Bioengineering / Biyomühendislik

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2’-Methylklavuzon Causes Lipid-Lowering Effects on A549 Non-Small Cell Lung Cancer Cells and Significant Changes on Dna Structure Evidenced by Fourier Transform Infrared Spectroscopy
(Elsevier, 2020) Ceylan, Çağatay; Aksoy, Hatice Nurdan; Çağır, Ali; Çetinkaya, Hakkı
Various chemical agents are used in the treatment of Non-Small Cell Lung Cancer (NSCLC). 2?-methylklavuzon was proposed as a potential chemotherapeutic agent in cancer treatment based on its topoisomerase inhibition activity. In this study the cellular effects of 2?-methylklavuzon was evaluated on A549 cancer cells using FTIR spectroscopy. 2?-methylklavuzon induced significant changes on both the whole cell lyophilizates and the lipid extracts of the A549 lung cancer cells. 2?-methylklavuzon caused significant structural changes in A549 cell DNA structure: T, A and G DNA breathing modes are lost after the drug application indicating the loss of topoisomerase activity. The level of transcription and RNA synthesis was enhanced. 2?-methylklavuzon induced single stranded DNA formation evidenced by the increase in the ratio of asymmetric/symmetric phosphate stretching modes. 2?-methylklavuzon induced band shifts only in the asymmetric mode of phosphate bonds not in the symmetrical phosphate bond stretching. 2?-methylklavuzon induced A form of DNA topography. In addition to the changes in the DNA structure and transcription 2?-methylklavuzon also caused lipid-lowering effect in A549 cancer cells. 2?-methylklavuzon suppressed lipid unsaturation, however, it induced formation of lipids with ring structures. 2?-methylklavuzon suppressed phosphate-containing lipids significantly and decreased carbonyl containing lipids and cholesterol slightly. 2?-methylklavuzon caused increases in the hydrocarbon chain length. Overall, 2?-methylklavuzon can be used as a lipid-lowering compound in the treatment of NSCLC and other cancer therapies. © 2020 Elsevier B.V.
Citation - WoS: 16
Citation - Scopus: 17
Antiproliferative Activity of (r)-4 '-methylklavuzon on Hepatocellular Carcinoma Cells and Epcam(+)/Cd133(+) Cancer Stem Cells Via Sirt1 and Exportin-1 (crm1) Inhibition
(Elsevier Ltd., 2019-10) Delman, Murat; Avcı, Sanem Tercan; Akçok, İsmail; Kanbur, Tuğçe; Erdal, Esra; Çağır, Ali
Cytotoxic effects of (R)-4'-methylklavuzon were investigated on hepatocellular carcinoma cells (HuH-7 and HepG2) and HuH-7 EpCAM(+)/CD133(+) cancer stem cells. IC50 of (R)-4'-methylklavuzon was found as 1.25 mu M for HuH-7 parental cells while it was found as 2.50 mu M for HuH-7 EpCAM(+)/CD133(+) cancer stem cells. (R)-4'-methylklavuzon tended to show more efficient in vitro cytotoxicity with its lower IC50 values on hepatocellular carcinoma cell lines compared to its lead molecule, goniothalamin and FDA-approved drugs, sorafenib and regorafenib. Cell-based Sirtuin/HDAC enzyme activity measurements revealed that endogenous Sirtuin/HDAC enzymes were reduced by 40% compared to control. SIRT1 protein levels were upregulated indicating triggered DNA repair mechanism. p53 was overexpressed in HepG2 cells. (R)-4'methylklavuzon inhibited CRM1 protein providing increased retention of p53 and RIOK2 protein in the nucleus. HuH-7 parental and EpCAM(+)/CD133(+) cancer stem cell spheroids lost intact morphology. 3D HepG2 spheroid viabilities were decreased in a correlation with upregulation in p53 protein levels. (C) 2019 Elsevier Masson SAS. All rights reserved.
