Yüksek Lisans Tezleri
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/5799
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Master Thesis RNA Etkileşimlerinin İn Silico Analizi(Abdullah Gül Üniversitesi, Fen Bilimleri Enstitüsü, 2024) Orhan, Mehmet Emin; Demirci, Müşerref Duygu SaçarMany supervised machine learning models have been developed for the classification and identification of non-coding RNA (ncRNA) sequences. These models play a significant role in the diagnosis and treatment of various diseases. During such analyses, positive learning datasets typically consist of known ncRNA examples, some of which may even be confirmed with strong experimental evidence. However, there is no database of validated negative sequences for ncRNA classes or standardized methodologies for generating high quality negative samples. To overcome this challenge, a new method for generating negative data called the NeRNA (Negative RNA) method has been developed in this study. NeRNA generates negative sequences using known ncRNA sequences and their octal representations, similar with frame shift mutations found in biology but without base deletions or insertions. In this thesis, the NeRNA method was tested separately with four different ncRNA datasets, including microRNA (miRNA), transfer RNA (tRNA), long non-coding RNA (lncRNA), and circular RNA (circRNA). Additionally, a species-specific case study was conducted to demonstrate and compare the performance of the study's miRNA predictions. The results of 1000-fold cross-validation on machine learning algorithms such as Decision Trees, Naive Bayes, Random Forest classifiers, and deep learning algorithms like Multilayer Perceptrons, Convolutional Neural Networks, and Simple Feedforward Neural Networks showed that models developed using datasets generated by NeRNA exhibited significantly high prediction performance. NeRNA has been published as an easy-to-use, updatable, and modifiable KNIME workflow, along with example datasets and required extensions that can be downloaded and utilized. NeRNA is designed specifically as a powerful tool for RNA sequence data analysis.Master Thesis Tasarlanmış Mikroorganizmalar ile Katma Değeri Yüksek Karotenoidlerin Biyosentezi(Abdullah Gül Üniversitesi, Fen Bilimleri Enstitüsü, 2024) Arslansoy, Nuriye; Fidan, ÖzkanCarotenoids are pigment molecules that play an important role in coloring plants, algae, and other organisms. These molecules exhibit various biological activities such as anticancer, antiviral and antioxidant activities. They have a huge market size and are mainly used in the food, feed, and cosmetic industries. The current supply chain for carotenoids is mostly relied on the extraction from plants and/or chemical synthesis for certain carotenoids. However, these strategies have various bottlenecks and disadvantages such as being affected by climate change, more difficult and costly extraction processes, and environmental issues. These can be overcome with microbial biosynthesis, which not only addresses the previous problems but also provides advantages of producing in a short time and scale-up for industrial production. In this research, we aimed to biosynthesize the high value-added carotenoids by engineered microorganisms. The genome of a native producer of zeaxanthin diglucoside, identified as endophytic Pseudomonas sp. 102515, was first edited by CRISPR-Cas9 to knock out zeaxanthin glucosyltransferase (CrtX), lycopene β-cyclase (CrtY) and beta-carotene hydroxylase (CrtZ). This led to ΔcrtX, ΔcrtY and ΔcrtZ mutant strains of Pseudomonas sp. 102515. On the other hand, overexpression plasmids carrying crtW, CaZEP and CaZEP-CaCCSm40 genes were constructed and transformed to ΔcrtX mutant to synthesize astaxanthin, violaxanthin and capsanthin/capsorubin. HPLC analysis of extracts from mutant strains and overexpression strains revealed that all the engineered strains produced the corresponding carotenoids such as zeaxanthin, β-carotene, and lycopene. Thus, this study paved the way for the biosynthesis of valuable carotenoids in the engineered endophytic bacteria.Master Thesis Escherichia Coli