Master Degree / Yüksek Lisans Tezleri

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

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Department: search.filters.department.Thesis (Master)--İzmir Institute of Technology, Molecular Biology and GeneticsSubject: search.filters.subject.Proteins

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Now showing 1 - 3 of 3
  • Master Thesis
    Investigation of Bcl-2 Proteins in Th17 Cell Functions
    (01. Izmir Institute of Technology, 2021) Nalbant Aldanmaz, Ayten; Nalbant Aldanmaz, Ayten; 04.03. Department of Molecular Biology and Genetics; 04. Faculty of Science; 01. Izmir Institute of Technology
    Interleukin 17 producing T helper 17 cells are the distinct subset of CD4⁺ T cells. Th17 cells are an important part of the immune response of host defense. Dysregulation of Th17 cells plays a role in various pathologies including autoimmune diseases and cancer types. Bcl-2 family proteins are mostly known regulators of apoptotic cell death. The apoptotic and survival mechanisms of Th17 cells are not well known yet. Therefore, this study aims to investigate Bcl-2 protein family functions in Th17 cell survival and to understand the regulation network of apoptotic mechanisms of Th17 cells. To do that, Peripheral Blood Mononuclear Cells were isolated from a healthy buffy coat by Ficoll separation. Naive T cells were sorted from PBMC and cultured under Th17 polarizing conditions. Th17 cells were phenotypically characterized by flow cytometry. Afterward, cell lysates were obtained from Th0 and Th17 cells at different time points. The expressions of human transcription factor RORC2, proapoptotic Bik, Bid, Puma and Bim and, antiapoptotic Mcl-1 and Bcl-xL at cell groups were detected by Western blotting. The increased expressions of Bcl-xL and Mcl-1 were detected where the diminished expressions of Bim and Puma were detected in proportional with Th17 differentiation by increased RORC2 and elevated RORC/IL17A levels. Bik was undetectable in both cell groups while non-truncated isoform of Bid was barely decreased among cell groups. Outputs of this study allow us to understand the dynamics of Bcl-2 family proteins in human Th17 cell survival. The understanding roles of Bcl-2 proteins in Th17 cells may help to develop different therapeutics for Th17 associated diseases in the future.
  • Master Thesis
    Role of Sema6d in Proliferation, Epithelial-Mesenchymal Transition and Migration of Breast Cancer Cell Lines
    (Izmir Institute of Technology, 2017) Şahi, Ece; Yalçın Özuysal, Özden; Yalçın Özuysal, Özden; 04.03. Department of Molecular Biology and Genetics; 04. Faculty of Science; 01. Izmir Institute of Technology
    Breast cancer is one of the most common cancer types around world and the second leading cause of cancer related deaths among women. Not the primary tumor but distant metastases are mainly the reason of deaths. For metastasis, the cells may go through epithelial-mesenchymal transition (EMT), and acquire migration and invasion abilities. SEMA6D is a transmembrane protein that belongs to a large semaphorin family. SEMA6D is involved in the migration of embryonic cardiac cells. Recently it was validated as an oncogene in osteosarcoma. Also, its oncogenic roles were investigated in gastric cancer and mesothelioma. According to in silico analysis of the Cancer Genome Atlas (TCGA), high SEMA6D expression level is associated with better survival of triple negative breast cancer patients. However, there is not any published study which investigates roles of SEMA6D in breast cancer yet, other than bioinformatic analysis. Therefore, we aimed to understand role of SEMA6D in proliferation, EMT and migration of breast cancer cells. We observed that overexpression of SEMA6D reduces proliferation but enhances migration in non-invasive breast cancer cell line MCF7. Thereby, SEMA6D may increase metastatic ability of MCF7 cells. Its metastatic ability was also supported by changes in EMT markers. On the other hand, proliferation of metastatic breast cancer cell line MDAMB231 was not significantly changed by overexpression of SEMA6D and migration ability was slightly reduced but mesenchymal markers tended to increase in SEMA6D overexpressing MDAMB231 cells. As a conclusion, SEMA6D tends to enhance proliferation, migration through EMT in MCF7 cell line whereas overexpression of SEMA6D did not demonstrate significant effect on metastatic MDA-MB-231 cell line. Therefore, we should separately evaluate role of SEMA6D in different breast cancer cell lines and further studies are required to understand role of SEMA6D in breast cancer.
  • Master Thesis
    A Computational Study on the Structures and Proton Affinities of B3+ Ions; Peptide Mass Fragment Product
    (Izmir Institute of Technology, 2015) Boz, Seçkin; Elmacı Irmak, Nuran; Elmacı Irmak, Nuran; 04.01. Department of Chemistry; 04. Faculty of Science; 01. Izmir Institute of Technology
    Mass spectrometry is the tool of choice during most of the proteomics studies to get amino acid sequence. However, unambiguously identifying amino acid sequence from mass spectra is not easy and straight forward task. Deeper understanding is needed to support both existing knowledge and develop newer models on dissociation patterns of protonated peptides and it will help to improve efficiency of current algorithms used in peptide identification. In this study, the structures of b3+ ions and their neutral forms were investigated by using computational methods. First, potential energy surface of b ions are scanned using molecular dynamics simulations and conformer samples are collected. Then, in order to reduce number of conformers, principal coordinate analysis was applied to find and select different structures within the sample. Selected conformers were optimized using density functional theory calculations. Proton affinities of b ions are determined by the energy difference between most stable conformers of the positively charged and neutral peptide fragments. Different amino acids were used to understand the role of side chain of amino acids on both structures and proton affinities of b3+ ions; XA2+ where X=N, H, C, Y, D, L and F. The results showed that, b3+ ions prefer to have linear oxazolone structure. However, in their neutral states, cyclic structures are relatively far more stable than linear isomers. Histidine display different behavior than other amino acids. Side chain of histidine holds protons and forms stable structures. The energies of cyclic and linear isomers of Histidine containing b ions are close to each other. Histidine containing peptide fragments have larger proton affinity comparing to others. Difference of proton affinities between linear and cyclic conformers varies based on amino acid used. This difference is lower than 10kcal/mol in histidine, asparagine and aspartic acid containing peptide fragments. There is no dramatic position preference of the X-amino acid for the N- or C- terminals or middle position with the exception of Asn and Asp (unlike the center) and Histidine which likes to be at C-terminal.