Bioengineering / Biyomühendislik
Permanent URI for this collectionhttps://hdl.handle.net/11147/4529
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Article Citation - WoS: 27Citation - Scopus: 28Biocomposite Scaffolds for 3d Cell Culture: Propolis Enriched Polyvinyl Alcohol Nanofibers Favoring Cell Adhesion(John Wiley and Sons Inc., 2021) Bilginer, Rumeysa; Özkendir İnanç, Dilce; Yıldız, Ümit Hakan; Arslan Yıldız, AhuThe objective of this work is generation of propolis/polyvinyl alcohol (PVA) scaffold by electrospinning for 3D cell culture. Here, PVA used as co-spinning agent since propolis alone cannot be easily processed by electrospinning methodology. Propolis takes charge in maximizing biological aspect of scaffold to facilitate cell attachment and proliferation. Morphological analysis showed size of the electrospun nanofibers varied between 172-523 nm and 345-687 nm in diameter, for non-crosslinked and crosslinked scaffolds, respectively. Incorporation of propolis resulted in desired surface properties of hybrid matrix, where hybrid scaffolds highly favored protein adsorption. To examine cell compatibility, NIH-3T3 and HeLa cells were seeded on propolis/PVA hybrid scaffold. Results confirmed that integration of propolis supported cell adhesion and cell proliferation. Also, results indicated electrospun propolis/PVA hybrid scaffold provide suitable microenvironment for cell culturing. Therefore, developed hybrid scaffold could be considered as potential candidate for 3D cell culture and tissue engineering.Article Citation - WoS: 5Citation - Scopus: 6Boosting Up Printability of Biomacromolecule Based Bio-Ink by Modulation of Hydrogen Bonding Pairs(Elsevier Ltd., 2020) Köksal, Büşra; Önbaş, Rabia; Başkurt, Mehmet; Şahin, Hasan; Arslan Yıldız, Ahu; Yıldız, Ümit HakanThis study describes low dose UV curable and bioprintable new bioink made of hydrogen bond donor-acceptor adaptor molecule 2-isocyanatoethyl methacrylate (NCO)modified gelatin (NCO-Gel). Our theoretical calculations demonstrate that insertion of 2-isocyanatoethyl methacrylate doubles the interaction energy (500 meV) between gelatin chains providing significant contribution in interchain condensation and self-organization as compared to methacrylic anhydride modified gelatin (GelMA). The NCO-Gel exhibits peak around 1720 cm?1 referring to bidentate hydrogen bonding between H-NCO and its counterpart O[dbnd]CN[sbnd]H. These strong interchain interactions drive chains to be packed and thereby facilitating UV crosslinking. The NCO-Gel is exhibiting a rapid, 10 s gelation process by the exposure of laser (3 W, 365 nm). The dynamic light scattering characterization also reveals that NCO-Gel has faster sol to gel transition as compared to GelMA depending on the UV curing time. The NCO-Gel was found to be more firm and mechanically strong that provides advantages in molding as well as bioprinting processes. Bioprinted NCO-Gel has shown sharp borders and stable 3D geometry as compared to GelMA ink under 10 s UV curing time. The cell viability tests confirm that NCO-Gel facilitates cell proliferation and supports cell viability. We foresee that NCO-Gel bioink formulation provides a promising opportunity when low dose UV curing and rapid printing are required. © 2020 Elsevier LtdArticle Citation - WoS: 2Citation - Scopus: 2Transition-Metal Direct C-H Arylation of Thiophene in Aqueous Media Via Potassium Peroxymonosulfate(John Wiley and Sons Inc., 2019) Özenler, Sezer; Kaya, Hakan; Elmacı, Nuran; Yıldız, Ümit HakanThis study covers the use of potassium peroxymonosulfate (PPS) which, is a mild and inexpensive catalyst, for direct coupling of C-H/C-H for water soluble thiophene. The 3-(4-methyl-3 '- thienyloxy)propyltriethylammonium bromide (M1) has been selected as model monomer that reacted PPS in 2.0, 0.20 and 0.020 monomer to PPS ratio. The reaction has been monitored via NMR spectroscopy revealing the monomer consumption and formation of dimers to tetramers as well as completion of reaction within 15 minutes. Resultant product is easily collected without tedious work up steps. The computational calculation has optimized the regularity of the coupling as head to tail, tail to tail, head to