Project description:We have previously reported that phosphoenolpyruvate carboxykinase(Pck) overexpression under glycolytic conditions enables Escherichia coli to harbor a high intracellular ATP pool resulting in enhanced recombinant protein synthesis and biohydrogen production. To understand possible reasons of the high ATP haboring cell, we carried out transcriptome and metabolic flux analysis.
Project description:The purpose of this study is to determine whether the presence of pathogenic Escherichia coli in colon is associated with psychiatric disorders.
Project description:This dataset is part of a study aimed at developing algorithms for the quantification of stable isotope content in microorganisms after labeling them with stable isotope-labeled substrates. In this dataset Escherichia coli cultures were labeled with different percentages (1% or 10%) of either single-carbon 13C glucose (13C2) or fully-labeled 13C glucose (13C1-6). Labeled cells were subsequently mixed with unlabeled E. coli cells in fixed ratios (50%, 90%, 95%, 99%). Cultures of E. coli were grown in M9 minimal medium in which a percentage of the glucose was replaced with 13C2 or 13C1-6 glucose for >10 generations to achieve close to complete labeling of cells. Triplicate cultures were grown for each percentage. Please note that the unlabeled glucose that was used of course had a natural content of 13C of around 1.1%, thus the 0% added label samples have an actual 13C content of 1.1% and all added label is on top of this value. We included a tab delimited table with this submission providing details on all raw files.
Project description:Escherichia coli release Extracellular Vesicles (EVs) which carry diverse molecular cargo. Pathogenic E.coli EVs contain virulence factors which assist during infection in the host in different mechanisms.The RNA cargo of E.coli EVs has not been assessed in their effect in the host. We used microarray data to asses and compare the global response of bladder cells to EV-RNA from pathogenic E.coli (Uropathogenic UPEC 536) and non-pathogenic E. coli (probiotic Nissle 1917)
Project description:Escherichia coli (E. coli) amine oxidase (ECAO) encoded by tynA gene has been one of the model enzymes to study the mechanism of oxidative deamination of amines to the corresponding aldehydes by amine oxidases. The biological roles of ECAO have been less addressed. Therefore we have constructed a gene deletion Escherichia coli K-12 strain, E. coli tynA-, and used the microarray technique to address its function by comparing the total RNA gene expression to the one of the wt. Our results suggest that tynA is a reserve gene for stringent environmental conditions and its gene product ECAO a growth advantage compared to other bacteria due to H2O2 production.
Project description:Despite the characterization of many aetiologic genetic changes. The specific causative factors in the development of sporadic colorectal cancer remain unclear. This study was performed to detect the possible role of Enteropathogenic Escherichia coli (EPEC) in developing colorectal carcinoma.
Project description:This dataset has been used to establish GroEL-SIP, coupling a targeted proteotyping approach for assessing bacterial community compositions using the taxonomic marker protein GroEL with stable isotope probing to link the identified taxa to substrate assimilation. This dataset contains raw data of four experiments: 1.) Pure cultures of T. aromatica cultivated with 13C or 12C benzoate mixed in defined ratios. 2.) Pure cultures of P. putida cultivated with 13C or 12C benzoate mixed in a 1:1 ratio. 3.) Pure cultures of E. coli cultivated with 12C acetate and 13C or 12C benzoate mixed in a 1:1 ratio. 4.) Co-cultivated biculture of T. aromatica and P. putida cultivated with 13C or 12C benzoate and mixed in a 1:1 ratio. 5.) Co-cultivated biculture of T. aromatica and E. coli cultivated with 12c acetate and 13C or 12C benzoate and mixed in a 1:1 ratio. 1)-3) were analyzed after in-solution digestion 4)-5) were analyzed after in-gel digestion of the 60 kDa band
Project description:This research focuses on the design, manufacturing and validation of a new E. coli whole-genome tiling micraorray platform for novel RNA transcript discovery. A whole-genome tiling microarray allows both annotated genes as well as previously unknown RNA transcripts to be detected and quantified at once. The E. coli MG1655 genome is re-acquired with next-generation sequencing and then used to design the tiling microarray with the thermodynamic analysis program Picky. Validations are performed by subjecting E. coli under various growth conditions and then using the tiling microarrays to verify expected gene expression patterns.
Project description:We used trimethylpsoralen intercalation to map supercoiling across the E. coli chromosome. We treated E. coli cells with trimethylpsoralen and exposed them to UV light. Psoralen enters cells, intercalates between DNA base pairs, and crosslinks the two strands of DNA at a rate proportional to the local superhelical density. We then fragmented DNA and hybridized crosslinked and non-crosslinked DNA fragments separately to tiling microarrays.
Project description:NsrR is a nitric oxide sensitive regulator of transcription. In Escherichia coli, NsrR is a repressor of the hmp gene encoding the flavohemoglobin that detoxifies nitric oxide. Several other transcription units (including ytfE, ygbA and hcp-hcr) are known to be subject to regulation by NsrR. In this study, chromatin immunoprecipitation and microarray analysis was used to identify NsrR binding sites in the chromosome of Escherichia coli strain MG1655. Keywords: ChIP-chip