Professional Education


  • PhD, Izmir Institute of Technology, Bioengineering (2020)
  • MS, Middle East Technical University, Biotechnology (2014)
  • BS, Ege University, Bioengineering (2011)

Stanford Advisors


All Publications


  • Size and density measurements of single sickle red blood cells using microfluidic magnetic levitation. Lab on a chip Goreke, U., Bode, A., Yaman, S., Gurkan, U. A., Durmus, N. G. 1800

    Abstract

    Single cells have unique biophysical signatures that can rapidly change during various disease states. For instance, cellular density is an inherent property differing between cell types. Characterizing changes in fundamental density properties down to the single-cell level can reveal sub-populations in pathological states. Here, we have developed a microfluidic, magnetic levitation-based assay (MagDense) that detects minute density differences of individual red blood cells (RBCs) down to 0.0001 g mL-1 resolution. This assay fractionates RBCs based on their density profiles in a non-ionic paramagnetic medium flowing in a capillary microchannel placed between magnets with same poles facing each other. Based on precisely measured levitation height and density of individual RBCs at their specific equilibrium state, we demonstrated that MagDense can accurately analyze the density of sickle hemoglobin (HbS)-containing RBCs and normal hemoglobin (HbA)-containing RBCs. In addition, the precise density and cell size measurements at the single cell level showed three different sub-populations of RBCs in blood samples from individuals with homozygous sickle cell disease receiving blood transfusions; where less dense, HbA-containing RBCs levitated higher, while the denser, HbS-containing RBCs levitated lower. We compared the mean RBC densities of sickle cell disease subjects with healthy controls and found distinctly separated bands of RBC density for each group denoting the likely range of cell densities seen in the blood samples. The high resolution of our method enabled measurement of deviation from the mean RBC density. Moreover, we introduced a new term as a measure of density dispersion, "RBC levitational density width, RLDW". Mean RBC density in sickle cell disease associated with hemoglobin from complete blood count (p = 0.032, linear regression) and RLDW associated with absolute reticulocyte count (ARC) and RBC distribution width (RDW) from complete blood count (p = 0.002 for ARC and p = 003 for RDW, linear regression). Our magnetic levitation-based assay enables rapid, accurate, density-based imaging, profiling and label-free monitoring of single RBCs. Our approach can be broadly applicable to investigate blood cell disorders and the effects of emerging pharmacological and curative therapies in patient outcomes.

    View details for DOI 10.1039/d1lc00686j

    View details for PubMedID 35094036

  • HologLev: A Hybrid Magnetic Levitation Platform Integrated with Lensless Holographic Microscopy for Density-Based Cell Analysis ACS SENSORS Delikoyun, K., Yaman, S., Yilmaz, E., Sarigil, O., Anil-Inevi, M., Telli, K., Yalcin-Ozuysal, O., Ozcivici, E., Tekin, H. 2021; 6 (6): 2191-2201

    Abstract

    In clinical practice, a variety of diagnostic applications require the identification of target cells. Density has been used as a physical marker to distinguish cell populations since metabolic activities could alter the cell densities. Magnetic levitation offers great promise for separating cells at the single cell level within heterogeneous populations with respect to cell densities. Traditional magnetic levitation platforms need bulky and precise optical microscopes to visualize levitated cells. Moreover, the evaluation process of cell densities is cumbersome, which also requires trained personnel for operation. In this work, we introduce a device (HologLev) as a fusion of the magnetic levitation principle and lensless digital inline holographic microscopy (LDIHM). LDIHM provides ease of use by getting rid of bulky and expensive optics. By placing an imaging sensor just beneath the microcapillary channel without any lenses, recorded holograms are processed for determining cell densities through a fully automated digital image processing scheme. The device costs less than $100 and has a compact design that can fit into a pocket. We perform viability tests on the device by levitating three different cell lines (MDA-MB-231, U937, D1 ORL UVA) and comparing them against their dead correspondents. We also tested the differentiation of mouse osteoblastic (7F2) cells by monitoring characteristic variations in their density. Last, the response of MDA-MB-231 cancer cells to a chemotherapy drug was demonstrated in our platform. HologLev provides cost-effective, label-free, fully automated cell analysis in a compact design that could be highly desirable for laboratory and point-of-care testing applications.

