Sürdürülebilir Yeşil Kampüs Koleksiyonu / Sustainable Green Campus Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7755
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Master Thesis Elecidation of Selenium Tolerance Mechanisms in Puccinellia Distans (jacq.) Parl, Using a Transcriptomic Approach(Izmir Institute of Technology, 2018) Kök, Aysu Başak; Frary, Anne; Frary, Anne; Eroğlu, Seçkin; 04.03. Department of Molecular Biology and Genetics; 04. Faculty of Science; 01. Izmir Institute of TechnologySelenium (Se) has a versatile chemistry. Therefore, it is present in a wide variety of materials on Earth. Although it is not an essential element for plants, Se provides several survival and ecological advantages. Puccinellia distans (P.distans) is weeping alkali grass which has a relatively fast growth rate and produces a large biomass. It can also hyperaccumulate extreme concentrations of boron and tolerate high levels of salinity. It is known that some plant species can tolerate high concentrations of soil salts and boron while hyperaccumulating Se in their leaves. Therefore, in this study, the Se accumulation and tolerance capacity of P. distans were investigated, and the plant’s Se tolerance mechanism was elucidated using a transcriptomic approach. The results of this study indicated that P. distans accumulated more than 100 mg Se kg-1 in its shoots. Therefore, P. distans was discovered to be a novel Se accumulator plant. Biochemical analyses and RNA sequencing results helped us to decipher the Se tolerance and accumulation mechanism of P. distans. Accordingly, the tolerance mechanism was found to be associated with the upregulation of genes involved in sulfate, selenocompound and antioxidant pathways. Here, we suggest that upregulation of Se assimilation and stress responses genes may have been due to induction of jasmonic acid signaling. In addition, we propose that the cell wall may play an important role in restriction of Se movement to the cytoplasm. Also, we put forward that sequestration of selenate inside the vacuole may be a way that Se accumulates in cells.Master Thesis Elucidation of Molecular Mechanisms Conferring Arsenic Tolerance To Yeast Cells(Izmir Institute of Technology, 2016) Işık, Esin; Karakaya, Hüseyin Çağlar; Karakaya, Hüseyin Çağlar; 04.03. Department of Molecular Biology and Genetics; 04. Faculty of Science; 01. Izmir Institute of TechnologyArsenic is a highly toxic metalloid available in the environment mainly as arsenite or arsenate. These compounds’ interference with many molecular mechanisms results in several diseases including cancer. Conversely, arsenic is used in therapeutic approaches, however, they are associated with drug resistance. Although some tolerance and toxicity mechanisms of arsenicals in yeast have been enlightened by previous studies, complete understanding, which is important for development of protection and therapy strategies, has not yet been achieved. Comprehensive genome-wide screening is a promising approach for the elucidation of novel genes involved in arsenic-associated mechanisms. The aim in this study was to screen a yeast genome library to characterize novel genes whose overexpression confers resistance to toxic concentrations of arsenate or arsenite in Saccharomyces cerevisiae. The plasmids from the colonies confirmed to be highly-resistant against arsenicals were sequenced to determine the genomic regions and seven genes were selected to clone into expression vectors. The overexpression of Pho86p and Vba3p provided yeast cells with the highest arsenate and arsenite resistance, respectively. Arsenate is a phosphate analogue and taken up by phosphate transporters. Pho86p is an ER-resident protein regulating ER-exit of the phosphate transporter. Therefore, it is reasonable that overexpression of Pho86p provides arsenate resistance. Vacuolar sequestration is a common route for the removal of toxic compounds from the cytosol and Vba3p is a vacuole-located transporter of basic amino acids with a likely role in arsenite resistance. Consequently, the screen in the current study revealed two genes with promising roles for tolerance mechanisms against arsenicals.Master Thesis Investigation of the Effects of Il-7 on the Th-17 Cell Apoptosis(Izmir Institute of Technology, 2015) Aydınlı, Fatmagül İlayda; Nalbant Aldanmaz, Ayten; Nalbant Aldanmaz, Ayten; 04.03. Department of Molecular Biology and Genetics; 04. Faculty of Science; 01. Izmir Institute of TechnologyTh17 cells known as Interleukin-17 (Inflammatory Cytokine) producing cells are differentiated subsets from naïve CD4+ T cells and have crucial roles in regulation of inflammation, host defense and autoimmunity. TCR (T Cell Receptor) activation is triggered under Th17 cell culture conditions and resulting naïve CD4+ T cells are induced to differentiate through Th17 cells. In the life time of activated T cells, the activation process also induces