Master Degree / Yüksek Lisans Tezleri
Permanent URI for this collectionhttps://hdl.handle.net/11147/3008
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Master Thesis Daha Etkili Aşı, Anti-viral Molekül, Survilas Geliştirilmesi için Rekombinant ve Rekombinant Olmayan Omicron-SARS-CoV2 Alt Soylarının Moleküler Evrimlerinin Biyoinformatik ve İstatistiksel Yöntemler ile Analiz Edilmesi(2025) Arlı, Meliscan; Sezgin, Efe; Eraltuğ, Nur Başak SürmeliCOVID-19'un ortaya çıkmasıyla birlikte SARS-CoV-2 virüsü birçok değişim geçirmiştir ve bunun sonucunda Alfa, Beta, Gama, Delta ve Omikron gibi çeşitli varyantlar ortaya çıkmıştır. Şu anda tespit edilen varyantların hepsi Omikron varyantına aittir ve en yüksek bulaşıcılık ile bildirilen varyant olma özelliğini sürdürmektedir. Bunun yanında, rekombinant suşlar da virüsün evriminde ve genetik çeşitlilik sağlamada önemli bir yere sahiptir. Hipotezimiz, Omikron rekombinant suşlarının ebeveynlerine göre farklı bir evrimsel süreçten geçtiğini popülasyon genetiği ve moleküler evrim analizleri yaparak göstermektir ve bu sayede pandemiye yol açabilecek bu suşlara karşı aşı/ilaç veya sürvilans metotları geliştirilmesine katkıda bulunmaktır. Bu doğrultuda, uygulanan testler ve analizlerden elde edilen bulgulara göre 8 rekombinantın çoğunda negatif seçilimin etkili olduğu görülmüştür. Gözlemlenen mutasyonların çoğu Spike gen bölgesinin RBD kısmındadır ve bunların immün kaçışı sağlayan ve enfeksiyonu etkileyen mutasyonlar olduğu bulunmuştur. Ayrıca, Spike gen bölgesindeki sinonim olmayan değişimlerin ve negatif Tajima, Fu ve Li değerlerinin suşların ortadan kaybolmasına katkıda bulunduğu ortaya çıkarılmıştır. Spike bölgesinin en korunmuş bölgelerden olması ve yapılan analizler sonucunda rekombinant suşlarla ilgili önemli bulgular vermesine dayanarak Spike geninin rekombinant suşlarda aşı/ilaç, sürvilans metotları geliştirmede potansiyel hedef olabileceği öngörülmektedir.Master Thesis Daha Etkili Aşı, Anti-viral Molekül ve Survilans Geliştirilmesi için Rekombinant ve Rekombinant Olmayan Omicron-SARS-CoV-2 Alt Soylarının Moleküler Evrimlerinin Biyoinformatik ve İstatistiksel Yöntemlerle Analizi(2025) Arlı, Meliscan; Sezgin, Efe; Eraltuğ, Nur Başak SürmeliCOVID-19'un ortaya çıkmasıyla birlikte SARS-CoV-2 virüsü birçok değişim geçirmiştir ve bunun sonucunda Alfa, Beta, Gama, Delta ve Omikron gibi çeşitli varyantlar ortaya çıkmıştır. Şu anda tespit edilen varyantların hepsi Omikron varyantına aittir ve en yüksek bulaşıcılık ile bildirilen varyant olma özelliğini sürdürmektedir. Bunun yanında, rekombinant suşlar da virüsün evriminde ve genetik çeşitlilik sağlamada önemli bir yere sahiptir. Hipotezimiz, Omikron rekombinant suşlarının ebeveynlerine göre farklı bir evrimsel süreçten geçtiğini popülasyon genetiği ve moleküler evrim analizleri yaparak göstermektir ve bu sayede pandemiye yol açabilecek bu suşlara karşı aşı/ilaç veya sürvilans metotları geliştirilmesine katkıda bulunmaktır. Bu doğrultuda, uygulanan testler ve analizlerden elde edilen bulgulara göre 8 rekombinantın çoğunda negatif seçilimin etkili olduğu görülmüştür. Gözlemlenen mutasyonların çoğu Spike gen bölgesinin RBD kısmındadır ve bunların immün kaçışı sağlayan ve enfeksiyonu etkileyen mutasyonlar olduğu bulunmuştur. Ayrıca, Spike gen bölgesindeki sinonim olmayan değişimlerin ve negatif Tajima, Fu ve Li değerlerinin suşların ortadan kaybolmasına katkıda bulunduğu ortaya çıkarılmıştır. Spike bölgesinin en korunmuş bölgelerden olması ve yapılan analizler sonucunda rekombinant suşlarla ilgili önemli bulgular vermesine dayanarak Spike geninin rekombinant suşlarda aşı/ilaç, sürvilans metotları geliştirmede potansiyel hedef olabileceği öngörülmektedir.Master Thesis Population Genomics of Crohn Disease Susceptibility(01. Izmir Institute of Technology, 2024) Narli, Bengisu; Sezgin, Efe; Büyükkileci, Ali OğuzCrohn Hastalığı (CD), gastrointestinal sistemin kronik inflamasyonuna neden olan inflamatuar bir bağırsak hastalığıdır. Modern popülasyonlarda CD'ye yatkınlığı artıran genetik yapının, enfeksiyonlara ve patojenlere direnç gibi belirli çevresel stres faktörlerine karşı seçici avantaj sağlayan türetilmiş bir özellik olduğu iddia edilmektedir. Bu nedenle, CD ile ilişkili genlerde seçilim belirtileri olmalıdır. CD riskinin türetilmiş seçilmiş bir özellik olup olmadığını test etmek için, literatür taramaları yoluyla CD ile ilişkili genler ve varyantlar belirlenmiştir. Allen veriseti ve 1000 Genom Projesi aracılığıyla eski ve modern nüfus verileri toplanmıştır. Veriler Plink ve R kullanılarak analiz edilmiştir. 