Citation - WoS: 17
Citation - Scopus: 15
Antiproliferative and Apoptotic Effects of Olive Leaf Extract Microcapsules on Mcf-7 and A549 Cancer Cells
(American Chemical Society, 2023) Bal, Yıldız; Sürmeli, Yusuf; Şanlı Mohamed, Gülşah
Alginate microcapsules are a talented means for the delivery of broad curative biomacromolecules. In this study, we immobilized olive leaf extract (OLE) by calcium alginate (CA) and chitosan-coated CA (CCA) and characterized the OLE-loaded CA and CCA. The cytotoxic effect, the cell cycle arrest, and the apoptotic effect of OLE and its microcapsules were investigated against breast adenocarcinoma (MCF-7) and lung carcinoma (A549). As a result, the loading capacity of OLE-CA and OLE-CCA was found to be 80 and 99%, respectively, in optimal conditions. Also, OLE-CA and OLE-CCA were characterized by unique FTIR peaks and morphological display relative to the empty CCA microcapsules. The cytotoxicity analysis showed that the IC50 values of OLE-CA and OLE-CCA were determined to be 312 and 0.94 μg mL-1 against A549, respectively, whereas these were found to be 865.4 and 425.5 μg mL-1 for MCF-7 cells. On the other hand, the OLE microcapsules did not possess in any concentration of cytotoxic influence on the BEAS 2B healthy cell line. Also, the exposure of OLE-CCA to MCF-7 and A549 resulted in the arrest of more MCF-7 and A549 cells at the G0/G1 phase compared to the OLE. A549 and MCF-7 cells were predominantly found in the late apoptosis phase and necrosis phase, respectively. Optical microscopy images confirmed that OLE microcapsules were more effective against MCF-7 and A549 than free OLE. The present work suggested that the OLE microcapsules might be administered as nutrition supplements for cancer therapy. © 2023 The Authors. Published by American Chemical Society.
Citation - WoS: 26
Citation - Scopus: 28
Biocomposite Scaffolds for 3d Cell Culture: Propolis Enriched Polyvinyl Alcohol Nanofibers Favoring Cell Adhesion
(John Wiley and Sons Inc., 2021-05) Bilginer, Rumeysa; Özkendir İnanç, Dilce; Yıldız, Ümit Hakan; Arslan Yıldız, Ahu
The 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.
Citation - WoS: 34
Citation - Scopus: 35
Biomimetic Hybrid Scaffold Consisting of Co-Electrospun Collagen and Pllcl for 3d Cell Culture
(Elsevier Ltd., 2019) Türker, Esra; Yıldız, Ümit Hakan; Arslan Yıldız, Ahu
Electrospun collagen is commonly used as a scaffold in tissue engineering applications since it mimics the content and morphology of native extracellular matrix (ECM) well. This report describes "toxic solvent free" fabrication of electrospun hybrid scaffold consisting of Collagen (Col) and Poly(L-lactide-co-epsilon-caprolactone) (PLLCL) for three-dimensional (3D) cell culture. Biomimetic hybrid scaffold was fabricated via co-spinning approach where simultaneous electrospinning of PLLCL and Collagen was mediated by polymer sacrificing agent Polyvinylpyrrolidone (PVP). Acidified aqueous solution of PVP was used to solubilize collagen without using toxic solvents for electrospinning, and then PVP was readily removed by rinsing in water. Mechanical characterizations, protein adsorption, as well as biodegradation analysis have been conducted to investigate feasibility of biomimetic hybrid scaffold for 3D cell culture applications. Electrospun biomimetic hybrid scaffold, which has 3D-network structure with 300-450 nm fiber diameters, was found to be maximizing cell adhesion through assisting NIH 3T3 mouse fibroblast cells. 3D cell culture studies confirmed that presence of collagen in biomimetic hybrid scaffold have created a major impact on cell proliferation compared to conventional 2D systems on long-term, also cell viability increased with the increasing amount of collagen. (c) 2019 Elsevier B.V. All rights reserved.
