Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Altered microRNAs expression and gene expression in allicin-treated ileal tissues revealed their potential roles in regulating host responses to antimicrobials

ABSTRACT: Allicin is a natural extract from garlic that has been used as an antibiotic alternative in livestock production. Limited knowledge is known about the effects of allicin on gut microbiota and tissue. The aim of this study was to investigate the effects of allicin on the expression of ileal miRNAs and the tissue-associated total bacterial density in pre-weaned calves. Different doses of allicin (0 mg, 0.5 mg, 5 mg, 50 mg and 500 mg) were used to treat in vivo ileal loop tissues in pre-weaned calves for different periods (1 day, 3 days and 12 days). A total of 15 miRNAs showed allicin dose-dependent differential expression patterns. Four miRNAs (miR-132, miR-423-5p, miR-429 and miR-6529a) were upregulated in 50 mg or 500 mg treated gut tissues, while 11 miRNAs (miR-190a, miR-193a-3p, miR-196a, miR-196b, miR-2285aa, miR-2285o, miR-2887, miR-2904, miR-409a, miR-6523a and miR-96) were downregulated in 50 mg or 500 mg treated gut tissues. Functional analysis of differentially expressed mRNAs showed that the upregulated mRNAs regulate functions that may be involved in “disrupted microtubule function”, and the downregulated miRNAs may be associated with the “inhibited leukocyte transendothelial migration” and “promoted cell phagocytosis”.

ORGANISM(S): Bos taurus

PROVIDER: GSE74503 | GEO | 2016/11/01

SECONDARY ACCESSION(S): PRJNA300570

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Expression data of ileal mucosa in developing piglets

Project description:The transcriptome changes of the ileal mucosa in suckling piglets during early postnatal life were analysed to contribute to the knowledge of a pig’s gut development. In addition, the ileal transcriptome of suckling piglets was compared with that of age-matched weaned piglets (weaned at the age of 21 days) to elucidate the effect of weaning on the developing gut. DNA microarray was used to analyse the change of transcriptome profiles and biological pathways in porcine ileum that occurred during the developmental or the weaning process.

2015-09-30 | GSE65008 | GEO

Potential regulatory role of microRNAs in the development of bovine gastrointestinal tract during early life

Project description:Purpose: The aims of this study were to profile miRNAs throughout the GIT during the early life of dairy calves and to investigate their potential regulatory roles in the development of bovine GIT. Results: The expression of miR-143 was abundant in all three gut regions and under all the time points and it targets genes involved primarily in the proliferation of connective tissue cells and muscle cells, suggesting its association with rapid tissue development during the early life of calves. The expression of miR-10, miR-146, miR-191, miR-33, miR-7, miR-96, miR-99/100, miR-486, miR-145, and miR-211 displayed significant temporal differences (FDR < 0.05), while miR-192/215, miR-194, miR-196,miR-205 and miR-31 revealed significant regional differences (FDR<0.05) throughout the GIT. Expression levels of miR-15/16, miR-29 and miR-196 were positively correlated with copy numbers of 16S rRNA gene of Bifidobacterium or Lactobacillus species or both of them (P < 0.05). Functional analysis using Ingenuity Pathway Analysis identified above mentioned differentially expressed miRNAs as potential regulators of gut tissue cells proliferation and differentiation, and bacterial density-associated miRNAs as modulators of development of lymphoid tissues (miR-196), maturation of dendritic cells (miR-29) and development of immune cells (miR-15/16). Conclusion: This present study revealed temporal and regional changes in miRNA expression, correlation between miRNA expression and microbial population during early life suggest their potential roles in host-microbial interactions during the gut development.

2016-10-29 | GSE52193 | GEO

Transcription profiling of piglet ileal tissues to assess the impact of environment on microbial diversity and global transcriptional responses in the developing gut

Project description:The study investigated the impact of environment on the composition of the gut microbiota and mucosal immune development and function at gut surfaces in early and adult life. Piglets of similar genotype were reared in indoor and outdoor environments and in an experimental isolator facility. Mucosa-adherent microbial diversity in the pig ileum was characterized by sequence analysis of 16S rRNA gene libraries. Host-specific gene responses in gut ileal tissues to differences in microbial composition were investigated using Affymetrix microarray technology and Real-time PCR. Experiment Overall Design: Animals were reared on the sow at an outdoor or indoor facility. Additional piglets from the indoor facility were transferred to individual isolator units at 24 hours of age, and given a daily dose of antibiotic cocktail for the duration of the study. Piglets were weaned at day 28. From day 29 onwards, piglets were fed creep feed ad libitum. Ileal tissue samples were excised from N=6 piglets per group at day 5, 28 and 56.

2009-12-05 | E-GEOD-15256 | biostudies-arrayexpress

Altered microRNA expression and pre-mRNA splicing events reveal new mechanisms associated with early stage Mycobacterium avium subspecies paratuberculosis infection

Project description:The molecular regulatory mechanisms of host responses to Mycobacterium avium subsp. paratuberculosis (MAP) infection during the early subclinical stage are still not clear. In this study, surgically isolated ileal segments in newborn calves (n = 5) were used to establish in vivo MAP infection adjacent to an uninfected control intestinal compartment. RNA-seq was used to profile the whole transcriptome (mRNAs) and the microRNAome (miRNAs) of ileal tissues collected at one-month post-infection. The most related function of the differentially expressed mRNAs between infected and uninfected tissues was “proliferation of endothelial cells”, indicating that MAP infection may lead to the over-proliferation of endothelial cells. In addition, 46.2% of detected mRNAs displayed alternative splicing events. The pre-mRNA of two genes related to macrophage maturation (monocyte to macrophage differentiation-associated) and lysosome function (adenosine deaminase) showed differential alternative splicing events, suggesting that specific changes in the pre-mRNA splicing sites may be a mechanism by which MAP escapes host immune responses. Moreover, 9 miRNAs were differentially expressed after MAP infection. The integrated analysis of microRNAome and transcriptome revealed that these miRNAs might regulate host responses to MAP infection, such as “proliferation of endothelial cells” (bta-miR-196b), “bacteria recognition” (bta-miR-146b), and “regulation of the inflammatory response” (bta-miR-146b).

