Master Degree / Yüksek Lisans Tezleri
Permanent URI for this collectionhttps://hdl.handle.net/11147/3008
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Master Thesis Bioinformatic Analysis and Biostatistical Modelling of Genetic Interactions Between Microbiota and Host(01. Izmir Institute of Technology, 2020) Sezgin, Efe; Sezgin, Efe; 03.08. Department of Food Engineering; 03. Faculty of Engineering; 01. Izmir Institute of TechnologyAdvances in genome sequencing technology have revolutionized the study of microorganisms. Recent genome-wide association studies (GWAS) on gut microbiota revealed fascinating discoveries about the effect of microbiota on our health. In this thesis, Drosophila Melanogaster samples were used to investigate the associations between the host's genotype and microbiota. The meta-analysis of microbiota data was performed using PhyloMAF, a novel, and comprehensive microbiome meta-analysis framework. The resulting microbial abundance tables were analyzed using alpha and phylogenetic beta bio-diversity metrics, which were used in the microbiome GWAS study. Significant variant associations were further analyzed in the post-GWAS analysis. The results of our study show that several genomic variants are significantly associated with bio-diversity estimates. Among identified variants, few were found to be associated with more specific phenotypes. Particularly, the gene involved in folate transport and linked to folate malabsorption was found to be associated with Proteobacteria. The latter for its part was found to be one of the primary phyla containing the highest number of genes responsible for de-novo folate synthesis. Similarly, the fly gene related to immune function with the human homologous gene linked to the inflammatory gut disease was found to be associated with the Acetobacter genus. This genus based on the literature survey was found to be associated with an immune deficiency in a fruit fly. In summary, this research revealed captivating findings of genetic factors associated with fruit fly microbiota. The limitations and future directions were stated in order to provide the basis for future prospective studies.Master Thesis Analysis of Temporal and Spatial Expression of Drosophila Embryonic Small Rnas by Deep-Sequencing Method(Izmir Institute of Technology, 2012) Coşacak, Mehmet İlyas; Akgül, Bünyamin; Akgül, Bünyamin; 04.03. Department of Molecular Biology and Genetics; 04. Faculty of Science; 01. Izmir Institute of TechnologyThe world of small RNAs is expanding and new types of small RNAs are being identified. By using deep-sequencing techniques in addition to most abundant small RNAs; miRNA and siRNA, piRNA and tRFs were further characterized and shown to be functional. The global behavior of small RNAs during MZT and their location in the cytoplasmic complexes has not been shown. By combining polysomal fractionation and deep-sequencing technique as well as the highly regulated developmental stages in Drosophila we have shown that the temporal and spatial expression of small RNAs changes during MZT. We have shown that each small RNA group has unique behaviour in cytoplasm and is enriched in specific polysomal fractions which shows that their local function in cytoplasmic complexes is mainly translational machinery.