WoS İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/394
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Article Citation - WoS: 3Citation - Scopus: 6Simple Staining of Cells on a Chip(MDPI, 2022-11-13) Kosker, Fatma Betul; Aydin, Omer; Icoz, KutaySimple staining of cells is a widely used method in basic medical diagnostics, education, and research laboratories. The stains are low-cost, but the extensive consumption results in excessive toxic waste generation. Thus, to decrease the amount of toxic waste resulting from the cell staining procedure is a need. In this study, we developed a magnetically driven and compartmentalized passive microfluidic chip to perform simple staining of human eukaryotic cells, K562 cells, and lymphocyte cells derived from patients. We demonstrated simple staining on cells with trypan blue, methylene blue, crystal violet, and safranin for high, medium, and low cell densities. The stained cells were imaged using a bright field optical microscope and a cell phone to count cells on the focal plane. The staining improved the color signal of the cell by 25-135-pixel intensity changes for the microscopic images. The validity of the protocol was determined using Jurkat and MDA-MB-231 cell lines as negative controls. In order to demonstrate the practicality of the system, lymphocyte cells derived from human blood samples were stained with trypan blue. The color intensity changes in the first and last compartments were analyzed to evaluate the performance of the chip. The developed method is ultra-low cost, significantly reduces the waste generated, and can be integrated with mobile imaging devices in terms of portability. By combining microfabrication technology with cell staining, this study reported a novel contribution to the field of microfluidic biosensors. In the future, we expect to demonstrate the detection of pathogens using this method.Article Citation - WoS: 50Citation - Scopus: 63Optical Detection of Microplastics in Water(Springer Heidelberg, 2021-01-19) Iri, Ahmet H.; Shahrah, Malek H. A.; Ali, Ali M.; Qadri, Sayed A.; Erdem, Talha; Ozdur, Ibrahim T.; Icoz, KutayUnfortunately, the plastic pollution increases at an exponential rate and drastically endangers the marine ecosystem. According to World Health Organization (WHO), microplastics in drinking water have become a concern and may be a risk to human health. One of the major efforts to fight against this problem is developing easy-to-use, low-cost, portable microplastic detection systems. To address this issue, here, we present our prototype device based on an optical system that can help detect the microplastics in water. This system that costs less than $370 is essentially a low-cost Raman spectrometer. It includes a collimated laser (5 mW), a sample holder, a notch filter, a diffraction grating, and a CCD sensor all integrated in a 3D printed case. Our experiments show that our system is capable of detecting microplastics in water having a concentration less than 0.015% w/v. We believe that the designed portable device can find a widespread use all over the world to monitor the microplastic content in an easier and cost-effective manner.Article Citation - WoS: 16Citation - Scopus: 19On-Demand Weighing of Single Dry Biological Particles Over a 5-Order Dynamic Range(Royal Soc Chemistry, 2014) Chan, Bin-Da; Icoz, Kutay; Huang, Wanfeng; Chang, Chun-Li; Savran, Cagri A.We report a simple and highly versatile system to select and weigh individual dry biological particles. The system is composed of a microtweezer to pick and place individual particles and a cantilever-based resonator to weigh them. The system can weigh entities that vary from a red blood cell (similar to 10(-11) g) to the eye-brain complex of an insect (similar to 10(-6) g), covering a 5-order-of-magnitude mass range. Due to its versatility and ease of use, this weighing method is highly compatible with established laboratory practices. The system can provide complementary mass information for a wide variety of individual particles imaged using scanning electron microscopy and determine comparative weights of individual biological entities that are attached to microparticles as well as weigh fractions of individual biological entities that have been subjected to focused ion beam milling.Article Citation - WoS: 12Citation - Scopus: 13Numerical Analysis and Experimental Verification of Optical Scattering From Microplastics(Royal Soc, 2023-08) Genc, Sinan; Icoz, Kutay; Erdem, TalhaAccurate and fast characterization of the micron-sized plastic particles in aqueous media requires an in-depth understanding of light interaction with these particles. Due to the complexity of Mie scattering theory, the features of the scattered light have rarely been related to the physical properties of these tiny objects. To address this problem, we reveal the relation of the wavelength-dependent optical scattering patterns with the size and refractive index of the particles by numerically studying the angular scattering features. We subsequently present a low-cost setup to measure the optical scattering of the particles. Theoretical investigation shows that the angular distribution of the scattered light by microplastics carries distinct signatures of the particle size and the refractive index. The results can be used to develop a portable, low-cost setup to detect microplastics in water.Article Citation - WoS: 16Citation - Scopus: 18Microfluidic Chip Based Direct Triple Antibody Immunoassay for Monitoring Patient Comparative Response to Leukemia Treatment(Springer, 2020-07-13) Icoz, Kutay; Akar, Unal; Unal, EkremWe report a time and cost-efficient microfluidic chip for screening the leukemia cells having three specific antigens. In this method, the target blast cells are double sorted with immunomagnetic beads and captured by the 3rd antibody immobilized on the gold surface in a microfluidic chip. The captured blast cells in the chip were imaged using a bright-field optical microscope and images were analyzed to quantify the cells. First sorting