Phd Degree / Doktora

Permanent URI for this collectionhttps://hdl.handle.net/11147/2869

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Access type: Open accessAuthor: search.filters.author.Bedir, Erdal

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  • Doctoral Thesis
    Effects of Telomerase Activators on Monoclonal Antibody-Producing Cell Lines and Stem Cells, and Their Utilization in Industrial Productions
    (01. Izmir Institute of Technology, 2024) Kuru, Gülten; Bedir, Erdal
    Aging is a physiological and multifactorial biological process of functional decline in any living organism. Telomere shortening, high levels of reactive oxygen species (ROS), and cellular senescence are the primary physiological changes that accompany aging. While there has been an increase in human life expectancy in recent decades, there has not been a concomitant increase in healthy aging. Degenerative diseases, including musculoskeletal disorders such as osteoporosis and osteoarthritis, have been found to be directly linked to aging. Age-related degenerative diseases are devastating diseases that cause millions of deaths worldwide each year and place an economic and psychological burden on society. Due to the ever-increasing number of patients, there is a huge demand for novel therapeutic approaches to treat degenerative diseases. Two main approaches are at the forefront of technology for the treatment of degenerative diseases: stem cell transplantation (regenerative medicine) and monoclonal antibody-based therapy. Indeed, it is well known that there is a strong correlation between disease pathology and telomeres. In fact, the possible therapeutic effects of telomerase activation have been evaluated in diverse backgrounds to cure and prevent various diseases. Within the scope of this thesis, we aim to investigate the effects of telomerase activator novel molecules from Astragalus sp., obtained in our previous studies by biotransformation of cycloastragenol (CG) via the plant's endophytic fungi on the health span/lifespan of mesenchymal stem cells (MSCs) during in vitro expansion and their osteogenic differentiation. Additionally, the efficacy of these compounds was investigated in the monoclonal antibody (mAb) production process in terms of mAb productivity. Based on the outcomes of the study, novel telomerase activators deriving from natural resources of our country have significant potential in stem cell research, thus regenerative medicine, since promising results were obtained for the clinical use of these novel molecules. Our data also suggest that molecules simultaneously promote osteogenic differentiation and telomerase activation.
  • Doctoral Thesis
    Preparation of Vaccine Formulations for Melanoma Using Potent Adjuvant Candidate Astragaloside Vii and Investigation of Anti-Tumor Activities of Formulations in Mouse Cancer Models
    (01. Izmir Institute of Technology, 2024) Özefe, Nilgün Yakuboğulları; Bedir, Erdal; Sağ, Duygu
    Kanser, genomdaki nokta mutasyonların birikmesi sonucu ortaya çıkan ve yapısal değişikliklerle ilerleyen bir hastalıktır. Kanser immünoterapisinin ana kategorilerinden biri, vücudun kansere karşı kendi bağışıklık sistemini harekete geçiren kanser aşısıdır. Geleneksel tedaviler güvenlik sorunları ve bağışıklık sisteminin uygun olmayan modülasyonu nedenleriyle etkili olmadığından, nanotıp temelli yaklaşımların uygulanması bu sorunların çözümü için bir potansiyel oluşturmaktadır. Bir taşıyıcı malzeme içinde immünostimülatör ajanların/adjuvanların formülasyonları, hedef hücreler tarafından alımı sağlar, sistemik etkiyi değiştirir, güvenli bir profil sağlar ve immünoterapötiklerin terapötik etkinliğini arttırır. Bu bakış açısıyla bu tez kapsamında, Astragalus polisakkariti temelli bir nanotaşıyıcıya MPLA/Astragaloside-VII entegre edilerek yeni bir adjuvan sistemi (MA-NP) tasarlanmış ve geliştirilmiştir. MA-NP'nin in vitro ve in vivo immünomodülatör özellikleri ve ardından iki fare melanoma modelinde profilaktik ve terapötik etkinliği araştırılmıştır. Biyouyumlu, 20-50 nm boyutunda, negatif yüklü, dendritik hücreler tarafından etkin bir şekilde alınabilen MA-NP başarılı bir şekilde üretilmiştir. Çoklu peptitler ile formülize edilen MA-NP, doğal ve kazanılmış bağışıklık hücreleri aktive etmiş, öncelikli olarak merkezi bellek CD8+ T hücre yanıtı gösteren antijen spesifik sitotoksik T hücre popülasyonunu arttırmış, fonksiyonel IFN-+CD8+ T hücrelerini indüklemiş, tümör içi CD4+, CD8+ T hücre, dendritik hücre ve M1 makrofajlarını arttırmış ve güçlü bir şekilde tümör büyümesini inhibe etmiştir. Ayrıca MA-NP ile oluşturulan nanoaşı, anti-PD1 antikorları ile birlikte farelere uygulandığında yerleşik B16-F10 tümörlerini ortadan kaldırmıştır. Bu bulgular, kanser aşılarında kullanılabilecek yeni bir saponin temelli adjuvan sistemini ve kanser immünoterapi yaklaşımını geliştirmek için umut verici bir kombine terapiyi ortaya koymaktadır.