2016-05-01 | GSE74394 | GEO

Intestinal proteomic response to oral challenge of enterotoxigenic Escherichia coli in weaned pigs

Project description:Enterotoxigenic Escherichia coli (ETEC) is a major cause of diarrhoea in children in resource-limited countries and of travellers diarrhoea. The ileal proteomics change after ETEC challenge is less characterised. Here in this study changes of ileal proteins post ETEC challenge in weaned pigs are studied. In total, 5151 ileal proteins were successfully annotated and 9 proteins had significantly different abundance between the ETEC and CON pigs.

2022-04-01 | PXD028066 | Pride

Transcriptome anlaysis of gastrointestinal tract of pre-weaned cavles

Project description:In order to test the development of gastrointestinal tract (GIT) in pre-weaned cavles, the GIT tissues were collected from day 0, day 7, day 21 and day 42 calves. RNA-seq was used to measure the transcriptome profiles. The RNA-seq analysis revealed the fast development of small intestine and rumen tissue during the first week after birth.

2016-05-01 | GSE74329 | GEO

Project description:Gut and nasal microbiota from pre-weaned calves

| PRJNA474385 | ENA

Transcriptomic analysis of adipose and muscle of dairy calves supplemented with 5-hydroxytryptophan

Project description:Serotonin is a monoamine that regulates processes such as energy balance and immune function. Manipulating this pathway in growing dairy calves could promote growth and development by modulating functions and signaling pathways within key organs. In this study, we characterized the adipose and muscle transcriptome of pre-weaned calves with increased serotonin bioavailability through the elucidation of differentially expressed genes.

2020-06-05 | GSE151781 | GEO

p53-regulated networks of protein, mRNA, miRNA and lncRNA expression revealed by integrated pSILAC and NGS analyses

Project description:We determined the effect of p53 activation on de novo protein synthesis using quantitative proteomics of newly synthesized proteins (pulsed stable isotope labeling with amino acids in cell culture, pSILAC) in combination with mRNA and non-coding RNA expression analyses by next generation sequencing (RNA-, miR-Seq) in the colorectal cancer (CRC) cell line SW480. Furthermore, genome-wide DNA binding of p53 was analyzed by chromatin-immunoprecipitation (ChIP-Seq). Thereby, we identified differentially regulated mRNAs (1258 up, 415 down), miRNAs (111 up, 95 down), lncRNAs (270 up, 123 down) and proteins (542 up, 569 down). Changes in mRNA and protein expression levels showed a positive correlation (r = 0.50, p < 0.0001). More transcriptionally induced genes displayed occupied p53 binding sites (4.3% mRNAs, 7.2% miRNAs, 6.3% lncRNAs, 5.9% proteins) than repressed genes (2.4% mRNAs, 3.2% miRNAs, 0.8% lncRNAs, 1.9% proteins), suggesting indirect mechanisms of repression. Around 50% of the downregulated proteins displayed seed-matching sequences of p53-induced miRNAs in the corresponding 3â??-UTRs. Moreover, proteins repressed by p53 significantly overlapped with those previously shown to be repressed by miR-34a. We confirmed upregulation of the novel direct p53 target genes LINC01021, MDFI, ST14 and miR-486 and showed that ectopic LINC01021 expression inhibited proliferation in SW480 cells. Furthermore, HMGB1, KLF12 and CIT mRNAs were confirmed as direct targets of the p53-induced miR-34a, miR-205 and miR-486-5p, respectively. In line with the loss of p53 function during tumor progression, elevated expression of HMGB1, KLF12 and CIT was detected in advanced stages of cancer. This study provides new insights and a comprehensive catalogue of p53-mediated regulations and p53 DNA binding in CRC cells.

2016-05-24 | MSV000079767 | MassIVE

Aberrant miR-29 is a predictive feature of severe phenotypes in pediatric Crohn’s disease

Project description:Crohn's disease (CD) is a chronic inflammatory gut disorder. Molecular mechanisms underlying the clinical heterogeneity of CD remain poorly understood. MicroRNAs (miRNAs) are important regulators of gut physiology and several have been implicated in the pathogenesis of adult CD. However, there is a dearth of large-scale miRNA studies for pediatric CD. We hypothesized that specific miRNAs uniquely mark pediatric CD. We performed small RNA-sequencing of patient-matched non-inflamed colon and ileum biopsies from treatment-naïve pediatric patients with CD (n=169) and a control cohort (n=108). Comprehensive miRNA analysis revealed 58 miRNAs altered in pediatric CD. Notably, multinomial logistic regression analysis revealed that index levels of ileal miR-29 are strongly predictive of severe inflammation and stricturing. Transcriptomic analyses of transgenic mice overexpressing miR-29 show a significant reduction of the tight junction protein gene Pmp22 and classic Paneth cell markers. The dramatic loss of Paneth cells was confirmed by histologic assays. Moreover, we also found that pediatric CD patients with elevated miR-29 exhibit significantly lower Paneth cell counts, increased inflammation scores, and reduced levels of PMP22. These findings strongly indicate that miR-29 up-regulation is a distinguishing feature of pediatric CD, highly predictive of severe phenotypes, and associated with inflammation and Paneth cell loss.

2022-12-23 | GSE221261 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data