Master Degree / Yüksek Lisans Tezleri
Permanent URI for this collectionhttps://hdl.handle.net/11147/3008
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Master Thesis Green Synthesis of Nanostructured Bioactive Glass for Dental Applications(01. Izmir Institute of Technology, 2023) Tüncer, Melisa; Yücesoy, Deniz Tanıl; Öksel Karakuş, CeydaBioactive glass is a biomaterial commonly used in dental care products and bone tissue engineering applications due to its biocompatibility, bone-forming ability, and remineralization capability. Bioactive glasses form a hydroxyapatite-like layer on dentinal tubules by releasing calcium and phosphorus ions after interaction with saliva. Bioactive 45S5 glass traditionally synthesized by wet chemical methods which require high-temperature heating and the use of a strong acid catalyst, bringing into question of the possibility of introducing toxic acid residues into the final product. Therefore, there is a need to develop environmental-friendly bioactive glass synthesis methods or to modify existing ones in a way to uplift their environmental friendliness. To satisfy this need, we greenized the traditional sol-gel method by replacing the acid catalyst with an environment-friendly alternative and successfully used it for the synthesis of nanostructured 45S5 bioactive glass. First, physicochemical characterization of the synthesized bioactive glasses was performed. Then, the apatite formation capability of bioglasses were investigated in saliva. Next, the mineralization kinetics of bioglasses were tested in Ca/P buffer. In vitro toxicity tests were performed to assess the cytotoxic potential of the synthesized bioactive glass. All analyses were repeated for the traditional synthesis method for comparison purposes. The results confirmed that green synthesis is more advantageous in terms of bioactivity and functionality required for dental applications. Increasing the safety and functionality of bioglass at the same time during the production phase has critical importance for ensuring the sustainability of current applications as well as creating new uses in the biomedical fieldMaster Thesis Centrifugal microfluidic-based platforms for in vitro diagnostics(01. Izmir Institute of Technology, 2024) Koç, Sadık; Tekin, Hüseyin Cumhurİn vitro tanı (IVD) yöntemleri, tanı koymak için kullanılan tüm araçları kapsarlar ve erken teşhis sağladıkları için büyük önem taşırlar. IVD'lerin gelişimi, hücreler arası iletişimi sağlayan eksozomların, özellikle hastalıkların erken teşhisinde biyomarker olarak kullanılmasına olanak tanımıştır. Geleneksel IVD'ler altın standart olarak kabul edilmesine rağmen, genellikle yüksek maliyetli ve zaman alıcıdır. Bu zorlukların üstesinden gelmek için IVD'lerin mikroakışkan sistemler kullanılarak hasta başı sistemlerine uyarlanması gerekmektedir. Bu bağlamda, polimetil metakrilat (PMMA) bazlı bir mikroakışkan çip üzerinde eksozomları izole etmek ve zenginleştirmek için yeni bir mikroakışkan üretim yöntemi geliştirilmiştir. Bu yöntemde, saf aseton hem yüzey iyileştirici hem de yapıştırıcı olarak kullanılmış, PMMA kanallarındaki yüzey pürüzlülüğü ve opaklık sorunlarını ortadan kaldırarak yüzeyin kendini onarmasını ve şeffaf hale gelmesini sağlamıştır. Elde edilen çipler, yalnızca daha dayanıklı olmakla kalmayıp, aynı zamanda uygun maliyetli ve kolay üretilebilir niteliktedir. Bu yöntem, nanoparçacık ve eksozom izolasyonu için kapalı bir kanal içeren santrifüjlü mikroakışkan bir çip üretmek için başarıyla uygulanmıştır. Çip, 9000 rpm (9418 g) hızında standart bir masaüstü santrifüjde 200 nm parçacıkları 20 dakikada, 100 nm parçacıkları 30 dakikada ve 50 nm parçacıkları 60 dakikada izole etmeyi başarmıştır. Özellikle, eksozomlar, belirteç kullanmadan, hücre ortamından bir saat içinde izole edilmiştir. Bu yenilikçi santrifüj tabanlı mikroakışkan platform, farklı IVD uygulamaları için umut vaat etmektedir.Master Thesis Effect of Gold Nanorod Properties on Lspr Response(01. Izmir Institute of Technology, 2023) Kılıç, Şebnem; Bulmuş Zareie, Esma Volga; Tekin, Hüseyin CumhurOptical qualities make gold nanorods (GNRs) excellent for plasmonic biosensors. Localized surface plasmon resonance (LSPR) phenomenon which occurs on GNR surfaces enables the creation of highly sensitive biosensors. The physical properties such as aspect ratio and size are directly related to the LSPR response of GNRs. The aim of this study is to investigate the impact of the aspect ratio (AR) and the interparticle distance on the localized surface plasmon resonance (LSPR) response of GNRs decorated glass sensor chips. For this aim, GNRs were first synthesized using a