Master Degree / Yüksek Lisans Tezleri
Permanent URI for this collectionhttps://hdl.handle.net/11147/3008
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Master Thesis Computational investigation of allostery in hydroxyacid oxidase(01. Izmir Institute of Technology, 2024) Gökoğlu, Gizem; Uyar, Arzu; Ceylan, ÇağatayUnderstanding allosteric regulation in proteins may enable the development of effective new-generation therapeutics for disease treatments. Computational methods are gaining importance daily due to their fast and effective nature in examining protein dynamics and discovering potential allosteric binding sites. In this context, computational methods were used to determine the potential binding sites of the human hydroxyacid oxidase 1 (hHAO1) protein, which is effective in the rare disease Primary hyperoxaluria type 1 (PH1). Then, potential binding sites were predicted in monomeric and homotetrameric crystal and modeled structures of hHAO1 using the Fragment–Based Mapping (FTMap) web server and the Essential Site Scanning Analysis (ESSA) method. In ESSA, first, the default parameters cut-off 10 Å and mode 10 were applied. Then, to examine the effect of the cut-off value (distance) (Å), the parameters cut-off 7 Å and cumulative mode 20, and cut-off 13 Å and cumulative mode 20 were applied in ESSA. The modeled structures for hHAO1 were successful in terms of conformation and predicted binding sites. In the results of hHAO1, more binding sites were determined in the monomeric forms of hHAO1 than in tetrameric forms. FTMap and especially ESSA successfully predicted allosteric and potential new binding sites for hHAO1. This thesis might contribute to the improvement of computational methods and the development of allosteric therapeutics for hHAO1 and PH1.Master Thesis Screening Spirulina Stranins for Protein Productivity Based on Cultivation Under Photobioreactor Conditionsy(01. Izmir Institute of Technology, 2022) Binkanat, Tahir Burak; Özkan, Altan; Büyükkileci, Ali OğuzSpirulina is an industrially produced algae for consumption as a nutritional supplement owing to its exceptionally high protein content. The delivery of the desired metabolite profiles highly depends on selecting the correct strains for growth. In this regard, the information in the literature is limited as the strains cultivated industrially are unknown, and the strains of academic research were mostly locally isolated or procured from local sources. The current study is the first step of research activities planned to assess the large-scale production potential of Spirulina in Izmir. Thus in this work, Spirulina platensis 2340, Spirulina maxima 84.79, Spirulina platensis 85.79, Spirulina platensis 86.79, and Spirulina platensis 29 were screened for biomass and protein productivity during cultivation under standardized process conditions of a bubble column photobioreactor. The final biomass concentrations were strain specific and ranged from 1.2 to 1.9 g/L. An inverse relationship existed between the logistic model-based final biomass concentrations and the production rate constants. Thus, the peak productivities were more evenly distributed and ranged between 0.15 to 0.20 g/L-day. SP 29 had the ideal protein content vs. cultivation time profile as it was consistently high and varied in the narrow range of 60 to 64%. Higher protein contents could be reached with the other strains, but they also had higher variations during the growth period. The final protein concentrations varied from 0.4 g/L to 1.4 g/L. The highest peak productivity obtained was about 0.11 g/L-day, which could be obtained by three of the strains. The results clearly show the importance of strain selection for sustaining protein-rich biomass production with Spirulina.Master Thesis Investigation of Bcl-2 Proteins in Th17 Cell Functions(01. Izmir Institute of Technology, 2021) Çimen, Tuğçe; Nalbant Aldanmaz, AytenInterleukin 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.