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.
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.
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.
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.
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.
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.