Bio

Professional Education


  • Bachelor of Science, Middle East Technical University (2007)
  • Master of Engineering, Boston University (2009)
  • Doctor of Philosophy, Brown University (2013)

Stanford Advisors


Publications

All Publications


  • Magnetic levitation of single cells PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Durmus, N. G., Tekin, C., Guven, S., Sridhar, K., Yildiz, A. A., Calibasi, G., Ghiran, I., Davis, R. W., Steinmetz, L. M., Demirci, U. 2015; 112 (28): E3661-E3668

    Abstract

    Several cellular events cause permanent or transient changes in inherent magnetic and density properties of cells. Characterizing these changes in cell populations is crucial to understand cellular heterogeneity in cancer, immune response, infectious diseases, drug resistance, and evolution. Although magnetic levitation has previously been used for macroscale objects, its use in life sciences has been hindered by the inability to levitate microscale objects and by the toxicity of metal salts previously applied for levitation. Here, we use magnetic levitation principles for biological characterization and monitoring of cells and cellular events. We demonstrate that each cell type (i.e., cancer, blood, bacteria, and yeast) has a characteristic levitation profile, which we distinguish at an unprecedented resolution of 1 × 10(-4) g⋅mL(-1). We have identified unique differences in levitation and density blueprints between breast, esophageal, colorectal, and nonsmall cell lung cancer cell lines, as well as heterogeneity within these seemingly homogenous cell populations. Furthermore, we demonstrate that changes in cellular density and levitation profiles can be monitored in real time at single-cell resolution, allowing quantification of heterogeneous temporal responses of each cell to environmental stressors. These data establish density as a powerful biomarker for investigating living systems and their responses. Thereby, our method enables rapid, density-based imaging and profiling of single cells with intriguing applications, such as label-free identification and monitoring of heterogeneous biological changes under various physiological conditions, including antibiotic or cancer treatment in personalized medicine.

    View details for DOI 10.1073/pnas.1509250112

    View details for Web of Science ID 000357878700008

    View details for PubMedID 26124131

  • Portable Microfluidic Integrated Plasmonic Platform for Pathogen Detection SCIENTIFIC REPORTS Tokel, O., Yildiz, U. H., Inci, F., Durmus, N. G., Ekiz, O. O., Turker, B., Cetin, C., Rao, S., Sridhar, K., Natarajan, N., Shafiee, H., Dana, A., Demirci, U. 2015; 5

    Abstract

    Timely detection of infectious agents is critical in early diagnosis and treatment of infectious diseases. Conventional pathogen detection methods, such as enzyme linked immunosorbent assay (ELISA), culturing or polymerase chain reaction (PCR) require long assay times, and complex and expensive instruments, which are not adaptable to point-of-care (POC) needs at resource-constrained as well as primary care settings. Therefore, there is an unmet need to develop simple, rapid, and accurate methods for detection of pathogens at the POC. Here, we present a portable, multiplex, inexpensive microfluidic-integrated surface plasmon resonance (SPR) platform that detects and quantifies bacteria, i.e., Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus) rapidly. The platform presented reliable capture and detection of E. coli at concentrations ranging from ~10(5) to 3.2 × 10(7) CFUs/mL in phosphate buffered saline (PBS) and peritoneal dialysis (PD) fluid. The multiplexing and specificity capability of the platform was also tested with S. aureus samples. The presented platform technology could potentially be applicable to capture and detect other pathogens at the POC and primary care settings.

    View details for DOI 10.1038/srep09152

    View details for Web of Science ID 000351699600001

    View details for PubMedID 25801042

  • Paper and flexible substrates as materials for biosensing platforms to detect multiple biotargets. Scientific reports Shafiee, H., Asghar, W., Inci, F., Yuksekkaya, M., Jahangir, M., Zhang, M. H., Durmus, N. G., Gurkan, U. A., Kuritzkes, D. R., Demirci, U. 2015; 5: 8719-?

