Biology subjects

Demirel, M. C.

Publications and source records attributed to Demirel, M. C..

4 recordsLinked to original sources

bioRxiv2026

A Low-Cost, High-Throughput Design-Build-Test Pipeline for Engineering Genetic Systems: Stress Testing with Complex Structural Proteins

Genetic systems engineering is constrained by high DNA synthesis costs, assembly inefficiencies, and challenges in expressing complex proteins. To address these limitations, we developed a highly parallel, low-cost pipeline for the design, assembly, and functional screening of genetic systems, which we stress-tested on highly repetitive structural proteins, including spider silk, biocements, reflectins, and talins. The integrated pipeline combines computational genetic systems design, low-cost many-plasmid DNA assembly from oligopools, automated many-to-many mapping using nanopore sequencing data, and a label-free biosensor to measure single-cell protein expression levels. We applied this pipeline to build 240 plasmids, achieving an 88% success rate (up to 2000 bp) using standard clonal isolation and 58% assembly efficiency (up to 5600 bp) without selective DNA purification, while lowering material costs by up to 24-fold. We applied the biosensor to identify genetic factors that create distinct cellular subpopulations with varying protein expression levels. Overall, the integrated pipeline will dramatically lower the cost of high-throughput synthetic biology, while demonstrating how designing genetic systems to improve build efficiency ("design for build") and directly incorporating biosensors into genetic systems ("design for test") will greatly accelerate design-build-test workflows.

synthetic biology↗

bioRxiv2021

Hydration-induced structural transitions in biomimetic tandem repeat proteins

A major challenge in developing biomimetic, high-performance, and sustainable products is the accurate replication of the biological materials striking properties, such as high strength, self-repair, and stimuli-responsiveness. The rationalization of such features on the microscopic scale, together with the rational design of synthetic materials, is currently hindered by our limited understanding of the sequence-structure-property relationship. Here, employing state-of-the-art nuclear magnetic resonance (NMR) spectroscopy, we link the atomistic structural and dynamic properties of an artificial bioinspired tandem repeat protein TR(1,11) to its stunning macroscopic properties including high elasticity, self-healing capabilities, and recordholding proton conductivity amongst biological materials. We show that the hydration-induced structural rearrangement of the amorphous Gly-rich soft segment and the ordered Ala-rich hard segment is the key to the materials outstanding physical properties. We found that in the hydrated state both the Ala-rich ordered and Gly-rich disordered parts contribute to the formation of the nanoconfined {beta}-sheets, thereby enhancing the strength and toughness of the material. This restructuring is accompanied by fast proline ring puckering and backbone cis-trans isomerization at the water-protein interface, which in turn enhances the elasticity and the thermal conductivity of the hydrated films. Our in-depth characterization provides a solid ground for the development of next-generation materials with improved properties.

biophysics↗

bioRxiv2020

Dielectrophoretic separation of randomly shaped protein particles

Recently, insoluble protein particles have been increasingly investigated for artificial drug delivery systems due to their favorable properties, including programmability for active drug targeting of diseases as well as their biocompatibility and biodegradability after administration. One of the biggest challenges is selectively collecting monodisperse particles in desirable morphologies and sizes to enable consistent levels and rates of drug loading and release. Therefore, technology that allows sorting of protein particles with respect to size and morphology will enhance the design and production of next-generation drug delivery materials. Here, we introduce a dielectrophoretic (DEP) separation technique to selectively isolate spherical protein particles from a mixture of randomly shaped particles. We tested this approach by applying it to a mixture of precipitated squid ring teeth inspired tandem repeat protein particles with diverse sizes and morphologies. The DEP trapping system enabled us to isolate specific-sized, spherical protein particles out of this mixture: after separation, the fraction of 2 m and 4 m spherical particles was increased from 28.64% of mixture to 80.53% and 74.02% with polydispersity indexes (PDIs) decreased from 0.93 of mixture to 0.19 and 0.09, respectively. The protein particles show high aqueous swelling capability (up to 74% by mass) that could enable delivery of drug solutions. This work is intended to inspire the future development of biocompatible drug-delivery systems.

bioengineering↗

bioRxiv2017

Squid Ring Teeth Coated Mesh Improves Abdominal Wall Repair

BackgroundHernia repair is a common surgical procedure with mesh often used. Current mesh materials have a high incidence of repair failures, due to poor tissue integration, and complications such as seroma and pain. Polypropylene (PP) mesh is the standard material in hernia repair secondary to its material durability; however, failures still approach 15%. In this first time animal study, we hypothesized that squid ring teeth (SRT), a biologically-derived high strength protein, coated polypropylene (SRT-PP) mesh, would offer enhanced tissue integration and strength compared to standard PP mesh, while proving biocompatibility for in vivo use.\n\nMaterials and methodsPolypropylene mesh was coated with SRT. Mechanical properties and cell proliferation studies of the composite mesh were performed in vitro. Rats underwent inlay mesh implantation in an anterior abdominal wall defect model. Repair was assessed clinically and radiographically, with integration evaluated by histology and mechanical testing.\n\nResultsCell proliferation was enhanced on SRT-PP composite mesh. This was corroborated by abdominal wall histology, dramatically diminished cranio-caudal mesh contraction, improved strength testing, and higher tissue failure strain following in vivo implantation. There was no increase in complications with SRT, with regard to seroma or visceral adhesion. No foreign body reactions were noted on liver histology.\n\nConclusionSRT-PP mesh showed better tissue integration than PP mesh. SRT is a high strength protein that is applied as a coating to augment mesh-tissue integration leading to improvements in abdominal wall stability with potential to reduce re-intervention for failures.

bioengineering↗