  • Doctoral Thesis
    Development of Computational Models To Predict the Toxicity of Advanced Materials
    (01. Izmir Institute of Technology, 2023) Bilgi, Eyüp; Karakuş, Ceyda Öksel; Bedir, Erdal
    The aim of this study is to harness computational power to enhance existing knowledge on NM safety and to optimize the use of existing nanotoxicity data. The primary goal is to support the safe(r)-by-design concept, necessitating early integration of safety considerations into NM design through structural manipulation strategies. This thesis focuses on three case studies: zinc oxide, silver, and gold NP, using data manually collected from the literature. Analyses with zinc oxide and silver NP revealed a correlation between their toxicity and both internal (intrinsic properties, size, shape, surface charge) and external (cell and analysis-related properties) factors. For zinc oxide, it was found that coating had significant influence on cell viability, with a critical threshold identified at 20 µg/ml concentration and 10 nm size. Similarly, for silver NPs, concentration, size, and exposure time were significant factors. Coating with organic macromolecules increased cell viability, whereas green-synthesized NPs (using bacteria, plant extracts, algae) decreased it. The gold NP study highlighted that ensemble methods were more effective in elucidating complex relationships, with cellular uptake linked to particle size, zeta potential, concentration, and exposure time. Overall, this thesis contributes to safer-by-design strategies, crucial for developing commercially viable and safe NMs. The findings advocate for a broader toxicity evaluation approach, considering various physicochemical aspects and experimental procedures. The complex interactions observed suggest that advanced algorithms are necessary for accurate modeling, supporting the optimization of experimental parameters in NP engineering for biomedical applications.
  • Doctoral Thesis
    Utilization of Endophytic Fungi and Their Enzymes for Transformation To Obtain Bioactive Compounds
    (01. Izmir Institute of Technology, 2022) Küçüksolak, Melis; Bedir, Erdal; Sağ, Duygu
    Biotransformation is a chemical reaction performed by biological systems or their components to modify molecules and has many applications in the pharmaceutical industry. In our previous project, biotransformation studies were carried out on Astragalus cycloartanes using endophytic fungi isolated from the tissues of Astragalus species, and the effects of the metabolites on telomerase activation were investigated. Among the isolated endophytic fungi, Alternaria eureka and Camarosporium laburnicola were identified as potent biocatalysts in developing molecule libraries and producing potent telomerase activators. This thesis aims to demonstrate the potential use of endophytic fungi in the production of bioactive metabolites. In the first part, biotransformation studies were performed on cyclocephagenol, a novel cycloartane-type sapogenin with tetrahydropyran unit, using Alternaria eureka and Camarosporium laburnicola, and twenty-eight new metabolites were obtained. According to the results of bioactivity studies, Alternaria eureka and Camarosporium laburnicola were found to be responsible for producing potent neuroprotective agents and potent telomerase activators, respectively. In parallel, biotransformation conditions were statistically optimized to afford potential telomerase activators, discovered in our previous studies (E-CG-01, E-AG-01 and E-AG-02). For this, nine parameters were screened by Plackett-Burman Design, and three significant parameters were optimized using Central Composite Design. As a result, production yields were increased by 1.95-fold for E-CG-01, 70-fold for E-AG-01, and 19-fold for E-AG-02. In the last part, the partial purification and characterization of alcohol dehydrogenase, Baeyer-Villiger monooxygenase, and lactone hydrolase enzymes, which were catalyzing the modifications in the production of telomerase activators, from Camarosporium laburnicola were performed.