tail (HT-TT-HT) for tetramer. The regularity of tetramer which is further satisfied via NMR analysis showing emergence of new peaks at 3.56 and 4.48. The shifts in the UV maximum of reactive species have been monitored by absorbance spectroscopy showing time dependent red shift corresponds to growing from monomer to tetramers. The reaction has self-stopped due to low solubility of moderate condensates (higher than trimer), however further experiments have performed in water-organic mixtures showed great promises to obtain higher condensates.Article Citation - WoS: 13Citation - Scopus: 13Single Chain Cationic Polymer Dot as a Fluorescent Probe for Cell Imaging and Selective Determination of Hepatocellular Carcinoma Cells(American Chemical Society, 2019) Özenler, Sezer; Yücel, Müge; Tüncel, Özge; Kaya, Hakan; Özçelik, Serdar; Yıldız, Ümit HakanThis letter describes formation of single chain cationic polymer dots (Pdots) made of poly[1,4-dimethy1-1-(34(2,4,5-trimethylthiophen-3-yl)oxy)propyl)piperazin-1-ium bromide] conjugated polyelectrolyte (CPE). The single chain Pdot formation relies on a simple process which is a rapid nanophase separation between CPE solution of ethylene glycol and water. Pdots show narrow monodisperse size distribution with a 3.6 nm in diameter exhibiting high brightness and excellent colloidal and optical stability. It has been demonstrated that photoluminescent Pdots provide selective nuclear translocation to hepatocellular carcinoma cells as compared to healthy liver cells. The Pdot labeling effectively discriminates cancer cells in the coculture media. Pdots hold great promise as a luminescent probe to diagnose cancer cells in histology and may guide surgeons during operations to precisely separate out cancerous tissue due to augmented fluorescence brightness.Article Citation - WoS: 17Citation - Scopus: 19Pixelated Colorimetric Nucleic Acid Assay(Elsevier, 2020) Aydın, Hakan Berk; Cheema, Jamal Ahmed; Arnmanath, Gopal; Toklucu, Cihan; Yücel, Müge; Özenler, Sezer; Yıldız, Ümit HakanConjugated polyelectrolytes (CPEs) have been widely used as reporters in colorimetric assays targeting nucleic acids. CPEs provide naked eye detection possibility by their superior optical properties however, as concentration of target analytes decrease, trace amounts of nucleic acid typically yield colorimetric responses that are not readily perceivable by naked eye. Herein, we report a pixelated analysis approach for correlating colorimetric responses of CPE with nucleic acid concentrations down to 1 nM, in plasma samples, utilizing a smart phone with an algorithm that can perform analytical testing and data processing. The detection strategy employed relies on conformational transitions between single stranded nucleic acid-cationic CPE duplexes and double stranded nucleic acid-CPE triplexes that yield distinct colorimetric responses for enabling naked eye detection of nucleic acids. Cationic poly[N,N,N-triethyl-3-((4-methylthiophen-3-yl)oxy)propan-1-aminium bromide] is utilized as the CPE reporter deposited on a polyvinylidene fluoride (PVDF) membrane for nucleic acid assay. A smart phone application is developed to capture and digitize the colorimetric response of the individual pixels of the digital images of CPE on the PVDF membrane, followed by an analysis using the algorithm. The proposed pixelated approach enables precise quantification of nucleic acid assay concentrations, thereby eliminating the margin of error involved in conventional methodologies adopted for interpretation of colorimetric responses, for instance, RGB analysis. The obtained results illustrate that a ubiquitous smart phone could be utilized for point of care colorimetric nucleic acids assays in complex matrices without requiring sophisticated software or instrumentation.Article Citation - WoS: 18Citation - Scopus: 19Hand-Held Volatilome Analyzer Based on Elastically Deformable Nanofibers(American Chemical Society, 2018) Yücel, Müge; Akın, Osman; Çayören, Mehmet; Akduman, İbrahim; Palaniappan, Alagappan; Liedberg, Bo; Hızal, Gürkan; İnci, Fatih; Yıldız, Ümit HakanThis study reports on a hand-held volatilome analyzer for selective determination of clinically relevant