    Abstract

    The need for sensitive, robust, portable, and inexpensive biosensing platforms is of significant interest in clinical applications for disease diagnosis and treatment monitoring at the point-of-care (POC) settings. Rapid, accurate POC diagnostic assays play a crucial role in developing countries, where there are limited laboratory infrastructure, trained personnel, and financial support. However, current diagnostic assays commonly require long assay time, sophisticated infrastructure and expensive reagents that are not compatible with resource-constrained settings. Although paper and flexible material-based platform technologies provide alternative approaches to develop POC diagnostic assays for broad applications in medicine, they have technical challenges integrating to different detection modalities. Here, we address the limited capability of current paper and flexible material-based platforms by integrating cellulose paper and flexible polyester films as diagnostic biosensing materials with various detection modalities through the development and validation of new widely applicable electrical and optical sensing mechanisms using antibodies and peptides. By incorporating these different detection modalities, we present selective and accurate capture and detection of multiple biotargets including viruses (Human Immunodeficieny Virus-1), bacteria (Escherichia coli and Staphylococcus aureus), and cells (CD4(+) T lymphocytes) from fingerprick volume equivalent of multiple biological specimens such as whole blood, plasma, and peritoneal dialysis effluent with clinically relevant detection and sensitivity.

    View details for DOI 10.1038/srep08719

    View details for PubMedID 25743880

  • Enhanced Efficacy of Superparamagnetic Iron Oxide Nanoparticles Against Antibiotic-Resistant Biofilms in the Presence of Metabolites ADVANCED MATERIALS Durmus, N. G., Taylor, E. N., Kummer, K. M., Webster, T. J. 2013; 25 (40): 5706-?

    Abstract

    Antibiotic resistance and the lack of new antibacterial agents cause major challenges for the treatment of infections. Here, we describe a simple, broad-spectrum, and low-cost dual-sided approach which uses superparamagnetic iron oxide particles (SPION) in combination with fructose metabolites as an alternative to existing antibacterial strategies. This strategy offers further improved efficacy of SPION against persistent gram-positive and gram-negative bacteria infections by manipulating the biofilm metabolic microenvironment and outperforms vancomycin (the antibiotic of last resort), creating a new nanotechnology-driven approach.

    View details for DOI 10.1002/adma.201302627

    View details for Web of Science ID 000330773400002

    View details for PubMedID 23963848

  • Effects of different sterilization techniques and varying anodized TiO2 nanotube dimensions on bacteria growth JOURNAL OF BIOMEDICAL MATERIALS RESEARCH PART B-APPLIED BIOMATERIALS Kummer, K. M., Taylor, E. N., Durmas, N. G., Tarquinio, K. M., Ercan, B., Webster, T. J. 2013; 101B (5): 677-688
  • BIOPRINTING Functional droplet networks NATURE MATERIALS Durmus, N. G., Tasoglu, S., Demirci, U. 2013; 12 (6): 478-479

    View details for DOI 10.1038/nmat3665

    View details for Web of Science ID 000319402200013

    View details for PubMedID 23695742

  • Eradicating Antibiotic-Resistant Biofilms with Silver-Conjugated Superparamagnetic Iron Oxide Nanoparticles ADVANCED HEALTHCARE MATERIALS Durmus, N. G., Webster, T. J. 2013; 2 (1): 165-171

    Abstract

    Concerns about antibiotic-resistant microorganisms, such as methicillin-resistant Staphylococcus aureus (MRSA), is causing a resurgence in the search for novel strategies which can eradicate infections without the use of antibiotics. In this study, the unique magnetic and antibacterial properties of superparamagnetic iron oxide nanoparticles (SPION) and silver have been combined through the design of silver-conjugated SPION. For the first time, it is demonstrated that MRSA biofilms can be eradicated by silver-conjugated SPION without resorting to the use of antibiotics. A significant decrease in biofilm mass, which corresponds to a seven orders of magnitude decrease in viability, is observed when MRSA biofilms are treated with 1 mg/mL of silver-conjugated SPION (p < 0.01). Moreover, SPION anti-biofilm efficacy is further improved in the presence of an external magnetic field. The anti-biofilm property of silver-conjugated SPION treatment is due to the significant increases in intracellular or membrane-bound iron (p < 0.001), sulfur (p < 0.05), and silver (p < 0.001) concentrations, thus increases in SPION uptake within the biofilms. For this reason, this study demonstrates for the first time that silver-conjugated SPION could be used as a targeted antibacterial therapy to the infection site. Thus, this novel infection eradication strategy holds great promise to be an alternative to the antibiotic of last resort, vancomycin, which bacteria have already started to develop a resistance towards.

