Master Degree / Yüksek Lisans Tezleri

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

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Author: search.filters.author.Pesen Okvur, DevrimSubject: search.filters.subject.Biotechnology

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Now showing 1 - 4 of 4
  • Master Thesis
    Invadopodia Formation on Nanometer Scale Protein Patterns
    (Izmir Institute of Technology, 2014) Batı, Gizem; Pesen Okvur, Devrim; Özyüzer, Lütfi
    How the positions of invadopodium in the cell are determined and if they have an adhesivefunction are not known. Using fluorescence microscopy and antibodies that recognize actin, cortactin and MT1-MMP proteins, invadopodia formed by breast cancer cells plated on protein nanopatterns of different geometeries and components after stimulation with epidermal growth factor which is known to induce invadopodia formation, were examined. Invadopodia formation was studied for the first time on nanometer scale, single and double active component, protein patterns with equal distance and gradient spacings. The results show that: • On K-casein-fibronectin nanopatterns, invadopodia prefer to form on K-casein which blocks cell adhesion rather than on fibronectin nanodots which promote cell adhesion. • On Laminin-fibronectin nanopatterns, invadopodia prefer to form on laminin rather than on fibronectin nanodots. • On gradient patterns, invadopodia prefer areas with wide spacings. These results support the hypotheses that the positions where invadopodia form can be determined by surface protein nanopatterns and that cell adhesion is not required at points where invadopodia will form.
  • Master Thesis
    Cell Adhesion on Nanomater Scale Fibronectin Patterns: a Comparision of Breast Cancer Cells and Normal Breast Epithelial Cells
    (Izmir Institute of Technology, 2014) Horzum, Utku; Pesen Okvur, Devrim
    Cell adhesion to extracellular matrix is an important process for both health and disease states. Surface protein patterns are topographically flat, and do not introduce other chemical, topographical or rigidity related functionality and, more importantly, that mimic the organization of the in vivo extracellular matrix are desirable. Previous work showed that vinculin and cytoskeletal organization are modulated by the size and shape of surface nanopatterns. However, a comparative and quantitative analysis on normal and cancerous cell morphology and focal adhesions as a function of micrometer scale spacings of protein nanopatterns was absent. Here, electron beam lithography was used to pattern fibronectin (FN) nanodots with micrometer scale spacings on a K-casein background (single active) on indium tin oxide (ITO) coated glass which, unlike silicon, is transparent and thus suitable for many light microscopy techniques. Exposure times were significantly reduced using the line exposure mode with micrometer scale step sizes. Micrometer scale spacings of 2, 4, 8 microns and gradients between FN nanodots modulated cell adhesion for both breast cancer and normal mammary epithelial cells, through modification of cell area, cell symmetry, actin organization, focal adhesion number, size and circularity under both static and flow conditions. Overall, cell behavior was shown to shift at the apparent threshold of 4 μm spacing. Results showed that there were significant differences in terms of cell adhesion between breast cancer and normal mammary epithelial cells: Breast cancer cells exhibited a more dynamic and flexible adhesion profile than normal mammary epithelial cells.
  • Master Thesis
    Design and Fabrication of Microfluidic Device That Allows Investigation of Distance Dependent Interactions of Two Different Cell Types
    (Izmir Institute of Technology, 2014) Sağlam, Murat; Pesen Okvur, Devrim; Özyüzer, Lütfi
    The main studies of in this thesis, the mold and a microfluidic device are achieved by using SU-8 photoresist and PDMS polymer. Firstly, molds are obtained which are thickness ranging from 30 to 400 μm by using SU-8 photoresist with UV lithography technique and this molding will use for shaping polydimethylsiloxane (PDMS) polymer. Finally, PDMS molds combined with the glass surface to create a three dimensional reservoirs. Microfluidic device that allows investigation of distance dependent interactions, two factors are positioned at certain distances from each other and the microfluidic device is allowed to investigation of distance dependent interaction of two factors. There is an alternating width channel between two channels which have each of two factors. These three channels are separated from each other by colonnades, not by walls, therefore physical, chemical and biological interactions are possible between the factors. Necessary physical, chemical, and biological conditioning can be provided by the reservoirs which are neighbor of channels including factors. Microfluidic chip has a lot of advantages that are small liquid volumes (pL-μL), precise spatial & temporal control, successfully mimic the physiological context, highthroughput analysis, low fabrication costs; portable and safer therefore it facilitates us to refine our methods of analysis and development in cell biology investigations and determining the content of chemical samples.
  • Master Thesis
    Method That Positions Cell-Laden or Cell-Free Matrices at Defined Positions From Each Other Inside a Single Microfluidic Channel
    (Izmir Institute of Technology, 2014) Tarım, Emre; Pesen Okvur, Devrim; Özyüzer, Lütfi
    In recent years, the use of microfluidic has increased in the field of many biological studies. Microfluidic technology has a large area which is a joint product of biology and industry covering all branches of science. The small size of the microfluidic chip offers many advantages in the use of microfluidic. During the analysis, the microfluidic chip offers many advantages such as, use of less material, less waste generation, temporal control, opportunity of analysis under the microscope and high throughput analysis. In addition to these, while microfluidic chip is providing a safe environment for users, via mimicking the physiological environment, it also provides a suitable environment in order to make cell, tissue and organs based assays. Microfluidic devices especially use in cancer studies, chemical analysis, tissue engineering, drug screening, immunology and stem cell differentiation. In this study, we aimed to develop methods depending on the distance to position the MDA-MB 231 breast cancer cells in the microfluidic channels. Firstly, the microfluidic channels were obtained by using the soft lithography and experiments with breast cancer cells were performed using these channels. Breast cancer cells containing matrix was loaded into microfluidic chips and precipitated onto blank matrix by using centrifuge. The aim of repeating this process was to position the breast cancer cells at different distanced locations.