Influence of nalidixic acid on gene expression of Escherichia coli
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ABSTRACT:
ORGANISM(S): Escherichia coli K-12 Escherichia coli
PROVIDER: GSE8674 | GEO | 2008/07/20
SECONDARY ACCESSION(S): PRJNA101887
REPOSITORIES: GEO
Similar Datasets
Project description:The intention of this study is to analyse the effect of antibiotics on the gene expression of Escherichia coli. Shaking-flask cultivations of Escherichia coli K12GFP-UTL2 were carried out with a medium containing nalidixic acid. Cultures with antibiotic-free medium, which were run in an identical way, served as reference. Samples were taken at different times during the cultivations, the RNA was isolated and hybridised on whole genome yeast microarrays. Keywords: Influence of toxins on gene expression in E. coli A timeserial experiment of the influence of nalidixic acid on the gene expression in Escherichia coli was performed. Effects of the growth curve were eliminated by bionformatic methods.
2010-05-25 | E-GEOD-8674 | biostudies-arrayexpress
Project description:Escherichia coli O157 presents a number of specific problems in terms of food safety and public health. It has been found that E. coli O157 is more resistant to a number of the stresses encountered during food production such as heat, pH and osmotic shock. This greater resistance is thought to contribute to the low infectious dose of E. coli O157 (<100 organisms). Moreover, E. coli O157 is associated with debilitating conditions such as haemorrhagic colitis and haemoytic uraemic syndrome, particularly in children and the elderly. We have been studying the stress responses of E. coli O157:H7 (Sakai) and comparing with a commensal strain of E. coli K-12, MG1655. We found that E. coli O157 (Sakai) is more resistant to heat stress than MG1655. A microarray study of these strains subjected to sub-lethal heat-stress at 45M-BM-0C was carried out. In E. coli O157 (Sakai), 380 genes responded significantly to the treatment compared to 410 genes in MG1655. Overnight cultures of E. coli O157 (Sakai) and E. coli K-12 MG1655 were grown in Neidhardt's EZ Rich Defined Medium and diluted 1:100 in 50 ml fresh medium in 125 ml Ehrlenmeyer flasks. The cultures were shaken at 37M-BM-0C until the optical density (OD600) reached 0.4. Each culture was divided into 2 equal parts in identical flasks. One flask flask was transferred to a shaking water bath and incubated at 45M-BM-0C for 10 min; the other flask was incubated at 37M-BM-0C for 10 min. After incubation, the cultures were transferred to 50 mL centrifuge tubes and treated with RNAprotectM-bM-^DM-" to stabilise the mRNA. The experiment was performed 3 times on different days. Six custom-made microarray slides were used in this study; each slide was hybridised with labelled cDNA made from untreated and heated E. coli O157 (Sakai) or MG1655.
2018-03-20 | E-MTAB-5912 | biostudies-arrayexpress
Project description:The effect of an extracellular acid shift on gene expression profiles of Escherichia coli K-12 W3110 was observed using Affymetrix E. coli arrays. In order to maximize aeration and maintain logarithmic growth, the overnight culture (LBK broth medium) was diluted 500-fold into a 250-ml baffled flask containing 55 ml of 20mM HOMOPIPES buffered medium (pH 7.6). Cultures were grown to OD600=0.2. A shift to acid external pH was conducted by rapid addition of 840 µl 1M HCl, which lowered the pH of the medium to pH 5.5. For each of five biological replicates, 10-ml samples were taken at times 0, 1, 5, and 10 min post addition of HCl. Each sample was added to 1 ml 10% phenol-ethanol stop solution in <5 sec. For each sample, cDNA synthesized from total RNA was hybridized onto Affymetrix E. coli arrays. Model-based gene expression intensities were determined using GCOS software. Gene-by-gene temporal differential expression was analyzed as a mixed-effects model using polynomial time functions as fixed effects and flask variation as a random effect. Keywords: Time Course
2008-02-20 | GSE4778 | GEO
Project description:Expression and use of motility genes is a potentially beneficial but costly process in bacteria. Interestingly, many isolate strains of Escherichia coli possess motility genes but have lost the ability to activate them in conditions in which motile cells are advantageous, raising the question of how they respond to these situations. Through transcriptome profiling of strains in the E. coli single-gene knockout Keio collection, we noticed drastic upregulation of motility genes in many of the deletion strains as compared to its typically non-motile parent strain (BW25113). This switch to a motile phenotype is not a direct consequence of the genes deleted, but is instead due to a variety of secondary mutations that increase the synthesis of the major motility regulator, FlhDC. We found that a phenotypic switch to motility at a population level can be induced in non-motile E. coli strains by incubation in non-shaking liquid medium overnight but not in shaking media. Individual isolates after the overnight incubation acquired distinct mutations upstream of the flhDC operon, including different insertion sequence (IS) elements and, to a lesser extent, point mutations. The rapid sweep in the non-shaking population shows that non-motile strains without existing regulatory mechanisms can quickly adapt to a motile lifestyle by quickly acquired genetic changes.