    View details for DOI 10.1002/adhm.201200215

    View details for Web of Science ID 000315121900015

    View details for PubMedID 23184367

  • Short communication: carboxylate functionalized superparamagnetic iron oxide nanoparticles (SPION) for the reduction of S. aureus growth post biofilm formation INTERNATIONAL JOURNAL OF NANOMEDICINE Leuba, K. D., Durmus, N. G., Taylor, E. N., Webster, T. J. 2013; 8: 731-736

    Abstract

    Biofilms formed by antibiotic resistant Staphylococcus aureus (S. aureus) continue to be a problem for medical devices. Antibiotic resistant bacteria (such as S. aureus) often complicate the treatment and healing of the patient, yet, medical devices are needed to heal such patients. Therefore, methods to treat these Biofilms once formed on medical devices are badly needed. Due to their small size and magnetic properties, superparamagnetic iron oxide nanoparticles (SPION) may be one possible material to penetrate Biofilms and kill or slow the growth of bacteria. In this study, SPION were functionalized with amine, carboxylate, and isocyanate functional groups to further improve their efficacy to disrupt the growth of S. aureus Biofilms. Without the use of antibiotics, results showed that SPION functionalized with carboxylate groups (followed by isocyanate then amine functional groups then unfunctionalized SPION) significantly disrupted Biofilms and retarded the growth of S. aureus compared to untreated Biofilms (by over 35% after 24 hours).

    View details for DOI 10.2147/IJN.S38256

    View details for Web of Science ID 000317922700066

    View details for PubMedID 23450111

  • Superparamagnetic Iron Oxide Nanoparticles (SPION) for the Treatment of Antibiotic-Resistant Biofilms SMALL Taylor, E. N., Kummer, K. M., Durmus, N. G., Leuba, K., Tarquinio, K. M., Webster, T. J. 2012; 8 (19): 3016-3027

    Abstract

    Bacterial infections caused by antibiotic-resistant strains are of deep concern due to an increasing prevalence, and are a major cause of morbidity in the United States of America. In particular, medical device failures, and thus human lives, are greatly impacted by infections, where the treatments required are further complicated by the tendency of pathogenic bacteria, such as Staphylococcus aureus, to produce antibiotic resistant biofilms. In this study, a panel of relevant antibiotics used clinically including penicillin, oxacillin, gentamicin, streptomycin, and vancomycin are tested, and although antibiotics are effective against free-floating planktonic S. aureus, either no change in biofilm function is observed, or, more frequently, biofilm function is enhanced. As an alternative, superparamagnetic iron oxide nanoparticles (SPION) are synthesized through a two-step process with dimercaptosuccinic acid as a chelator, followed by the conjugation of metals including iron, zinc, and silver; thus, the antibacterial properties of the metals are coupled to the superparamagnetic properties of SPION. SPION might be the ideal antibacterial treatment, with a superior ability to decrease multiple bacterial functions, target infections in a magnetic field, and had activity better than antibiotics or metal salts alone, as is required for the treatment of medical device infections for which no treatment exists today.

