Effect of STOP1 dificiency under low oxygen condition.
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ABSTRACT: Comparison of stop1-mutant vs. wild type (WT;Col-0) treated with low-oxygen stress, and gene expression responses to low-oxygen in Arabidopsis shoots. Biological replicates: 3 replicates of shoot sample.
Project description:The genome-wide transcriptional responses of the strictly aerobic -proteobacterium Gluconobacter oxydans 621H to oxygen limitation, to the absence of the cytochrome bc1 complex, and to low pH were studied using DNA microarray analyses. Oxygen limitation caused expression changes of 486 genes, representing 20% of the chromosomal genes. Genes with an increased mRNA level included those for terminal oxidases, the cytochrome bc1 complex, transhydrogenase, two alcohol dehydrogenases, heme biosynthesis, PTS proteins, proteins involved in cyclic diGMP synthesis and degradation, two sigma factors, flagella and chemotaxis proteins, several stress proteins, and a putative exporter protein. The downregulated genes comprised those for respiratory dehydrogenases, enzymes of central metabolism, PQQ biosynthesis, outer membrane receptors, Sec proteins, and proteins involved in transcription and translation. A M-NM-^TqrcABC mutant of G. oxydans showed a growth defect during cultivation on mannitol at pH 4 under oxygen saturation. Comparison of the transcriptomes of this mutant versus the wild type under these conditions revealed 51 differentially expressed genes. Interestingly, almost all of the 45 genes with increased expression in the M-NM-^TqrcABC mutant at pH 4 were also upregulated in the wild type grown at pH 6 under oxygen limitation. These results support an active role of the cytochrome bc1 complex in G. oxydans respiration. The transcriptome comparison of G. oxydans wild type at pH 4 versus pH 6 in mannitol medium under oxygen-saturated conditions uncovered only 72 differentially expressed genes. The 35 upregulated genes included those for cytochrome bd oxidase, major polyol dehydrogenase, iron storage and oxidative stress proteins. Among the 37 downregulated genes were some encoding enzymes dealing with carbon dioxide, such as biotin carboxylase, biotin carboxyl carrier protein, and carboanhydrase. These results give first insights into global transcriptional responses of G. oxydans. DNA microarray experiments were repeated independently three times for G. oxydans M-NM-^TqrcABC versus wild type and G. oxydans grown at pH 4 versus pH 6 and four times for G. oxydans grown at oxygen limitation versus pH oxygen saturation in biological replicates.
Project description:Whole genome expression profiles in response to different suspected stresses including heat, hypo-tonic conditions, oxygen and blood exposure were examined.
Project description:Bifidobacterium longum strain BBMN68 is resistant to low concentrations of oxygen. In this study, a transcriptomic study was performed to detail the cellular response of B. longum strain BBMN68 to oxidative stress. Oxygen and its intermediate metabolites, reactive oxygen species (ROS), induced abundant changes in gene expression at the mRNA level. Increased expression was found for genes involved in ROS detoxification and the redox homeostasis system, protein and DNA synthesis and repair, the FeâS cluster assembly system, and biosynthesis of branched-chain amino acids and tetrahydrofolate. Among them, two classes of ribonucleotide reductase (RNR), which are important for deoxyribonucleotide biosynthesis, were rapidly and persistently induced: first, the class Ib RNR NrdHIEF and then the class III RNR NrdDG. The increased resistance to oxygen and hydrogen peroxide conferred by NADH oxidase was confirmed by its heterogeneous overexpression in B. longum strain NCC2705. In addition, cell-membrane and cell-wall compositions were modified, probably by an increase in cyclopropane fatty acids and a decrease in polysaccharides, respectively, resulting in improved cell hydrophobicity and autoaggregation; this subsequently reduced the permeation of dissolved oxygen into the cell. Taken together, the proposed cell model of B. longum responses to oxygen stress suggests that this bacterium employs a complex molecular defense mechanism against oxygen-induced stresses. Whole mRNA profiles of B. longum BBMN68 grown in the absence or presence of 3% oxygen were generated using AB SOLiD technology and differentially expressed genes were analyzed.
Project description:This SuperSeries is composed of the following subset Series: GSE24073: Transcriptional profile of Candida albicans during Hypoxic conditions. GSE24074: Transcriptional profile of Candida albicans DAY286 culture without ketoconazole versus DAY286 culture with 0.04 μg/ml ketoconazole, both at 20% oxygen (normoxia). GSE24075: Transcriptional profile of Candida albicans DAY286 versus UPC2 delete, both at 1% oxygen (hypoxia). Refer to individual Series
Project description:In order to find out the vital genes during retinal neovascularization (RNV), we set up OIR (oxygen-induced retinopathy; induced with 75%±2% oxygen) and wild-type C57BL/6J murine models. We observed the retinal vascular growth process daily both in OIR and wild-type mice through retinal flat-mount, and isolated total retinal RNA at different time points (P8, P9, P12, P13, P30) both in OIR and wild-type mice for gene expression analysis. At least three different retinae were accessed at each time point for observing the retinal vascular growth process. Ten neural retinae from five mice were harvested and pooled into one sample for gene expression analysis. Three biological replicates were used for each time point. Dye-swaps were performed.