an apoptotic mechanism which is called activation-induced cell death (AICD) for elimination of activated cells from the environment for maintenance of homeostasis. AICD is known as the main programmed cell death mechanism for T cells by Fas-FasL signaling resulting activation of early and late apoptotic caspase proteins such as caspase-3 and caspase-8. Moreover, Interleukin-7, which is a member of Interleukin-2 family, has a survival mechanism in T cells by the activation and maintenance of anti-apoptotic proteins mainly Bcl-2 and inhibition of pro-apoptotic proteins such as Bax and Bim. This research analyzes apoptosis mechanism in Th17 cells in terms of AICD and the effects of IL-7 on that apoptosis signaling pathway. Our results showed that IL-7 did not have any effect to AICD throughout Fas-FasL signaling and activation of caspase-3 and caspase-8 protein.Master Thesis Deciphering Functions of Aberrant Hemichannels Formed by Connexin 26- I30n and D50y Mutations(Izmir Institute of Technology, 2015) Meşe Özçivici, Gülistan; Meşe Özçivici, Gülistan; 04.03. Department of Molecular Biology and Genetics; 04. Faculty of Science; 01. Izmir Institute of TechnologyCells need to communicate with each other for maintenance cellular and tissue homeostasis. Gap junctions are channel-forming structures that are formed by docking of two hemichannels on the plasma membrane of adjacent cells. Connexins are subunits of gap junctions. Connexin 26 (Cx26) is one of the connexin isoform and mutations on the Cx26 gene (GJB2) cause non-syndromic and syndromic deafness. Keratitis-ichthyosis-deafness (KID) syndrome is one of the syndromic deafness disorders caused by Cx26 mutations. Among these mutations, Cx26-I30N and D50Y missense mutations were shown to form aberrant hemichannels but their effect on protein biosynthesis and functions have not studied. In this study, we aimed to decipher in vitro functions of aberrant hemichannels formed by Cx26-I30N and D50Y mutations. First of all, the effect of Cx26-I30N and D50Y mutations on localization, mRNA expression and protein synthesis properties were investigated in HeLa, N2A and HaCaT cells. Results suggested that Cx26-I30N and D50Y mutants were not able to form gap junction plaques on the plasma membrane and were localized in the Golgi apparatus. In addition, mutations resulted in a reduction in mRNA expression and protein synthesis. After, functional analysis was performed in Cx26-I30N and D50Y transfected N2A and HaCaT cells. Internal Ca2+ content measurement, measurement of released ATP, measurement of cell size and apoptosis assays were performed. Ca2+ measurement results showed that both Cx26-I30N and D50Y mutations deregulate Ca2+ balance in both N2A and HaCaT cells. Result of ATP release assay indicated that ATP amount in the extracellular environment decreased in N2A cells having Cx26-I30N and D50Y clones. Finally, apoptosis assay showed that number of necrotic cells increased when N2A cells were transfected with Cx26-I30N and D50Y constructs. Therefore, it was shown that aberrant hemichannels formed by Cx26-I30N and D50Y mutations may induce necrotic cell death by disrupting Ca2+ balance and ATP amount in cells.Master Thesis Proteomic Analysis of Boron Stress Response in Yeast Saccharomyces Cerevisiale(Izmir Institute of Technology, 2011) Avşar, Kadir; Koç, Ahmet; Koç, Ahmet; 04.03. Department of Molecular Biology and Genetics; 04. Faculty of Science; 01. Izmir Institute of TechnologyBoron is a versatile element distributed in every part of the environment but most of its deposit reserves are localized in a few countries, Turkey being one of the most prominent. Boron is known to be an essential micronutrient for plants and some animals. Like any other essential element it has toxicity in high concentrations. Herein the mechanism of toxicity and the elements of the boron stress response were investigated in Saccharomyces cerevisiae with a proteomics approach. Boron is believed to have played a role in the evolution of life on earth. It has strongly electrophile organic compounds, the most important physiological form being boric acid. Boric acid has a capacity to bind cis-located hydroxl groups and some amino groups. Some of these groups are located at the active sites of some enzymes and at the carbohydrates with five-membered furanose rings. The riboses of some metabolically important molecules like S-adenosyl methionine, diadenosine phosphate family members and 3'end of RNAs are prone to be affected. The yeast cells subjected to boron in this study expressed higher amounts of carbohydrate metabolic enzymes, proteins involved in protein synthesis, protein folding and catabolism, redox homeostasis and nucleotide synthesis. All of these proteins are common to metal stress responses in yeasts. Some of them involve in other stress responses like peroxide, salt or herbicide stresses showing complex interplay between responses.