Master Degree / Yüksek Lisans Tezleri
Permanent URI for this collectionhttps://hdl.handle.net/11147/3008
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Master Thesis Magnetic Based Cell Sorting in Microfluidic Devices(01. Izmir Institute of Technology, 2024) Özcan, Hatice Ahsen; Tekin, Hüseyin CumhurKan, hastalıkla ilişkili hücreleri heterojen örneklerden ayırarak hastalık teşhisi ve tedavisi için kullanılır. Bu hücrelerin bazıları, örneğin damar hasarı ve kanser için biyobelirteçler olarak kullanılan dolaşımdaki endotel hücreleri (CEC'ler) gibi nadirdir. Bu nadir hücrelerin kesin olarak ayrılması çok önemli ve zordur. Bu sorunu çözmek için etiketsiz bir mikroakışkan sistem geliştirildi. Bu sistem, parçacıkları etiketlemeden belirli konumlara kaldırmak için manyetik, yerçekimsel ve sürükleme kuvvetlerinden yararlanan Manyetik Levitasyon ilkelerini kullanarak CEC'leri beyaz kan hücrelerinden (WBC'ler) izole eder. Mikroakışkan çipin bir girişi ve iki çıkışı vardır: üst çıkış, CEC'lerin bir taklidi olarak düşük yoğunluklu İnsan Göbek Ven Endotel Hücrelerini (HUVEC'ler) toplarken, alt çıkış, bir geri çekme yöntemi kullanarak WBC'lerin bir taklidi olarak yüksek yoğunluklu U937 hücrelerini toplar. Ayrıştırma verimliliğini optimize etmek için paramanyetik ortam olarak kullanılan gadolinyumunun (Gd3+) çeşitli konsantrasyonları, akış hızları ve oranları test edildi. Çıkışlar arasındaki akış hızı oranlarının ayarlanması, sanal bir ayraç oluşturarak ayıklama verimliliğini artırdı. Toplam 0,2 mL/saat geri çekme akış hızıyla 30 mM Gd3+ kullanılması, üst çıkıştan HUVEC'lerin %86,67 ± 10,4'te ve U937 hücrelerinin %20,83 ± 7,93'te ayrıştırma verimliliğine ulaştı. Ek olarak, aynı mikroakışkan çip kullanılarak canlı/ölü MDA-MB-231 kanser hücresi ayrımı gerçekleştirildi. Canlı/ölü ayırmanın amacı, daha fazla sayıda canlı hücrenin sferoid oluşum verimliliğini arttırması nedeniyle, sferoid oluşum gibi doku mühendisliği uygulamalarında kullanılmak üzere canlı hücreler elde etmekti. Toplam 0,25 mL/saat geri çekme akış hızıyla 75 mM Gd3+ kullanılması, üst çıkıştan canlı hücrelerin %86,03 ± 2,54'te ve ölü hücrelerin %11,02 ± 5,81 oranında ayrıştırma verimliliğine ulaştı.Master 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 Development of Magnetic and Image Based Cell Cytometry Techniques(01. Izmir Institute of Technology, 2024) Keleş, Şeyda; Tekin, Hüseyin CumhurAkış sitometrisi çeşitli parametreler kullanılarak hücrelerin veya tek hücre özelliklerinin ölçülmesine olanak tanır. Bu tezde etiketlemeye gerek kalmadan hücrelerin veya mikropartiküllerin farklı yoğunluklarına göre ayrıştırılmasına olanak tanıyan manyetik levitasyon yöntemi kullanılmıştır. Ayrıca mikroakışkan çip içindeki mikropartiküllerin ve hücrelerin akış koşulları altında yoğunluğunu ölçen derin öğrenme tabanlı yeni bir görüntü sitometri tekniği üstünde çalışılmıştır. Bu bağlamda You Only Look Once (YOLO) algoritmasını kullanılarak parçacık yarıçapının ve levitayon yüksekliklerinin otomatik ve doğru analizini sağlayan bir yöntem geliştirilmiştir. Bununla birlikte farklı iki yoğunluğa sahip mikroparçacıklar birbirinden başarılı şekilde yoğunluklarına göre ayrıştırılmıştır. Devamında aynı şekilde insan monosit hücresinin (U-937) ölü ve canlı analizi yapılmıştır. Böylece, geliştirilen görüntü tabanlı sitometri yöntemi, mikropartiküllerin ve hücrelerin yoğunluklarına ve yarıçaplarına göre otomatik analizini kolaylaştırmıştır. Bu yaklaşım farklı uygulamalar için mikropartikül/hücre popülasyonlarının gerçek zamanlı, etiketsiz tanımlanmasına imkan tanıyabilecektir. Ayrıca bu sistemin akış altında ayrıştırma amacı ile kullanılabilmesi için mikrovalfler üzerinde çalışmalar gerçekleştirilmiştir. Bu kapsamda mikro pnömatik valf üretimi üzerinde çalışılmıştır. Polidimetilsiloksan (PDMS) membran yapıları ile oluşturulan pnömatik valfler, sağlam işleyişleri sayesinde hızlı akış manipülasyonuna olanak tanımaktadır. 3B baskı yöntemi ile üretilen kalıplar kullanılarak pnömatik valf yapıları hızlı ve basit bir şekilde üretilmiştir. Ayrıca, bu valfler çok düşük basınçlarda kapatılabilir ve manyetik levitasyon kurulumunda kullanılabilir olduğu gösterilmiştir. Bu nedenle, sunulan teknikle gelecekteki çalışmalarda yeni manyetik levitasyon tabanlı sitometri uygulamaları yürütülebilir.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 CumhurMicrofluidics 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 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 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 Cell Separation in Microfluidic Devices(01. Izmir Institute of Technology, 2022) Öksüz, Cemre; Tekin, Hüseyin CumhurCell separation is used to separate homogeneous and individual cell classes from a heterogeneous cell population. The efficiency and purity of these separated cells are of great importance in personalized medicine, regenerative medicine, disease monitoring and drug testing as well as in the therapeutic and diagnostic research. In this thesis, different microfluidic approaches were presented for cell separation. With this regard, a closed channel vacuum-integrated microfluidic chip was developed using an air permeability of a Polydimethylsiloxane and density-based separation of microparticles was performed. Besides, a centrifugal