seed-mediated growth method. The effect of AgNO3 concentration on the AR of GNRs was investigated. It was observed that increasing AgNO3 concentration resulted in GNRs with higher AR and a red shift in the longitudinal plasmon peak wavelength. GNRs with an AR of 4, 6 and 8 were successfully synthesized. Next, the effect of the stabilizer molecule type and molecular weight on the distribution of GNRs on the silanized glass surface was investigated. It was found that the APTES modified glass surfaces cannot be coated with CTAB stabilized GNRs. Using GNRs stabilized with PEG5K resulted in a more homogeneous distribution of GNRs on the glass surface with respect to GNRs stabilized with PEG2K. The interparticle distance between GNRs on the glass surface was successfully controlled by simply concentrating or diluting the GNR solution used for coating the glass surfaces. It was observed that the LSPR peak shifts decreased upon binding of analytes as the interparticle distance between GNRs decreased in the studied range. On the other hand, as the AR decreased, the LSPR response of the GNRs shifted blue. The results presented in this thesis may contribute to future research to improve the potential of LSPR-based biosensors for diverse biomedical and diagnostic applications.Master Thesis Genetics and Etiopathology of Childhood Obesity, and Development of a Genetic Risk Calculation Panel Based on the Polygenic Risk Score Approach(01. Izmir Institute of Technology, 2023) Yurt, Dudu Seher; Sezgin, EfeObesity is the disease that significantly affects human life as a combination of genetic and physiological environment. The polygenic background of the disease causes of childhood or adulthood obesity are still not fully understood. Childhood obesity and adulthood obesity are usually expressed in terms of body fat mass and body mass index (BMI). Obesity is a comorbid disease that is often associated with T2D, cardiovascular diseases, fatty liver and various mental health problems. Therefore, examining the genetic background of the disease is also important for epidemiological studies. Obesity, which is one of the multi-gene diseases, is revealed by genome-wide research studies, candidate gene studies by SNP genotyping assays. SNP genotyping analyzes not only provide information about the transmission of childhood obesity, but also provide significant guidance on the biological pathways of the disease. Genome-wide association studies (GWAS) provide effective research in association studies between anthropometric body characteristics and the genome. The aim of this thesis is to investigate childhood related obesity variants, adulthood related obesity variants, to identify relationship of these two groups of genetic variants. In addition, the purpose of the thesis, is to understand effects of the variants on metabolic pathways, the difference of childhood and adulthood obesity related pathways and calculation of polygenic risk.Master Thesis Uv-C Irradiation and Lantibiotic Nisin Applications for Food Biopreservation(01. Izmir Institute of Technology, 2023) Altundaş, İlker; Baysal, Ayşe Handan; Sezgin, EfeThe antibacterial and antifungal activity of Lantibiotic Nisin and Essential oil Carvacrol against pathogenic and spoilage-forming microorganisms was investigated in this study. The antimicrobial activities of these compounds were observed in vitro on one Gram-positive (Listeria monocytogenes), two Gram-negative (Cronobacter sakazakii andS. Typhimurium) bacterial strains, and one fungus (Candida albicans). The study investigated the effect of combined treatments involving UV-C irradiation along with Nisin and carvacrol as antimicrobial agents on microbial growth, both at 4°C refrigerator temperature storage for two weeks, and on artificially inoculated chicken drumsticks with L. monocytogenes and S. Typhimurium. Total Aerobic Mesophilic, Yeast & Mold, and Enterobacter/Coliform populations were examined using plate counting on PCA, PDA, and VRBA media, for L. monocytogenes, and S. Typhimurium. PALCAM, OXFORD, and Bismuth Sulphite Agar, respectivelyMaster Thesis Development of Doxorubicin-Loaded Liposomes Self-Assembled With Polysaccharides for Breast Cancer Therapy(01. Izmir Institute of Technology, 2023) Önol, Ayşenur Başar; Kılıç Özdemir, Sevgi; Polat, HürriyetThis thesis aimed to develop Tariquidar and Doxorubicin-loaded liposomes decorated by Fucoidan coating for breast cancer treatment. Fucoidan is a negatively charged polysaccharide with a special affinity to p-selectins expressed on MDA-MB-231 breast cancer cells and, at the same time, possesses anti-cancer activity. Different liposomes were prepared