Master Degree / Yüksek Lisans Tezleri
Permanent URI for this collectionhttps://hdl.handle.net/11147/3008
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Master Thesis Investigation of Long Non-Coding Rna and Chromatin Interactions in Hela Cells(Izmir Institute of Technology, 2022) Atbinek, Melis; Akgül, BünyaminThe DNA in the cells is surrounding histone proteins to form nucleosomes. The structure is packed further into chromatin. The chromatin structure is dynamic and flexible. It is regulated by many factors including long non-coding RNAs (lncRNAs). LncRNAs are a class of non-coding RNAs, transcripts that do not encode protein. They are longer than 200 nucleotides and might contain a polyA tail and a 5’ cap. Thus, they are localized in the nucleus. lncRNAs interact with chromatin in two ways, indirect and direct. Direct interaction occurs via two mechanisms: R-loop and triplex formation. These interactions affect the folding of chromatin inducing gene expression under various cellular conditions. LncRNAs interacting with chromatin regulating genes are found in HEK cells. Thus, it is hypothesized that lncRNA – chromatin interactions may differ in cancerous cells as well. In this study, the iMARGI method is optimized to be used in adenocarcinoma HeLa cells. The chromatin digestion and incubation conditions are adjusted to give optimal results for HeLa cells. iMARGI is a recently developed method employed to investigate such interactions in a genome-wide manner. iMARGI allows the isolation of all lncRNAs interacting with the whole genome. The interacting RNA – DNA molecules are pulled down with streptavidin conjugated beads after linker ligation. The chimeric molecules are amplified with PCR forming lncRNA – chromatin libraries of HeLa cells. In the future, new libraries can be formed after inducing apoptosis in HeLa cells. Identification of lncRNAs involved in chromatin remodeling in apoptotic conditions can facilitate new therapeutic methods for fighting tumor initiation and development.Master Thesis Investigation of Anticancer Properties of the Novel Synthesixed Pyrrole Derivatives as Potential Tyrosine Kinase Inhibitors(Izmir Institute of Technology, 2017) Kaya, Meltem; Şanlı Mohamed, GülşahIn cancer treatment, chemotherapy has some serious side effects, because it targets active cells which might not be cancer cells. Mouth, hair, nail, bone marrow cells are some examples of active cells. For the reason that chemotherapy has side effects, targeted therapy become more important. Tyrosine kinases are most interested target, because they are necessary for cell growth and metastasis. Active form of tyrosine kinases can cause tumour growth and proliferation, angiogenesis, metastasis and antiapoptotic effects. Based on these vital role of tyrosine kinases, they became more important target in cancer treatment. Pyrrole derivatives have been used chemotherapy drugs for years. Semaxanib and Sunitinib, indole derivatives, are tyrosine kinase inhibitors. The main purpose of this research is to investigate the biologic activities of novel synthesized seven pyrrole derivatives, their activities on migration, apoptosis, cell cycle, and mTOR downstream as a potential tyrosine kinase inhibitor. The results of this research proved that these seven compounds have toxicity on HeLa cells with the IC50 values of 140.60 μM, 382.82 μM, 366.44 μM, 542.00 μM, 255.86 μM, 148.59 μM, 171.40 μM, respectively, but toxicity effects of drugs do not depend on apoptosis mechanism. Beside this, D1 and D3 were able to effect cell cycle by arresting at S phase for D1 and G1 phase for D3. It was demonstrated that D1 and D3 inhibited cell migration. And this inhibition was reported as in a relation with overexpression of p- 4EBP1, inhibition of p-p70S6K (Thr) and p-p70S6K (Shr) proteins. Considering all results, D1 and D3 might be potent inhibitory of metastasis of HeLa cells with respect to its effect on cell cycle, migration, p-4EBP1, p-p70S6K (Ser), and p-p70S6K (Thr) protein levels.