Citation - WoS: 5
Citation - Scopus: 6
Boosting 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 Hakan
This 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 Ltd
Citation - Scopus: 3
Development of Chrono-Spectral Gold Nanoparticle Growth Based Plasmonic Biosensor Platform
(Elsevier, 2024) Sözmen, Alper Baran; Elveren, Beste; Erdoğan, Duygu; Mezgil, Bahadır; Baştanlar, Yalın; Yıldız, Ümit Hakan; Arslan Yıldız, Ahu
Plasmonic sensor platforms are designed for rapid, label-free, and real-time detection and they excel as the next generation biosensors. However, current methods such as Surface Plasmon Resonance require expertise and well-equipped laboratory facilities. Simpler methods such as Localized Surface Plasmon Resonance (LSPR) overcome those limitations, though they lack sensitivity. Hence, sensitivity enhancement plays a crucial role in the future of plasmonic sensor platforms. Herein, a refractive index (RI) sensitivity enhancement methodology is reported utilizing growth of gold nanoparticles (GNPs) on solid support and it is backed up with artificial neural network (ANN) analysis. Sensor platform fabrication was initiated with GNP immobilization onto solid support; immobilized GNPs were then used as seeds for chrono-spectral growth, which was carried out using NH2OH at varied incubation times. The response to RI change of the platform was investigated with varied concentrations of sucrose and ethanol. The detection of bacteria E.coli BL21 was carried out for validation as a model microorganism and results showed that detection was possible at 102 CFU/ml. The data acquired by spectrophotometric measurements were analyzed by ANN and bacteria classification with percentage error rates near 0% was achieved. The proposed LSPR-based, label-free sensor application proved that the developed methodology promises utile sensitivity enhancement potential for similar sensor platforms. © 2024 The Author(s)
Citation - WoS: 33
Citation - Scopus: 38
Glucuronoxylan-Based Quince Seed Hydrogel: a Promising Scaffold for Tissue Engineering Applications
(Elsevier, 2021) Güzelgülgen, Meltem; Özkendir İnanç, Dilce; Yıldız, Ümit Hakan; Arslan Yıldız, Ahu
Natural gums and mucilages from plant-derived polysaccharides are potential candidates for a tissue-engineering scaffold by their ability of gelation and biocompatibility. Herein, we utilized Glucuron-oxylanbased quince seed hydrogel (QSH) as a scaffold for tissue engineering applications. Optimization of QSH gelation was conducted by varying QSH and crosslinker glutaraldehyde (GTA) concentrations. Structural characterization of QSH was done by Fourier Transform Infrared Spectroscopy (MR). Furthermore, morphological and mechanical investigation of QSH was performed by Scanning Electron Microscopy (SEM) and Atomic Force Microscopy (AFM). The protein adsorption test revealed the suitability of QSH for cell attachment. Biocompatibility of QSH was confirmed by culturing NIH-3T3 mouse fibroblast cells on it. Cell viability and proliferation results revealed that optimum parameters for cell viability were 2 mg mi(-1)of QSH and 0.03 M GTA. SEM and DAPI staining results indicated the formation of spheroids with a diameter of approximately 300 pm. Furthermore, formation of extracellular matrix (ECM) microenvironment was confirmed with the Collagen Type-I staining. Here, it was demonstrated that the fabricated QSH is a promising scaffold for 3D cell culture and tissue engineering applications provided by its highly porous structure, remarkable swelling capacity and high biocompatibility. (C) 2021 Published by Elsevier B.V.
Citation - WoS: 17
Citation - Scopus: 18
Hand-Held Volatilome Analyzer Based on Elastically Deformable Nanofibers
(American Chemical Society, 2018-04) Yücel, Müge; Akın, Osman; Çayören, Mehmet; Akduman, İbrahim; Palaniappan, Alagappan; Liedberg, Bo; Hızal, Gürkan; İnci, Fatih; Yıldız, Ümit Hakan
This 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.