Konak Organizmada GLP-1 Analoğunun Rekombinant Üretimi(Abdullah Gül Üniversitesi, Fen Bilimleri Enstitüsü, 2024) Çalış, Burak; Fidan, ÖzkanDiabetes is the most serious metabolic disorder correlated with obesity, hypertension and cardiovascular conditions. High prevalence of Type II Diabetes Mellitus (T2DM) indicates the need for new medication development. In developing therapeutics, higher efficiency and fewer adverse effect features are targeted primarily. Recombinant protein-based biotechnological drug molecules have been developed and used for the treatment of T2DM. Especially, GLP-1 analogues are known by their self-limiting mechanism and insulinotropic effect. In this study, a novel GLP-1 analogue with increased stability and efficiency is produced using recombinant E. coli. The expression plasmid was constructed and confirmed by restriction digestion and whole plasmid sequencing. Then, itwas transformed into various E. coli strains followed by optimized lysis, growth and expression conditions to maximize the yield of the GLP-1 analogue. Various parameters such as pre-induction time, induction point, induction IPTG concentration and post-induction temperature were tested for the succesfull expression with maximum yield. Consequently, it was achieved that E. coli BL21(DE3) as strain, 0.2 mM IPTG induction at OD600nm of 0.6 and 18 °C overnight post-induction growth was the most promising conditions. Under these conditions, the GLP-1 analogue was obtained in the insoluble fraction. Following protein analysis and purification, quantification was performed and the highest titer of GLP-1 analogue was measured as 626 µg/ml. As future prospect, using another host organism and changing growth conditions can provide obtaining target protein in the soluble form. Keywords: T2DM, GLP-1 analogue, recombinant DNA technology, protein expression, E. coliMaster Thesis Potansiyel Gen Dağıtımı Uygulamaları için Poegma ve Sistaminle Modifiye Plazmit DNA'lar İçeren Polimerik Konjugatlar(Abdullah Gül Üniversitesi, Fen Bilimleri Enstitüsü, 2024) Yıldız, Gizem; İşoğlu, İsmail Alper; İşoğlu, Sevil DinçerPolymer-based gene delivery systems have revealed significant advancements in the treatment of various diseases in recent years. Considering the potential of polymeric vectors, it is observed that the improvements in the field of gene therapy enable effective gene transfection and induced therapeutic protein production. In this thesis study, a strategy based on a new conjugation procedure is designed to increase the gene transfer and cellular uptake rate of plasmid DNAs. According to the findings, POEGMA-based carrier and cystamine-modified plasmid DNAs demonstrated successful conjugation through disulfide bond formation. MDA-MB-231 in vitro cellular uptake results of conjugates showed 94-98% cell internalization, indicating excellent results compared to the well-known polymers in the literature. As a result, the new delivery system we developed in this study determined the success of cystamine-modified plasmid DNAs binding to POEGMA polymer chains via a covalent linkage for the first time in the literature and provided a start for future studies.Master Thesis COVID-19 Virüs Pandemisinde Haftalık Döngünün Kökeni ve Sosyo-Ekonomik Faktörlerle İlişkisinin Araştırılması(Abdullah Gül Üniversitesi, Fen Bilimleri Enstitüsü, 2024) Yağmur, İsmail Emre; Ercan, AltanThe Covid-19 virus, which started in China in 2019 and affected the whole world, has caused a global pandemic. Looking at the worldwide data of this pandemic, the number of daily cases appears to have a weekly cycle that is underestimated as an artifact of the number of daily tests administered. In this thesis study, a new model is developed to calculate the daily infection numbers from daily case numbers by using the Weibull distribution and the natural characteristics of the COVID-19 virus. According to the results obtained, it is found that the number of daily cases has a real weekly cycle. It has been determined that the daily infection numbers calculated in this weekly cycle are minimum on weekdays. According to the analysis by the new