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Graduate Students' Thesis Topics

Method development and optimization for nucleic acid detection platforms by
Esra Sengul

Currently: Ongoing masters

Abstract: Integration of microfabricated, single-cell resolution and traditional, population-level biological assays to investigate the direct and indirect influence of macrophages on glioma cell behavior. Quantification of proliferation, morphology, motility, migration, and deformation properties of glioma cells at single-cell level and compared these results with population-level data.

Development of training box for thyroidectomy operations by Pouya Sharbati

Currently: Ongoing masters

Abstract: This thesis aims to develop realistic anatomical model, to provide performance evaluation for the thyroidectomy operations by using sensors and to measure the success of the trainee by using machine learning. Considering these features, it is expected to be a more efficient training alternative than the conventional training boxes for the thyroid surgeries.

Development of microfluidic ecosystems to understand antibiotic action mechanisms by Sumeyra Vural

Currently: Ongoing doctorates

Abstract: This research aims to investigate antibiotic killing mechanisms via developing artificial microfluidic niches those mimics several habitats for various types of microorganisms. Therefore, new antibiotic treatment strategies can be established and new diagnostics tests can be developed for clinics and farms.

Development of biosensors to detect microorganisms in the field of agriculture and water pollution
by Unal Akar

Currently: Ongoing doctorates

Abstract: Development and advancement of DNA- or RNA-based detection sensors to be used in the field or farms for agriculture, and water pollution. These technologies will provide low-cost, reliable, particle to detection tools for microorganism identification and evaluation of treatment strategies.

Characterization of hematopoietic cells using 3d corbon-dielectrophoresis
by Yagmur Yildizhan

Currently: PhD student at KU Leuven

Abstract: Tumor-associated macrophages (TAM), one of the key players in tumor microenvironment, involves in tumor development and progression in many cancers. Here, we will present carbon electrode dielectrophoresis (carbon-DEP) as a characterization tool to identify and separate U937 monocytes and macrophages. First, we will differentiate monocytes to obtain macrophages. Next, we will apply carbon-DEP to determine specific crossover frequencies as signatures. Since DEP does not require any pre-labelling for the cells, it will allow direct characterization of cells based on their physical properties without altering their genetic and phenotypic properties. Finally, we will verify our results using traditional biochemical assays. When we obtain their dielectrophoretic signatures, we will isolate and enrich them for high-throughput biochemical analysis.

Development of artificial cell culture platforms using microfluidics
by Hande Karamahmutoglu

Currently: PhD student at KU Leuven

Abstract: Understanding the interactions between tumor cells and immune cells in a quantitative manner will provide valuable information to reveal the mechanism of diseases, immune defense and discovery of new drugs and new treatment strategies. Today one of the biggest limitations relies on the traditional methods and tools that we use to investigate rare cells and specific events in biology particularly in immunology. Since conventional techniques are not adequate to be selective, specific and precise, the rare cells such as the metastatic or drug resistant ones or the events such as onset symptoms of tumors or infections are being masked by the majority of the cells or events in the population. Consequently, our diagnosis or treatment approaches might not target the right cells at the right time in the right microenvironment. Therefore, missed, and delayed diagnosis or wrong treatment strategies emerges. To overcome the limitations, microfabricated tools in conjunction with live-cell imaging provide quantitative, accurate, reproducible, and repeatable information at single-cell resolution related to behavior of rare cells in their natural microenvironments. Moreover, these modern methods reduce the assay time, sample consumption and waste production, while improving the throughput and precision. Herein, we present microfabricated platforms for cell culture and drug exposure studies that could be used for immune cell-tumor cell investigations.

