Master Degree / Yüksek Lisans Tezleri

Permanent URI for this collectionhttps://hdl.handle.net/11147/3008

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Author: search.filters.author.Özçivici, EnginPublisher: search.filters.publisher.01. Izmir Institute of Technology

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Now showing 1 - 5 of 5
  • Master Thesis
    Characterization and Biofabrication of Keratinocytes at the Single-Cell Level in Normal and Pathological Conditions
    (01. Izmir Institute of Technology, 2024) Kara, Alara; Özçivici, Engin; Özçivici, Engin; 03.01. Department of Bioengineering; 03. Faculty of Engineering; 01. Izmir Institute of Technology
    Keratinositler cildin korunması ve dolayısıyla genel sağlık için çok önemlidir. Yapısal bütünlüğü ve yara iyileşmesini desteklemek amacıyla hücre kültürü çalışmalarında sıklıkla modellenmektedirler. Bu çalışma, keratinosit yoğunluğunu tek hücre düzeyinde ölçmek için manyetik kaldırma tekniğini kullanarak hassas yöntemler geliştirmeyi ve ölçümlerdeki varyasyonların normal ve patolojik koşullarda keratinosit davranışını ve işlevini nasıl etkilediğini araştırmayı amaçlamaktadır. Buna ek olarak, MagLev teknolojisi aracılığıyla 3D keratinosit yapıları oluşturmayı ve bunların doku mühendisliği için yapısal bütünlüğünü ve işlevselliğinin değerlendirilmesi amaçlanmaktadır. Bu çalışmada, manyetik alandaki davranışlarını incelemek için dört farklı HaCaT hücre grubu kullanılmıştır. Tek hücre yoğunluğu ölçümlerimiz, özellikle G45E grubunda HaCaT hücreleri için standardizasyon ve tekrarlanabilirliği gösteren önemli farklılıklar ortaya koymuştur. Önceki çalışmalarda çeşitli hücre tiplerinin yoğunluğu belirlenmiştir, ancak keratinositler bu bağlamda ilk kez incelenmiştir. Biyofabrikasyon deneylerinde, G45E grubunda deneysel standardizasyonumuzu daha da doğrulayan önemli levitasyon yüksekliği farklılıkları kaydedilmiştir. Agaroza aktarılan manyetik levitasyon kültürü, dağınık yapılar oluşturan doğrudan aktarıma kıyasla daha tutarlı sferoid yapılarla sonuçlanmıştır. Böylece, keratinosit yapıları manyetik kaldırma ile bütünlüklerini korumuş ve daha fazla 3D kültürü oluşumunu kolaylaştırmıştır. Sonuçlar keratinositlerin biyofiziksel özelliklerinin anlaşılmasını geliştirmekte ve etiketsiz, iskelesiz manyetik kaldırmanın doku mühendisliği için pratik bir alternatif olabileceğini göstermektedir. Bu yaklaşım negatif manyetoforez yoluyla, geleneksel iskeleler olmadan karmaşık 3D yapılar oluşturmak için hücre ve doku düzeyinde biyomühendislik çalışmalarına önemli bir potansiyel sunmakta ve yeni, yoğunluğa dayalı bir tespit yöntemi sağlamaktadır.
  • Master Thesis
    Development of a Natural Tubular Scaffold From Decellularized Parsley Stems To Be Used in Vascular Tissue Engineering Applications
    (01. Izmir Institute of Technology, 2024) Çevik, Merve; Dikici, Serkan; Özçivici, Engin; Dikici, Serkan; Özçivici, Engin; 03.01. Department of Bioengineering; 03. Faculty of Engineering; 01. Izmir Institute of Technology
    Cardiovascular diseases (CVD) are usually associated with narrowing or blockage of blood vessels and are the leading cause of death globally. By 2030, the annual incidence of CVD-related deaths is estimated to increase 23.3 million. Considering the advancements in endovascular surgery, the use of vascular grafts in cardiovascular surgery is becoming increasingly common. Autografts are the gold standard but have limitations, including limited tissue availability and complications from vessel isolation. Recently, synthetic grafts have emerged as alternatives, though they often fail due to thrombosis, atherosclerosis, intimal hyperplasia, or infection. Thrombosis, the main cause of post-implantation failure, is associated with damage or absence of the endothelial cell lining on the luminal surface of the vascular graft. To overcome the limitations mentioned so far, tissue-engineered vascular grafts (TEVG) have come into prominence. The use of decellularized plant tissues in tissue engineering applications has recently gained great importance. Accordingly, in this study, we fabricated tubular scaffolds from decellularized parsley stems and evaluated them in vitro as potential TEVGs. Our results demonstrated that native plant DNA was successfully removed, and biocompatible tubular biomaterials were successfully fabricated via chemical decellularization of parsley stems. The decellularized parsley stems showed suitable mechanical and biological properties for use as TEVG material. Finally, they were found to provide a convenient environment to form a pseudo-endothelium by recellularization with human endothelial cells prior to implantation. This study is the pioneer in the literature that reports on the potential of parsley stems to be used as a potential TEVG biomaterial.
