Project description:To obtain a broader understanding of the effects of the N. caninum on S. gregaria adults, we examined the parasite impact on host gene expression using Affymetrix DNA microarray and Cross Species Hybridisation (CSH) analysis. Since N. caninum infection induced neurological injuries in locusts, it was important to test whether N. caninum infection had altered gene expression within locust brains. The analysis was designed to gain further understanding of the mechanisms for N. caninum neuropathy, and in particular, of the genes responsible for the capacity of N. caninum to establish brain infection. Using a cross species hybridisation (CSH) approach, RNA samples from brains of mock- and N. caninum-infected locusts were labeled and hybridised to Affymetrix Gene Chip Drosophila Genome 2.0 Arrays. Data were analysed using Partek Genomics Suite Version 6.4. Of the 28,593 transcripts represented on the GeneChip, approximately 18,500 were expressed in the N. caninum-infected locust’s brain. PCA quality control analysis shows that the uninfected and infected samples were biologically noisy but generally well separated .
Project description:Small RNA libraries from N. caninum tachyzoites were analyzed using a high-throughput RNA sequencing technology combined with systematic bioinformatics analysis.
Project description:Recent advances in high throughput sequencing methodologies allow the opportunity to probe in depth the transcriptomes of organisms including N. caninum. In this project, we are using Illumina sequencing technology to analyze the transcriptome (RNA-Seq) of experimentally accessible stages (e.g. tachyzoites at different times points) of N. caninum NCLiv. The aim is to make transcriptional landscape maps at different time points at different life cycle stages of N. caninum and compare it with equivalent datasets from the closely related parasite Toxoplasma gondii
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.
