Phd Degree / Doktora

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Department: search.filters.department.Thesis (Doctoral)--İzmir Institute of Technology, BioengineeringScopus Q: search.filters.scopusQuartile.N/A

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Now showing 1 - 10 of 24
  • 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
    Development of a Telemedicine Platform for Remote Monitoring of Patients
    (01. Izmir Institute of Technology, 2023) Tarım, Ergün Alperay; Tekin, Hüseyin Cumhur; Mevsim, Vildan
    Telemedicine supports patients and healthcare professionals to provide remote medical services and to ensure that medical operations, services, and applications. Telemedicine provides mobile health services, doctor-patient communication, relationship and consultation, medical clinic, and operation service for the diagnosis, monitoring, treatment, and rehabilitation by remote health services. In this thesis, telemedicine-based applications and integrated devices are developed to assist in the diagnosis, monitoring, and treatment processes of specific diseases. In this regard, a WebRTC-based telemedicine application has been developed to ensure the transfer of health data and doctor-patient communication for monitoring diseases. The developed telemedicine application performance of providing doctor-patient communication and its effect on the management of chronic heart failure disease were examined. Thereupon, medical diagnosis and wearable devices have been developed that can be integrated into the telemedicine application that has been proven for disease monitoring. As part of this study, vital health data, biomarkers, and pathogen analysis were performed by developed devices to diagnose and monitor three chronic diseases, namely sleep apnea, chronic kidney disease, and COVID-19. First, a wearable device platform has been developed that can analyze breathing patterns via diaphragm acceleration and breath temperature and diagnose and monitor sleep apnea. Afterward, electromechanical LOC platforms used for colorimetric determination of serum creatinine levels for the diagnosis of chronic kidney disease by two methods were characterized and presented in detail. Finally, a real-time LAMP-based electromechanical device used to detect SARS-CoV-2 viral RNA has been produced, and a colorimetric rapid test system has been developed and tested for COVID-19 diagnosis. In this way, devices and systems integrated into the telemedicine platform have been developed for use in different diseases and medical applications. With these developed platforms, disease diagnosis, treatment and rehabilitation, remote monitoring and patient management are provided with inexpensive, portable, user-friendly, easy-to-use solutions without the need for professional service providers.
  • Doctoral Thesis
    Development and Characterization of Novel Bioink by Using Decellularized Extracellular Matrix for Bone Tissue Engineering Applications
    (01. Izmir Institute of Technology, 2023) Kara Özenler, Aylin; Tıhmınlıoğlu, Funda; Havıtçıoğlu, Hasan
    Bone tissue engineering has focused on the development of functional scaffolds that can organize bone regeneration with appropriate structures and properties. Three-dimensional (3D) printing technology enables the development of personalized scaffolds. In addition, biological scaffolds obtained by decellularization have various advantages for developing natural-based scaffolds. The development of printable, patient-specific bioinks derived from decellularized extracellular matrix could provide 3D fabrication of tissues and organs with high potential to mimic native tissues. The presented thesis study demonstrates the development of various bioink compositions for bone tissue engineering applications. In this regard, bone tissues were decellularized with a novel method and then characterized in order to verify the removal of whole cellular components for eliminating immunological reactions. After the pulverization of tissues, decellularized bone (DB) particles were used as an additive within various ink combinations (alginate-, gelatin- and alginate-gelatin-based). Thus, various bioink formulations were developed containing DB particles, biopolymers and mesenchymal stem cells (MSC). All prepared bioinks were bioprinted, then the viability, proliferation and differentiation capacity of the cells inside the structures as well as the physical, rheological, and printability properties of the inks were assessed. The results revealed that all bioink combinations were suitable for bioprinting and the addition of DB particles improved cell proliferation and osteogenic differentiation in all bioink formulations. Alginate-based bioinks exhibited the greatest printability and shape fidelity, gelatin-based bioinks showed the highest cell proliferation and attachment, also, gelatin incorporation into alginate-based bioinks improved the biological activity of cells. In conclusion, cytocompatible, functional composite bioinks developed in this thesis study are of value for bone tissue engineering research in future to explore their functions in the living system and show complete bone regeneration while maintaining their stability for a long time.
  • 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.