methos, these weekly minimums are controlled by socio-economic factors such as human development index and annual national income per capita. During the ascending and descending phases of the pandemic, the weekly minimum shifts from Monday to Friday, exposing the presence of two separate environments for the transmission of the virus among people: working and social. Moreover, the data reveal a variable rather than a fixed reproduction number. As a result, the model we developed in this study successfully identifies the socio-economic factors as the effectors of the progression of the pandemic by taking into account the time of infection for the first time in the literature and is expected to guide the future pandemic studies and pandemic, itself.Master Thesis Geleneksel Gıda Ürünlerinden İzole Edilen Laktik Asit Bakterilerinin Probiyotik Özelliklerinin Belirlenmesi(Abdullah Gül Üniversitesi, Fen Bilimleri Enstitüsü, 2023) Yiğit, Mehmet Burak; Aydın, Aysun CebeciProbiotics are microorganisms that live in our bodies and positively affect health when consumed regularly. One of the ways to have a healthy body is to have a healthy microbiota. Because of that, the importance given to the consumption of probiotic foods among the public is increasing. Since probiotics are especially abundant in fermented and traditional foods, consuming these foods is vital to have a healthy microflora. In this thesis, probiotic potentials of bacteria isolated from tarhana, einkorn sourdough, Turkish and Bulgarian-type boza and pickled beetroot foods were investigated, and obtained results were discussed. Based on acid and bile salt tolerance tests, MRS ES-2-3-7-11-12-17, MRS PT-2-14-16, MRS N-1, MRS EB-3, MRS T-1, M17 N-2 -3-4 showed higher viability in acidic environments (pH 2.0 and 3.0) than the control groups, M17 N-3-4 and M17 TB-1-2 strains showed higher viability at 0.3% and 0.5% bile salt conditions than other strains. For 10 strains which are selected for further tests, in the adhesion to Caco-2 cells, MRS ES-3, MRS N-1, MRS T-2, M17 BB-7, M17 N-2 and M17 N-3 showed over 35% adhesion, especially, MRS N-1 and M17 N-2 showed over 85% adhesion to Caco-2 cells. For the antimicrobial activity test, ES-3 strain showed limited effect on S. aureus ATCC 6538 and K. pneumoniae ATCC 4352 pathogens, while other strains showed no inhibitory effect on pathogens. Finally, according to the results of 16S rRNA sequencing, it was determined that MRS ES-3, ES-7, PT-14 strains belonged to L. plantarum, MRS ES-11 strain belonged to L. brevis, M17 BB-7 strain belonged to E. faecium and M17 TB-2 strain belonged to E. durans species.Master Thesis Peynirden İlk Defa İzole Edilen Loigolactobacillus Coryniformis FOL-19'un Yeni Nesil Dizilenmesi ve Diğer L. Coryniformis Suşlarıyla Karşılaştırmalı Genomik Analizleri(Abdullah Gül Üniversitesi, Fen Bilimleri Enstitüsü, 2023) Gümüştop, İsmail; Ortakcı, FatihLoigolactobacillus coryniformis is a member of lactic acid bacteria isolated from various ecological niches. We isolated a novel L. coryniformis strain FOL-19 from artisanal Tulum cheese and performed the whole-genome sequencing for FOL-19 using Illumina NextSeq. Then, genomic characterization of FOL-19 against ten available whole genome sequences of the same species isolated from kimchi, silage, fermented meat, air of cowshed, and dairy was performed. The average genome size of 2.93 ±0.1 Mb, GC content of 42.96% ±0.002, number of CDS of 2905 ±165, number of tRNA of 56 ±10, and number of CRISPR elements of 6.55 ±1.83 was achieved. Both Type I and II Cas clusters were observed in L. coryniformis. Only one strain (CECT 5711) was predicted to encode a Carnocin CP52 bacteriocin gene cluster. The presence of CRISPR elements and Cas clusters suggests that L. coryniformis holds a promising potential for being a reservoir for new CRISPR-based tools. These findings put a step forward for the genomic characterization of L. coryniformis strains for biotechnological applications via genome-guided strain selection to identify industrially relevant traits.Master Thesis 32-mer MaSP1 Geninin pBbB6c Plazmid Vektörüne Klonlanması ve Escherichia