Development of loop-mediated isothermal amplification (LAMP) based biosensor set for detection of genetically
by Dogukan Kaygusuz

Abstract: The worldwide usage of products with genetically modified organisms (GMOs) is constrained by different legal frameworks. GMO’s usage limits are determined by the related regulations in each country. “Regulation on Genetically Modified Organisms and Products” named law – effective since 2010 – draws the conditions in Turkey. Consequently, a variety of products are monitored by undergoing a GMO detection and classification processes. Researchers have been proposing different works regarding the specifically important problem of GMO-based products’ detection. Various methods such as Polymerase Chain Reaction, Ligase Chain Reaction, Rotating Circle Amplification are commonly used for DNA amplification, a crucial preprocessing step of the detection process. In this work, the loop-based isothermal amplification (LAMP) method which provides fast results and requires fewer temperature cycles is used. For the LAMP method to be properly implemented, the sample should be kept at 60-65⁰C between 35-120 minutes. Conventional laboratory devices used for this purpose can be characterized – on average – to be heavy (1-12 kg), expensive (1300-15000 €), unmovable and only operable by trained experts. In this thesis, we present the design, implementation and performance analysis of two prototype GMO-based product and bacteria detection devices that are portable (108-240 g) , fast (<30-40 minutes), affordable (<25-30 €) and pocket-size (6x6x3-9.7×6.8×5 cm) provided with battery system that allows its functionality outside laboratory environment. The temperature level controller, heater design, feedback circuit and the exterior of the device are prepared via different mechanical and electronic design software. Different heating elements (Peltier, Wire winding, Cartridge heater) have experimented for selection purposes. In these experiments, the heaters were found to be not flexible and cannot be adapted to device requirements. Accordingly, new customized heaters are mathematically modeled and then embedded on the flexible PCB. A Proportional Integral Derivative (PID) control-based feedback control scheme is used to adjust the temperature with a high accuracy of (± 0.2⁰C). To achieve this sensitivity, parameters of PID control were fine-tuned by Ziegler-Nichols Method.

In this work, we extended the devices uses to E. coli bacteria detection as well. The detection was done using the LAMP method and is presented as the second device with its customized design providing high output (105 microchannels). Roundup Ready Soybean (RRS), gts40-3-2) with 0%, 0.1%, 1% and 10% GMO content were used for GMO analysis part and E. ColiATCC 10536 bacteria for bacterial analysis. Both GMO and Bacteria detection and analysis results were done by the proposed devices showed similar performance in terms of accuracy and sensitivity when compared to the laboratory or commercial correspondents in the market while successfully outperforming them in the other already mentioned aspects.

Method development and optimization for nucleic acid detection platforms
by Sumeyra Vural

Currently: PhD student at Sabanci University

Abstract: The nucleic acid tests abbreviated as NAT, is a technique requires amplification and detection to provide guidance on the diagnosis of genetic materials. Although the genetic material of every living consists of DNA or RNA, there are variations in genome sequences. This genetic variation makes NAT an ideal technique for identifying, genetically modified organisms (GMOs), infectious diseases, cancer, genetic disorders, and mitochondrial disorders, helping to improve diagnostic technologies. Nucleic acid amplification requires a laboratory environment with special equipment and technical expertise. Loop Mediated Isothermal Amplification (LAMP) is technically simpler than Polymerase Chain Reaction (PCR). LAMP has ideal properties for nucleic acid detection applications. LAMP assays are robust and has ability of pyrophosphate production in the presence of target, which enables detection with naked eye. Polymerase inhibitors in samples do not affect the amplification process. Most importantly, LAMP makes the reaction suitable for simple target-response diagnostic systems with simplified sample preparation. In this thesis, LAMP was primarily developed and optimized according to highlight the strong diagnostic aspects of detection platforms, and their effects on healthcare and its benefits to society. The systems we worked on enlarges the target DNA using LAMP method. In less than 30 minutes, it reacts with pH-dependent dyes (such as hydroxynaphtol blue (HNB)) and enables colorimetric DNA detection with naked-eye. Detection of DNA fragments were performed parallelly in thermal cycler and our platforms. Results show LAMP is an advantageous method because it is highly sensitive, cheap, user-friendly, and safe; in addition, does not usually require DNA extraction (in colony-LAMP). The LAMP reaction is believed to be a simple and reliable tool for laboratory purposes because it needs only very basic instruments, and the results can be observed and visually contrasted.