  • Doctoral Thesis
    Development of Conducting Polymer-Based Fluorescence On/Off Biosensor for Biomolecule Analysis
    (01. Izmir Institute of Technology, 2022) Arslantaş, Duygu; Arslan Yıldız, Ahu
    Sensitive and selective detection of biomolecules and cells is essential for early diagnosis of diseases, prognosis monitoring, and effective therapy. This thesis aimed to develop a novel fluorescence ‘‘turn-on/off’’ biosensor for biomolecules and cells detection. In this study, cationic polythiophene derivative poly(1,4-dimethyl-1-(3-((4- methylthiophen-3-yl)oxy)propyl)piperazin-1-ium bromide) (PT–Pip) was used as an efficient fluorescence transduction element to discriminate proteins, mammalian cells, and amino acids for the first time. Initially, pH–dependent spectroscopic characterization of the PT–Pip was performed to monitor the conformational and optical changes. The pH sensitivity of the PT–Pip was demonstrated for the first time. Afterwards, the fluorescence ‘‘turn–off’’ phenomena were investigated in detail using citrate–capped gold nanoparticles as an efficient fluorescence quencher. Further, the interaction of target analytes such as proteins, mammalian cells, and amino acids with pre–quenched non–covalent PT–Pip–AuNP complexes was examined. Disruption of the binding equilibrium between PT–Pip and AuNP by analytes resulted in the selective displacement of PT–Pip, which generated signal output as a fluorescence ‘‘turn–on’’ mode. Consequently, for the sensitive detection of biomolecules and cells, chemical tongue sensor arrays were developed utilizing differential sensing approaches. PCA was used for the statistical evaluation of the multi–dimentional fluorescence response patterns. As a result, unique fingerprints were rapidly obtained by the direct sensing of proteins, ratiometric sensing of mammalian cells, and indirect sensing of amino acids. The combination of a differential sensing strategy with an appropriate multivariate statistical technique enabled the selective and sensitive detection and identification of proteins, mammalian cells, and amino acids.
  • Doctoral Thesis
    Development and Use of Contactless Magnetic Manipulation Methodologies for the Formation of 3d Cardiac Models
    (01. Izmir Institute of Technology, 2022) Önbaş, Rabia; Arslan Yıldız, Ahu
    In this thesis, two contactless magnetic manipulation methodologies were introduced, which are magnetic levitation (MagLev) and biopatterning techniques. The optimization steps of both techniques were completed with NIH/3T3 mouse fibroblast cells. Later, 3D cardiac models were developed using H9c2 rat cardiomyocytes. For the MagLev technique, tunable 3D spheroids were obtained with changing initial cell seeding number, gadobutrol concentrations, and culturing time. For the biopatterning approach, a new bio-ink formulation, which comprises alginate, magnetic nanoparticles, and cells, was developed. Further, biopatterned cellular structures were fabricated in different shapes such as discs, rings, and rectangles under an external magnetic field. Later, characterization was done successfully via immunostaining of collagen I, F-actin, and DAPI. Moreover, cardiac-specific markers; cardiac troponin T and MYH6 were analyzed for both 3D cardiac spheroids and patterned 3D cardiac structures. Finally, doxorubicin was applied to evaluate the drug responses. IC50 values were calculated as 14.7 μM and 8.1 μM for 3D cardiac spheroids and 3D cellular structures respectively, while standard 2D cell culture was 3.5 μM which indicated 3D cardiac models were more resistant to drug exposure. In the last part of thesis, patterned 3D cardiac structures were fabricated using co-cultured hiPSC-derived cardiomyocytes and cardiac fibroblast cells via biopatterning methodology. Characterization was carried out successfully by immunostaining of α-actinin, collagen I, Cx-43, Troponin T, and DAPI. Taken together, to fabricate 3D cell culture models, MagLev and biopatterning-based contactless manipulation methodologies may be good alternatives to conventional 2D cell culture methods for tissue engineering applications, especially for drug screening.
  • Doctoral Thesis
    Multi-organ-on-a-chip for cancer drug testing
    (Izmir Institute of Technology, 2022) Mohammed, Abdurehman Eshete; Pesen Okvur, Devrim; Erdal Bağrıyanık, Şerife Esra
    Cancer is one of the devastating and fatal severe diseases worldwide that kills millions of people every year. Globally cancer is the second leading cause of death after cardiovascular disease and was responsible for 10 million deaths in 2020. Breast cancer is one of the predominant cancers in females and is the cause of more than half a million females death each year. The primary cause of cancer patients' death is cancer metastasis. Triple-negative BREAST cancer (TNBC) is mainly treated by chemotherapy. In the current drug discovery and development processes, the efficacy and toxicity of chemotherapies identify using 2D and animal testing but not simulating the in vivo microenvironment. This research designed multiorgan-on-a-chip with liver and breast cell line compartments, and drug PKPD modeling was done by Monolix software. In this research, a unique multiorgan-on-a-chip (MOC) was designed and fabricated, generated experimental PK and PD data using the new MOC device, and modeled and simulated PK and PD using the experimental data. To conclude, we developed a new multiorgan-on-a-chip (MOC) platform used for PKPD modeling and PKPD simulations that would be helpful in the preclinical research to evaluate the effectiveness and toxicity of drugs. In the future, using calceinAM, a fluorescent cell viability dye, generating PD data for each cell type and determining side effects of doxorubicin in each cell line is essential. Adding more organs to the MOC, such as heart tissue, to study the cytotoxicity of doxorubicin in different organs gives more efficient data for PKPD modeling.
