Master Degree / Yüksek Lisans Tezleri

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  • Master Thesis
    Interactions Between Metal Surfaces and Sulfur-Containing Amino Acids
    (01. Izmir Institute of Technology, 2022) Çevlikli, Mustafa; Ataman, Evren
    With Covid-19 pandemic, the scientific studies over viruses gained a big acceleration. Some of these studies show that SARS-CoV-2 can infect through direct ways from a patient. Besides that, surfaces that are contaminated from adsorption of the virus can indirectly infect a person. Because of this, the studies on the interaction between viruses and environment is an important field on virus studies. Spike proteins which project out from protective structure called lipid bilayer and they are outmost elements of SARS-CoV-2 viruses. Spike proteins play a vital role on functions like viral entry to the host cell and attachment to the surfaces. Purpose of this study is to contribute to the existing knowledge about surface interaction of these proteins which have an important role on virus-surface interactions. Because of the complicated physical and chemical form of proteins, in this study, the interaction of amino acids, which are building block of proteins, with metal surfaces are investigated. 0.01M, 0.02M and 0.05M L-cysteine and L-methionine aqueous solution was dropped to the metals frequently used in daily life, chrome (Cr) and iron (Fe) polycrystalline substrates and left to dry out at room temperature and under atmospheric conditions. Since the water solubility of L-cystine is low, only a saturated solution of Lcystine was prepared and same process was applied. After, dried out samples were analyzed with x-ray photoelectron spectroscopy (XPS). Functional sulfur groups on L-cysteine/Cr, L-methionine/Cr and L-Methionine/Fe system stayed intact. On the other hand, sulfur atoms on L-Cysteine/Fe system oxidized and formed --SO x species. While all other systems behaved oppositely, the amount of protonated functional amino species (􀵆􀜰􀜪􀬷 􀬾) on L-methionine/Fe system decreased relative to functional amino group (􀵆􀜰􀜪􀬶) with increase in coverage. Due to surface amino acid interaction of L-methionine in different substrates, binding energy of sulfur on iron was measured 1 eV lower than on chromium. In L-cystine/Cr system, while disulfide bonds stayed intact, 􀵆􀜰􀜪􀬶 and 􀵆􀜰􀜪􀬷 􀬾 functional groups were observed on the surface together.
  • Master Thesis
    Examination of Covid-19 Outbreak Dynamics, and Identification of Better Vaccine and Viral Drug Targets Through Genomic Analyses of Sars-Cov
    (01. Izmir Institute of Technology, 2022) Gürbüz, Bahar Anıl; Sezgin, Efe
    Since the emergence of the SARS-CoV-2 virus, which causes the COVID-19 disease, it continues despite the application of many vaccines and drug treatments. It has continuously mutated, therefore the effect of vaccines and drug treatments has begun to decrease and a permanent solution has not been found. The main hypothesis of thesis is that the conserved regions in the SARS-CoV-2 genome can be potential targets for new vaccines and drugs to eradicate the Covid-19 pandemic. In this study, a total of 807 sequences of the first emerging clades (L, O, S) of the SARS-CoV-2 human virus and its variants in the category of Variants of Concern (Alpha, Beta, Gamma, and Delta) were taken from different dates, and population genetic statistical tests were conducted. Human specific SARS-CoV-2 sequence analyses showed that the evolution of all viral proteins are primarily driven by negative selection. Interspecies tests using the RaTG13 Bat coronavirus, which has the most similar genome to the SARS-CoV-2 virus genome, showed that there was no fixed amino acid change divergence between the bat and human virus sequences for Membrane, Nsp8, Nsp10, and Nsp16, indicating high conservation. Then, a list of the amino acid changes among the SARS-CoV-2 human clades and variants was prepared for Membrane, Nsp8, Nsp10, and Nsp16. Since the regions outside of these changes are the most conserved, the functions of the Membrane, Nsp8, Nsp10, and Nsp16 and and interactions with other viral proteins should be investigated as potential targets for new vaccines and drug treatments.