Citation - WoS: 2
Citation - Scopus: 5
Immobilization of Olive Leaf Extract With Chitosan Nanoparticles as an Adjunct To Enhance Cytotoxicity
(American Chemical Society, 2023) Özdamar, Burcu; Sürmeli, Yusuf; Şanlı Mohamed, Gülşah
We immobilized the olive leaf extract (OLE) with chitosannanoparticles(CNPs) by optimizing the effect of various immobilization conditions,and OLE-loaded CNPs (OLE-CNPs) were then elaborately characterizedphysicochemically by scanning electron microscopy (SEM), Fourier transforminfrared (FT-IR) spectroscopy, dynamic light scattering (DLS), andatomic force microscopy (AFM). Under optimal conditions, CNPs wereable to accommodate the OLE with a loading capacity of 97.5%. Theresulting OLE-CNPs had a spherical morphology, and their average diameterwas approximately 100 nm. The cytotoxic influence, cell cycle distribution,and apoptosis stage of OLE and OLE-CNPs were analyzed on lung carcinoma(A549) and breast adenocarcinoma (MCF-7) cell lines. In an in vitrocytotoxic assay, IC50 values of OLE-CNPs were determinedto be 540 & mu;g/mL for A549 and 810 & mu;g/mL for MCF-7. Thetreatment of both A549 and MCF-7 with OLE-CNPs caused the highestcell arrest in G0/G1 in a dose-independent manner. OLE-CNPs affectedcell cycle distribution in a manner different from free OLE treatmentin both cancer cells. A549 and MCF-7 cells were predominantly foundin the late apoptosis and necrosis phases, respectively, upon treatmentof 1000 & mu;M OLE-CNPs. Our results suggest that CNPs enhance theutility of OLEs as nutraceuticals in cancer and that OLE-CNPs canbe utilized as an adjunct to cancer therapy.
Citation - WoS: 1
Immunomodulatory Mechanisms of Astragalus Saponins
(Wiley, 2021) Yakuboğulları, Nilgün; Çağır, Ali; Bedir, Erdal; Sağ, Duygu
Citation - WoS: 15
Citation - Scopus: 17
Improved Activity of Alpha-L From Geobacillus Vulcani Gs90 by Directed Evolution: Investigation on Thermal and Alkaline Stability
(John Wiley and Sons Inc., 2019) Sürmeli, Yusuf; İlgü, Hüseyin; Şanlı Mohamed, Gülşah
alpha-L-Arabinofuranosidase (Abf) is a potential enzyme because of its synergistic effect with other hemicellulases in agro-industrial field. In this study, directed evolution was applied to Abf from Geobacillus vulcani GS90 (GvAbf) using one round error-prone PCR and constructed a library of 73 enzyme variants of GvAbf. The activity screening of the enzyme variants was performed on soluble protein extracts using p-nitrophenyl alpha-L-arabinofuranoside as substrate. Two high activity displaying variants (GvAbf L307S and GvAbf Q90H/L307S) were selected, purified, partially characterized, and structurally analyzed. The specific activities of both variants were almost 2.5-fold more than that of GvAbf. Both GvAbf variants also exhibited higher thermal stability but lower alkaline stability in reference to GvAbf. The structural analysis of GvAbf model indicated that two mutation sites Q90H and L307S in both GvAbf variants are located in TIM barrel domain, responsible for catalytic action in many Glycoside Hydrolase Families including GH51. The structure of GvAbf model displayed that the position of L307S mutation is closer to the catalytic residues of GvAbf compared with Q90H mutation and also L307S mutation is conserved in both variants of GvAbf. Therefore, it was hypothesized that L307S amino acid substitution may play a critical role in catalytic activity of GvAbf. (C) 2018 International Union of Biochemistry and Molecular Biology, Inc.