    View details for DOI 10.1002/smll.201200575

    View details for Web of Science ID 000309454800014

    View details for PubMedID 22777831

  • Nanostructured titanium: the ideal material for improving orthopedic implant efficacy? NANOMEDICINE Durmus, N. G., Webster, T. J. 2012; 7 (6): 791-793

    View details for DOI 10.2217/NNM.12.53

    View details for Web of Science ID 000305713400001

    View details for PubMedID 22734635

  • Fructose-enhanced reduction of bacterial growth on nanorough surfaces INTERNATIONAL JOURNAL OF NANOMEDICINE Durmus, N. G., Taylor, E. N., Inci, F., Kummer, K. M., Tarquinio, K. M., Webster, T. J. 2012; 7: 537-545

    Abstract

    Patients on mechanical ventilators for extended periods of time often face the risk of developing ventilator-associated pneumonia. During the ventilation process, patients incapable of breathing are intubated with polyvinyl chloride (PVC) endotracheal tubes (ETTs). PVC ETTs provide surfaces where bacteria can attach and proliferate from the contaminated oropharyngeal space to the sterile bronchoalveolar area. To overcome this problem, ETTs can be coated with antimicrobial agents. However, such coatings may easily delaminate during use. Recently, it has been shown that changes in material topography at the nanometer level can provide antibacterial properties. In addition, some metabolites, such as fructose, have been found to increase the efficiency of antibiotics used to treat Staphylococcus aureus (S. aureus) infections. In this study, we combined the antibacterial effect of nanorough ETT topographies with sugar metabolites to decrease bacterial growth and biofilm formation on ETTs. We present for the first time that the presence of fructose on the nanorough surfaces decreases the number of planktonic S. aureus bacteria in the solution and biofilm formation on the surface after 24 hours. We thus envision that this method has the potential to impact the future of surface engineering of biomaterials leading to more successful clinical outcomes in terms of longer ETT lifetimes, minimized infections, and decreased antibiotic usage; all of which can decrease the presence of antibiotic resistant bacteria in the clinical setting.

    View details for DOI 10.2147/IJN.S27957

    View details for Web of Science ID 000302710600001

    View details for PubMedID 22334783

  • Microengineering methods for cell-based microarrays and high-throughput drug-screening applications BIOFABRICATION Xu, F., Wu, J., Wang, S., Durmus, N. G., Gurkan, U. A., Demirci, U. 2011; 3 (3)

    Abstract

    Screening for effective therapeutic agents from millions of drug candidates is costly, time consuming, and often faces concerns due to the extensive use of animals. To improve cost effectiveness, and to minimize animal testing in pharmaceutical research, in vitro monolayer cell microarrays with multiwell plate assays have been developed. Integration of cell microarrays with microfluidic systems has facilitated automated and controlled component loading, significantly reducing the consumption of the candidate compounds and the target cells. Even though these methods significantly increased the throughput compared to conventional in vitro testing systems and in vivo animal models, the cost associated with these platforms remains prohibitively high. Besides, there is a need for three-dimensional (3D) cell-based drug-screening models which can mimic the in vivo microenvironment and the functionality of the native tissues. Here, we present the state-of-the-art microengineering approaches that can be used to develop 3D cell-based drug-screening assays. We highlight the 3D in vitro cell culture systems with live cell-based arrays, microfluidic cell culture systems, and their application to high-throughput drug screening. We conclude that among the emerging microengineering approaches, bioprinting holds great potential to provide repeatable 3D cell-based constructs with high temporal, spatial control and versatility.

    View details for DOI 10.1088/1758-5082/3/3/034101

    View details for Web of Science ID 000294955200003

    View details for PubMedID 21725152

  • Living Bacterial Sacrificial Porogens to Engineer Decellularized Porous Scaffolds PLOS ONE Xu, F., Sridharan, B., Durmus, N. G., Wang, S., Yavuz, A. S., Gurkan, U. A., Demirci, U. 2011; 6 (4)

    Abstract

    Decellularization and cellularization of organs have emerged as disruptive methods in tissue engineering and regenerative medicine. Porous hydrogel scaffolds have widespread applications in tissue engineering, regenerative medicine and drug discovery as viable tissue mimics. However, the existing hydrogel fabrication techniques suffer from limited control over pore interconnectivity, density and size, which leads to inefficient nutrient and oxygen transport to cells embedded in the scaffolds. Here, we demonstrated an innovative approach to develop a new platform for tissue engineered constructs using live bacteria as sacrificial porogens. E.coli were patterned and cultured in an interconnected three-dimensional (3D) hydrogel network. The growing bacteria created interconnected micropores and microchannels. Then, the scafold was decellularized, and bacteria were eliminated from the scaffold through lysing and washing steps. This 3D porous network method combined with bioprinting has the potential to be broadly applicable and compatible with tissue specific applications allowing seeding of stem cells and other cell types.

