Contributed Projects 

1. Minimally-Instrumented Home HIV Detection and Care Linkage System (NIH - 4R33HD101937-04)
[ 09/2019 – 08/2025 ]

According to recent estimates, ~37 million adults and 3.4 million children live with HIV. High-sensitivity diagnostic tests for HIV are needed to reduce the spread and burden of the disease and allow detection during the seroconversion window to enable “test and treat” and modify behavior. There is also a great need for inexpensive, home / point-of-care viral load tests for HIV patients undergoing therapy to individualize treatment, control the emergence and spread of drug-resistant strains of HIV, and monitor adherence. To address these needs, an interdisciplinary team of scientists from Penn Engineering, Penn Center for Aids Research (CFAR), and Centers of Disease Control and Prevention (CDC) is proposing a system consisting of an inexpensive disposable diagnostic cassette and inexpensive reusable processor. Our cassette will carry out all unit operations from sample introduction, including plasma separation from whole blood, to multi-plex enzymatic amplification, facilitating co-detection and quantification of HIV-1 clade B, Hepatitis B (HBV), Hepatitis C (HCV), and beta Globin (positive control) with detection limit of 10 targets in a sample (e.g., 350 copies/mL when whole blood sample volume is 100μL) and of HIV-1 Group M (subtype- independent) in under 40 minutes. The cassette stores all reagents refrigeration-free with a shelf-life exceeding 12 months. Our cassette mates with a simple battery-powered processor that provides temperature control, actuation, and an interface for a smartphone. The smartphone instructs the user in operating the device; controls device operation, monitors and analyzes enzymatic amplification processes; reports test results to the patient, to the medical team and public health officials (in compliance with prevailing laws); and provides counseling. Our system carries out all the necessary unit operations from sample introduction to test results. At the conclusion of this effort, we will have developed a remarkable system for home/point-of-care molecular detection of HIV-1 and co-infections with minimal instrumentation. Our system will be able to detect HIV during seroconversion to encourage individuals to start therapy early and modify transmission behavior, monitor viral rebound to detect the development of drug- - resistance and non-adherence, and enable personalized therapy with novel long-acting agents such as broadly neutralizing antibody infusions likely to emerge over the next decade; and detect infection in infants born to HIV– infected mothers (particularly in the developing world). As such, this system has the potential to allow rapid detection of viremia and rapid intervention to prevent HIV transmission to the uninfected and reduce the complications of HIV in those infected. More broadly, our system will enable individuals to assume responsibility for their own care.

2. Detection and Sorting of Cancer Microemboli in a Microfluidic Chip with Image Processing Algorithms (TÜBİTAK 1001 – Scientific and Technological Research Projects Funding Program - 119M052)
[ 11/2019 – 11/2023 ]

Circulating tumor microemboli (CTM) is a structure formed by two or more tumor cells. CTMs are very rare compared to circulating tumor cells (CTC) in blood, and it is believed that they are extremely aggressive in cancer metastasis. CTMs are also important indicators for cancer diagnosis, therapeutics, and prognostics. But, CTM sorting methods have focused on properties such as cell size, density, or membraneprotein differences. In studies of CTM separation, reliable results can’t be obtained due to low isolation purity, efficiency, cell viability, long processing times, and the need for high-cost equipment. Since CTMs can’t maintain their integrity under high mechanical stress, up-to-date methods can’t separate CTMs with high efficiency. This project will use a new method based on microfluidic chip filtering and image processing to differentiate CTMs from leukocytes according to their size and morphology. With this method, CTMs captured on a microfluidic filter will be detected in real-time with image processing algorithms and will be transferred to the collection reservoir. Thus, long-term mechanical stress derived from the fluidic flow on CTMs will be eliminated, and CTMs will maintain their integrity and viability. The cells collected in the reservoir will be visualized, and with a trained neural network, CTMs will be detected automatically without using any staining method. In our device, a lensless holographic microscope system will be used to achieve high-quality cell imaging. With a digital holographic microscopy system, recorded hologram images can be processed using algorithms to obtain detailed images. This method can obtain phase information containing 3D geometrical and structural properties of objects. It also provides cost-effective and portable imaging. In the experimental setup, CTM separation operations will be performed automatically. For that, syringe pumps generating flows and microfluidic valves guiding flows in the chip will be controlled by using a house-developed program, and by adding CTM detection algorithms to this program, automation of CTM separation protocols will be ensured. CTMs will be separated on a microfluidic chip according to their size and morphological differences without structural damage with the successful completion of the project. With this method, sensitive, specific, and rapidly separated CTMs can be used for cancer diagnosis and treatment, allowing single-cell/ cell cluster studies. Applying advanced analysis methods to extract CTMs efficiently will also contribute to the widespread application of personalized treatment methods.

