Master Degree / Yüksek Lisans Tezleri
Permanent URI for this collectionhttps://hdl.handle.net/11147/3008
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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 Magnetic Manipulation of Gravitational Force During Cell Culture(01. Izmir Institute of Technology, 2022) Kaptan, Sinem; Özçivici, EnginWith 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) Çağan, Melike; Özçivici, EnginTissue 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.Master Thesis Optimizing the Transfection Conditions for the Generation of Stable Transgenic Cell Lines(Izmir Institute of Technology, 2020) Kreekman, Karin; Özçivici, Engin; Sürmeli Eraltuğ, Nur BaşakTransgenic cell lines that produce biopharmaceutical proteins are widely utilized in the biotech industry and the demand is not predicted to decline in the near future. For obtaining an industrially usable cell line, process components like expression vector, host cell line and transfection method need to be carefully selected. Due to all practical reasons, the industry prefers to use the most conventional Chinese hamster ovary (CHO) cell line. The generation of recombinant cell lines is known to be time-consuming, labor-intensive and expensive. Therefore, the several steps of this process are under constant development. One of the first work packages is transfection, where genes encoding for the therapeutic protein are taken into mammalian host cells. In this study, we aimed to generate a more cost-effective transfection procedure using the electroporation based technology of nucleofection. This method is favored by the researchers for its high and reproducible transfection efficiency, but also known for the high cost and lack of public information on its components and related consumables. As a result of this study, a novel nucleofection solution was developed for the transfection of CHO-DG44 cells, showing comparable if not better performance over the commercial Lonza's solution in terms of transient and stable expression of recombinant proteins. The transfection was further improved by selecting a more effective nucleofection program and by linearizing the plasmid prior to transfection. These enhancements, optimized on the basis of the biotherapeutic protein production, are potentially advantageous for any research requiring a large number of efficient transfection experiments.Master Thesis Environmental Factors Influencing Bacterial Biofilm Formation and Inactivation(Izmir Institute of Technology, 2020) Üreğen, Mert; Baysal, Ayşe Handan; Özçivici, EnginObjective of this study was to evaluate effect of UV-C radiation (0, 1.16 and 3.21 kJ/cm2), pomegranate (Punica granatum) seed essential oil (PGEO) and lemon (Citrus lemonum) plant essential oil (CLEO) on decontamination of Candida albicans, Listeria monocytogenes, Staphylococcus aureus and Esherichia coli O157:H7 biofilms formed at +4°C and 20°C on polystyrene, stainless steel and glass surfaces. After 16, 32 and 64 sec UV-C treatment 0.24 log CFU/cm2, 1.61 log CFU/cm2, 1.59 log CFU/cm2 reductions were achieved in the numbers of C. albicans biofilms formed at 20°C on polystyrene. In the numbers of S. aureus biofilms formed at 20°C on polystyrene 0.99 log CFU/cm2, 1.9 log CFU/cm2, 3.91 log CFU/cm2 reductions were obtained after 16, 32 and 64 sec UV-C treatments, respectively. In general C. albicans biofilm formed at 20°C on stainless steel was found as the most UV-C resistant biofilm. CLEO inhibited the growth of C. albicans, L. monocytogenes and S. aureus at MIC values of 186 µg/ml, 103.5 µg/ml and 103.5 µg/ml, respectively. The results of the study showed that UV-C radiation and CLEO can be used as an anti-biofilm agent to control or to prevent biofilm formation of foodborne bacterial pathogens. It was suggested that UV-C radiation and CLEO treatments have potential as a biofilm control interventions for the food industry.Master Thesis Cellular Mechanosensing at a Distance(Izmir Institute of Technology, 2019) Can, Ali; Pesen Okvur, Devrim; Özçivici, EnginThe goal of the project is to determine differences in mechanical sensing at a distance between breast cancer cells and normal mammary epithelial cells. To achieve this goal, we aim to: 1. Optimize the device for mechanical sensing at a distance 2. Determine the effect of mechanical sensing at a distance on cell proliferation 3. Determine the effect of mechanical sensing at a distance on cell migration Breast cancer is one of the cancers with the highest incidence and mortality rates in women in Turkey as well as in the world. Tumor microenvironment comprises of cancer and normal cells, extracellular matrix, soluble biological and chemical factors. Biochemical aspects of the interactions of cancer cells with the constituents of the microenvironment are widely studied whereas biophysical studies are at limited numbers. There is increasing evidence that extracellular matrix can change the mechanics and function of cancer and stroma cells. It has been observed that cancer cells show different responses to soft and stiff tissues they are in direct contact with than normal cells. However, it is not known whether the distance at which cancer cells can feel the stiffness of a distant tissue is longer, the same or shorter than that of normal cells. The hypothesis we will test in this project is as follows: The distance at which cancer cells can feel the stiffness of a distant tissue is shorter than that of normal cells.Master Thesis Detection of Bone Marrow Stem Cell Differentiation With Magnetic Levitation(Izmir Institute of Technology, 2019) Sarıgil, Öykü; Özçivici, EnginAdipocytes are the major energy depots which primarily compose adipose tissue in the body. They are mainly responsible for energy balance and also play a crucial role as endocrine and paracrine cells. Hypertrophy (cell size increase) and hyperplasia (cell number increase) are two mechanisms for adipose tissue growing, relating to some diseases such as obesity, osteoporosis, diabetes and anorexia nervosa. In this context, to detect and identify adipocytes has become critical to determine increase in cell size and cell number, thereby, it facilitates to understand mechanisms and process of adipocyte differentiation and provide to develop therapeutic strategies for the treatment and prevention of obesity and obesity-related diseases. Traditional or advanced techniques used for adipocyte detection and examination are available with their accomplished applications. However, they have some restrictions on adipocyte detection, such as being complicated and expensive operations or causing cell defects. Magnetic levitation is a