352 CD risk aleli tanımlanmıştır ve CD ile ilişkili alellerin hastalık risk durumu (koruyucu ve duyarlı) atasal ve türetilmiş durumlarıyla karşılaştırılmıştır. Dünya çapındaki dört metapopülasyonun bu alellere göre farklılaşması incelenmiştir. Ayrıca, eski ve modern popülasyonlar arasındaki alel frekansı farklılıkları karşılaştırılmıştır. Günümüz metapopülasyonları arasındaki genetik farklılaşma ve ayrımın, CD ile ilişkili PUS10 ve PPBP_CXCL5 genlerinin etkisine bağlı olduğu, antik ve modern metapopülasyonlardaki ayrımın ise PPP5C, PPBP_CXCL5 ve AIMP1P2 genlerinin etkisi olduğu gözlemlenmiştir. CD prevalansının daha yüksek olduğu popülasyonlarda daha yüksek risk alel frekanslarına sahip olduğu belirlenmiştir. CD ile ilişkili IRGM, OR2B11 ve IL10 genlerindeki varyantlar, atasal ve modern Avrupa popülasyonları karşılaştırıldığında zaman içinde yüksek alel frekansı değişiklikleri göstermiştir. Gen bazlı son seleksiyon analizleri, CD ile ilişkili HERC2, MACROD2, RBFOX1, ITLN1 ve RNFT1P2 genlerinde etkili olan olası pozitif seçilime işaret etmiştir.Master Thesis Molecular Evolutionary and Population Genetics Analyses of Human H1n1 Ha and Na Genes in Pandemic and Non-Pandemic Years(2023) Naycı, Kıvanç; Sezgin, EfeThe 1918 H1N1 pandemic, known as Spanish Flu, is one of the deadliest pandemics on recorded history. It is estimated that the Spanish Flu pandemic affected over 500 million people across the globe, and the death toll is estimated to be between 20 to 50 million. Ever since this, scientists worked hard to find an effective vaccine for influenza, but its very rapidly evolving nature made this task quite the challenge. In this thesis we performed molecular evolution and population genetics analyses on 35714 hemagglutinin and 36302 neuraminidase nucleotide sequences to better understand the evolution of these proteins. The Tajima's D values showed strong positive selection on the pandemic year of 2009 and the BEAST analysis results also suggested there was a greater exponential growth compared to other years. The relaxation of selection and lack of exponential population growth was inferred from the calculations for 2021 sequences, whereas the positive selection on the hemagglutinin and neuraminidase proteins was evident for the 2022 sequences. Outgroup tests also confirmed the positive selection was acting on the pandemic and non-pandemic years, the tests also confirmed the divergence of human influenza neuraminidase from the swine influenza neuraminidase. HA2 part of hemagglutinin and 475-500 nt part of neuraminidase proteins were found to be the most conserved parts of these proteins. In conclusion, the positive selection on these two proteins returned after the year 2021, which was a very unusual year for influenza that caused the positive selection on the virus and the exponential growth rates of the virus to decline. The most conserved regions can be a good candidate for small molecule/drug and vaccine studies.Master Thesis Polymorphisms in Reverse-Cholesterol Transport Pathway Related Genes and Their Relationship With Complex Heart Diseases in Human Populations(01. Izmir Institute of Technology, 2023) Yasdı, Burak Kaan; Sezgin, EfeCardiovascular diseases have been one of the major causes of mortality worldwide. Genetic factors within the underlying mechanisms are extensively studied but still remain unclear at certain points of views. This master's thesis investigates the genetic factors as single nucleotide polymorphisms and their relationship with complex heart diseases in human populations. The study employs a comprehensive approach integrating molecular genetics, epidemiology and biostatistics to analyze diver range of genetic variations within the reverse cholesterol pathway (RCT) playing a role in the cholesterol homeostatis. In a systematic review perspective, by conducting meta-analyses of existing clinical data in literature, the study aims to examine and identify single nucleotide polymorphisms with an increased risk of complex heart disease. Furthermore, the study aims to enrich the set of variants related to coronary heart disease (CHD) and high-density lipoprotein cholesterol (HDL-C) by determination of additional variants in linkage disequilibrium pairs and functional annotation of variants with