Escherichia coli
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ABSTRACT:
PROVIDER: PRJNA238565 | ENA |
REPOSITORIES: ENA
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Project description:Wild type and hemA strains of Escherichia coli MG1655 were grown under anaerobiosis in batch culture in custom-made, stirred (200 rpm) 250 ml mini-fermenter vessels at 37 °C during continuous sparging with 100 % nitrogen gas. Cells were grown in defined medium (pH 7.0) containing 0.5 % glucose as the sole and limiting source of energy and carbon. The medium was supplemented with 0.1 % casamino acids and 5 % LB to support the growth of the hemA mutant. For maintenance of the hemA mutation, 50 mg/ml kanamycin were added to cultures of the heme-deficient mutant only. CORM-3 (final concentration of 100 uM) was added to wild type and mutant cultures at an OD600 of 0.2. iCORM-3 (final concentration of 100 uM) was added to only mutant cultures at an OD600 of 0.2. Samples were taken immediately prior to the addition of CORM-3 or iCORM-3 and at consecutive time-points thereafter (10, 20, 40, 60 and 120 min) for microarray analysis. Cells were harvested directly into phenol:ethanol to stabilise RNA and total RNA was purified using Qiagen’s RNeasy Mini Kit, according to the manufacturer's instructions. Time-course experiments with samples taken immediately prior to or 10, 20, 40, 60 and 120 min after addition of 100 uM CORM-3, or 100 uM iCORM-3 for the hemA mutant only, under 100 % anaerobiosis; 2 independent biological experiments were performed for each condition with 2 technical (dye swap) repeats per biological experiment.
2015-04-01 | E-GEOD-55097 | biostudies-arrayexpress
Project description:Wild type and hemA strains of Escherichia coli MG1655 were grown under anaerobiosis in batch culture in custom-made, stirred (200 rpm) 250 ml mini-fermenter vessels at 37 °C during continuous sparging with 100 % nitrogen gas. Cells were grown in defined medium (pH 7.0) containing 0.5 % glucose as the sole and limiting source of energy and carbon. The medium was supplemented with 0.1 % casamino acids and 5 % LB to support the growth of the hemA mutant. For maintenance of the hemA mutation, 50 mg/ml kanamycin were added to cultures of the heme-deficient mutant only. CORM-3 (final concentration of 100 uM) was added to wild type and mutant cultures at an OD600 of 0.2. iCORM-3 (final concentration of 100 uM) was added to only mutant cultures at an OD600 of 0.2. Samples were taken immediately prior to the addition of CORM-3 or iCORM-3 and at consecutive time-points thereafter (10, 20, 40, 60 and 120 min) for microarray analysis. Cells were harvested directly into phenol:ethanol to stabilise RNA and total RNA was purified using Qiagen’s RNeasy Mini Kit, according to the manufacturer's instructions.
2015-04-01 | GSE55097 | GEO
Project description:The present study investigated the role(s) of RNase I (encoded by the rna gene) in Escherichia coli by comparative gene expression analysis of an rna mutant and the isogenic wild-type E. coli strain BW25113. The transcriptomic analysis aims to provide mechanistic insight into aberrant phenotypes observed in the RNase I-deficient mutant.
2020-01-04 | E-MTAB-6095 | biostudies-arrayexpress
Project description:Treatment of urinary tract infections is today a challenge due to the increasing prevalence of multidrug-resistant ESBL-producing uropathogenic Escherichia coli (UPEC). There is an urgent need for new treatment strategies for multidrug-resistant UPEC and preferably with targets that have low potential for development of resistance. Carbon monoxide-releasing molecules (CORMs) are novel and potent antibacterial agents. The present study examines the transcriptomic targets of CORM-2 in a multidrug-resistant ESBL-producing UPEC isolate (ESBL7) in response to a single exposure to CORM-2 and after repeated exposure to CORM-2. The bacterial viability and minimal inhibitory concentration (MIC) were also examined after repeated exposure to CORM-2. Microarray analysis revealed that a wide range of processes were affected by CORM-2, including a general trend of down-regulation in energy metabolism and biosynthesis pathways and up-regulation of the SOS response and DNA repair. Several genes involved in virulence (ibpB), antibiotic resistance (marAB, mdtABC) and biofilm formation (bhsA, yfgF) were up-regulated, while some genes involved in virulence (kpsC, fepCEG, entABE), antibiotic resistance (evgA) and biofilm formation (artIP) were down-regulated. Repeated exposure to CORM-2 did not alter the gene expression patterns, the growth inhibitory response to CORM-2 or the MIC values for CORM-2, cefotaxime, ciprofloxacin and trimethoprim.
