Project description:Chromosomal instability (CIN) occurs at high frequency during early in vitro embryogenesis and is known to be associated with early embryonic loss in humans. The chromosomal stability of in vivo-conceived cleavage stage embryos largely remains unknown. Here, we applied haplotyping and copy number profiling to investigate genomic architecture of 171 single bovine blastomeres and to compare the nature and frequency of CIN between in vivo embryos, in vitro embryos produced from ovum pick up with ovarian stimulation (OPU-IVF), and in vitro produced embryos from in vitro matured oocytes without ovarian stimulation (IVM-IVF). Our data shows that CIN is significantly lower in in vivo conceived cleavage stage embryos when compared to in vitro cultured embryos, as genomic stability of single blastomeres in both IVF embryos was severely compromised (P<0.0001)
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:NO-CUT is a one-stage phase II trial seeking to establish whether an oxaliplatin-based chemotherapy preceding standard neo-adjuvant fluoropyrimidines-based chemo radiotherapy, can safely spare demolitive surgical intervention in patients with operable rectal cancer, without increasing the risk of distant relapse. The trial also has a translational component aimed at establishing whether selected genomic, epigenetic, and transcriptomic markers are predictive of tumor and patient outcome.
Project description:The purpose of this study is the investigation of new host-microbiome interactions promoting adenoma formation and adenocarcinoma progression. For that purpose, the investigators will collect saliva, stool and colon biopsy specimens from patients referred to colonoscopy or surgical resection of colorectal tumor. Besides, a questionnaire about diet, lifestyle and medical history will be collected. Sample analysis will involve simultaneous characterization of host and microbiota genomic and transcriptomic components.