potential effects. Publicly available clinical data regarding to the relationships of variants and their effects enabled us to explore the underlying genetic factors of higher CHD risk. The findings have the potential to improve future research directions, clinical practice, and public health initiatives aimed at reducing the global burden of cardiovascular diseases.Master Thesis Development of a Functional Snack(01. Izmir Institute of Technology, 2023) Maşa, Zeynep Tuğba; Korel, Figen; Sezgin, EfeNowadays, with the increasing animal food prices, many people in our country are malnourished because they cannot get the necessary protein in their bodies. Additionally, with the Corona virus, which entered our lives in 2019, many people had to struggle with various mental disorders. Although we have left behind the pandemic period, negative emotional states such as depression and unhappiness are still observed in many people today. In this direction, vegetables rich in protein were investigated and used in developing functional snacks. In this study, vegetable chips dough was prepared with 40% pea flour content 15, 17.5, 20, 22.5, and 25% radish, 20, 22.5, 25, 27.5, and 30% zucchini, and 10, 12.5, 15, 17.5, and 20% pumpkin seeds. Each vegetable chip mix was cooked at 50°C, 55°C, and 60°C with the aid of a tray dryer. The proximate analyses (moisture, ash, fat and protein), chemical analyses (antioxidant activity and total phenolic content), physical analyses (color and texture) and sensory analysis were carried out. Mixture design was created with the help of MINITAB 16.0 (Minitab Inc., State College, PA, USA) program, the results of the analyses were evaluated statistically. Based on the design, it was decided to bake thirteen different mixtures at three different temperatures and to perform all the analyzes mentioned above. As a result of the evaluation of all analyses results, the optimized sample was determined as the vegetable chips sample with 40% pea flour, 22.5% zucchini, 25% radish, and 12.5% pumpkin seeds baked at 60°C. The vegetable chips, with this mixture, were baked at 50°C, 55°C and 60°C in the a tray dryer, and in addition to all analyses, sensory analysis and antioxidant activity analysis for all samples baked at 50°C, 55°C and 60°C were conducted. The sample baked at 60°C was the most liked sample.Master Thesis Genetics and Etiopathology of Childhood Obesity, and Development of a Genetic Risk Calculation Panel Based on the Polygenic Risk Score Approach(01. Izmir Institute of Technology, 2023) Yurt, Dudu Seher; Sezgin, EfeObesity is the disease that significantly affects human life as a combination of genetic and physiological environment. The polygenic background of the disease causes of childhood or adulthood obesity are still not fully understood. Childhood obesity and adulthood obesity are usually expressed in terms of body fat mass and body mass index (BMI). Obesity is a comorbid disease that is often associated with T2D, cardiovascular diseases, fatty liver and various mental health problems. Therefore, examining the genetic background of the disease is also important for epidemiological studies. Obesity, which is one of the multi-gene diseases, is revealed by genome-wide research studies, candidate gene studies by SNP genotyping assays. SNP genotyping analyzes not only provide information about the transmission of childhood obesity, but also provide significant guidance on the biological pathways of the disease. Genome-wide association studies (GWAS) provide effective research in association studies between anthropometric body characteristics and the genome. The aim of this thesis is to investigate childhood related obesity variants, adulthood related obesity variants, to identify relationship of these two groups of genetic variants. In addition, the purpose of the thesis, is to understand effects of the variants on metabolic pathways, the difference of childhood and adulthood obesity related pathways and calculation of polygenic risk.Master Thesis Uv-C Irradiation and Lantibiotic Nisin Applications for Food Biopreservation(01. Izmir Institute of Technology, 2023) Altundaş, İlker; Baysal, Ayşe Handan; Sezgin, EfeThe antibacterial and antifungal activity of Lantibiotic Nisin and Essential oil Carvacrol against pathogenic and spoilage-forming microorganisms was investigated in this study. The antimicrobial activities of these compounds