Master Degree / Yüksek Lisans Tezleri
Permanent URI for this collectionhttps://hdl.handle.net/11147/3008
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Master Thesis Development and Characterization of Biomimetic Peptide-Based Bioink for Dental Tissue Engineering(01. Izmir Institute of Technology, 2023) Altan, Zeynep; Arslan Yıldız, AhuRecently, the role of molecular control in the tooth mineralization process has received much attention. Biomimetic scaffolds have been started to use in dental tissue engineering and regeneration due to their high applicability, biocompatibility, biodegradability, and mineralization capability. In this thesis, a hybrid biomimetic bio-ink; P11-4 peptide-based Quince Seed Hydrogel (QSH)/Gelatin (Gel) is used in 3D cell culture studies for dental tissue engineering applications. Pristine QSH, QSH/Gel, and P11-4/QSH/Gel bio-inks were characterized by FTIR and viscosity analysis, and their 3D bioprinting parameters were optimized. Hydrogels were crosslinked via 1-Ethyl-3-(3-dimethylaminopropyl) Carbodiimide (EDC)/N-Hydroxysuccinimide (NHS) coupling reaction and various hydrogel concentrations were investigated for scaffold fabrication. Characterization of produced scaffolds was performed by SEM imaging, mechanical testing, protein adsorption, and swelling analyses. As a result, the mechanical strength, viscosity, swelling properties, and surface characteristics of the biomaterial were evaluated. SaOS-2 human osteosarcoma cell line was used for 3D bioprinting studies. Cell viability analyses were performed via Live/Dead and MTT assays. Mineralization was investigated and assay was carried out with Alizarin Red Staining. According to obtained results, P11-4/QSH/Gel scaffolds provide high cell viability and proliferation rate compared to pristine QSH and QSH/Gel control groups. Also, with the addition of P11-4 to QSH/Gel, a certain amount of increase in mineralization was observed after day 7 on long-term cultured scaffolds. As a result of this study, it was concluded that P11-4-based QSH/Gel has a high potential to be used as a bio-ink in the production of 3D scaffolds for dental tissue engineering applications.Master Thesis Development and Characterization of Magnesium Alginate Hydrogels for 3d Cell Culture Formation(01. Izmir Institute of Technology, 2021) Çoban, Başak; Arslan Yıldız, AhuCell culture is an important tool for biological research. Two-dimensional (2D) cell culture is still used but growing cells on plastic surfaces offering unnatural growth kinetics and cell attachment. Three-dimensional (3D) cell culture allows cells to growth in their 3D physical shape and interact with their surroundings which represent the natural microenvironment. Hydrogels are crosslinked networks, have become increasingly used biomaterial for 3D cell culture with their ability to simulate the nature of most soft tissues. In this thesis, a new methodology based on bio-patterning was developed to fabricate (3D) cellular structures by using Mg-alginate hydrogel and fabricated 3D cellular structures was utilized for drug screening studies. Mg-alginate hydrogel has a specific gelation/de-gelation characteristics compared to other types of hydrogels due to its weak polymer-ion interaction. In this study slow gelation and de-gelation property of Mg-alginate hydrogel was used for biopatterning of 3D cellular structures. Plackett-Burman and Box-Behnken design models were used to optimize parameters of Mg alginate-based biopatterning method while using HeLa cells as a model cell line. Then, the applicability of newly developed methodology was successfully demonstrated by using SaOS-2 and SH-SY5Y cells to fabricate 3D cellular structures. Cell proliferation and migration profiles were observed during long-term culturing with time-dependent light microscopy images. Also cell proliferation and viability of long-term cultured tumor models were analyzed by using Alamar Blue and Live/Dead assays. Moreover, F-actin, Collagen I, and DAPI staining/immunostaining was done to investigate cellular and extracellular components of 3D cellular structures for short and long-term culture times. Finally, the dose-response of fabricated 3D structures was evaluated and compared with standard 2D cell culture by applying doxorubicin (DOX). The IC50 values were calculated for 3D cellular structure of HeLa, SaOS-2 and SH-SY5Y cells as 8.2, 7.8, and 2.1 µM respectively while IC50 values of 2D controls obtained as 3.2, 4.4, and 0.2 µM respectively. These results were also statistically analyzed and dose responses were found significantly different according to t-test, which means 3D cellular structures were more resistant to drug exposure compared to 2D cell culture.Master Thesis Design and Development of Paper-Based Microfluidics for Point-Of Applications(01. Izmir Institute of Technology, 2020) Özefe, Fatih; Arslan Yıldız, Ahu; Yıldız, Ümit HakanPaper-based microfluidics is a subarea of microfluidics which is recently used in various applications from diagnostics to environmental monitoring, and to food safety. In such microfluidic systems, a test platform is formed from a paper substrate instead of silicon and polymers, such as poly-dimethylsiloxane, poly-methyl methacrylate, and etc. The main goal of this thesis is the development and fabrication of a paper-based microfluidic device (μPAD), which could be used in point-of-care (POC) applications. The characterizations of μPADs, which were fabricated via laser ablation methodology, were performed in terms of their surface and barrier characteristics, and liquid sample flows within μPADs. Depending on the characterization, nine different fabrication parameters, 10P40S (10%Power & 40%Speed), 10P60S, 20P90S, 30P50S, 30P100S, 40P80S, 40P100S, 70P80S, and 70P100S, were identified as optimized fabrication parameters. Also, two designed models of μPADs, 1S4T-Type2 and 1S4T-Type3, were selected to be used in the detection of BSA and recombinant Hepatitis C Virus (HCV) protein. The BSA and HCV (1 mg/ml) in PBS solution were successfully detected via naked eye depending on the colorimetric sensing through micro-paper enzyme linked immunosorbent assay (μP-ELISA) protocol. Moreover, the limit of detection (LoD) values for HCV were determined in 1S4T-Type2 μPAD as 1.000, 0.883, and 0.796 ng/ml when the detection was performed via naked eye, smart-phone, and bright-field microscope, respectively. Also, the easily-disposable 1S4T-Type2 μPAD provided 14 times faster and 45 times cheaper detection of HCV compared to conventional ELISA techniques. Consequently, the developed 1S4T-Type2 μPAD presented low-cost, easy-to-use, and rapid detection of HCV as POC devices.Master Thesis Characterization and Utilization of Injectable Hydrogels for Tissue Engineering Applications(Izmir Institute of Technology, 2020) Güzelgülgen, Meltem; Arslan Yıldız, AhuTissue engineering combines the knowledge of the engineering aspects with life sciences to improve human health. Recent studies in tissue engineering have focused on investigating biocompatible scaffold materials and design. Quince seed hydrogel(QSH) has been used in traditional and modern medicine for skin wound and burn treatments, synovial lubrication, cough and asthma removal, and oral drug delivery with its antioxidant potential and biocompatible aspects. This thesis focuses on developing QSH and evaluating its potential as an injectable hydrogel in treating bone tissue defects as a totally new tissue scaffold and also as a promising tissue filling material. For this purpose, QSH scaffold optimization was carried out using various concentrations of hydrogel and crosslinkers which were glutaraldehyde(GTA) and 1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide(EDC)/N-hydroxysuccinimide(NHS). Morphological and chemical analysis of QSH was done using SEM, FTIR, AFM, and protein adsorption test. Thus, porosity, swelling ratio, degradation rate and surface characteristics were evaluated. NIH-3T3 and SaOS-2 cell lines were utilized for 3D cell culture formation. Afterward, 3D spheroids were analyzed for cell viability and proliferation by using AlamarBlue and LiveDead assays, and also cell imaging technics. Results showed that QSH scaffolds did not show any cytotoxic effect on NIH-3T3 and SaOS-2 cells. The optimum results were achieved with 2mg/mL of QSH and 0.03M GTA concentrations; where 76.59µm average pore size, 56.8 fold water holding capacity and at least 80% cell viability was observed. Therefore, it was concluded that QSH has a high potential to promote tissue engineering applications with its injectable texture as a filling material.Master Thesis Ultra-Porous Interconnected Hydrogel Structures for Tissue Engineering Applications(Izmir Institute of Technology, 2018) Yıldız, Büşra; Yıldız, Ümit Hakan; Arslan Yıldız, AhuTissue engineering aims to repair and regenerate tissue and organs with functional defects. The most significant developments in tissue engineering emerging as modification of the scaffold used to mimic native extracellular matrix (ECM) and support cell proliferation and differentiation. Hydrogel-based biomaterials are one of the most utilized materials as scaffold providing excellent chemical, physical/biophysical properties, high biocompatibility and functionality necessary for the applications in tissue engineering. In this study, Gelatin methacryloyl hydrogel (GelMA) and Gelatin-urethane hydrogels (GelatinK) are successfully synthesized as scaffold material for tissue engineering applications. Gelatin is modified with methacrylic anhydride for GelMA polymer and with 2-isocyanatoethly methacrylate for GelatinK polymer. The hydrogels of these two novel polymer are produced with photopolymerization reactions in aqueous media using Irgacure 2959 as redox initiator. Hydrogels are freeze-dried to remove solvent in the gel matrix and then they immersed in distilled water to reach equilibrium swelling ratio. The swelling capacity of GelMA hydrogels ranges between 1200 and 300% whereas GelatinK hydrogels has swelling capacity in between 1900-380%. Also, morphology of the hydrogels were investigated with Scanning Electron Microscopy (SEM). GelMA hydrogels has pore sizes between 142-14 µm while GelatinK hydrogels has between 160-56 µm pore sizes. The cell viability assay were also conducted using GelMA and GelatinK hydrogels. The results showed that both hydrogels provide high viability as compared to 2D control assay.Master Thesis Green Synthesis of Metal Nanoparticles and Their Applications as Plasmonic Substrates(Izmir Institute of Technology, 2018) Elveren, Beste; Arslan Yıldız, Ahu; Yıldız, Ümit HakanGold nanoparticles (GNPs) have been widely used in diagnostic, tissue engineering, and drug delivery fields, in the last decades. Generally, reducing