Browsing by Author "Ozkan A.D."

Now showing 1 - 9 of 9

Open Access
Atomic force microscopy for the investigation of molecular and cellular behavior
(Elsevier, 2016-10) Ozkan A.D.; Topal, A. E.; Dana, A.; Güler, Mustafa O.; Tekinay, A. B.
The present review details the methods used for the measurement of cells and their exudates using atomic force microscopy (AFM) and outlines the general conclusions drawn by the mechanical characterization of biological materials through this method. AFM is a material characterization technique that can be operated in liquid conditions, allowing its use for the investigation of the mechanical properties of biological materials in their native environments. AFM has been used for the mechanical investigation of proteins, nucleic acids, biofilms, secretions, membrane bilayers, tissues and bacterial or eukaryotic cells; however, comparison between studies is difficult due to variances between tip sizes and morphologies, sample fixation and immobilization strategies, conditions of measurement and the mechanical parameters used for the quantification of biomaterial response. Although standard protocols for the AFM investigation of biological materials are limited and minor differences in measurement conditions may create large discrepancies, the method is nonetheless highly effective for comparatively evaluating the mechanical integrity of biomaterials and can be used for the real-time acquisition of elasticity data following the introduction of a chemical or mechanical stimulus. While it is currently of limited diagnostic value, the technique is also useful for basic research in cancer biology and the characterization of disease progression and wound healing processes.
Open Access
Chromium(VI) biosorption and bioaccumulation by Live and acid-modified biomass of a novel morganella morganii isolate
(Taylor and Francis, 2014) Ergul-Ulger, Z.; Ozkan A.D.; Tunca E.; Atasagun, S.; Tekinay, T.
Conventional methods of chromium removal are often insufficient for the remediation of chromium-contaminated natural environments, necessitating the development of alternative strategies. In this paper, we report the isolation of a novel Morganella morganii strain capable of reducing hexavalent chromium to its less-toxic and less-soluble trivalent form. Cr(VI) reduction by this strain was evaluated in both acidic environments and conditions reflecting natural freshwater sources. The isolate achieved equilibrium within 3 h and displayed a specific uptake rate of 24.30 ± 1.67 mg Cr(VI)/g biomass following HCl treatment. Without acid treatment, a reduction of over 90% was recorded within 72 h for an initial Cr(VI) concentration 20 mg/L, corresponding to a Cr(VI) removal capacity of 19.36 ± 1.89 mg/g. Absorption data of acid-treated STB5 biomass most closely followed the Toth and Langmuir models. FTIR results indicate that hydroxyl groups and extracellular or cell membrane polysaccharides may be potential adsorption sites for hexavalent chromium. Our results suggest that the isolate may be used in situ for treatment of polluted freshwater environments. Copyright © Taylor & Francis Group, LLC.
Open Access
Effects of temperature, pH and counterions on the stability of peptide amphiphile nanofiber structures
(Royal Society of Chemistry, 2016) Ozkan A.D.; Tekinay, A. B.; Güler, Mustafa O.; Tekin, E. D.
Peptide amphiphiles are a class of self-assembling molecules that are widely used to form bioactive nanostructures for various applications in bionanomedicine. However, peptide molecules can exhibit distinct behaviors under different conditions, suggesting that environmental variables such as temperature, pH, electrolytes and the presence of biological factors may greatly affect the self-assembly process. In this work, we used united-atom molecular dynamics simulations to understand the effects of three counterions (Na+, Ca2+ at pH 7 and Cl- at pH 2) and temperature change on the stability of the lauryl-VVAGERGD peptide amphiphile self-assembly. This molecule contains a bioactive RGD peptide sequence and has been shown to support cellular adhesion and proliferation in vitro. A 19-layered peptide nanostructure, containing 12 peptide amphiphile molecules per layer, was previously shown to exhibit optimal stability and it was used as the model nanofiber system. Peptide backbone stability was studied under increasing temperatures (300-358 K) using the number of hydrogen bonds and root-mean-square deviations of nanofiber size. At higher temperatures, fiber disintegration was observed to be dependent on the type of counter-ion used for nanofiber formation. Interestingly, rapid heating to higher temperatures could sometimes reestablish the integrity of the nanofiber backbone, possibly by allowing the system to bypass an energy barrier and assuming a more thermodynamically stable configuration. As counterion identity was observed to exhibit remarkable effects on the thermal stability of peptide nanofibers, we suggest that these behaviors should be considered while developing new materials for potential applications.
