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:Comparative genomic hybridization between Escherichia coli strains to determine core and pan genome content of clinical and environmental isolates
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:Background: This study aimed to explore potential tobramycin-resistant mutagenesis of Escherichia coli (E. coli) strains after spaceflight. Methods: A spaceflight-induced mutagenesis of multi-drug resistant E.coli strain (T1_13) on the outer space for 64 days (ST5), and a ground laboratory with the same conditions (GT5) were conducted. Both whole-genome sequencing and RNA-sequencing were performed. Results: A total of 75 SNPs and 20 InDels were found to be associated with the resistance mechanism. Compared to T1_13, 1242 genes were differentially expressed in more than 20 of 38 tobramycin-resistant E. coli isolates while not in GT5. Function annotation of these SNPs/InDels related genes and differentially expressed genes was performed. Conclusion: This study provided clues for potential tobramycin-resistant spaceflight-induced mutagenesis of E. coli.
Project description:Comparative genomic hybridization between Escherichia coli strains to determine core and pan genome content of clinical and environmental isolates Two color experiment, Escherichia coli Sakai (reference), clinical and environmental Escherichia coli strains (testers): At least two replicates including a single dye swap for each reference-tester comparison
Project description:we designed a CRISPR-based chromosome-doubling technique to construct an artificial diploid Escherichia coli cell. The stable diploid E. coli was confirmed by quantitative PCR and third-generation genome sequencing.
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: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:The model prokaryote Escherichia coli can exist as a either a commensal or a pathogen in the gut of diverse mammalian hosts. These associations, coupled with its ease of cultivation and genetic variability, have made E. coli a popular indicator organism for tracking the origin of fecal water contamination. Source tracking accuracy is predicated on the assumption that E. coli isolates recovered from contaminated water present a genetic signature characteristic of the host from which they originated. In this study, we compared the accuracy with which E. coli isolated from humans, bear, cattle and deer could be identified by standard fingerprinting methods used for library-based microbial source tracking (repetitive element PCR and pulsed-field gel electrophoresis) in relation to microarray-based analysis of genome content. Our results show that patterns of gene presence or absence were more useful for distinguishing E. coli isolates from different sources than traditional fingerprinting methods, particularly in the case of human strains. Host-associated differences in genome composition included the presence or absence of mobile IS1 elements as well as genes encoding the ferric dicitrate iron transporter (fec), E. coli common pilus (ECP), type 1 fimbriae and the CRISPR associated cas proteins. Many of these differences occurred in regions of the E. coli chromosome previously shown to be “hot spots” for the integration of horizontally-acquired DNA. PCR primers designed to amplify the IS1 and fec loci confirmed array results and demonstrated the ease with which gene presence/absence data can be converted into a diagnostic assay. The data presented here suggest that, despite the high level of genetic diversity observed among isolates by PFGE, human-derived strains may constitute a distinct ecotype distinguished by multiple potential library-independent source tracking markers.