2019-07-11 | GSE129161 | GEO
Project description:A microarray study was performed to identify the Escherichia coli SlyA regulon. The wild-type (parental) Escherichia coli MG1655 strain was compared to an isogenic slyA deletion mutant, whilst a slyA-overexpression strain (in pET28a) was compared to an empty (pET28a) vector control. Continuous chemostat cultures were obtained (Evans medium pH 6.9, 0.2 h-1 dilution rate, 1 culture volume per hour air input, 400 rpm). Samples were eluted directly into RNAprotect, RNA purified and then hybridised in a reference-style format to micorarrays.
2017-01-25 | E-MTAB-5220 | biostudies-arrayexpress
Project description:Long-term experiment (150 days) of Escherichia coli MC1000 with daily transfers into fresh LB medium and under three different oxygen regimes. An overnight culture of E coli (ancestor culture) was propagated in LB media with three different oxygen regimes during 150 days. One regime involved transfers under constant shaking (200rpm): Treatment A-Replica populations 1 and 2 , second regime consisted in a daily shift between shaking and static (no shaking) conditions: Treatment B-replica populations 3,4 and 5. The third regime involved transfers in constant static conditions: Treatment C-Populations 6 and 7. After 150 days and plating, 3 different colony types were selected by population (populations 6 and 7 only had 2 different morphologies). Morpholigies were marked as a, b, c in each population. cDNA was obtainned from each morphology after growing separately in LB medium, under they correspondant evolving condition until late logaritmic phase (0,6-0,7 in OD600). A total of 19 evolved forms were analyzed plus one ancestor. Each morphology was labeled in a dye-swap design and hybridized to the ancestor into genome-wide multi-strain E. coli (8x15K) microarrays.
2013-03-01 | E-GEOD-44614 | biostudies-arrayexpress
Project description:The pyruvate dehydrogenase regulator protein (PdhR) of Escherichia coli acts as a transcriptional regulator in a pyruvate dependent manner to control central metabolic fluxes. However, the complete PdhR regulon has not yet been uncovered. To achieve an extended understanding of its gene regulation network, we combined large-scale network inference and experimental verification of results obtained by a systems biology approach. We determined the gene expression of four different strains of E. coli on three different media. The four strains corresponded to the wild-type E. coli (LJ110), a PdhR knockout mutant (LJ110deltapdhR), a strain carrying an empty plasmid (LJ110/pTM30) and a PdhR overexpression strain (LJ110/pTM30PdhRhis). These strains were cultivated on Luria-Bertani broth (LBo), standard phosphate minimal medium supplemented with acetate and standard phosphate minimal medium supplemented with pyruvate. We obtained an overall 24 microarray experiments from two replicates of each of these cultivations.
2011-12-21 | E-GEOD-31333 | biostudies-arrayexpress
Project description:The effect of an extracellular acid shift on gene expression profiles of Escherichia coli K-12 W3110 was observed using Affymetrix E. coli arrays. In order to maximize aeration and maintain logarithmic growth, the overnight culture (LBK broth medium) was diluted 500-fold into a 250-ml baffled flask containing 55 ml of 20mM HOMOPIPES buffered medium (pH 7.6). Cultures were grown to OD600=0.2. A shift to acid external pH was conducted by rapid addition of 840 µl 1M HCl, which lowered the pH of the medium to pH 5.5. For each of five biological replicates, 10-ml samples were taken at times 0, 1, 5, and 10 min post addition of HCl. Each sample was added to 1 ml 10% phenol-ethanol stop solution in <5 sec. For each sample, cDNA synthesized from total RNA was hybridized onto Affymetrix E. coli arrays. Model-based gene expression intensities were determined using GCOS software. Gene-by-gene temporal differential expression was analyzed as a mixed-effects model using polynomial time functions as fixed effects and flask variation as a random effect. Experiment Overall Design: Gene expression profiles of Escherichia coli K-12 W3110 were compared as a function of time versus change in external pH. Overnight cultures were diluted 1:500 in potassium-modified Luria-Bertani medium (LBK) buffered with 20 mM HOMOPIPES at 7.6. Bacteria were cultured in baffled flasks (less than 10% volume) with rotation at 225 rpm, incubated at 37°C to an optical density at 600 nm of 0.2. External pH was lowered to pH 5.5 by adding 840 µl of 1M HCl to 40 mls of culture within 5 seconds. Four samples were taken from each of five replicate cultures, corresponding to time 0 (before HCl addition),1, 5, and 10 min post HCl addition.
2008-04-07 | E-GEOD-4778 | biostudies-arrayexpress
Project description:Responses of Escherichia coli as they are treated to Gamma radiation in Davis medium Keywords: time course
2006-03-08 | GSE4377 | GEO
Project description:The goal of this study is to analyse how the gene expression in Saccharomyces cerevisiae changes in dependency on the glucose concentration. Therefore, fed batch cultivations were carried out, during which the glucose concentration was maintained stable for several hours. Samples were taken at different times during the cultivations, the RNA was isolated and hybridised on whole genome yeast microarrays. Results from cultivations with the glucose concentrations 50, 70, 100 and 500 mg/L are presented. In addition, one sample from a starvation period (0 mg/L glucose) was analysed. Keywords: Dependency on glucose concentration
2007-12-02 | GSE6358 | GEO