by extrusion method from the DSPC, Cholesterol, and cationic lipid DSTAP mixtures for coating negatively charged Fucoidan. The most stable liposomes with a size of 200 nm were obtained at a molar ratio of DSPC/Cholesterol/DSTAP:55/30/15, exhibiting a zeta potential above +30 mV. Tariquidar was encapsulated into the liposome bilayer by passive loading, and Doxorubicin into the core of the liposome by active loading. In the final step, liposomes were coated with Fucoidan by electrostatic interaction. Tariquidar loading was determined by UV-Vis spectrophotometry, indicating an optimum TRQ/Lipid molar ratio of 0.012 with encapsulation and loading efficiencies of 50% and 20%, respectively. Fluorescence spectrophotometry determined Doxorubicin loading, showing insignificant encapsulation efficiency change (exhibiting around 70%) by neither Tariquidar content in the bilayer nor DSTAP% in the formulation. An optimum amount of Fucoidan was determined by incubating the liposomes with varying amounts of fucoidan at different dilutions. Size and zeta potential measurements monitored the coating of liposomes with Fucoidan. Our finding showed that zeta potentials of liposomes go from positive to negative with increasing fucoidan, while no trend was observed in the size of liposomes. However, smaller sizes were observed when incubation was performed in diluted solutions.Master Thesis Antimicrobial, Antioxidant, Antiproliferative and Cytotoxic Activities of Aronia Fruit Extract(01. Izmir Institute of Technology, 2023) Tanağardı, Dilaranur; Baysal, Ayşe Handan; Sezgin, EfeAronia melanocarpa contains high amounts of phenolic compounds, especially anthocyanins. Because of its high chemical content and significant antioxidant action, this food is known as a functional food, and its use is spreading worldwide. Within the scope of this thesis research, studies were carried out on Aronia melanocarpa dry extract and liquid extract. For these purposes, chromatographic and chemical profile were determined in detail by HPLC (High-Pressure Liquid Chromatography), Fourier-Transform Infrared Spectroscopy (FTIR) and Q-TOFF- MS (Quadrupole Time of Flight Mass Spectrometry), and significant bioactive were determined. Spectroscopic methods were used to characterize phenolic, anthocyanin, and flavonoid components. Aronia melanocarpa dry and liquid extracts were tested for antioxidant activity using DPPH and ABTS methods. The antioxidant potential of the Aronia melanocarpa dry and liquid extracts studied is high. To test the antiproliferative and cytotoxic effects, cytotoxic studies were performed on the CaCo2 cell line. Cell migration was also studied in HUVEC and HaCat cell lines. The antimicrobial activity of Aronia melanocarpa dry extract and liquid extract was tested against Saccharomyces cerevisiae, a yeast species, and bacterial strains of Staphylococcus aureus, Escherichia coli O157:H7, Salmonella Typhimurium. The extracts analyzed showed an antimicrobial effect on the tested bacteria at different concentrations. The results obtained in this study emphasize that the tested Aronia melanocarpa dry extract and liquid extract have antimicrobial properties. Chromatographic, chemical, and cytological data reveal that Aronia melanocarpa liquid and dry extracts can be used as antioxidative and antiproliferative products as food supplements in the health field.Master Thesis Development of an Advanced Lspr-Based Biosensor Chip for Rapid Detection of Border Disease Virus(01. Izmir Institute of Technology, 2023) Alakbarov, Abdullah; Bulmuş Zareie, Esma Volga; Tekin, Hüseyin CumhurThe Border Disease Virus (BDV) is responsible for causing fetal deathly infection, leading to annual occurrences of affected farms. BDV, along with other pestiviruses such as classical swine fever virus (CSFV) and bovine viral diarrhea virus (BVDV), are known to cause major losses in stock farming. These losses can result in reproductive failure, expensive inspections, and other impacts on livestock health. The current detection methods of BDV include various techniques such as RT-PCR, ELISA, VNT, and immunofluorescence assays. These methods, although reliable, may require specialized equipment, time-consuming procedures, and laboratory facilities, making them less suitable for rapid on-site detection. Hence, it is imperative to employ diverse methodologies for detection of BDV. LSPR-based biosensors are a subset of plasmonic biosensors that exhibit numerous advantages for diverse applications. LSPR-based biosensors are particularly well-suited for the production of compact, practical devices for rapid, on-site detection of analytes. The aim