  • Master Thesis
    In Silico Design of Chimeric Peptides for Infection Resistant Implant Coatings
    (01. Izmir Institute of Technology, 2023) Yücesoy, Deniz Tanıl; Özçivici, Engin; Yücesoy, Deniz Tanıl; Özçivici, Engin; 03.01. Department of Bioengineering; 03. Faculty of Engineering; 01. Izmir Institute of Technology
    Tooth 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
    Magnetic Manipulation of Gravitational Force During Cell Culture
    (01. Izmir Institute of Technology, 2022) Özçivici, Engin; Özçivici, Engin; 03.01. Department of Bioengineering; 03. Faculty of Engineering; 01. Izmir Institute of Technology
    With the development of space technologies, one of the most important problems that astronauts will encounter in the planned manned space travels to the Moon and Mars in the near future is the reduced (<1g) gravitational force. Knowledge of the biological effects of partial gravitational force on long-duration space missions is limited. Therefore, it is important to investigate effects of partial gravitational force on physiological adaptation mechanisms. However, methodology to induce partial gravity is expensive and subjected to ethical constraints, therefore there is a need for new ground-based simulation platforms that are able to mimic the partial gravitational force. In this master's thesis, a new partial gravity platform was developed that manipulates gravitational force during cell culture using magnetic fields. First, the platform system was designed and fabricated, and then detailed protocols were described for its use in cell culture. In addition, the effect of simulated partial gravity on cell viability and morphology at the cellular level was examined. The results show that the simulated partial gravity of Mars and the Moon affects the viability and morphology of cells. This new low-cost and easy-to-use partial gravity platform can be used as a ground-based simulation system for gravitational space biology research at the cellular and molecular levels.
  • Master Thesis
    Cell Patterning With Magnetic Manipulation
    (01. Izmir Institute of Technology, 2020) Özçivici, Engin; Özçivici, Engin; 03.01. Department of Bioengineering; 03. Faculty of Engineering; 01. Izmir Institute of Technology
    Tissue engineering is a biomedical engineering field that provides solutions to restore, maintain, improve or replace tissues or whole organs. The main goal tissue engineering is to overcome the restrictions of existing treatments that are based on organ transplantation. Cells and biomaterials can be used to form functional tissues and organs. Actually, the goal is to produce structures that resemble and mimic the real tissues. One of the useful mimicking technique is cell patterning. Cell patterning is a technique that provides cell clusters are located at a proper position for function of tissues. Some of the patterning techniques uses cell adhesion ligands, optical tweezers, acoustic tweezers, dielectrophoresis and magnetic force. In addition to the advantages of all these techniques, there are also disadvantages. However, Magnetic force-based cell patterning techniques provide excellent advantages such as low adverse effects to cell. Magnetophoresis is one of the magnetic force-based cell patterning technique that forms cell patterns without labeling cells in a short time using the principle of movement of the cells to lower magnetic field region in a paramagnetic medium. In this study, a cell patterning system was used to form cell patterns via magnetophoresis. Results showed that cell patterns were formed in different shapes in a short time and they maintained integrity even if magnetic force was removed.