Kanser Öntanısı için Hücredışı Veziküller Kullanılarak Plazmonik Temelli Metodoloji Geliştirme
(Institute of Electrical and Electronics Engineers Inc., 2017-02) Erdoğan, Duygu; Alduran, Yeşim; Yıldız, Ümit Hakan; Arslan Yıldız, Ahu
Son 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.
Citation - WoS: 16
Citation - Scopus: 18
A Novel Thermostable Xylanase From Geobacillus Vulcani Gs90: Production, Biochemical Characterization, and Its Comparative Application in Fruit Juice Enrichment
(Wiley, 2021) Algan, Müge; Sürmeli, Yusuf; Şanlı Mohamed, Gülşah
Xylanases have great attention to act as a potential role in agro-industrial processes. In this study, production, characterization, and fruit juice application of novel xylanase from thermophilic Geobacillus vulcani GS90 (GvXyl) were performed. GvXyl was purified via acetone precipitation and gel-filtration chromatography. The results showed that GvXyl had 1,671.4 U/mg of specific activity and optimally worked at pH 8 and 55 degrees C. It was also active in a wide pH (3-9) and temperature (30-90oC) ranges. GvXyl was highly stable at 90oC and relatively stable at pH 3-9. The kinetic parameters of GvXyl were obtained as K-m, V-max, and k(cat); 10.2 mg/ml, 4,104 mu mol min(-1) mg(-1), and 3,542.6 s(-1), respectively. GvXyl had higher action than commercial xylanase in fruit juice enrichment. These results revealed that GvXyl might possess a potential influence in fruit juice processing because of its high specific activity and great thermal stability. Practical applications Polysaccharides include starch, pectin, and hemicellulose create problems by lowering fruit juice quality in beverages. To overcome this problem, various clarification processes might be applied to natural fruit juices. Even though chemicals are widely used for this purpose, recently enzymes including xylanases are preferred for obtaining high-quality products. In this study, we reported the production and biochemical characterization of novel thermostable xylanase from thermophilic G. vulcani GS90 (GvXyl). Also, apple and orange juice enrichment were performed with the novel xylanase to increase the quality in terms of yield, clarity, and reducing sugar substance. The improved quality features of apple and orange juices with GvXyl was then compared to commercially available beta-1,4-xylanase. The results revealed that GvXyl might possess a potential influence in fruit juice processing because of its high specific activity and great thermal stability.
Citation - WoS: 16
Citation - Scopus: 19
Pixelated Colorimetric Nucleic Acid Assay
(Elsevier, 2020) Aydın, Hakan Berk; Cheema, Jamal Ahmed; Arnmanath, Gopal; Toklucu, Cihan; Yücel, Müge; Özenler, Sezer; Yıldız, Ümit Hakan
Conjugated 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.
Semi-Synthetic Studies on Astragaloside Vii and Immunomodulatory Activities of the Derivatives
(Georg Thieme Verlag, 2019) Yakuboğulları, Nilgün; Sağ, Duygu; Çağır, Ali; Bedir, Erdal
Adjuvants have been used in vaccine sector since 1920s to increase the immunogenicity of antigens, reduce the dosage and minimize frequency of immunizations [1]. The use of saponins as adjuvant in the prophylactic/therapeutic human and veterinary vaccines, and investigation of their immunomodulatory activities have gained importance in recent years [2],[3]. Astragaloside VII (AST VII), a triterpenoid saponin isolated from Astragalus species, stimulates Th1 mediated immune response, antigen-specific antibody response and splenocyte proliferation.
Citation - WoS: 12
Citation - Scopus: 12
Single 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 Hakan
This 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.