microfluidic system, Spinochip, was developed with one reservoir as inlet and outlet for the first time and different fluid manipulations were shown in the system. The system was applied to clinical tests of hematocrit measurements and white blood cell estimation using real patient samples. The developed system offered correlated results with clinical results. In addition to closed channel microfluidics, negative-magnetophoresis microfluidic chip was demonstrated for the size-based separation of microparticles and cells. In this regard, capturing rate of breast cancer cells (MCF-7) and human monocyte cells (U937) was investigated. The results showed that the approaches presented here could promote to the microfluidic studies for size-based cell separation.Master Thesis Magnetic-Based Cell Manipulation in Microfluidic Devices(01. Izmir Institute of Technology, 2022) Özçelik, Özge Solmaz; Tekin, Hüseyin CumhurCell manipulation is the concept of altering cell movement. Different manipulation techniques have been demonstrated with microfluidic systems for various studies such as tissue engineering, circulating tumor cell (CTC) filtering, and other biomedical applications. For instance, cell patterning and filtering studies are being developed through different manipulation approaches in microfluidic platforms where one of these approaches is the magnetophoresis principle method. Positive and negative magnetophoresis can be utilized generally through labeling or non-labeling, respectively. In this thesis, two different cell manipulation platforms using negative magnetophoresis were developed for cell patterning and cell filtration applications. These platforms allow several advantages such as simple fabrication, easy control, and low cost. Compared to other devices, the developed microfluidic platforms do not require any labeling process for cells for magnetic manipulation. In the patterning platform, microparticle and cell patterns were formed inside a simple microfluidic channel with different tilted angles in <1.5 hours. Furthermore, in the filtration platform, large microparticles were separated from small microparticles with 98.25% trapping efficiency. Live/dead cell separation of human monocyte macrophage cells (U937) under different flow rates was also investigated. The suggested platforms could be useful for label-free magnetic cell patterning and filtering in biomedical applications.Master Thesis Quantitative Phase Analysis in Lensless Digital Inline Holographic Microscopy(01. Izmir Institute of Technology, 2021) Demir, Ali Aslan; Tekin, Hüseyin Cumhur; Varlıklı, CananComputational imaging modalities replace the bulky, complex, and expensive optical components of traditional imaging procedures with numerical reconstruction steps. Digital holographic microscopy is one of the most prominent ones with the possibility of obtaining quantitative phase information by measuring the phase shift change caused by the refractive index of objects. In the lensless digital holographic microscopy system, a pinhole and a light-emitting diode are sufficient to create a holographic pattern on the camera sensor. Here, the optimization of a digital lensless inline holographic microscopy setup was performed to obtain optimal phase value. Also, to retrieve the lost phase information during the recording step, the numerical solution was performed with the single and multi-shot phase retrieval methods. Then, human breast adenocarcinoma (MDA-MB-231) and human myeloid leukemia (U937) cells were analyzed to obtain phase shift, perimeter, and circularity values. These parameters were used to obtain a quantitative differentiation model to replace the traditional labeling or visual confirmation steps with a direct analysis manner. The analysis of respective cells with the classification, object detection, and conditional generative adversarial models can be used directly with pre-trained weights to lessen the computational workloads. With this study, the quantitative analysis with lensless holographic microscopy setup was shown to be a label-free differentiation mechanism to separate cancer cells from monocytes cells which could be used for the early diagnosis of cancer. Also, the proposed method has the potential to be used to identify other cells with links to the diagnosis of different diseases.Master Thesis Design and Fabrication of a Wearable, Flexible Pulse Oximeter(01. Izmir Institute of Technology, 2020) Aydın, Ahmed; Tekin, Hüseyin CumhurOxygen is vital for the healthy functioning of tissues and organs. For this reason, it is indispensable to monitor the oxygen saturation of the human body during daily activities in order to improve the quality of life, in the detection and tracking of respiratory diseases. Pulse Oximeter is an electro-optic device that non-invasively measures peripheral oxygen saturation and provides information about how well oxygen diffuses the tissues. Conventional devices are not suitable for daily use due to their bulky structure and designs that restrict movement. With this thesis, the design and production of a flexible reflectance type Pulse Oximeter device that is conformally adapt to measurement suite, can be used all day long and is intended for continuous measurement has been realized.