2016-10-06 | GSE87627 | GEO
Project description:Escherichia coli strain MG1655 was grown in a New Brunswick Scientific Bioflow III Biofermentor under continuous culture (chemostat) conditions. Cells were grown in defined media containing 2 mM glycerol as the sole and limiting source of energy and carbon. The working volume was 200 ml, and the dilution rate 0.2 h-1. For aerobic growth, the air-flow rate was 0.1 l/min, and the dissolved oxygen tension was maintained at ~7% air saturation by measuring oxygen dissolved in the culture using a Broadley James D140 OxyProbeM-BM-. electrode. For anaerobic growth, cells are grown on 100 % nitrogen gas bubbled at 0.1 l/min Cells were grown as above to steady-state, At steady-state, CORM-3 or iCORM-3 was added to the chemostat culture at a final concentration of 40 uM. Samples were taken immediately prior to the addition of CORM-3 or iCORM-3 and over a time course of 2.5, 5, 10, 20, 40 and 80 min exposure to (i)CORM-3 for subsequent analysis using microarrays. Cells were harvested directly into phenol:ethanol to stabilize RNA, and total RNA was purified using QiagenM-bM-^@M-^Ys RNeasy Mini kit as recommended by the suppliers. Time course experiment with samples taken immediately prior to or 2.5, 5, 10, 20, 40 or 80 minutes after addition of either 40uM CORM-3 or iCORM-3 under either 0 or 100 % perceived aerobiosis. 2 biological repeats were performed for each condition with 2 technical (dye swap) repeats per biological repeat.
2013-08-21 | E-GEOD-40811 | biostudies-arrayexpress
Project description:Escherichia coli strain MG1655 was grown in a New Brunswick Scientific Bioflow III Biofermentor under continuous culture (chemostat) conditions. Cells were grown in defined media containing 2 mM glycerol as the sole and limiting source of energy and carbon. The working volume was 200 ml, and the dilution rate 0.2 h-1. For aerobic growth, the air-flow rate was 0.1 l/min, and the dissolved oxygen tension was maintained at ~7% air saturation by measuring oxygen dissolved in the culture using a Broadley James D140 OxyProbe® electrode. For anaerobic growth, cells are grown on 100 % nitrogen gas bubbled at 0.1 l/min Cells were grown as above to steady-state, At steady-state, CORM-3 or iCORM-3 was added to the chemostat culture at a final concentration of 40 uM. Samples were taken immediately prior to the addition of CORM-3 or iCORM-3 and over a time course of 2.5, 5, 10, 20, 40 and 80 min exposure to (i)CORM-3 for subsequent analysis using microarrays. Cells were harvested directly into phenol:ethanol to stabilize RNA, and total RNA was purified using Qiagen’s RNeasy Mini kit as recommended by the suppliers.
2013-08-21 | GSE40811 | GEO
Project description:The purpose of this study is to determine whether the presence of pathogenic Escherichia coli in colon is associated with psychiatric disorders.
| 2230352 | ecrin-mdr-crc
Project description:We recently reported that carbon monoxide (CO) has bactericidal activity. To understand its mode of action we analysed the gene expression changes occurring when Escherichia coli, grown aerobically and anaerobically, is treated with the carbon monoxide releasing molecule, CORM-2. The E. coli microarray analysis shows that E. coli CORM-2 response is multifaceted with a high number of differentially regulated genes spread through several functional categories, namely genes involved in inorganic ion transport and metabolism, regulators, and genes implicated in posttranslational modification, such as chaperones. CORM-2 has higher impact in E. coli cells grown anaerobically, as judged by the existence of repressed genes belonging to eight functional classes which are absent in aerobically CORM-2 treated cells. In spite of the relatively stable nature of the CO molecule, our results show that CO is able to trigger a significant alteration in the transcriptome of E. coli which necessarily has effects in several key metabolic pathways.
2008-12-17 | GSE13982 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE12877: Transcriptional profiling of Escherichia coli after addition of CO-RMs to aerobically growing cells GSE12878: Transcriptional profiling of Escherichia coli after addition of CO-RMs to anaerobically growing cells Refer to individual Series
2010-06-24 | E-GEOD-13048 | biostudies-arrayexpress
Project description:Escherichia coli strain MG1655 was grown in a New Brunswick Scientific Bioflow III Biofermentor under continuous culture (chemostat) conditions. Cells were grown in Evans media containing 2 mM glucose as the sole and limiting source of energy and carbon. The working volume was 200 ml, and the dilution rate 0.2 h-1. For aerobic growth, the air-flow rate was 0.1 l/min, and the dissolved oxygen tension was maintained at ~7% air saturation by measuring oxygen dissolved in the culture using a Broadley James D140 OxyProbe® electrode. For anaerobic growth, cells are grown on 100 % nitrogen gas bubbled at 0.1 l/min Cells were grown as above to steady-state, At steady-state, CO gas was bubbled through the culture at 0.1L/min. Samples were taken immediately prior to the addition of CORM-401 and over a time course of 2.5, 5, 10, 20, 40 and 80 min exposure to CORM-401 for subsequent analysis using microarrays. Cells were harvested directly into phenol:ethanol to stabilize RNA, and total RNA was purified using Qiagen’s RNeasy Mini kit as recommended by the suppliers.
2017-05-31 | GSE71784 | GEO