gold salts to zero valent gold has been accomplished by harsh chemicals and strong reducing agents, which cause toxicity and eventually limiting the bioapplications. Green synthesis is a newly developing methodology to synthesize GNPs. Especially natural products and plants extracts are commonly preferred for green synthesis based on their natural content. Biological molecule-capped GNPs, are more biofriendly and biocompatible nano-materials that can be used for varied applications.1-3 Sensor applications; varying from biosensing to environmental analysis, are an important field that GNPs were intensively utilized.4-5 Cyanide ion (CN-) has been considered as one of the main pollutants of water, because of its rapid discharge. CN- is currently being used in industry such as; polymer synthesis6, noble metal mining7, pest control8, plastics production etc., at large scale. However, there is an unmet need for CN- detection and monitoring. Colorimetric detection of CN- that utilizes GNPs has been done by several researchers.9-10 However, in all these studies reduction of GNPs were done by strong reducing agents. Green synthesis of GNPs eliminates the toxic side-products that can be harmful to both environment and human health. To overcome this problem green synthesized GNPs were used to establish the sensor platform, which can be further employed for CN- detection. Oxidation of GNPs in the presence of cyanide molecules is a direct-forward, colorimetric and optical method that requires no toxic chemicals; therefore it is a greener approach towards CN- detection in water resources.Master Thesis Polymer Based Extracellular Matrix Mimetics for 3d Cell Culture(Izmir Institute of Technology, 2018) Türker, Esra; Arslan Yıldız, AhuTissue engineering combines engineering principles and knowledge of life sciences to improve biological substituents. Three dimensional (3D) supporting structures, namely scaffolds obtained from biomaterials to mimic extracellular matrix (ECM) that provides suitable microenvironment for cell proliferation, migration and differentiation. In this study, poly (L-lactide-co-ε-caprolactone) (PLLCL) and collagen type I was used to fabricate scaffold by electrospinning method. In literature, collagen was often dissolved in toxic and harmful solvents that creates the major problem for cell culture applications. To overcome this problem “co-spinning” methodology is utilized for the formation of non-toxic collagen-based ECM mimetic scaffold. Collagen mixed with water-soluble carrier materials which is either polyvinylpyrrolidone (PVP) or polyvinyl alcohol (PVA) and co-electrospinning is carried out with PLLCL. Fabricated scaffolds were immersed into water to remove co-spinning agent; PVA or PVP, so only PLLCL/Collagen remained. PLLCL has homogeneous fibers in a diameter of 1.312 ± 0.22μm. The contact angle of PLLCL (136.6° ± 2.6) proved hydrophobic behavior of PLLCL material. The contact angle of the scaffold decreased up to 86.7° ± 0.1 confirming that hydrophobic behavior is decreased with the addition of collagen. Also, collagen-containing scaffolds were saturated at lower amount of protein than PLLCL, PLLCL/PVA and PLLCL/PVP scaffolds. Cytotoxicity analysis of scaffolds showed that PVA containing scaffolds had lower viability than PVP containing scaffolds; so most of the cell studies were carried out with PLLCL/ Collagen scaffolds fabricated by PVP cospinning. Cell proliferation on PLLCL/Collagen scaffolds found to be more favorable than PLLCL and PLLCL/PVP scaffolds.Master Thesis Development of Gold Nanoparticle-Based Plasmonic Assay Platform for Esherichia Coli Detection(Izmir Institute of Technology, 2017) Erdoğan, Duygu; Yıldız, Ümit Hakan; Arslan Yıldız, AhuThe traditional methods for pathogen detection have long detection time and insufficient sensitivity. Optical methods can overcome these drawbacks. There are solution based nanoparticle growth in the literature to enhance a surface sensitivity for biosensing applications. In this project, surface refractive index (RI) sensitivity was enhanced on solid support via gold growth to develop a label free, simple and costeffective methodology for bacteria screening. The gold nanoparticles (GNPs) were grown on solid support by using 20 μl of HAuCl4 / 80 μl of NH2OH at varied incubation times. Firstly, about 20 nm GNPs were synthesized and immobilized on polystyrene surfaces. Then, these GNPs were utilized as seed particles, and grown on solid support. During GNPs growth, a red shift in the plasmonic wavelength was observed. Morphological characterization showed that almost uniform gold growth could be achieved. The plasmonic platform sensitivity was validated by varied concentrations of sucrose, ethanol and BSA solutions, showing that the plasmonic platform gave a response to any small RI change. Next, two different E.coli bacterial strains’ adsorption was tested. Adsorption screenings for about 107 E.coli DH5-alpha cells/ml and 107 E.coli BL21(DE3) cells/ml in Phosphate Buffer Saline were made on growth gold surfaces. Further, E.coli BL21(DE3) containing milk and apple juice were also adsorbed on these gold surfaces with a 30 min incubation time. The results showed that these gold surfaces exhibit higher binding kinetics for bacteria. Therefore, the proposed LSPR-based label free methodology can be an alternative to the bacteria screening in water or food samples.