Open Access
Force and time-dependent self-assembly, disruption and recovery of supramolecular peptide amphiphile nanofibers
(Institute of Physics Publishing, 2018) Dikecoglu, F. B.; Topal, A. E.; Ozkan A.D.; Tekin, E. D.; Tekinay, A. B.; Güler, Mustafa O.; Dana, A.
Biological feedback mechanisms exert precise control over the initiation and termination of molecular self-assembly in response to environmental stimuli, while minimizing the formation and propagation of defects through self-repair processes. Peptide amphiphile (PA) molecules can self-assemble at physiological conditions to form supramolecular nanostructures that structurally and functionally resemble the nanofibrous proteins of the extracellular matrix, and their ability to reconfigure themselves in response to external stimuli is crucial for the design of intelligent biomaterials systems. Here, we investigated real-time self-assembly, deformation, and recovery of PA nanofibers in aqueous solution by using a force-stabilizing double-pass scanning atomic force microscopy imaging method to disrupt the self-assembled peptide nanofibers in a force-dependent manner. We demonstrate that nanofiber damage occurs at tip-sample interaction forces exceeding 1 nN, and the damaged fibers subsequently recover when the tip pressure is reduced. Nanofiber ends occasionally fail to reconnect following breakage and continue to grow as two individual nanofibers. Energy minimization calculations of nanofibers with increasing cross-sectional ellipticity (corresponding to varying levels of tip-induced fiber deformation) support our observations, with high-ellipticity nanofibers exhibiting lower stability compared to their non-deformed counterparts. Consequently, tip-mediated mechanical forces can provide an effective means of altering nanofiber integrity and visualizing the self-recovery of PA assemblies.
Open Access
Interactions between metals accumulated in the narrow-clawed crayfish Astacus leptodactylus (Eschscholtz, 1823) in Dikilitaş Lake, Turkey
(Taylor and Francis Ltd., 2015) Ergen, Ş. F.; Tunca, E. Ü.; Ozkan A.D.; Ölmez, T. T.; Acaröz, E.; Altındağ, A.; Tekinay, T.; Tunca E.
The accumulations of Al, Cd, Cr, Cu, Fe, Ni, Pb and Zn in the exoskeleton, gills, hepatopancreas and abdominal muscles of crayfish Astacus leptodactylus (Eschscholtz, 1823) were determined. The strongest correlation observed was between Cr and Ni in the gills (r = 0.904); moderate to strong correlations between Al, Cr, Fe, Ni and Cu were also observed in gill tissue. Disregarding the gills, the strongest correlation was found between Cu and Zn in the hepatopancreas (r = 0.808); the correlation between these two metals might have been a result of metallothionein activity. The accumulation of Pb was found to correlate with that of Cd in the exoskeleton, Cd and Zn in the gills, Zn and Cu in the hepatopancreas and Cu in the abdominal muscle. None of these correlations were present in lakewater and sediment samples, suggesting that the crayfish metabolism may be responsible for the co-accumulation of metal–metal pairs. As all correlations in non-gill tissues are observed between divalent metals, a shared transporter such as divalent metal transporter 1 might be involved in the accumulation of these metals. © 2015 Taylor & Francis.
Open Access
Nanomechanical characterization of osteogenic differentiation of mesenchymal stem cells on bioactive peptide nanofiber hydrogels
(Wiley-VCH Verlag, 2017-08) Topal, A. E.; Tansik, G.; Ozkan A.D.; Güler, Mustafa O.; Dana, A.; Tekinay, A. B.
Stem cell differentiation is known to be influenced by the mechanical properties of the surrounding extracellular matrix (ECM); however, little is known about the mechanical phenotypes of differentiating stem cells within the ECM. Here, this study uses osteoinductive, ECM-mimetic peptide nanofibers to investigate the changes in the mechanical properties of rat mesenchymal stem cells (rMSCs) during osteogenic differentiation. In addition, octafluorocyclobutane (C4F8)-coated atomic force microscopy (AFM) cantilevers are developed to minimize tip–sample adhesion during the nanomechanical characterization of rMSCs, and osteogenic differentiation is monitored through molecular analysis in conjunction with AFM measurements. rMSCs cultured on osteoinductive peptide nanofibers differentiate at substantially higher rates, form osteogenic cell clusters, deposit calcium to the surrounding matrix, and strikingly increase their Young's moduli throughout the osteogenic differentiation process compared to controls. These results show that the elasticity profiles of differentiating rMSCs may change significantly depending on environmental factors and especially the degree of biomineralization, and that the natural elasticity responses of cells cultured on scaffolds may be considerably different from those observed on non-bioactive surfaces. This is important for the identification of cell elasticity as a biophysical marker of osteogenic differentiation of MSCs, and indicates that biomineralization might have a predominant role on cell mechanics.
