IeProBifi
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB73660 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR12737281_1.fastq.gz | Fastqsanger.gz | |||
| ERR12737281_2.fastq.gz | Fastqsanger.gz | |||
| ERR12736887.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 3 of 3 |
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Project description:Bifidobacteria constitute a specific group of commensal bacteria which inhabit the gastrointestinal tract of humans and other mammals. Bifidobacterium breve UCC2003 has previously been shown to utilise several plant-derived carbohydrates that include cellodextrins, starch and galactan. In the current study, we investigate the ability of this strain to utilise the mucin- and human milk oligosaccharide (HMO)-derived carbohydrate, sialic acid. Using a combination of transcriptomic and functional genomic approaches, we identified a gene cluster dedicated to the uptake and metabolism of sialic acid. Furthermore, we demonstrate that B. breve UCC2003 can cross feed on sialic acid derived from the metabolism of 3’ sialyllactose, a HMO, by Bifidobacterium bifidum PRL2010.
2014-05-29 | GSE56291 | GEO
Project description:Analysis of gene expression in Caco-2 intestinal epithelial cells stimulated with Bifidobacterium bifidum PRL2010. We used microarrays to investigate gene expression in intestinal epithelial cells in response to Bifidobacterium bifidum PRL2010, in particular genes involved in mucin pathways.
2010-10-01 | GSE21976 | GEO
Project description:Identify candidate different expression genes in HT-29 cells after incubation with Bifidobacterium bifidum ATCC 29521. The results of microarray provide importment information for different genes expression in HT-29 cell after incubation withBifidobacterium bifidum ATCC 29521, up or down-regulated.
2015-10-19 | GSE74119 | GEO
Project description:Analysis of gene expression in Caco-2 intestinal epithelial cells stimulated with Bifidobacterium bifidum PRL2010. We used microarrays to investigate gene expression in intestinal epithelial cells in response to Bifidobacterium bifidum PRL2010, in particular genes involved in mucin pathways. Caco-2 cells were grown in transwell plates to 4 days post-confluence. Cells were then incubated for 2h and 4h with Bifidobacterium bifidum PRL2010. The experiment was performed in duplicate. Caco-2 RNA was extracted and hybridized to Affymetrix NuGO_Hs1a52018 arrays.
2010-10-01 | E-GEOD-21976 | biostudies-arrayexpress
Project description:Analyses of new genomic, transcriptomic or proteomic data commonly result in trashing many unidentified data escaping the ‘canonical’ DNA-RNA-protein scheme. Testing systematic exchanges of nucleotides over long stretches produces inversed RNA pieces (here named “swinger” RNA) differing from their template DNA. These may explain some trashed data. Here analyses of genomic, transcriptomic and proteomic data of the pathogenic Tropheryma whipplei according to canonical genomic, transcriptomic and translational 'rules' resulted in trashing 58.9% of DNA, 37.7% RNA and about 85% of mass spectra (corresponding to peptides). In the trash, we found numerous DNA/RNA fragments compatible with “swinger” polymerization. Genomic sequences covered by «swinger» DNA and RNA are 3X more frequent than expected by chance and explained 12.4 and 20.8% of the rejected DNA and RNA sequences, respectively. As for peptides, several match with “swinger” RNAs, including some chimera, translated from both regular, and «swinger» transcripts, notably for ribosomal RNAs. Congruence of DNA, RNA and peptides resulting from the same swinging process suggest that systematic nucleotide exchanges increase coding potential, and may add to evolutionary diversification of bacterial populations.
2017-12-18 | PXD006238 | Pride
Project description:Gordius_albopunctatus, genomic and transcriptomic data
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Project description:We got insights into the B. bifidum PRL2010 genes whose expression resulted to be affected when bacterial cells were cultivated on kefir and kefiran as the unique carbon source. In order to exploit the transcriptome of PRL2010 grown on kefir and hefiran we performed global transcription profiling using PRL2010 microarrays hybridized with cDNA from the RNA samples of B. bifidum PRL2010 cultivated on these substrates. We isolated mRNA from B. bifidum PRL2010 cells collected from a culture of kefir grains and from PRL2010 cultivated on MRS plus kefiran at upon 12 hours following inoculation. Microarray analysis was performed with an oligonucleotide array based on the B. bifidum PRL2010 genome: a total of 8,130 oligonucleotide probes of 60bp in length were designed on 1707 ORFs using eArray5.0 (Agilent Technologies). 5 Oligos were designed for each gene on a 4x44k Agilent Microarrays(Agilent Technologies, Santa Clara, CA, USA). Replicates were distributed on the chip at random, non-adjacent positions.
2016-07-03 | E-GEOD-50506 | biostudies-arrayexpress
Project description:We have shown that pre-incubation with Bifidobacterium bifidum (B. bifidum) strain BF-1, a probiotic strain known to improve H. pylori-associated gastritis, suppresses the induction of IL-8 by the pathogen. To investigate how BF-1 affects gene expression in H. pylori-infected cells, we performed microarray analysis to assess gene expression in epithelial cells, which had been pre-incubated with BF-1 and infected with H. pylori.
2010-10-13 | GSE20171 | GEO
Project description:Dendritic cells (DC) play a pivotal regulatory role in activation of the innate as well as the adaptive part of the immune system by responding to environmental microorganisms. We have previously shown that some lactobacilli strains induce a strong production of the pro-inflammatory and Th1 polarizing cytokine IL-12 in DC. Contrary, bifidobacteria do not induce IL-12, but are able to inhibit the IL-12 production induced by lactobacilli. In the present study, genome wide microarrays were used to investigate the maturation and gene expression pattern murine bone marrow derived DC stimulated with Lactobacillus acidophilus NCFM and Bifidobacterium bifidum Z9. L. acidophilus NCFM strongly induced expression of interferon (IFN)-β, multiple virus defence genes, and cytokine and chemokine genes related to both the adaptive and the innate immune response. Contrary, B. bifidum Z9 mostly up-regulated genes encoding cytokines and chemokines related to the innate immune response. Moreover, B. bifidum Z9 inhibited the expression of the genes initiating the adaptive immune response induced by L. acidophilus NCFM and had an additive effect on genes of the innate immune response and some Th2 skewing genes. The gene encoding Jun dimerization protein 2 (JDP2), a key regulator in cell signalling, was one of the few genes only induced by B. bifidum Z9. Blocking of the JNK1/2 pathway completely inhibited the gene expression of Ifn-β. We suggest that B. bifidum Z9 employs an active mechanism to inhibit induction of genes in DC triggering the adaptive immune system and that JPD2 is involved in the regulatory mechanism. In the experiment saline control, Lactobacillus acidophilus NCFM, Bifidobacterium bifidum Z9 or both bacteria were were added to murine dendritic cells and stimulated for 10 hours. Experiments were run in triplicates and analyzed in a Two-way ANOVA design.
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