Master Degree / Yüksek Lisans Tezleri

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

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  • Master Thesis
    Development of Microfluidic Devices for Investigating Small Molecule Induced Chemotaxis of Dendritic Cells
    (01. Izmir Institute of Technology, 2023) Khurram, Muhammad Maaz; Bedir, Erdal; Tekin, Hüseyin Cumhur
    Microfluidics is the core branch of science and technology in which interdisciplinary research is conducted with a low amount of samples in microchannels ranging from 10-100 μm. The main objective of this thesis is to design and fabricate a chemotaxis microfluidic device (CMD) from the poly-methyl methacrylate (PMMA) substrate to analyze the immune cell behavior against cancer cells. The patterns of the three-layered CMD were generated using laser ablation. During the fabrication, Power (P) and Speed (S) values were varied to determine the optimal P-S combination. Then, the structural properties of microfluidic channels in the CMD were examined via microscope. The mechanical properties and liquid handling abilities of CMDs were also investigated through tensile and leakage tests, respectively. Moreover, cell viability of DC2.4 dendritic cells (DCs) and B16-F10 murine melanoma (B16-F10) cells in CMDs sterilized through either autoclaving or UV treatment were determined to test the suitability of CMDs via Live/Dead Assay. The highest cell viability for DCs and B16-F10 was obtained in autoclaved CMDs. For the maturation of DCs before seeding into CMD, DCs were stimulated with lipopolysaccharide (LPS) and Astragaloside VII (AST-VII) at various concentrations. While the cytotoxicity of LPS and AST-VII were determined by the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) assay, the expression levels of specific chemokine receptors were also analyzed through flow cytometry. Lastly, stimulated DCs and B16-F10 were simultaneously cultured in the CMD, and the migratory behavior of DCs against B16-F10 was time-dependently studied. Consequently, CMD that provided cost-effective and rapid analysis of intercellular interactions was successfully developed.
  • 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 Hakan
    Paper-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
    Evaluation of Biophysical Aspedts of Cancer Using Lab-On Chip Devices
    (Izmir Institute of Technology, 2019) Tahmaz, İsmail; Pesen Okvur, Devrim; Sürmeli, Nur Başak
    Breast cancer metastasis is really crucial point from cancer related deaths. As cancer cells from primary tumor are travelling through blood, they hang on to blood vessel and finally they exit from blood vessel into secondary site where is extracellular matrix and/or tissue/organ. This process commonly known as extravasation. Cancer cells sometimes can be highly aggressive when it exposed to hypoxia referred low oxygen amount by activating HIF1α. This transcription factor is activated in malignant cells, normal cells and endothelial cells in blood vessel when oxygen amount decreased to certain levels and it induce several genes expression such as VEGF, LOX, Angiopoietin-like-4 etc. In this study we investigated effect of HIF1α which is hypoxia indicator on breast cancer extravasation by comparing to normal oxygen level. This study represents both anemic hypoxia physiologically and lead to understand underlying mechanism of extravasation into extracellular matrix related to low oxygen circulating through blood. In addition to HIF1α effects, dynamic perfusion mimicking blood flow was applied to determine effects on extravasation. For this purpose, lab-on-a chip device was utilized for real time visualization. In conclusion, although hypoxia is giving permission MDAMB231 to extravasate because of reshaping of vascular geometry, less extravasated cancer cells observed in matrix during hypoxia under both static and flow condition when compared to normoxic and static conditions. Moreover, it was shown that flow triggers extravasation distance in normoxia against static condition and normal breast epithelial cells extravasated away in hypoxia comparing breast cancer cells by means of flow.
  • 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.