Biology subjects

Durmus, N. G.

Publications and source records attributed to Durmus, N. G..

4 recordsLinked to original sources

bioRxiv2025

3D-Printed Magnetic Levitation Device with Deep Learning-Assisted Particle Tracking and Analysis for High-Throughput Sorting

Intrinsic density-based particle separation is fundamental to biomedical research and materials science. Magnetic levitation offers an accessible and label-free approach; however, current platforms are limited by throughput, complex fabrication requirements, and manual analysis methods. Here, we demonstrate a high-throughput magnetic levitation-based microfluidic device fabricated using commercial 3D printing, integrated with dual automated analysis systems. The device features optimized magnet configurations and wide channel design (1 mm x 1 mm) that enables gentle separation (<1 PSI) at throughputs of 66 mL/hr-- a ten-fold improvement over existing levitation platforms. We developed two complementary analysis tools: "Phase" for static levitation height measurements, and a deep learning pipeline combining CNN-based particle classification (>95% accuracy) with SORT (Simple Online and Realtime Tracking) algorithm for dynamic analysis. The automated system showed excellent correlation with manual counting (Pearson coefficients: 0.91-0.99, p<0.001). Through systematic optimization of magnet spacing and paramagnetic medium concentration (150 mM Gd), the platform achieved robust continuous-flow sorting while maintaining exceptional purity (>90%) and resolving density differences as small as 0.03 g/mL. This work establishes a versatile platform for particle sorting, enabling sophisticated analysis without specialized facilities or extensive operator training, with broad applications in biomedical research and diagnostics.

bioengineering↗

bioRxiv2022

Magnetic Levitation and Sorting of Neoplastic Circulating Cell Hybrids

Circulating hybrid cells (CHCs) are a novel, rare cell population that harbor tumor and immune cell phenotypes and genotypes and are detectible in peripheral blood. Several recent reports implicated CHCs in the metastatic cascade and found their enumeration to provide better prognostic value than conventionally-defined circulating tumor cells (CTCs). However, methods for isolation and enrichment of CHCs are not well-studied or established. Here, we developed an ultrasensitive, antigen-independent platform leveraging the principles of magnetic levitation for the detection and isolation of disseminated neoplastic CHCs. For the first time, we demonstrate that CHCs can be magnetically focused to different levitation heights, under various paramagnetic conditions using a static levitation system, and we quantified the biophysical properties of CHCs (i.e., levitation heights). In addition, we investigated whether magnetic levitation approach can be combined with the affinity-based strategies to enrich CHCs under the magnetic field. Using clinical samples from breast and colorectal cancer patients, we demonstrated that neoplastic cells can be sorted with a magnetic levitation-based sorting device, without relying on any surface markers. Overall, we demonstrated the feasibility of the magnetic levitation method for unbiased enrichment of rare neoplastic-immune hybrid cells from peripheral blood specimens from cancer patients. This approach can be expanded to more clinical samples and cancer types to unprecedentedly explore the biology of rare neoplastic cells and develop metastasis-tailored therapies broadly impacting personalized and precision clinical treatments.

bioengineering↗

bioRxiv2020

Levitational Cell Cytometry for Forensics

Here, a method for label-free, real-time interrogation, monitoring, detection and sorting of biological rare cells in magnetically-suspended heterogeneous samples is developed. To achieve this, heterogeneous populations of cells were levitated and confined in a microcapillary channel. This strategy enables spatiotemporal differential magnetic levitation of rare fragile dead cells equilibrating at different heights based on the balance between magnetic and corrected gravitational forces. In addition, sorting of fragile rare dead cell populations is monitored in real-time. This technique provides a broadly applicable label-free tool for high resolution, real-time research, as well as forensic evidence processing of rape kits. This method is validated with forensic mock samples dating back to 2003, isolating sperm from epithelial fraction with >90% efficiency and >97% purity. Overall, this method reduces the processing time by over 20-fold down to 20 minutes, eliminating centrifugation and labels, and providing an inexpensive and a high-yield alternative to the current centrifuge-based differential extraction techniques. It can potentially facilitate the forensic downstream genomic analyses, accelerating the identification of suspects, and advancing public safety.

bioengineering↗

bioRxiv2020

CelLEVITAS: Label-free, rapid sorting and enrichment of live cells via magnetic levitation

Sorting methods that remove non-viable cells and debris, while retaining a high yield of viable cells, are crucial for many applications in biotechnology, genomics, tissue engineering and medicine. However, a significant challenge is gentle sorting of these different cell states based on very minute differences in density and magnetic signatures, without relying on any labels, tags or markers. Here, a new magnetic levitation-based technology, CelLEVITAS, is developed for the label-free sorting and enrichment of live cells. This work reports the first use of magnetic levitation for sorting of viable and non-viable cells within a microfluidic device and demonstrates extremely effective removal of dead cells and debris from heterogeneous samples. First, the levitation conditions for separating viable and non-viable cells under a magnetic field were fine-tuned. Levitation trajectories of live and dead cell states were then monitored in real-time, as cells magnetically focused to their corresponding levitation bands. CelLEVITAS successfully sorted and enriched live cells from a variety of input cell concentrations (100-200,000 cells/mL) and a variety of input purities (10-50%) into consistently high output purities (>80%). This method is sensitive, does not impair cell viability during sorting, and significantly increases the input sample viability up to 7-fold. Overall, this new magnetic levitation-based sorting strategy drastically reduces the processing time to a single-step, 30-minute sorting protocol and eliminates the manual pre-processing and labeling steps that are required for traditional flow cytometry techniques.

bioengineering↗