    View details for DOI 10.1371/journal.pone.0019344

    View details for Web of Science ID 000290020700050

    View details for PubMedID 21552485

  • Microporous Cell-Laden Hydrogels for Engineered Tissue Constructs BIOTECHNOLOGY AND BIOENGINEERING Park, J. H., Chung, B. G., Lee, W. G., Kim, J., Brigham, M. D., Shim, J., Lee, S., Hwang, C. M., Durmus, N. G., Demirci, U., Khademhosseini, A. 2010; 106 (1): 138-148

    Abstract

    In this article, we describe an approach to generate microporous cell-laden hydrogels for fabricating biomimetic tissue engineered constructs. Micropores at different length scales were fabricated in cell-laden hydrogels by micromolding fluidic channels and leaching sucrose crystals. Microengineered channels were created within cell-laden hydrogel precursors containing agarose solution mixed with sucrose crystals. The rapid cooling of the agarose solution was used to gel the solution and form micropores in place of the sucrose crystals. The sucrose leaching process generated homogeneously distributed micropores within the gels, while enabling the direct immobilization of cells within the gels. We also characterized the physical, mechanical, and biological properties (i.e., microporosity, diffusivity, and cell viability) of cell-laden agarose gels as a function of engineered porosity. The microporosity was controlled from 0% to 40% and the diffusivity of molecules in the porous agarose gels increased as compared to controls. Furthermore, the viability of human hepatic carcinoma cells that were cultured in microporous agarose gels corresponded to the diffusion profile generated away from the microchannels. Based on their enhanced diffusive properties, microporous cell-laden hydrogels containing a microengineered fluidic channel can be a useful tool for generating tissue structures for regenerative medicine and drug discovery applications.

    View details for DOI 10.1002/bit.22667

    View details for Web of Science ID 000276844500014

    View details for PubMedID 20091766

  • Engineered 3D tissue models for cell-laden microfluidic channels ANALYTICAL AND BIOANALYTICAL CHEMISTRY Song, Y. S., Lin, R. L., Montesano, G., Durmus, N. G., Lee, G., Yoo, S., Kayaalp, E., Haeggstrom, E., Khademhosseini, A., Demirci, U. 2009; 395 (1): 185-193

    Abstract

    Delivery of nutrients and oxygen within three-dimensional (3D) tissue constructs is important to maintain cell viability. We built 3D cell-laden hydrogels to validate a new tissue perfusion model that takes into account nutrition consumption. The model system was analyzed by simulating theoretical nutrient diffusion into cell-laden hydrogels. We carried out a parametric study considering different microchannel sizes and inter-channel separation in the hydrogel. We hypothesized that nutrient consumption needs to be taken into account when optimizing the perfusion channel size and separation. We validated the hypothesis by experiments. We fabricated circular microchannels (r = 400 microm) in 3D cell-laden hydrogel constructs (R = 7.5 mm, volume = 5 ml). These channels were positioned either individually or in parallel within hydrogels to increase nutrient and oxygen transport as a way to improve cell viability. We quantified the spatial distribution of viable cells within 3D hydrogel scaffolds without channels and with single- and dual-perfusion microfluidic channels. We investigated quantitatively the cell viability as a function of radial distance from the channels using experimental data and mathematical modeling of diffusion profiles. Our simulations show that a large-channel radius as well as a large channel to channel distance diffuse nutrients farther through a 3D hydrogel. This is important since our results reveal that there is a close correlation between nutrient profiles and cell viability across the hydrogel.

    View details for DOI 10.1007/s00216-009-2935-1

    View details for Web of Science ID 000268866800021

    View details for PubMedID 19629459

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