were observed in vitro on one Gram-positive (Listeria monocytogenes), two Gram-negative (Cronobacter sakazakii andS. Typhimurium) bacterial strains, and one fungus (Candida albicans). The study investigated the effect of combined treatments involving UV-C irradiation along with Nisin and carvacrol as antimicrobial agents on microbial growth, both at 4°C refrigerator temperature storage for two weeks, and on artificially inoculated chicken drumsticks with L. monocytogenes and S. Typhimurium. Total Aerobic Mesophilic, Yeast & Mold, and Enterobacter/Coliform populations were examined using plate counting on PCA, PDA, and VRBA media, for L. monocytogenes, and S. Typhimurium. PALCAM, OXFORD, and Bismuth Sulphite Agar, respectivelyMaster Thesis Antimicrobial, Antioxidant, Antiproliferative and Cytotoxic Activities of Aronia Fruit Extract(01. Izmir Institute of Technology, 2023) Tanağardı, Dilaranur; Baysal, Ayşe Handan; Sezgin, EfeAronia melanocarpa contains high amounts of phenolic compounds, especially anthocyanins. Because of its high chemical content and significant antioxidant action, this food is known as a functional food, and its use is spreading worldwide. Within the scope of this thesis research, studies were carried out on Aronia melanocarpa dry extract and liquid extract. For these purposes, chromatographic and chemical profile were determined in detail by HPLC (High-Pressure Liquid Chromatography), Fourier-Transform Infrared Spectroscopy (FTIR) and Q-TOFF- MS (Quadrupole Time of Flight Mass Spectrometry), and significant bioactive were determined. Spectroscopic methods were used to characterize phenolic, anthocyanin, and flavonoid components. Aronia melanocarpa dry and liquid extracts were tested for antioxidant activity using DPPH and ABTS methods. The antioxidant potential of the Aronia melanocarpa dry and liquid extracts studied is high. To test the antiproliferative and cytotoxic effects, cytotoxic studies were performed on the CaCo2 cell line. Cell migration was also studied in HUVEC and HaCat cell lines. The antimicrobial activity of Aronia melanocarpa dry extract and liquid extract was tested against Saccharomyces cerevisiae, a yeast species, and bacterial strains of Staphylococcus aureus, Escherichia coli O157:H7, Salmonella Typhimurium. The extracts analyzed showed an antimicrobial effect on the tested bacteria at different concentrations. The results obtained in this study emphasize that the tested Aronia melanocarpa dry extract and liquid extract have antimicrobial properties. Chromatographic, chemical, and cytological data reveal that Aronia melanocarpa liquid and dry extracts can be used as antioxidative and antiproliferative products as food supplements in the health field.Master Thesis Evolutionary Genetics of Behcet's Disease(01. Izmir Institute of Technology, 2022) Kaplan, Elif; Sezgin, EfeBehcet’s Disease (BD) is an auto-immune/autoinflammatory complex disease that causes inflammation of the blood vessels. The underlying cause of BD is unknown. The highest prevalence is seen in populations along the ancient silk road, raising the possibility that it may have its origins along these historic trade routes. The genetic makeup that increases BD susceptibility in modern populations might have been advantageous for certain environmental stress factors such as resistance to infections and pathogens. Such an advantage is expected to leave signs of selection on the genes associated with BD. We have observed a possible recent selection on HLA-B as suggested in previous reports, but recent selection signature was not unique to HLA-B, 14 other BD-associated genes also showed recent selection including other MHC loci such as HLA-G, and other genes such as KCKN9 and NOD2 showed even a stronger selection than HLA-B. Results indicate that the BD alleles are not specific to East Asians. They are present in other world populations with appreciable frequencies. This shows that there is no selection favouring specifically these variants in populations with high BD prevalence. In conclusion, a variety of evolutionary processes have shaped the genetic diversity in BD risk genes, and it is difficult to understand the precise mechanisms of selection that underlie these processes. There are some common genes with BD and other inflammatory diseases. Consequently, our findings may not only apply to BD but also to other inflammatory illnesses in general.