Project description:Rho-associated protein kinase (ROCK) inhibitors are highly present in different ocular tissues, and upregulation of ROCK pathway has been shown related to the pathogenesis of multiple ocular disorders, including glaucoma, diabetic retinopathy and age-related macular degeneration (AMD). However, the effect of ROCK inhibitor on AMD is still unknown. The protein profile changes in human retinal pigment epithelium (ARPE-19) cells after two days treatment with a ROCK inhibitor were studied using label-free Zeno SWATH acquisition. These results provided significant data of key protein candidates underlying the effect of ROCK inhibitor. Using the sensitive label-free mass spectrometry approach with data-independent acquisition (SWATH-MS), we established a comprehensive ARPE-19 proteome library. This project describes the use of Zeno SWATH MS to examine the underlying biological protein changes following ROCK inhibitor treatment of APRE-19 cells. This knowledge may allow more specific anti-AMD drugs to be developed
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:Microarray expression data from three different cell lines of human embrionic stem cells (Hs181, Hs293, Hs420), grown under feeder and feeder-free conditions (matrigel) with the addition of Y-27632 (ROCK Inhibitor) We assessed the difference between cell lines and the impact of feeder-free vs matrigel conditions upon the addition of the ROCK Inhibitor Y-27632