Citation - WoS: 1
Citation - Scopus: 1
The Soft Nanodots as Fluorescent Probes for Cell Imaging: Analysis of Cell and Spheroid Penetration Behavior of Single Chain Polymer Dots
(Wiley, 2024) Yücel, Müge; Onbaş, Rabia; Arslan Yıldız, Ahu; Yıldız, Ümit Hakan
This study describes the formation, size control, and penetration behavior of polymer nanodots (Pdots) consisting of single or few chain polythiophene-based conjugated polyelectrolytes (CPEs) via nanophase separation between good solvent and poor solvent of CPE. Though the chain singularity may be associated with dilution nanophase separation suggests that molecules of a good solvent create a thermodynamically driven solvation layer surrounding the CPEs and thereby separating the single chains even in their poor solvents. This statement is therefore corroborated with emission intensity/lifetime, particle size, and scattering intensity of polyelectrolyte in good and poor solvents. Regarding the augmented features, Pdots are implemented into cell imaging studies to understand the nuclear penetration and to differentiate the invasive characteristics of breast cancer cells. The python based red, green, blue (RGB) color analysis depicts that Pdots have more nuclear penetration ability in triple negative breast cancer cells due to the different nuclear morphology in shape and composition and Pdots have penetrated cell membrane as well as extracellular matrix in spheroid models. The current Pdot protocol and its utilization in cancer cell imaging are holding great promise for gene/drug delivery to target cancer cells by explicitly achieving the very first priority of nuclear intake. The penetration capability of cationic soft nanodots in to tumor models of breast cancer is demonstrated. The image analysis based on fluorescence intensity variation reveals the characteristics of translocation of nanodots in dense mediums such as tumor models.image
Citation - WoS: 2
Citation - Scopus: 3
Structural and Functional Analyses of Gh51 Alpha-L of Geobacillus Vulcani Gs90 Reveal Crucial Residues for Catalytic Activity and Thermostability
(Wiley, 2022) Sürmeli, Yusuf; Şanlı Mohamed, Gülşah
Alpha-L-arabinofuranosidase (Abf) is of big interest in various industrial areas. Directed evolution is a powerful strategy to identify significant residues underlying Abf properties. Here, six active variants from GH51 Abf of Geobacillus vulcani GS90 (GvAbf) by directed evolution were overproduced, extracted, and analyzed at biochemical and structural levels. According to the activity and thermostability results, the most-active and the least-active variants were found as GvAbf51 and GvAbf52, respectively. GvAbf63 variant was more active than parent GvAbf by 20% and less active than GvAbf51. Also, the highest thermostability belonged to GvAbf52 with 80% residual activity after 1 h. Comparative sequence and structure analyses revealed that GvAbf51 possessed L307S displacement. Thus, this study suggested that L307 residue may be critical for GvAbf activity. GvAbf63 had H30D, Q90H, and L307S displacements, and H30 was covalently bound to E29 catalytic residue. Thus, H30D may decrease the positive effect of L307S on GvAbf63 activity, preventing E29 action. Besides, GvAbf52 possessed S215N, L307S, H473P, and G476C substitutions and S215 was close to E175 (acid–base residue). S215N may partially disrupt E175 action. Overall effect of all substitutions in GvAbf52 may result in the formation of the C–C bond between C171 and C213 by becoming closer to each other.
Citation - Scopus: 3
Tissue Engineering Applications of Marine-Based Materials
(Springer, 2022) Polat, Hürriyet; Zeybek, Nuket; Polat, Mehmet
Tissue engineering is a promising approach in replacing or improving tissues lost or has become nonviable due to disease or trauma by the use of scaffold materials by combining engineering and biochemical/physicochemical methods. Its purpose is to create suitable matrices that support cell differentiation and proliferation toward the formation of new and functional tissue. Marine-based natural compounds are potential scaffold feedstock material in tissue engineering owing to their biocompatibility and biodegradability while providing excellent biochemical/physicochemical properties. Numerous application areas and various fabrication routes techniques described in the literature attest to the importance of these materials in tissue regeneration. This review has been carried to merge the information from a large number of studies on the marine-based scaffold materials in tissue engineering into a coherent summary. © The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd. 2022.

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Browsing Bioengineering / Biyomühendislik by Department "İzmir Institute of Technology. Chemistry"