Master Degree / Yüksek Lisans Tezleri

Permanent URI for this collectionhttps://hdl.handle.net/11147/3008

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2005 - 200912010 - 20193

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Language: search.filters.language.enSubject: search.filters.subject.Gene expression

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Now showing 1 - 4 of 4
  • Master Thesis
    Effect of Interleukin-10 Pathway Genes and Diet on Behcet's Disease
    (Izmir Institute of Technology, 2019) Arpaz, Goncagül; Sezgin, Efe; Sezgin, Efe; 03.08. Department of Food Engineering; 03. Faculty of Engineering; 01. Izmir Institute of Technology
    Behcet's disease (BD) is an inflammatory disease characterized by recurrent oral and genital aphthae with unknown etiology. The disease is most prevalent along the Silk Road populations. BD is complex disease influenced by genetic and environmental factors. Identification of contribution of these factors to BD is an active research question. The first aim of the thesis is to determine the biological pathways in the etiopathology of BD by a comprehensive literature review of published genetic research. The second aim of the thesis is to investigate the genetic changes and gene expression in IL-10, an anti-inflammatory pathway cytokine, and its primary receptor. IL-10R1 in BD. The third aim of the thesis is to discover potential novel functional foods that can benefit patients with BD. 241 variants from 119 genes were identified to be associated with BD. Frequency distribution of the 241 variants among world populations was rather different. IL-10 was idendified to be most significantly associated with BD and differentiated high BD risk populations from the rest based on principal component analyses. Sequence analyses of IL-10 and IL-10R1 identified rs3024498 and rs9610 variants, respectively, in Turkish BD patients. Rs3024498 wa not associated with BD risk; however, IL-10R1 rs 9610 variant showed a marginally significant relationship with BD. IL-10 gene expression was 9.6 fold higher in BD compared to normal controls. As an anti-inflammatory IL-10 pathway is identified to influence BD, novel food supplements with high anti-inflammatory ingredients need to be developed to benefit patients with BD.
  • Master Thesis
    Mining the Toxoplasma Gondii Genome for Microrna Regulatory Patterns
    (Izmir Institute of Technology, 2017) Acar, İlhan Erkin; Allmer, Jens; Acar, İlhan Erkin; Allmer, Jens; 01. Izmir Institute of Technology; 04.03. Department of Molecular Biology and Genetics; 04. Faculty of Science
    Toxoplasma gondii is a parasite that causes mental retardation, blindness or nearblindness, and decreased psycho-motor performance if the patient is congenitally infected. There have been efforts to vaccinate humans against this parasite, yet it was not achieved. Therefore, a better understanding of Toxoplasma gondii can be provided by examining its microRNA regulation. MicroRNAs are known to regulate messenger RNAs and prevent translation. This results in different effects in different biological pathways. In this study, the Toxoplasma gondii genome was used to predict precursor and mature microRNAs, while experimentally validated microRNAs were taken into consideration. This was further explored in terms of microRNA targeting, with the known genes of Toxoplasma gondii. Furthermore, RNA Sequencing data of this organism was obtained and analysed in terms of gene expression and possible microRNA expression outcomes. Combining gene expression analyses with targeting predictions, it was possible to create a microRNA - gene interaction network. Gene expression analyses showed that there was no differentially expressed genes, microRNAs or interactions between two developmental stages of Toxoplasma gondii, tachyzoite and bradyzoite. This result was added to interactions to determine up and down regulations. Then, all of these interactions were connected where they intersect, to create a regulation network of microRNAs. This network was further explored and compared to random networks of the same size. It was seen that the biological network contains many larger sized cliques. This knowledge can be further analysed in future work, to create drug leads that will target vital pathways of Toxoplasma gondii.
  • Master Thesis
    Identification of Complexes That Interact With Trna-Derived Small Rnas by Gene Expression Methods
    (Izmir Institute of Technology, 2013) Öztürk, Saniye Elvan; Akgül, Bünyamin; Akgül, Bünyamin; 04.03. Department of Molecular Biology and Genetics; 04. Faculty of Science; 01. Izmir Institute of Technology
    tRNA is a vital molecule of life and has been a focus of biochemical research since long. New aspects of tRNA biology have been drawn to light recently. Accumulating data indicates that tRNA has many diverse biological functions other than its canonical role in coding for amino acids. tRNA halves are produced by cutting the tRNA molecule from its anti-codon loop by angiognenin and even smaller RNA fragments (tRFs) produced from 5’ or 3’ ends of mature tRNA have been shown to have biological functions, most notable of which is the inhibition of the initiation of protein synthesis. In our study, the aim was to show the interaction between tRFs and RNA binding proteins. For this reason, two proteins were determined: Rox8 and D-La which are Drosophila homologs of human TIA-1 and La. In the beginning of study, we overexpressed FLAG-tagged versions of these proteins in S2 cells. Then immunoprecipitation experiments were performed with the tagged proteins. At the end of our research the potential interaction between tRFs and tRF related proteins are demonstrated.
  • Master Thesis
    Expression Profiles of Differentially Expressed Genes of Rat Mammary Adenocarcinoma in Various Tumor Cell Lines and Effects of Some Antioxidants
    (Izmir Institute of Technology, 2005) Certel, Seçil; Güneş, Hatice; Güneş, Hatice; 04.03. Department of Molecular Biology and Genetics; 04. Faculty of Science; 01. Izmir Institute of Technology
    Cancer is the most frequent reason of death in humans after heart disease. Most of the cancers are caused by mutations in tumor suppressor genes that play distinct roles in tumor formations. If a tumor suppressor gene is mutated, it loses its function to control cell division which may lead to overgrowth of cells that leads to tumor formation. It is important to identify the genes involved in tumor formation and metastasis to develop new cancer prevention and treatment methods. In a previous study, differentially expressed genes were identified between poorly metastatic and highly metastatic cell lines of rat mammary adenocarcinoma R3230AC. Eight cDNA clones from poorly metastatic CAb.D5 cell line and six cDNA clones from highly metastatic LN4.D6 cell line were identified (Gunes and Carlsen, 2003). The aim of this study was to investigate expression profiles of these differentially expressed genes in a set of different adenocarcinoma cell lines to find if they have any relation with metastasis. Cell culture and stocks of sixteen different cell lines were prepared and RNA from these cells were isolated. After synthesizing cDNA, RT-PCR analysis was carried out using primers specific for each cDNA clone. It was found that the gene clones FF-10 and SG-1 were expressed in non-metastatic cells but not in metastatic cells suggesting that they may have a tumor suppressive potential. Antioxidants are chemicals that prevents oxidation and free radical damages on cells. Because there is some evidence that antioxidants may prevent tumor formation, effects of antioxidants such as green tea catechins, beta carotene, lycopene as well as zeolite were examined on cancer cell growth and expression profiles of the differentially expressed genes. The cells were treated with different amounts of antioxidants and the cell growth was determined by MTT assay. The effects of antioxidants in gene expression were identified by RT-PCR analysis. At 100µM and higher concentrations, epigallocatechingallate (EGCG), epigallocatechin (EGC) and beta carotene significantly inhibited cell growth. Lycopene affected the cell growth at 3µM concentration. FH-2 expression decreased by 1.8-fold with lycopene treatment. In addition, EGCG increased the SG-1 expression by 1.14-fold. No effects of antioxidants as well as zeolite on the expression of other differentially expressed genes were observed. For further studies, investigation of expression profiles of differentially expressed genes in primary and secondary tumors of human will give more definitive results for the metastatic relevance of these genes.