Project description:B. cenocepacia J2315 was grown on LB medium to mid-stationary phase at OD 0.3 under full aeration and then transferred into a 50 ml centrifuge tube and placed upright into a CampyGen Compact (Oxoid, Basingstoke, UK) plastic pouch containing the gas generating paper sachet. The pouch was sealed immediately and then the cap of the centrifuge tube loosened to allow exchange of atmosphere between centrifuge tube and pouch. <br>The culture was further incubated at 37 degrees centigrade and 150 rpm for 2-3 hours until it reached OD 0.5. The centrifuge tube was sealed before opening the pouch and then snap-cooled before harvest to minimise exposure to atmospheric oxygen and to ensure expression profiles reflect the lower oxygen concentration.<br>The expression profile was compared to cells grown to OD 0.5 at atmospheric oxygen concentrations.<br>
Project description:Transcriptional profiling of human PC-3 prostate cancer cells lentivirally infected with non-target control (NTC) short hairpin (sh)RNA comparing with lentivirally shRNA mediated human ETV4 knock-down. Cells were either cultured for 24 hours at 20% oxygen tension or 0.2% oxygen. Goal was to determine (i) genes affected by hypoxia in PC-3 NTC cells and (ii) identification of hypoxically induced genes requiring ETV4 for hypoxic regulation. four condition experiment, shNTC at 20% and 0.2% oxygen and shETV4 at 20% and 0.2% oxygen for 24 hours. Biological replicates: 3 for each of the 4 conditions
Project description:Low-oxygen stress associated with natural phenomena such as waterlogging, results in widespread transcriptome changes and a metabolic switch from aerobic respiration to anaerobic fermentation. High-throughput sequencing of small RNA libraries obtained from low-oxygen stressed and control root tissue identified a total of 65 unique microRNA (miRNA) sequences from 46 families, and 14 trans-acting small interfering RNA (tasiRNA) from 3 families. Low-oxygen stress resulted in changes to the abundance of 46 miRNAs from 19 families, and all 3 tasiRNA families. Chemical inhibition of mitochondrial respiration caused similar changes in expression in a majority of the low-oxygen responsive small RNAs analysed. Our data indicate that miRNAs and tasiRNAs play a role in gene regulation and possibly developmental responses to low oxygen, and that a major signal for these responses is likely to be dependent on mitochondrial function. Keywords: Small RNA transcriptome analysis Examination of root tissue under 2 different environments, control and low oxygen
Project description:B. cenocepacia J2315 was exposed to heat stress and to stress form reactive oxygen species. <br>To expose the cultures to heat stress, cells were grown at 37ºC to an O.D. of 0.4 to 0.45 and then transferred into a different shaking incubator at 42.5ºC, incubated for 1 hour at 150 rpm and harvested.<br>To expose cultures to oxidative stress by reactive oxygen species, cells were grown at 37ºC to an OD of 0.5. Then t butyl hydroperoxide or hydrogen peroxide solution were added to the culture at 0.001% and 0.15% final concentration. The culture was further incubated for 15 min and then harvested. <br>The expression profiles were compared to cells grown in LB medium without exposure to stress.<br>
Project description:Microarray transcriptional profiling was utilized to observe the global cellular state correlates of the physiological responses to temperature and oxygen changes. We provide evidence for the existence of correlations of Escherichia coli transcriptional responses to temperature and oxygen perturbations-precisely mirroring the co-occurrence of these parameters upon transitions between the outside world and the mammalian gastrointestinal-tract. Keywords: time course Physiological perturbations were carried out under a controlled environment in the context of bioreactor (Bioflo 110, New Brunswick Scientific) growth. Thermoelectric sensors and heaters were used to shift temperature profiles between 25 C and 37 C, and polarographic dissolved oxygen sensors (Mettler Toledo) and nitrogen gas was used to rapidly change oxygen saturation between anaerobic (0% dissolved oxygen) and aerobic (16-21% dissolved oxygen) condition. The cultures were maintained in exponential phase (O.D.600 0.2-0.4) through controlled dilution, where fresh media is pumped in and spent media is pumped out at a controlled rate. Prior to the perturbations, cells were maintained in the pre-transition environment for at least eight generations (8-24 hours). All experiments were performed in duplicate.