Master Degree / Yüksek Lisans Tezleri
Permanent URI for this collectionhttps://hdl.handle.net/11147/3008
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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.Master Thesis Microbial Mapping in Air and Surface Samples Collected From Schools(Izmir Institute of Technology, 2022) Alkan, Kutlu Şafak; Ökten, Hatice Eser; Sezgin, EfeIndoor environmental quality has gained attention in the past decades due to the increased periods of time spent enclosed in buildings. Parameters such as ventilation, water damage, type of paints used, use of carpets, etc. affect the indoor air quality significantly. With the rising concern regarding outbreaks and pandemic, it is important to investigate the microbial load and consortium structure in schools. This thesis aims at determining the microbial loads in three selected schools in the Balçova District of İzmir, Türkiye. Two sampling campaigns were conducted, one in the winter break (February 2022) and one in the spring semester (May 2022). Surface swab samples and settle-plate air samples were collected from pre-defined spots at schools. Surface swab samples and settle-plate air samples were examined via both classical microbial culture methods and modern DNA analysis methods. Via classical microbial culture methods, culture comparison from the database, fungi cultures were dedicated up to genus level. Via modern DNA analysis method, Sanger sequencing, bacterial cultures were dedicated up to genus level too. All the results indicated that three schools were hosting possibly dangerous genera of both fungi and bacteria. But, this also showed that genus-level discrimination is still not enough to utter exact indoor air quality from the perspective of indoor microbiota to the identification of possible health risks for occupants. For further studies, microbial mapping should discriminate up to species level to demonstrate exact indoor air quality and indoor microbiota vie high throughput sequencing methods.Master Thesis An Investigation of Genetic Factor in Soft Tissue Injuries and Muscle Types Within Football Players(01. Izmir Institute of Technology, 2022) Ük, Yasemin; Sezgin, EfeWhen it comes to athletic performance, genes that affect many factors such as increased aerobic capacity, gene regions associated with strength and athletic ability, oxygen capacity, muscle structure, energy metabolism, and gene variants that cause these genes to be affected at different levels in each individual have been the subject of research for a long time. is addressed. Amateur and professional athletes train according to their injury history after the problems they encounter. However, such measures are insufficient to prevent new injuries in the long run and ensure that the athlete has a healthy season. Similarly, anthropometric tests used in athlete selection and systems that are insufficient to process the data are insufficient to predict the physiological characteristics of this individual in the future and the development of the athlete. In this research, it is aimed to associate detailed genetic parameters by including the genetic marker of the athlete that affects a successful and healthy sports life, and to inform the trainers by reporting the genes that are statistically meaningful with physical data; In this direction, it is aimed to develop and widely provide new test technologies. The aim is to test the hypothesis that athletes who have been genetically scored and matched with the right training accordingly show more improvement. With this setup, the project will be one of the comprehensive studies in sports genetics studies conducted in Turkey, which includes scoring, enables quantitative measurements, and combines genetic factors with physical tests in the international literature.Master Thesis Molecular Evolution and Population Genetics of Acid Resistant Pathway Glutamate Decarboxylase in Lactic Acid Bacteria(Izmir Institute of Technology, 2022) Tekin, Burcu; Sezgin, EfeThe Glutamate Decarboxylase(GAD) Pathway (GDP) is a major acid resistance mechanism that allows Lactic acid bacteria (LABs) to survive in low pH food environments. In the thesis, we aimed to study the molecular evolution and population genetics of GDP genes in LABs to understand evolutionary processes shaping adaptation to high acid environments by contrasting species where the GDP genes are organized as an operon structure (Levilactobacillus brevis) versus lack of an operon structure (Lactiplantibacillus plantarum). Intraspecies molecular population genetic analyses with GDP genes of L. brevis and L. plantarum from various environments revealed that synonymous and non-synonymous nucleotide diversity is driven mainly by low-frequency changes. Neutrality tests revealed mostly negative values indicating negative selection against replacement changes. Similarly, molecular structure and amino acid characteristic analyses showed that none of the replacement changes on the GDP genes alter the important residues of the proteins supporting negative selection against non-conservative amino acid changes. Interspecies analyses were used to identify the closely related LABs. Moreover, phylogenetic analyses showed that the GDP gene tree topologies differed from the LAB species tree, indicating divergent evolutionary histories. The functionally preserved two gad copies of the L. brevis grouped separate phylogenetic clades, showing that the origin of the second gad gene might be via horizontal gene transfer from a phylogenetically distant LAB species rather than gene duplication. In conclusion, GDP in LABs exhibits a dynamic molecular evolutionary history that enables organisms to thrive in high acid environments.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, EfeSince 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.Master Thesis Discovery of Biological Pathways That Have a Role in the Etiopathogenesis of Macular Degeneration by Genetic Investigations(01. Izmir Institute of Technology, 2021) Karayanık, Gizem; Sezgin, EfeMacular Degeneration is a common, progressive, multifactorial, and complex eye disorder among people over 50 years old. The etiology of Macular Degeneration is still not known. The main hypothesis of this thesis is that chronic inflammation and oxidative stress are the major factors for the development of AMD. Therefore, we focused on firstly an overview of the current Literatureto understand risk factors of AMD development, transcriptomic of Retina, and molecules that changing with aging. The genetic, and nongenetic factors associated with AMD are reviewed. Age, smokinghistory, gender, race, cardiovascular disease, hypertension, diabetes, hyperlipidemia, kidney disease, and HIV infection status were chosen as non-genetic factors. Genetic factors included ARMS2, C2, C3, CFH, CFI, CX3CR1, IL10RA, IL28B, LIPC, and SYN3. Secondly, the influence of these factors on early AMD development was investigated by focusing on patients with chronic HIV infection. Based on the idea that patients with acquired immunodeficiency syndrome (AIDS) can be a good model for Aging. Older age was observed to be the primary risk factor for AMD development. Smoking, cardiovascular disease, hypertension, diabetes and injection drug use, CFH (RS800292), IL10RA (RS3135932) and IL10RA (RS2229113) were also observed to be significantly associated with AMD development. According to pathway enrichment analyses, complement activation pathways, lipid metabolism pathways, cholesterol transport, receptor-mediated endocytosis, and extracellular matrix organization mechanism can be involved in AMD development. Multivariable modelsaccounting for other variables identified IL10RA (RS3135932) and injection drug as risk factors for AMD. For the first time, a significant association betweenIL10RA(RS3135932)and AMD is observed. As a conclusion, chronic inflammation and oxidative stress can be mainly risk factor for AMD development.