Project description:Reported here are the transcriptomic changes resulting from extinction learning, in the brain of an anuran amphibian. RNA sequencing was utilized to investigate gene expression patterns resulting from conditioned learning in the fire-bellied toad, Bombina orientalis. As a basal tetrapod lineage, B. orientalis represents a robust candidate for investigating the evolution of molecular mechanisms underlying learning in vertebrates. The gene expression patterns associated with extinction learning in this species shared similarities with to those found in mammals submitted to extinction, but interesting divergent profiles highlighted potential differences in the mechanisms of learning and memory among tetrapods.
Project description:Reported here are the transcriptomic changes resulting from learning, in the brain of an anuran amphibian. RNA sequencing was utilized to investigate temporal gene expression patterns resulting from conditioned learning in the fire-bellied toad, Bombina orientalis. As a basal tetrapod lineage, B. orientalis represents a robust candidate for investigating the evolution of molecular mechanisms underlying learning in vertebrates. Differential expression following learning reveled activity in molecular pathways related to immediate early gene expression, cytoskeletal modification, axon guidance activity, and apoptotic processes. Learning in the fire-bellied toad is characterized by early IEG activity coinciding with transcriptional activity and structural modification, followed by axon guidance and adhesion activity, and late neural pruning.
Project description:We performed proteomic analyses of the roots in non-root pruned (control) and root-pruned Platycladus orientalis seedlings at different sampling times.
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.