Coli NEB 10-beta'ya Transformasyonu(Abdullah Gül Üniversitesi, Fen Bilimleri Enstitüsü, 2023) Benk, Ruveyda; Ortakcı, Fatih; Öz, YahyaThe main purpose of my thesis was to clone Masp1 spider silk protein encoding gene from dragline type spider into E.coli NEB 10-beta organism. The recombinant microbial production of spider silk protein and converting it into a fiber format would ultimately produce a biomaterial also called as biosteel with high toughness and elasticity whereas low density compared to Kevlar, steel and carbon fiber. For this purpose, the gene encoding the dragline spider protein (MaSP1) was cloned into E. coli NEB 10-beta using recombinant molecular methods. First, 8-mer MaSP1 was synthesized and cloned via pGSI high copy cloning vector by sticky end cutting with restriction enzymes of KpnI,Kpn2I followed by heat-shock transformation into E.coli. Second, we performed restriction of the 8-mer plasmid by NheI and Kpn2I to extract the 8-mer. Later, the restriction was performed by SpeI and Kpn2I to obtain linearized pGSI containing 8-mer Masp1. A ligation was applied to merge 8-mer and pGSI plasmid carrying 8-mer Masp1 to achieve 16-mer Masp1 containing pGSI. Again, this plasmid was heat-shock transformed into E.coli. Following the same restriction 32-mer Masp1 containing pGSI plasmid was achieved. Finally, 32-mer Masp1 fragment was cut from pGSI cloning vector and ligated to pBbB6c low copy expression plasmid followed by electroporation into E.coli. The band size of 32-mer Masp1 gene was aligned between 3 kb and 5 kb which is an agreement with the calculated size of 32-mer Masp1 gene. Future studies should focus on the expression of Masp1 and the efficient production of this valuable recombinant protein under bioreactor conditions with cutting edge bioprocessing techniques.Master Thesis İn Siliko Analizlerle Yeni Patojenik Varyantlar Bulmak(Abdullah Gül Üniversitesi, Fen Bilimleri Enstitüsü, 2022) Zorluer, Ziya Furkan; Kaplan, Oktay İsmailInherited diseases are health problems caused by one or more abnormalities in the genome. It can be caused by changes in a single gene (monogenic) or multiple genes (polygenic), or by a damage on chromosomes. Genetic variation is the differences in the DNA sequences that can be observed within a species or in alleles. Evaluation of genetic variants, together with reported phenotypic or pathogenic annotations from non-human organisms, facilitates the comparison of these variants with their human counterparts. In this work, we combined pathogenic and phenotypic annotations with variants, and these phenotypic orthologous variants from seven organisms can provide clues to the functional consequences of human genetic variants.Master Thesis Histon Deasetilaz İnhibisyonu ve Otofaji Modülasyonunun Kolanjiokarsinoma Hücrelerine Etkisi(Abdullah Gül Üniversitesi, Fen Bilimleri Enstitüsü, 2022) Yenigül, Münevver; Yenigül, Münevver; Akçok, Emel Başak Gencer; Akçok, İsmailCholangiocarcinoma (CCA), also known as biliary tract cancer, is a heterogeneous group of malignancies formed by the differentiation of epithelial cells in the biliary tract. CCA is the second most common primary liver tumor and it has both an increasing rate and high mortality worldwide with its late diagnosis, refractory type, and aggressiveness. The effects of autophagy modulators and HDAC inhibitors in CCA are not fully known. This study is proposed a novel treatment approach with the combinational therapy of autophagy and HDAC inhibitors for CCA patients. In results obtained with alone HDACis, alone autophagy modulators, and combinations of HDACis and autophagy modulators, Nocodazole from autophagy modulators and MS-275 and Romidepsin from HDAC inhibitors showed a better synergistic effect on the TFK-1 and EGI-1 cell lines of the cholangiocarcinoma. In cell cycle analysis of the combination, was achieved arrest at the S phase and G2/M phase. In conclusion, this study highlights the important combination of HDAC inhibitors and autophagy modulators, which is a promising therapy in CCA. Keywords: Cholangiocarcinoma, HDAC inhibitors, Autophagy modulators, Combination therapy