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
Project description:This study explores the effects of glycerol, on whole genome expression of Escherichia coli. DNA microarray analysis imply that E. coli in the presence of glycerol generates acidic metabolites to which it adapts by upregulation of genes involved in acid stress and by simultaneously downregulating genes involved in high pH stress.
Project description:Escherichia coli culture was subjected to two different types of nutritional scenarios, abundant carbon/ nitrogen sources and scarce carbon/nitrogen medium. Study revealed that scarce medium adapted culture were more tolerant to hydrogen peroxide than abundant medium.
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.
Project description:Investigation of whole genome gene expression level changes in a Escherichia coli MG1655 K-12 ∆hns/∆stpA strain from exponental growth under aerobic and anaerobic growth conditions. The results are further described in the article Genome-scale Analysis of E.coli FNR Reveals the Complex Features of Transcrtipion Factor Binding.
Project description:Purpose: In this study, Escherichia coli DH5alpha whole transcriptome sequencing was performed in order to compare the different gene expression profiles between control and exposed to Wi-Fi radiofrequency radiations. Methods:Escherichia coli DH5alpha were exposed to Wi-Fi radiations. Total RNA samples( control and exposed ) were extracted by bacteria protect-Rneasy kit,treated with DNAase and subjected to sequnecing using an Illumina-NovaSeq 6000 platform. Library preparation and sequencing were performed by Macrogen (south korea).Trimmed reads are mapped to reference genome with Bowtie. HTseq was used for expression profiling. Expression profile was calculated for each sample and gene as read count.
Project description:Investigation of whole genome gene expression level changes in a Escherichia coli MG1655 K-12 M-bM-^HM-^Fhns/M-bM-^HM-^FstpA strain from exponental growth under aerobic and anaerobic growth conditions. The results are further described in the article Genome-scale Analysis of E.coli FNR Reveals the Complex Features of Transcrtipion Factor Binding. A four chip study using total RNA recovered from two separate cultures of Escherichia coli MG1655 K-12 M-bM-^HM-^Fhns/M-bM-^HM-^FstpA mutant strain under aerobic and anaerobic growth conditions. Each chip measures the expression level of 4,661 genes from Escherichia coli MG1655 K-12 using a high-density tiling array consisting of ~385,000 60mer probes spaced every 12 bp.
Project description:Transcription profiling of wild type E. coli MG1655, intestine-adapted E. coli MG1655star, and E. coli MG1655 flhD mutant grown on glucose, mannose, and mucus. We previously isolated a spontaneous mutant of E. coli K-12, strain MG1655, following passage through the streptomycin-treated mouse intestine, which has colonization traits superior to the wild-type parent strain (Leatham, et. al., 2005, Infect Immun 73:8039-49) The intestine-adapted strain (E. coli MG1655star) grew faster on several different carbon sources compared to the wild-type and was non-motile due to deletion of the flhD gene. To further characterize E. coli MG1655star, we used several high-throughput genomic approaches. Whole-genome pyrosequencing did not reveal any changes on its genome, aside from the deletion at the flhDC locus, that could explain the colonization advantage of E. coli MG1655star. Microarray analysis revealed modest, yet significant induction of catabolic gene systems across the genome in both E. coli MG1655star and the isogenic flhD mutant. Catabolome analysis with Biolog GN2 Microplates revealed an enhanced ability of both E. coli MG1655star and the isogenic flhD mutant to oxidize a wide variety of carbon sources. The results show that intestine-adapted E. coli MG1655star is more fit than the wild-type for intestinal colonization because loss of FlhD results in elevated expression of genes involved in carbon and energy metabolism, leading to more efficient carbon source utilization, which results in a higher population size in the intestine. Hence mutations that enhance metabolic efficiency confer a colonization advantage.
Project description:Counting DNA reads using whole genome sequencing is providing new insight into DNA double-strand break repair (DSBR) in the model organism Escherichia coli. We describe the application of RecA chromatin immunoprecipitation coupled to genomic DNA sequencing (RecA-ChIP-seq) and marker frequency analysis (MFA) to analyse the genomic consequences of DSBR.
Project description:Counting DNA reads using whole genome sequencing is providing new insight into DNA double-strand break repair (DSBR) in the model organism Escherichia coli. We describe the application of RecA chromatin immunoprecipitation coupled to genomic DNA sequencing (RecA-ChIP-seq) and marker frequency analysis (MFA) to analyse the genomic consequences of DSBR.
