Browsing by Author "Swartz, Aidan"
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- ItemProteogenomics of the Spotted Hyena (Crocuta crocuta)(Stellenbosch : Stellenbosch University, 2021-03) Swartz, Aidan; Tabb, David L.; Miller, Michele; Stellenbosch University. Faculty of Medicine of Health Sciences. Dept. Biomedical Sciences: Molecular Biology and Human Genetics.ENGLISH ABSTRACT: The spotted hyena (Crocuta crocuta) is an important yet understudied organism that could provide insights into the fields of disease resistance, pathogen movement and disease evolution. They exist in matrilineally controlled, transient, clan-like groups that feed on a variety of organic matter and, subsequently, control the spread of pathogenic infections within an environment. Due to this, they appear to possess a high degree of resistance to pathogens. In this project, RNA-Seq data were utilized to assemble a transcriptome for the spotted hyena and tissue samples were further used to acquire protein data via MS/MS analysis. The aim of this study was to produce an accurate assembly via the transcriptomic data and subsequently further validate this assembly through the use of proteomics to better prove the quality therein. The assembly was produced using the Trinity de novo assembly software tool and assessed via the BUSCO and TransRate analysis tools. Orthology detection was carried out using ProteinOrtho, using closely related species (tiger, house cat, leopard, cheetah). Finally, LC-MS/MS data (consisting of tissue samples from peripheral, abdominal, head and thoracic lymph, as well as lung and liver tissue), and fractionated data from the sample containing the most diverse spectra, were searched against both the assembly itself and the translated genome data from the NCBI. These data served as the means by which the proteomic data were assessed and to determine whether the fractionation was successful, based on the comparative quantity of spectra between initial and fractionated analyses, in diversifying the sample. Further, these data were utilized to determine whether the translated transcriptome assembly could be successfully aligned against the proteomic data. The analysis of the quality control results found that the assembly was of appropriate quality when compared to the standards found within NCBI and within those described by the quality analysis tools. This coupled with the analysis of the proteomic data suggest that the assembly is useable, though requires further refinement. Based on the above, the inclusion of more data for assembly, is required for it to be a completely viable and ideal model assembly, however, current results are promising.