    View details for DOI 10.1021/acssensors.0c02587

    View details for Web of Science ID 000668374500016

    View details for PubMedID 34124887

  • Magnetic Susceptibility-Based Protein Detection Using Magnetic Levitation ANALYTICAL CHEMISTRY Yaman, S., Tekin, H. 2020; 92 (18): 12556-12563

    Abstract

    Magnetic levitation, which is a magnetic phenomenon of levitating particles suspended in a paramagnetic liquid under a nonuniform magnetic field, is a powerful tool for determining densities and magnetic properties of micro- and nanoparticles. The levitation height of particles in the magnetic field depends on the magnetic susceptibility and density difference between the object and the surrounding liquid. Here, we developed a magnetic susceptibility-based protein detection scheme in a low-cost and miniaturized magnetic levitation setup consisting of two opposing magnets to create a gradient of a magnetic field, a glass capillary channel to retain the sample, and two side mirrors to monitor inside the channel. The method includes the use of polymeric microspheres as mobile assay surfaces and magnetic nanoparticles as labels. The assay was realized by capturing the target protein to the polymer microspheres. Then, magnetic nanoparticles were attached onto the resulting microsphere-protein complex, creating a significant difference in the magnetic properties of polymer microspheres compared to those without protein. The change in the magnetic properties caused a change in the levitation height of the microspheres. The levitation heights and their distribution were then correlated to the amount of target proteins. The method enabled a detection limit of ∼110 fg/mL biotinylated bovine serum albumin in serum. With the sandwich immunoassay developed for mouse immunoglobulin G, detection limits of 1.5 ng/mL and >10 ng/mL were achieved in buffer and serum, respectively. This approach sensed the minute changes in the volume magnetic susceptibility of the microspheres with a resolution of 4.2 × 10-8 per 1 μm levitation height change.

    View details for DOI 10.1021/acs.analchem.0c02479

    View details for Web of Science ID 000572832900060

    View details for PubMedID 32811142

  • Magnetic Force-Based Micro fluidic Techniques for Cellular and Tissue Bioengineering FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY Yaman, S., Anil-Inevi, M., Ozcivici, E., Tekin, H. 2018; 6: 192

    Abstract

    Live cell manipulation is an important biotechnological tool for cellular and tissue level bioengineering applications due to its capacity for guiding cells for separation, isolation, concentration, and patterning. Magnetic force-based cell manipulation methods offer several advantages, such as low adverse effects on cell viability and low interference with the cellular environment. Furthermore, magnetic-based operations can be readily combined with microfluidic principles by precisely allowing control over the spatiotemporal distribution of physical and chemical factors for cell manipulation. In this review, we present recent applications of magnetic force-based cell manipulation in cellular and tissue bioengineering with an emphasis on applications with microfluidic components. Following an introduction of the theoretical background of magnetic manipulation, components of magnetic force-based cell manipulation systems are described. Thereafter, different applications, including separation of certain cell fractions, enrichment of rare cells, and guidance of cells into specific macro- or micro-arrangements to mimic natural cell organization and function, are explained. Finally, we discuss the current challenges and limitations of magnetic cell manipulation technologies in microfluidic devices with an outlook on future developments in the field.

    View details for DOI 10.3389/fbioe.2018.00192

    View details for Web of Science ID 000454340700001

    View details for PubMedID 30619842

    View details for PubMedCentralID PMC6305723

  • Biofabrication of in situ Self Assembled 3D Cell Cultures in a Weightlessness Environment Generated using Magnetic Levitation SCIENTIFIC REPORTS Anil-Inevi, M., Yaman, S., Yildiz, A., Mese, G., Yalcin-Ozuysal, O., Tekin, H., Ozcivici, E. 2018; 8: 7239

    Abstract

    Magnetic levitation though negative magnetophoresis is a novel technology to simulate weightlessness and has recently found applications in material and biological sciences. Yet little is known about the ability of the magnetic levitation system to facilitate biofabrication of in situ three dimensional (3D) cellular structures. Here, we optimized a magnetic levitation though negative magnetophoresis protocol appropriate for long term levitated cell culture and developed an in situ 3D cellular assembly model with controlled cluster size and cellular pattern under simulated weightlessness. The developed strategy outlines a potential basis for the study of weightlessness on 3D living structures and with the opportunity for real-time imaging that is not possible with current ground-based simulated weightlessness techniques. The low-cost technique presented here may offer a wide range of biomedical applications in several research fields, including mechanobiology, drug discovery and developmental biology.