was performed with nano size immunomagnetic beads and followed by 2nd sorting where micron size immunomagnetic beads were used. The low-cost microfluidic platform is made of PMMA and glass including micro size gold pads. The developed microfluidic platform was optimized with cultured B type lymphoblast cells and tested with the samples of leukemia patients. The 8 bone marrow samples of 4 leukemia patients on the initial diagnosis and on the 15th day after the start of the chemotherapy treatment were tested both with the developed microfluidic platform and the flow cytometry. A 99% statistical agreement between the two methods shows that the microfluidic chip is able to monitor the decrease in the number of blast cells due to the chemotherapy. The experiments with the patient samples demonstrate that the developed system can perform relative measurements and have a potential to monitor the patient response to the applied therapy and to enable personalized dose adjustment.Article Citation - WoS: 28Citation - Scopus: 34Micro- and Nanodevices Integrated With Biomolecular Probes(Pergamon-Elsevier Science Ltd, 2015-12) Alapan, Yunus; Icoz, Kutay; Gurkan, Umut A.Understanding how biomolecules, proteins and cells interact with their surroundings and other biological entities has become the fundamental design criterion for most biomedical micro- and nanodevices. Advances in biology, medicine, and nanofabrication technologies complement each other and allow us to engineer new tools based on biomolecules utilized as probes. Engineered micro/nanosystems and biomolecules in nature have remarkably robust compatibility in terms of function, size, and physical properties. This article presents the state of the art in micro- and nanoscale devices designed and fabricated with biomolecular probes as their vital constituents. General design and fabrication concepts are presented and three major platform technologies are highlighted: microcantilevers, micro/nanopillars, and microfluidics. Overview of each technology, typical fabrication details, and application areas are presented by emphasizing significant achievements, current challenges, and future opportunities. (C) 2015 Elsevier Inc. All rights reserved.Article Citation - WoS: 15Citation - Scopus: 16Magnetic Micro/Nanoparticle Flocculation-Based Signal Amplification for Biosensing(Dove Medical Press Ltd, 2016-06) Mzava, Omary; Tas, Zehra; Icoz, KutayWe report a time and cost efficient signal amplification method for biosensors employing magnetic particles. In this method, magnetic particles in an applied external magnetic field form magnetic dipoles, interact with each other, and accumulate along the magnetic field lines. This magnetic interaction does not need any biomolecular coating for binding and can be controlled with the strength of the applied magnetic field. The accumulation can be used to amplify the corresponding pixel area that is obtained from an image of a single magnetic particle. An application of the method to the Escherichia coli 0157: H7 bacteria samples is demonstrated in order to show the potential of the approach. A minimum of threefold to a maximum of 60-fold amplification is reached from a single bacteria cell under a magnetic field of 20 mT.Article Citation - WoS: 14Citation - Scopus: 15Image-Analysis Based Readout Method for Biochip: Automated Quantification of Immunomagnetic Beads, Micropads and Patient Leukemia Cell(Pergamon-Elsevier Science Ltd, 2020-06) Uslu, Fatma; Icoz, Kutay; Tasdemir, Kasim; Dogan, Refika S.; Yilmaz, BulentFor diagnosing and monitoring the progress of cancer, detection and quantification of tumor cells is utmost important. Beside standard bench top instruments, several biochip-based methods have been developed for this purpose. Our biochip design incorporates micron size immunomagnetic beads together with micropad arrays, thus requires automated detection and quantification of not only cells but also the micropads and the immunomagnetic beads. The main purpose of the biochip is to capture target cells having different antigens simultaneously. In this proposed study, a digital image processing-based method to quantify the leukemia cells, immunomagnetic beads and micropads was developed as a readout method for the biochip. Color, size-based object detection and object segmentation methods were implemented to detect structures in the images acquired from the biochip by a bright field optical microscope. It has been shown that manual counting and flow cytometry results are in good agreement with the developed automated counting. Average precision is 85 % and average error rate is 13 % for all images of patient samples, average precision is 99 % and average error rate is 1% for cell culture images. With the optimized micropad size, proposed method can reach up to 95 % precision rate for patient samples with an execution time of 90 s per image.Article Citation - WoS: 5Citation - Scopus: 6Capturing B Type Acute Lymphoblastic Leukemia Cells Using Two Types of Antibodies(Wiley, 2018-11-20) Icoz, Kutay; Gercek, Tayyibe; Murat, Ayseguel; Ozcan, Servet; Unal, EkremOne way to monitor minimal residual disease (MRD) is to screen cells for multiple surface markers using flow cytometry. In order to develop an alternative microfluidic based method, isolation of B type acute lymphoblastic cells using two types of antibodies should be investigated. The immunomagnetic beads coated with various antibodies are used to capture the B type acute lymphoblastic cells. Single beads, two types of beads and surface immobilized antibody were used to measure the capture efficiency. Both micro and nanosize immunomagnetic beads can be used to capture B type acute lymphoblastic cells with a minimum efficiency of 94% and maximum efficiency of 98%. Development of a microfluidic based biochip incorporating immunomagnetic beads and surface immobilized antibodies for monitoring MRD can be an alternative to current cost and time inefficient laboratory methods. (c) 2018 American Institute of Chemical Engineers Biotechnol. Prog., 35: e2737, 2019