Yüksek Lisans Tezleri
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/5799
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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 K-mer Sekans Gösterimine Dayalı MicroRNA-Hastalık İlişkilerinin ve MicroRNA-Tür İlişkilerinin Sınıflandırılması(Abdullah Gül Üniversitesi, Fen Bilimleri Enstitüsü, 2022) Erbaşı, Yalçın Han; Güngör, BurcuThe dysregulated gene expression brings about a variety of diseases, and dysregulation of microRNA (miRNA) has a wide impact on disease development and cellular physiology. Thus, miRNAs play important roles in a variety of fundamental and significant biological processes related to human diseases. There are a lot of research about changes in the function of miRNAs have been published in many human diseases. Computational methods serve as a complementary process to traditional wet-lab experiments, which require many resources and time in terms of detecting potential miRNA-Disease associations. Furthermore, there is a need to present a novel approach that allows assignment of an unknown miRNA to its most likely species. An easy way to filter new data would be to ensure that the new miRNA is classified below the maximum distance to the species known to originate from. In this thesis, a computational model has been proposed for identifying miRNA-disease and miRNA-Species associations by depicting the miRNAs with their k-mer sequence representation and by utilizing machine learning methodologies. The difference of our approach is which we reveal disease and species associated the sequences of miRNA store information. This put a question about the miRNA's chemical compounds and their associations with different types of species and diseases. With this study, the new disease-disease and species-Species associations disclosed can be calculated for many different species and diseases, these approaches can develop to species and disease classification. Lastly, our study may open a door to redefine species and diseases classifications which have been used nowadays, also it may provide the improvement of treatment strategies and early diagnosisMaster Thesis Yeni Bir Silya Geni Olan TMEM145'in Karakterizasyonu(Abdullah Gül Üniversitesi, Fen Bilimleri Enstitüsü, 2020) Pir, Mustafa Samet; Kaplan, Oktay İsmailSilya ve flagella çoğu organizmada bulunan, mikrotübül yapılı, yüksek korunumlu hücresel bir yapıdır. Bunlar, protozoalarda hareket sağlamadan, çok hücreli canlılarda sinyal iletimine kadar bir çok fonksiyona sahiptir. Silyanın yapısında veya fonksiyonunda meydana gelen bozulmalar insanlarda silyopati denilen çeşitli hastalıklara sebep olur. Silyada meydana gelen bu bozukluklar silya genlerinde veya silya fonksiyonunu etkileyen silya geni olmayan genlerde meydana gelen mutasyonlardan kaynaklanır. Bu yüzden silyopatilerin moleküler temelini ortaya çıkarmaya yardımcı olacak yeni silya genleri keşfetmeye ihtiyaç vardır. GPCR proteini olan, insan TMEM145 geninin ortoloğu olan ve Caenorhabditis elegans'ta bulunan C15A7.2 genini silya geni olarak tanımladık. C15A7.2 geni tarafından kodlanan TMEM-145 proteinin fonksiyonunu araştırdık ve C15A7.2 mutantlarda intraflagellar transport sisteminin hızının yavaşladığını bulduk. Ne tekli, ne de çeşitli çiftli mutantlarda herhangi bir yapısal bozukluk gözlemlemedik. Bu da TMEM-145'in silya yapımında görev almadığını gösteriyor. Silyada bulunan bu genin tam fonksiyonunu öğrenmek için ilave analizler yapılmalıdır.