of this study is to design and fabricate a biosensor chip utilizing LSPR technology for potential BDV detection. For this aim, glass surfaces were functionalized with gold nanorods modified with a BDV-specific primer sequence, complementary single-strand DNA sequence of 19 bases, and fabricated with PMMA microchannels. Different concentrations of target BDV-DNAsequence ranging from 0.01 pM to 100 nM were exposed to the channels, and the LSPR response was quantified using a Vis-NIR spectrometer. The limit of quantification of the biosensor chips was determined to be 10 pM, while the limit of detection was found to be less than or equal to 1 pM. The sensitivity of the biosensor chips was calculated to be 0.0567 nm/RIU. The dynamic range of the biochips lies between 10 pM to 100 pM.Master Thesis In Silico Design of Chimeric Peptides for Infection Resistant Implant Coatings(01. Izmir Institute of Technology, 2023) Kan, İlker; Yücesoy, Deniz Tanıl; Özçivici, EnginTooth loss has been a widespread dental problem affecting patients of various ages. Replacement of lost teeth with implants is a common practice for managing tooth loss due to their mechanical properties and natural-looking aesthetics. One of the persistent problems associated with dental implants is the risk of infection (periimplantitis) which can occur when bacteria colonize the implant surface leading to inflammation and tissue damage with an eventual implant failure. Infection-resistant antimicrobial coatings have been one of the promising solutions to combat implant infections. The purpose of this study was to design functional chimeric peptides using antimicrobial peptides and hydroxyapatite binding peptides in order to provide an antimicrobial effect to hydroxyapatite-coated titanium dental implants. For this purpose, since titanium implants coated with hydroxyapatite show long-term biocompatibility, chimeric peptides that can provide antimicrobial resistance have been designed by considering antimicrobial peptides in addition to these coatings. Computational analysis, solubility analysis, secondary structure analysis, and conformational change analysis were performed to examine the ability of these formed chimeric peptides to retain their antimicrobial properties. Promising candidates obtained from secondary structure analysis and solubility analysis were examined to preserve their structure and stability by performing conformational change analysis, and the most suitable candidates were decided. Although the results give candidates computationally according to the analysis, these candidates should be confirmed experimentally. When the results from the computational analysis are validated by the experimental analysis, it will set the standard for antimicrobial chimeric peptide design.Master Thesis Enhancement of Bioavailability of Vitamin D by Nano-Sized Delivery Systems(01. Izmir Institute of Technology, 2023) Sağlam, Ezgi İrem; Kılıç Özdemir, Sevgi; Bulmuş Zareie, Esma VolgaStudies have indicated that Vitamin D (VitD) may decrease tumor invasiveness and propensity to metastasize. Cholecalciferol (VitD3) is the passive form of VitD3 and converts to active calcitriol through two-step hydroxylation reactions in the body, promoting binding to VitD-receptors (VDR). However, some breast cancer cells, especially MDA-MB-231, have very low levels of VDR. Besides, VitD3 suffers from first pass-effect of the liver which causes deactivation of VitD3. Therefore, new approaches are needed to increase VitD3 level in the cancerous sites. In this study, VitD3 was loaded into liposomes, which were subsequently coated by Fucoidan (FUC) to promote their binding to MDA-MB-231 cancer cells. Fucoidan strongly binds to P-selectins overexpressed in the breast cancer cells, blocking the cancer cells to adhere on the platelets to carry within the body, causing metastasis. Doxorubicin (DOX), being considered as the one of the most effective chemotherapeutic agents against breast cancer, was also loaded into liposomes in a similar manner. By liposomal encapsulations and fucoidan coating, it was aimed to deliver the all-cargo directly to the cancerous site and enhance the bioavailability of both agents at the target site. It was seen that liposomal VitD3 was more effective than free form to inhibit cell proliferation and, therapeutic potential of DOX increased with VitD3.VitD3 loaded FUC coated liposomes at optimized concentrations has a comparable effect with DOX-loaded liposomes with and without FUC coating. Overall, these results suggested that VitD3 and DOX loaded and FUC coated liposomes can be applied as combined therapy in cancer treatment.