    View details for DOI 10.1038/s41598-018-25718-9

    View details for Web of Science ID 000431627300016

    View details for PubMedID 29740095

    View details for PubMedCentralID PMC5940762

  • Beet molasses-based feeding strategy enhances recombinant thermostable glucose isomerase production by Escherichia coli BL21 (DE3) BIOTECHNOLOGY AND APPLIED BIOCHEMISTRY Yaman, S., Calik, P. 2017; 64 (6): 944-954

    Abstract

    The aim of this work was to develop an effective fed-batch feeding strategy to enhance recombinant glucose isomerase (r-GI) production by recombinant Escherichia coli BL21 (DE3) pLysS on an industrially relevant feedstock without the application of an exogenous inducer. Following the batch operation (0 < t < 7 H), the effects of pulse and/or continuous feeding of hydrolyzed beet molasses were investigated under five different feeding strategies. The two most promising strategies with respect to r-GI activity were (i) PM-0.05, designed with one pulse feed (t = 7 H) followed by a continuous feed and (ii) 2PMF -0.05, designed with two consecutive pulse feeds (t = 7 and 10 H) followed by a continuous feed. The continuous feeding of molasses for both fermentation strategies employed the same precalculated feeding rate, μo = 0.05 H-1 . The maximum r-GI activities exhibited by PM-0.05 and 2PMF -0.05 were 29,050 and 30,642 U dm-3 , respectively. On the one hand, compared to PM-0.05 r-GI activity reached its maximum within a shorter cultivation time (∆tmax = 2 H) at 2PMF -0.05, which could be preferable in terms of manufacturing costs and possible risks; on the other hand, PM-0.05 is a simpler fermentation regime compared to 2PMF -0.05 with respect to manipulations that should be considered in large-scale production.

    View details for DOI 10.1002/bab.1549

    View details for Web of Science ID 000418111300020

    View details for PubMedID 27958654

  • Synthesis of adsorbents with dendronic structures for protein hydrophobic interaction chromatography JOURNAL OF CHROMATOGRAPHY A Mata-Gomez, M. A., Yaman, S., Valencia-Gallegos, J. A., Tari, C., Rito-Palomares, M., Gonzalez-Valdez, J. 2016; 1443: 191-200

    Abstract

    Here, we introduced a new technology based on the incorporation of dendrons-branched chemical structures-onto supports for synthesis of HIC adsorbents. In doing so we studied the synthesis and performance of these novel HIC dendron-based adsorbents. The adsorbents were synthesized in a facile two-step reaction. First, Sepharose 4FF (R) was chemically modified with polyester dendrons of different branching degrees i.e. third (G3) or fifth (G5) generations. Then, butyl-end valeric acid ligands were coupled to dendrons via ester bond formation. UV-vis spectrophotometry and FTIR analyses of the modified resins confirmed the presence of the dendrons and their ligands on them. Inclusion of dendrons allowed the increment of ligand density, 82.5 ± 11 and 175.6 ± 5.7 μmol ligand/mL resin for RG3 and RG5, respectively. Static adsorption capacity of modified resins was found to be ∼ 60 mg BSA/mL resin. Interestingly, dynamic binding capacity was higher at high flow rates, 62.5 ± 0.8 and 58.0 ± 0.5mg/mL for RG3 and RG5, respectively. RG3 was able to separate lipase, β-lactoglobulin and α-chymotrypsin selectively as well as fractionating of a whole proteome from yeast. This innovative technology will improve the existing HIC resin synthesis methods. It will also allow the reduction of the amount of adsorbent used in a chromatographic procedure and thus permit the use of smaller columns resulting in faster processes. Furthermore, this method could potentially be considered as a green technology since both, dendrons and ligands, are formed by ester bonds that are more biodegradable allowing the disposal of used resin waste in a more ecofriendly manner when compared to other exiting resins.

    View details for DOI 10.1016/j.chroma.2016.03.057

    View details for Web of Science ID 000374362600023

    View details for PubMedID 27018188