biomarkers in exhaled breath. The sensing platform is based on electrospun polymer nanofiber-multiwalled carbon nanotube (MWCNT) sensing microchannels. Polymer nanofibers of poly(vinylidene fluoride) (PVDF), polystyrene (PS), and poly(methyl methacrylate) (PMMA) incorporated with MWCNT exhibits a stable response to interferences of humidity and CO2 and provides selective deformations upon exposure of exhaled breath target volatilomes acetone and toluene, exhibiting correlation to diabetes and lung cancer, respectively. The sensing microchannels "P1" (PVDF-MWCNT), "P2" (PS-MWCNT), and "P3" (PMMA-MWCNT) are integrated with a microfluidic cartridge (μ-card) that facilitates collection and concentration of exhaled breath. The volatilome analyzer consists of a conductivity monitoring unit, signal conditioning circuitries and a low energy display module. A combinatorial operation algorithm was developed for analyzing normalized resistivity changes of the sensing microchannels upon exposure to breath in the concentration ranges between 35 ppb and 3.0 ppm for acetone and 1 ppb and 10 ppm for toluene. Subsequently, responses of volatilomes from individuals in the different risk groups of diabetes were evaluated for validation of the proposed methodology. We foresee that proposed methodology provides an avenue for rapid detection of volatilomes thereby enabling point of care diagnosis in high-risk group individuals.Conference Object Citation - Scopus: 2Utilization of Near Ir Absorbing Gold Nanocolloids by Green Synthesis(Trans Tech Publications, 2018) Elveren, Beste; Yıldız, Ümit Hakan; Arslan Yıldız, AhuThe rapid developments in nanoscience, and its applications on biomedical areas have a large impact on drug delivery, tissue engineering, sensing, and diagnosis. Gold is widely investigated nanomaterial for the last couple of decades, since it has unique surface properties and very low toxicity to biological environment. In this work, we present a novel synthesis of gold nanoparticles (GNPs) exhibiting both visible and near-IR absorbance without agglomeration. The surface of GNPs were analyzed by routine methods and the binding kinetics were investigated by Surface Plasmon Resonance (SPR) Spectroscopy. The unique optical properties of near-IR asorbing GNP colloids hold promise for biological applications.Conference Object Kanser Öntanısı için Hücredışı Veziküller Kullanılarak Plazmonik Temelli Metodoloji Geliştirme(Institute of Electrical and Electronics Engineers Inc., 2017) Erdoğan, Duygu; Alduran, Yeşim; Yıldız, Ümit Hakan; Arslan Yıldız, AhuSon yıllarda, vücut sıvılarında bulunan hücredışı veziküller kanserde tanı biyobelirteci olarak kullanılmaktadır. Veziküllerin içeriği kanserin türünü ve seviyesini belirlemede rol oynayabilmektedir. Bu vezikülleri yakalama işleminde, genel olarak, Akış Sitometrisi (Flow cytometry), Western Blot, Enzime-bağlı İmmunosorbent Deneyi (ELISA) ve Yüzey Plazmon Rezonansı (SPR) metodolojileri kullanılmaktadır. Bu çalışmada vezikülleri yakalamaya yönelik plazmon temelli bir deney platformu üretilmesi önerilmiştir. Bu plazmonik platform, yüzeyde yapılacak modifikasyonlarla, yüksek hassasiyet oluşturabileceğimiz Lokalize Yüzey Plazmon Resonansı temellidir.Conference Object Üç Boyutlu Hücre Kültürü için Polimer Esaslı Ekstrasellüler Matriks Mimetiği(Institute of Electrical and Electronics Engineers Inc., 2017) Türker, Esra; Yıldız, Ümit Hakan; Arslan Yıldız, AhuElektro-eğirme metodu gelişmiş üretim teknolojilerindendir ve biyomedikal uygulamalarında yaygın olarak kullanılmaktadır. Özellikle doku mühendisliğinde amaç, çalışılacak doku üzerine doğal veya sentetik destek materyali (iskele) üreterek hücrenin uyum sağlayabileceği bir ortam oluşturmaktır. Bu projenin amacı üç boyutlu (3D) hücre kültürü çalışmaları için elektro-eğirme-metodu ile poli(L-laktik-co-epsilon-kaprolakton) (PLLCL) kullanılarak iskele üretilmesidir. Homojen lifler ve uygun gözenek boyutu elde etmek amacıyla optimizasyon çalışmaları yapılmıştır. Elde edilen liflerin çapı, akış hızı ve voltajın artmasıyla azalmaktadır. Taramalı uç elektron mikroskop incelemeleri (SEM) lif morfolojik yapılarının doku iskelesi fabrikasyonu için ideale yakın olduğunu ortaya çıkarmıştır.