed at S and then, after removal of HP at 135 minutes , continued the cell cycle, only to arrest at G2/M. Growth was carried out in 30C with shaking (295 rpm). Two time course experiments were performed with each oxidative stress agent, designated as H2O2 and H2O2_II, MD and MD_II. Keywords = oxidative stress Keywords = menadione Keywords = hydrogen peroxide Keywords = time course Keywords = cell cycle Keywords = yeast
Project description:Yeast cells were grown up in SD media containing all required amino acids. Each strain set was performed in triplicate. One set had no changes, the second set had 1mM methionine supplenting the media for the duration of growth and the third set was exposed to 0.5mM hydrogen peroxide for 15 minutes prior to harvesting
Project description:Yeast cells response during recovery after hydrogen peroxide stress. Comparison of yeast cells treated with 1.5mM hydrogen peroxide for 30 min with cells allowed to recover for 60 min
Project description:To gain insight into the basic mechanism of Hydrogen peroxide detoxification in the methylotrophic yeast, H. polymorpha, we analyzed changes in transcriptional profiles in response to hydrogen peroxide exposure. Total RNA samples were collected from H. polymorpha cells after 30 min incubation with 0.5mM hydrogen peroxide. Using the RNA sample obtained prior to hydrogen peroxide addition as a reference, the differential fluorescence intensities of each RNA sample prepared at the indicated time was measured after labeling with Cy3 or Cy5 fluorochromes. For all analyses, we performed dye swapping experiments to avoid dye bias.
Project description:In the present study, we employed Affymetrix Staphylococcus aureus GeneChip arrays to investigate the dynamics of global gene expression profiles during the cellular response of Staphylococcus aureus to hydrogen peroxide-induced oxidative stress, which involved initial growth inhibition and subsequent recovery. Keywords: Time course Overall design: We conducted three independent microarray experiments (biological replicates) in the absence (control) and the presence (experimental) of hydrogen peroxide. We calculated fold change as the ratio between the signal averages of three untreated (control) and three hydrogen peroxide-treated (experimental) cultures for 10 and 20 min exposures.
Project description:Transcripitonal profiling of Escherichia coli K-12 W3110 comparing cells with and without hydrogen peroxide treatment, two biological replicates each One-condition experiment, cells with or without hydrogen peroxide treatment for 10min
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:Transcriptional profiling of A. oleivorans DR1 treated Ampicillin 100 µg/ml for 15min . To identify effect of ampicillin in A. oleivornas DR1, the cells were grown to exponential phase (OD600 ~0.4) and treated ampicillin 100 µg/ml for 15 min.