A collection of files associated with a project I contributed to as as final-year Bioinformatics student at the University of Saskatchewan.
Proteoglycans are a class of macromolecules comprised of proteins to which carbohydrate groups are attached. They serve important functions in the synthesis of bone and cartilage. In addition, proteoglycans are known to function as extracellular signal molecules and have been identified intracellularly as well. The loss of proteoglycans is associated with debilitating diseases such as osteoarthritis. Therefore, an enriched knowledge of proteoglycans may aid osteoarthritis research by suggesting significant genes of the synthesis pathway, which can become subjects for more detailed studies. This research focused on collecting Homo sapiens orthologs of the proteoglycan synthesis pathway genes. Data for this study were collected from Ensembl. Multiple sequence alignments were performed to investigate gene sequence conservation across organisms. Phylogenetic analyses and an investigation of non-synonymous vs. synonymous mutation ratios of proteoglycan synthesis genes were conducted with the intent of verifying whether organisms that synthesize bone and cartilage exhibit higher mutation ratios compared to organisms that do not synthesize bone and cartilage. Organisms that synthesize bone and cartilage were hypothesized to showcase higher non-synonymous vs. synonymous mutation ratios compared to organisms that do not as a consequence of evolutionary pressures caused by environmental factors, such as the transition from water to land. Contrary to expectation, the research identified that organisms that synthesize bone and cartilage exhibit lower non-synonymous vs. synonymous mutation ratios compared to organism that do not synthesize bone and cartilage.
See first presentation here.