3. Quantitative Analysis of Creatinine Using Automated ELISA Protocols Lab on a Chip Platform (TÜBİTAK 1001 – Scientific and Technological Research Projects Funding Program - 217S518)
[ 06/2018 – 06/2021 ]

Chronic kidney disease (CKD) is a high-cost disease that affects approximately one in ten people in the world and progresses rapidly and results in kidney failure or dialysis, also triggering other diseases. Regular monitoring and control of the disease are important to reduce the death rate caused by the disease. In order to control the kidney functions of a CKD patient, the glomerular filtration rate (GFR) test is applied regularly in health institutions to determine the patient's serum creatinine value, and with this value, the patient's GFR is calculated based on data such as age, gender, and race. Currently, serum creatinine tests can only be done in health centers, and the results can be reached after at least one day. Although there are clinically used point-of-care creatinine tests, these tests are not suitable for frequent and regular control at home due to their high cost. This complicates the monitoring of kidney functions and makes it difficult to immediately intervene in the deterioration of kidney functions. Lab-on-a-chip technology not only allows biomarkers to be used automatically at the point of care but also provides sensitive and low-cost testing by shortening analysis times. This project aims to perform automatic serum creatinine analysis by applying direct enzyme-linked immunoassay (ELISA) protocols in a new lab-on-a-chip platform. In the presented project, a PMMA chip with reservoirs containing ELISA solutions, a bar coated with an antibody that selectively captures creatinine and an electromechanical platform that automatically moves the bar were designed and developed. Detection of creatinine in the concentration range of 0-15 μg/mL dissolved in phosphate-buffered saline (PBS) was performed on the electromechanical platform, and the detection limit and half-maximal inhibition concentration (IC50) were calculated as 9.74 μg/mLand 5 μg/mL, respectively. Using the calculated IC50 value, the storage conditions of the chip and antibody-coated bars were examined. In addition, to test similar patient sample conditions, creatinine concentrations of 0-150 μg/mL (0-15 mg/dL) dissolved in dialyzed fetal bovine serum (FBS) were also analyzed on the platform. The electromechanical platform, which will be obtained as a project output with the successful conclusion of the project, can be used to provide automatic point-of-care analysis of the creatinine molecule, as well as to be applied to point-of-care tests by applying it to different biomarkers in the future.

4. Automated Detection of Viral RNA with the Lab on a Chip Platform (İzmir Institute of Technology - Scientific Research Project - Project Number: 2020IYTE42)
[ 04/2020 – 03/2021 ]