  • Doctoral Thesis
    Xylan Based Composite Nanoparticles and Biofoams for Drug Delivery and Tissue Engineering
    (01. Izmir Institute of Technology, 2022) Zeybek, Nüket; Büyükkileci, Ali Oğuz
    Xylan is a hemicellulosic polysaccharide, which can be obtained from forest and agricultural wastes. Similar to some other polysaccharides, xylan can find application in drug delivery and tissue engineering due to its availability, structural diversity, biocompatibility, biodegradability, and low cost. In the first part of the study, xylan-based nanoparticles were developed for colontargeted oral drug delivery. Xylan is resistant to digestion and absorption in the upper GIT and is degraded by hydrolysis of glycosidic bonds by the colon microbiota; this makes it prominent in targeted drug delivery to the colon. The drug carrier was combined with a polymeric micelles system to increase the bioavailability of hydrophobic bioactive molecules in the colon targeting. The model hydrophobic molecule, curcumin, was loaded in the core of the triblock copolymer P-123 micelles by the thin-film hydration method. Curcumin-loaded micelles were coated with xylan supported by chitosan and tripolyphosphate using the ionic gelation method. In another approach, xylan was also used to coat curcumin-loaded mesoporous silica nanoparticles to prevent premature drug release in the upper GIT in colon-targeted delivery. In both approaches, the drugcontaining structures were maintained up to the colon and the drug was released upon bacterial hydrolysis of xylan. In the second part, xylan-based biofoams were synthesized by the oil in water emulsion templated method. Several physicochemical and mechanical tests have shown that at the optimal conditions foams with promising properties could be synthesized. Besides, to develop a more effective tissue therapy by utilizing the synergistic effect of the drug delivery and scaffold system, a model drug was successfully loaded into biofoams. This study showed that xylan is a promising feedstock for the synthesis of stable and biocompatible materials in biomedical applications, which reveals its potential capability in drug carriers and scaffolds.
  • Doctoral Thesis
    Magnetic Levitation of Cells From Bone Marrow Origin
    (Izmir Institute of Technology, 2021) Anıl İnevi, Müge; Özçivici, Engin; Güven, Sinan
    Magnetic levitation via negative magnetophoresis is a new label-free technology that is important in cell- and tissue-level bioengineering applications. Biofabrication applications of the technology is an area that still needs to be developed. In this doctoral thesis, 3D cellular structures with contrable size and cellular arrangement were formed and cultured with magnetic levitation using bone marrow-derived stem cells in both a miniature system that provides levitation between two magnets and a ring magnet-based large-scale system. First, a miniaturized magnetic levitation system that allows real-time imaging was produced and comprehensive protocols were described for its use for both single-cell level analysis and cell culture. With this setup, complex in situ 3D cellular aggregates were formed and their culture was maintained by levitation. Then, a new system that provides levitation on a single ring magnet was produced and used for biofabrication for the first time to overcome the reservoir volume constraint in the existing system and thus to create larger and symmetrical 3D cellular clusters. With the elimination of the upper limit in the system, the volume of the chamber was increased and the medium and biological structure transfer became easily applicable. It has been shown that this ring magnet-based magnetic levitation setup is suitable for cell culture, formation of millimeter-sized cellular structures with various cell types, and that pre- formed cellular structures can be combined by levitation. The low-cost and easy-to-use systems presented in this thesis have the potential to be applied in many areas such as tissue engineering and drug testing.
  • Doctoral Thesis
    Development of Novel Polymeric Carriers for Gene Therapy
    (01. Izmir Institute of Technology, 2021) Zelçak, Aykut; Bulmuş Zareie, Esma Volga
    The development of effective delivery systems is a limiting step in gene therapy. In this work, new linear block copolymers and star polymers were synthesized, and their siRNA delivery abilities were investigated. For this aim, diblock copolymers consisting of alternative "stealth" polymer blocks (PEG, P(OEGMA) (Poly(oligo(ethylene glycol) methyl ether methacrylate)) or P(OEtOxMA) (Poly(oligo(2-ethyl-2-oxazoline) methacrylate))); and same cationic polymer block (P(AEAEMA) (Poly(2-((2-aminoethyl)amino)ethyl methacrylate))), have been prepared via RAFT polymerization or combination of CROP and RAFT polymerizations. Additionally, to demonstrate the effect of polymeric architecture, P(OEGMA)/P(AEAEMA) miktoarm star polymers have also been synthesized via RAFT polymerization. Polymers were characterized by SEC, NMR and DLS. siRNA complexation was investigated by gel electrophoresis, DLS, SEM and TEM. Compared to star polymers, linear block copolymers could bind the siRNA molecules easier and tighter due to their more flexible natures and sterically accessible amine groups. The diameter of star polymer-siRNA complexes at N/P of 50 was found to be approximately 20 nm. Compared to this, linear block copolymers formed smaller particles (≈ 10 nm) at the same N/P ratio. The viability of linear block copolymer-treated cells was found to be 50% or better at the polymer concentration of 5 µM. In contrast, star polymers showed more detrimental effects at the same polymer concentrations. P(OEGMA)43-b-P(AEAEMA)45-siRNA complexes at N/P of 50 were taken up by 63.5% and 74.1% of H460 and Mda-mb-231 cells, respectively. In contrast, P(AEAEMA)40-b-P(OEtOxMA)38 complexes showed much lower uptake profile at the same conditions. Remarkably, P(OEGMA)43-b-P(AEAEMA)45-siRNA complexes showed potent gene silencing effect on Mda-mb-231 cells as shown by luciferase and RT-qPCR assays. Overall, it has been found that "stealth" polymers and polymeric architecture have a very significant effect on siRNA delivery.