Ausgem Porcine and Human E. coli
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB21464 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| ERR2228580_1.fastq.gz | Fastqsanger.gz | |||
| ERR2228580_2.fastq.gz | Fastqsanger.gz | |||
| ERR2228590_1.fastq.gz | Fastqsanger.gz | |||
| ERR2228590_2.fastq.gz | Fastqsanger.gz |
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Project description:Epigenetic changes such as DNA methylations regulate gene expression patterns in response to environmental cues including infections. Microbial infections induced DNA methylation may play a potential role in modulating host-immune response. In the present study, we sought to determine DNA methylation changes induced by the mastitis causing Escherichia coli (E coli) in porcine mammary epithelial cells (PMEC). Two time points (3hr and 24 hr) were selected based on the specific transcriptomic changes as early and late phase immune responses. Genome-wide methylation information was obtained to identify significant differential methylation patterns in E coli infected PMEC.
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Project description:AusGEM-Australian Pathogen Genomics One Health E. coli
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Project description:Background: Members of E. coli serogroup O45 are porcine enteropathogenic E. coli (PEPEC) strains which cause post-weaning diarrhea and produce characteristic attaching and effacing (A/E) lesions. Most of O45 PEPEC strains possess the locus of enterocyte effacement (LEE), encoding the virulence factors for A/E lesions, and often possess the paa gene, which is thought to contribute to the early stages of PEPEC virulence. Methodology: Nine O45 PEPEC strains and a rabbit enteropathogenic (REPEC) strain, known to produce A/E lesions, were characterized using an E. coli O157-E. coli K12 whole genome microarray and a virulence gene-specific microarray, and by PCR experiments. Results: Based on their virulence genes profiles, the 10 strains were characterized as atypical EPEC. The differences in their genomes pointed to two distinct evolutionary groups of O45 PEPEC, Group I and Group II, and to the contribution these genetic differences have on virulence in pigs. Group I contained the REPEC strain and four O45 PEPEC strains known to induce severe A/E lesions in challenged pigs whereas Group II was composed of five other O45 PEPEC strains which induced less severe or no A/E lesions in challenged pigs. Significant differences between Groups I and II were found in the presence or absence of 50 O-Islands (OIs) or S-loops and 13 K-islands (KIs) or K-loops, including the virulence-associated islands OI#1 (S-loop#1), OI#47 (S-loop#71), OI#57 (S-loop#85), OI#71 (S-loop#108), OI#115, OI#122, and OI#154 (S-loop#253).
2009-07-11 | GSE17036 | GEO
Project description:Porcine mammary epithelial cell (PMEC) cultures of three lactating sows were treated with potential mastitis-causing pathogens E. coli and S. aureus in vitro. Subsequently transcriptome profiles were analysed after 3 h and 24 h post-challenge, respectively.
2015-12-18 | GSE64246 | GEO
Project description:To better understand the molecular effects of Enterotoxigenic Escherichia coli (ETEC) F4ab/ac infection, we performed a genome-wide comparison of the changes in DNA methylation in ETEC F4ab/ac infected porcine intestinal epithelial cells. Our data provides further insight into the epigenetic alterations of ETEC F4ab/ac infected porcine intestinal epithelial cells and may advance the identification of biomarkers and drug targets for predicting susceptibility to and controlling ETEC F4ab/ac induced diarrhea.
2020-04-06 | GSE143661 | GEO
Project description:The enteric nerve system (ENS) coordinates diverse gastrointestinal functions. The porcine gastrointestinal tract is increasingly regarded as a useful translational model. However, porcine ENS molecular profiling and its similarity to that of human are lacking. Bulk RNA sequencing (RNA-seq) coupled with laser-capture microdissection and single-cell RNA-seq on myenteric ganglia (MG) addressed that discrepant transcriptional programs explained the functional characteristics between inner submucosal and/or MG in porcine proximal or/and distal colon (p-pC, p-dC). Comparative bulk transcriptomics of MG in corresponding colonic regions of porcine and human revealed highly conserved programs existing in p-pC and p-dC, which interpreted >90% of their transcriptomic responses to vagal nerve stimulation (VNS), suggesting that p-pC and p-dC could serve as predictors in translational studies. At bulk and single-cell resolution, we highlighted specific conserved programs, executing inflammatory modulation in porcine with VNS. This study offers rich foundations to understand human colonic functions and neuromodulation using porcine model.
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Project description:Background While more than 700 microRNAs (miRNAs) are known in human, a comparably low number has been identified in swine. Because of the close phylogenetic distance to humans, pigs serve as a suitable model for studying e.g. intestinal development or disease. Recent studies indicate that miRNAs are key regulators of intestinal development and their aberrant expression leads to intestinal malignancy. Results Here, we present the identification of hundreds of apparently novel miRNAs in the porcine intestine. MiRNAs were first identified by means of deep sequencing followed by miRNA precursor prediction using the miRDeep algorithm as well as searching for conserved miRNAs. Second, the porcine miRNAome along the entire intestine (duodenum, proximal and distal jejunum, ileum, ascending and transverse colon) was unraveled using customized miRNA microarrays based on the identified sequences as well as known porcine and human ones. In total, the expression of 332 intestinal miRNAs was discovered, of which 201 represented assumed novel porcine miRNAs. The identified hairpin forming precursors were in part organized in genomic clusters, and most of the precursors were located on chromosomes 3 and 1, respectively. Hierarchical clustering of the expression data revealed subsets of miRNAs that are specific to distinct parts of the intestine pointing to their impact on cellular signaling networks. Conclusions In this study, we have applied a straight forward approach to decipher the porcine intestinal miRNAome for the first time in mammals using a piglet model. The high number of identified novel miRNAs in the porcine intestine points out their crucial role in intestinal function as shown by pathway analysis. On the other hand, the reported miRNAs may share orthologs in other mammals such as human still to be discovered.
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