It aims to design and manufacture an electromechanical system using an on-chip laboratory platform for the diagnosis of COVID-19. For this purpose, inner (FIP, BIP), outer (F3, B3), and loop (LF, LB) primers were designed by using NEB LAMP Primer Design Tool Version 1.0.1 software for the N gene used in the detection of COVID-19. By synthesizing 295 base pairs (bp) gene fragments on which the designed primer regions are located, LAMP experiments were reduced to 107 copy numbers/mL. In the developed system, the color change of the colorimetric-based LAMP reaction was measured using a plate-based spectrometer device, and the signal level was examined by proportioning the absorbance values at 432 nm for yellow color and 560 nm for red color, corresponding to the maximum values (New England BioLabs 2021; Zhang, Ren. , et al. 2020). It is anticipated that this electromechanical platform, which can perform LAMP protocols, can be used as a different viral DNA/RNA diagnostic kit, as well as for the diagnosis of many DNA/RNA-related diseases. Thus, it is thought that it can be used as point-of-care testing for various diseases by making traditional diagnostic tests faster, cheaper, and more portable. Within the scope of this project, the electromechanical system integrated with the on-chip laboratory system was designed and manufactured. Thanks to the electromechanical system that was produced, the effect of the mixing process on the amplification was investigated. In the study, primer design software was used for the N gene region of the coronavirus, primers were designed, and WarmStart Colorimetric LAMP technology containing pH indicator was used for easy detection of target viral DNA with a Peltier heater in the on-chip laboratory system. The presence of viral DNA was evaluated as positive when the reaction color changed from pink to yellow, and the absorbance values in the literature were also examined. Amplification was completed in 45 minutes at 65 °C, and the intensity of the reaction color was measured simultaneously with the spectrometer. The primer mixture and WarmStart Colorimetric loop-mediated isothermal amplification solution was dripped into the reservoir, enabling rapid analysis with the aid of active mixing. In this context, it is anticipated that this automatic detection system, which is portable and portable at the bedside and provides rapid diagnosis as an alternative to existing diagnostic methods, will contribute to the detection of viral gene regions and shed light on this field.

5. Development of a Wearable Sensor-Integrated Telemedicine Platform for Remote Diagnosis and Monitoring of Sleep Apnea (TÜBİTAK 1501 - Industrial R&D Projects Grant Programme - 147081)

The aim of the project is to develop a telemedicine-integrated wearable device that uses an image-based strategy that detects breathing profiles in real-time, including the processes of inhalation, exhalation, and breathlessness, to diagnose sleep apnea. The device to be developed will measure the diaphragm movement resulting from breathing with an accelerometer placed on the diaphragm. The data collected from the wearable device will be transmitted wirelessly remotely and visualized for personalized monitoring in the telemedicine system for breath analysis. Deep learning algorithms will process these data, and breathing profiles will be automatically analyzed to determine sleep apnea. Thus, remote diagnosis and monitoring of sleep apnea will be effectively provided.

6. Spheroid Culture and Drug Testing with Magnetic Levitation Methods on Microfluidic System (TÜBİTAK 1004 – Center of Excellence Support Program - Project Number: 22AG032)
[ 12/2020 – 08/2023 ]

Two-dimensional (2D) cell culture methods are commonly employed to understand the biophysical and biochemical cellular responses. However, these culture methods, where cells are monolayered on a surface, do not accurately represent cell-cell and cell-extracellular matrix (ECM) interactions. In contrast, three-dimensional (3D) cell culture methods facilitate the transport of nutrients, gases, and growth factors between cells and their microenvironments. As a result, 3D cell cultures exhibit cell proliferation, apoptosis, and differentiation characteristics similar to in vivo conditions. Spheroids, spontaneously forming 3D cell clusters, closely mimic the cell microenvironment in vitro due to cell-cell and cell-matrix interactions. Spheroids, reproducing the cell microenvironment and demonstrating functional tissue-like properties in vivo, find applications in medical and clinical research. Various techniques are employed for spheroid production, with microfluidic systems particularly enabling highly efficient spheroid generation. In this project, we are demonstrating high-efficiency spheroid production using magnetic effects in microfluidic systems for the first time. Additionally, the impact of drugs on spheroids is assessed in real-time and label-free manners, with spheroid mass and sizes measured in real-time. The creation of 3D cell clusters using the magnetic levitation technique and their responses to drugs have been demonstrated in our previous studies. This project aims to present an integrated device within an innovative microfluidic system for efficient drug testing on spheroids. This device will also be provided to Yeditepe R&D and Analysis Center, another project component, for testing innovative cancer drugs. With the successful completion of the project, the prototype of the comprehensive drug testing device will enable high-efficiency and accurate testing of drugs on 3D tissues. Thus, a nationally competitive technology will be developed for international-level drug development endeavors.