Open Access
Probe microscopy methods and applications in imaging of biological materials
(Elsevier Ltd, 2018) Ozkan A.D.; Topal, A. E.; Dikecoglu, F. B.; Güler, Mustafa O.; Dana, A.; Tekinay, A. B.
Atomic force microscopy is an emerging tool for investigating the biomolecular aspects of cellular interactions; however, cell and tissue analyses must frequently be performed in aqueous environment, over rough surfaces, and on complex adhesive samples that complicate the imaging process and readily facilitate the blunting or fouling of the AFM probe. In addition, the shape and surface chemistry of the probe determine the quality and types of data that can be acquired from biological materials, with certain information becoming available only within a specific range of tip lengths or diameters, or through the assistance of specific chemical or biological functionalization procedures. Consequently, a broad range of probe modification techniques has been developed to extend the capabilities and overcome the limitations of biological AFM measurements, including the fabrication of AFM tips with specialized morphologies, surface coating with biologically affine molecules, and the attachment of proteins, nucleic acids and cells to AFM probes. In this review, we underline the importance of probe choice and modification for the AFM analysis of biomaterials, discuss the recent literature on the use of non-standard AFM tips in life sciences research, and consider the future utility of tip functionalization methods for the investigation of fundamental cell and tissue interactions. © 2017 Elsevier Ltd
Open Access
Production and structural characterization of biosurfactant produced by newly isolated staphylococcus xylosus STF1 from petroleum contaminated soil
(Elsevier BV, 2015) Keskin, N. O. S.; Han, D.; Ozkan A.D.; Angun, P.; Umu, O. C. O.; Tekinay, T.
Petroleum-contaminated soil was used to isolate and characterize biosurfactant producing bacteria. The strain could produce higher amount of biosurfactant in medium supplemented with motor oil as sole source of carbon and energy. A new biosurfactant producing bacterium, designated as Staphylococcus xylosus STF1 based on morphological, physiological, biochemical tests and 16S rRNA gene sequencing. The isolated bacterium was first screened for the ability to produce biosurfactant. Partial sequence of STF1 strain of 16S rDNA gene was highly similar to those of various members of the family Staphylococcaceae. Biochemical characterizations including FT-IR, Raman spectroscopy and Mass spectroscopy studies suggested the biosurfactant to be lipopeptide. Study also confirmed that the cell free supernatant exhibited high emulsifying activity against the different hydrocarbons. Moreover, the partially purified biosurfactant exhibited antimicrobial activity by inhibiting the growth of several bacterial species. The strain could be a potential candidate for the production of polypeptide biosurfactant which could be useful in a variety of biotechnological and industrial processes, particularly in the food and oil industry. © 2015 Elsevier B.V.
Open Access
Removal of a reactive dye and hexavalent chromium by a reusable bacteria attached electrospun nanofibrous web
(Royal Society of Chemistry, 2015) Keskin, N. O. S.; Celebioglu A.; Sarioglu O.F.; Ozkan A.D.; Uyar, Tamer; Tekinay, T.
A contaminant resistant Lysinibacillus sp. NOSK was isolated from a soil sample and its Reactive Black 5 (RB5) and Cr(vi) removal efficiencies were investigated as a function of changes in the initial pH values, temperature, static/shaking conditions, reactive dye and Cr(vi) concentrations. In this study, an electrospun polysulfone nanofibrous web (PSU-NFW) was found to be effective in attachment of bacterial cells. Bacteria attached PSU-NFWs (bacteria/PSU-NFW) have shown highly efficient removal of RB5, as 99.7 ± 0.9% and 35.8 ± 0.4% for the pristine PSU-NFW. Moreover, the highest Cr(vi) removal efficiencies measured were 98.2 ± 0.6% for bacteria attached PSU-NFW and 32.6 ± 0.6% for the pristine PSU-NFW. Simultaneous removal of RB5 and Cr(vi) were also investigated. Reusability test results indicate that, bacteria/PSU-NFW can be reused for at least 7 cycles with 28.1 ± 0.6% and 66.7 ± 0.8% removal efficiencies for RB5 and Cr(vi), respectively.