novel technique with the capability of label-free, density-based detection using the principle of movement of the cells to lower magnetic field region in a paramagnetic medium. In this study, we used magnetic levitation system for detection of adipogenic-differentiated cells in heterogeneous cell populations. Results showed that levitation platform could detect the changes in lipid content of mesenchymal stem cells during adipogenic differentiation. This microfluidic system has a promising future with modification to sort adipogenic cells.Master Thesis Development of a Cell Sorting Platform Based on Magnetic Levitation Principle(Izmir Institute of Technology, 2019) Yılmaz, Esra; Tekin, Hüseyin Cumhur; Özçivici, EnginCirculating Tumor Cells (CTCs) play a vital role in cancer diagnosis, prognosis and personalized medicine. However, CTCs are extremely rare in blood (i.e., down to 1- 100 CTC per 1 mL human blood) and hard to isolate because of the heterogeneity of CTCs in biomarker expression. The current CTC separation techniques use numerous differences between cells such as size, electric charges, density and expression of cell surface markers. However, these techniques have many limitations in terms of manual sample preparation steps, inconsistent results caused by low specificity and efficiency, and increased cost. Hence, there is no standard method for isolating CTCs yet. With this study, it was aimed to fill the gap in CTC isolation by proposing a new method based on magnetic levitation principle, which has recently been demonstrated as a highly acceptable method for biological characterization of cells and monitoring of their cellular events. Short while ago, magnetic levitation technology has been used to measure cell densities at single-cell level. By using this technology, unique differences in levitation height and so in density have been identified between cancer cells and blood cells. In this study, we have been developed a new label-free microfluidic cell sorter that is based on the principles of magnetic levitation. After successfully completing this master thesis, this device can be used for rapid, low cost and label-free in-vitro diagnosis of cancer by sorting CTCs from whole blood in a high-throughput manner. The sorted cells might further be collected for downstream analysis for personalized and precision medicineMaster Thesis Molecular Characterization of Adult Stem Cells' Adaptations To Mechanical Signals During Adipogenic Commitment(Izmir Institute of Technology, 2015) Baskan, Öznur; Özçivici, Engin; Baskan, Öznur; Yalçın Özuysal, Özden; Özçivici, Engin; Yalçın, ÖzdenPrevalence of obesity have increased across the years based on technological developments that supported nutritional availability and sedentary lifestyles. Restoring mechanical activity with physical exercise suppresses obesity, and mechanical loading can also be delivered passively with whole body vibrations with high frequency and low magnitude. Anabolic effects of high frequency low magnitude mechanical vibrations on adult stem cells are well identified whereas sensing mechanism of cells and their response to mechanical stimuli is largely unknown. Here, we hypothesed that daily bouts of low intensity vibrations will affect molecular, physical and ultrastructural profile of the cells and the effect will interact with the adipogenic induction. To test this hypothesis mouse bone marrow stem cell line D1 ORL UVA were subjected to mechanical vibrations (0.15g, 90 Hz, 15min/d) for 7 days to both during quiescence and adipogenic commitment. Ultrastructural changes were identified on cellular and molecular levels. Atomic force microscopy was used to characterize the changes on cell surface and significant increase was observed in cell surface height. Moreover, in order to identify the changes in cytoskeleton structure and physical properties, actin were stained with phalloidin and imaged with inverted microscope. To quantify phalloidin amount, signal intensities and physical features of the cells were measured. It was observed that mechanical stimulation and adipogenic induction affect actin content and the physical structure of the cells significantly. Molecular level analysis of cytoskeleton elements and adipogenic markers were performed with Real time PCR. Dramatic increases in adipogenic markers were detected with adipogenic induction. These results indicate that mesenchymal stem cells responds to mechanical vibrations by altering their molecular and ultrastructure during both quiescence and adipogenesis.Master Thesis Characterization of Changes Induced by Lineage Commitment and External Mechanical Stimuli on Cellular Ultrastructure of Adult Mesenchymal Stem Cells(Izmir Institute of Technology, 2014) Demiray, Levent; Özçivici, EnginMechanical vibrations have great impact on the regulation of bone cells and their precursor’s Mesenchymal stem cells. Anabolic effects of high frequency low magnitude mechanical vibrations on these cells are well identified whereas sensing mechanism of cells and their early response to mechanical stimuli is largely unknown. Here, we hypothesed that daily bouts of low intensity vibrations will affect cellular ultrastructure and the effect will interact with the osteogenic induction. To test this hypothesis mouse bone marrow stem cell line D1 ORL UVA were subjected to mechanical vibrations (0.15g, 90 Hz, 15min/d) for 7 days to both during quiescence and osteogenic commitment. Ultrastructural changes were identified on cellular and molecular levels. To characterize alterations in cell surface, Atomic force microscopy is used. Mechanical vibrations increased cell surface height, cell surface roughness and nucleus height significantly during quiescence and under osteogenic conditions. Moreover, in order to identify the changes in cytoskeleton structure, actin were stained with phalloidin and imaged with inverted microscope. To quantify phalloidin signals pixel frequency analysis were performed, signal intensities and thickness of actin fibers were measured. It was observed that mechanical stimulation and osteogenic induction effects number of actin fibers and their thickness significantly. Molecular level analysis of cytoskeleton elements and osteogenic markers were performed with Real time RT-PCR. Significant increases in osteogenic markers were detected with osteogenic induction. Unlikely, no relation between mechanical stimulation and osteogenic marker expression was observed. These results indicate that mesenchymal stem cells responds to mechanical vibrations by altering their ultrastructure in particular cytoskeleton during both quiescence and osteoblastogenesis.