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Öğe Bifunctional sharkskin mimicked chitosan/graphene oxide membranes: Reduced biofilm formation and improved cytocompatibility(Elsevier, 2021) Rostami, Sabra; Puza, Fatih; Ucak, Meltem; Ozgur, Erdogan; Gul, Ozgur; Ercan, Utku Kursat; Garipcan, BoraAntibacterial activity and cytocompatibility are the two essential characteristics that an ideal implantable biomaterial must possess simultaneously. Biomaterials with these characteristics can be fabricated via combination of chemical and topographical features. Herein, design and fabrication of a sharkskin mimicked Graphene Oxide modified Chitosan membrane with enhanced antibacterial and cytocompatibility properties was investigated. As a measure of antibacterial properties, viability of planktonic and bacterial biofilm was measured using gram-positive Staphylococcus aureus and gram-negative Escherichia coil. Results showed a significant reduction in bacterial adhesion and biofilm growth induced by sharkskin surface topography regardless of chemical modifications for both strains, hence proving the superior antibacterial activity of sharkskin topography. Furthermore, the highest level of cell viability and proliferation of cultured human keratinocyte (HaCaT) and mouse fibroblast (L929) cell lines belonged to Graphene Oxide (GO) coated sharkskin mimicked membranes. Our results indicate that GO coated (GOc) sharkskin mimicked membranes can significantly reduce bacterial biofilm formation in stationary culture conditions while promoting cytocompatibility. The duo of sharkskin surface topography and GO coating provides remarkable potentials as a cytocompatible and antibacterial biomaterial for diverse biomedical applications.Öğe Decellularization and characterization of leek: a potential cellulose-based biomaterial(Springer, 2020) Toker, Melis; Rostami, Sabra; Kesici, Muge; Gul, Ozgur; Kocaturk, Ozgur; Odabas, Sedat; Garipcan, BoraCellulose, which is easily attainable in nature, has been studied due to its biocompatibility, low cytotoxicity, adjustable biomechanical properties and cost effectiveness as a biomaterial. Recently, plant-derived cellulose-based biomaterials were given attention for numerous applications including bone, cartilage and cardiac tissue engineering. In this study, leek (Allium porrum) was chosen as a plant tissue model for the fabrication of a potential biomaterial due to its structural morphology (interconnected and elongated channel like structural morphology). Leek tissues were decellularized by a detergent solution. The degree of residual cell content was evaluated by DNA and protein quantification as well as immunostaining. Chemical and mechanical properties were tested for both native and decellularized leek samples in order to investigate the effect of decellularization on the structure. Swelling, degradation and protein adsorption behavior of decellularized leek samples were also studied. In order to enhance cell adhesion, decellularized leek samples were modified with 3-aminopropyltriethoxysilane, octadecyltrichlorosilane and coated with graphene oxide prior to cell seeding. SH-SY5Y human neuroblastoma cells were used for mammalian cell culture studies. MTT cell viability assay and SEM imaging were performed to observe the cell adhesion and morphology. Decellularized leek tissues are expected to be cellulose based biomaterial for candidate biomedical applications both in vitro and in vivo in future studies. Graphic abstractÖğe Design and Implementation of a Low-Cost High-Performance Syringe Pump System(IEEE, 2017) Coskun, Hilmi; Gul, Ozgur; Ferhanoglu, Onur; Gokdel, Y. DaghanThis study describes design and implementation of a high-performance, low-cost, syringe pump device. Proposed device can be used with different injectors having volumes that are ranging from a common 0.5 mL to a larger 60 mL. This adaptable and programmable syringe pump provides high accuracy and adjustable flow rate in a simple mechanical manner and costs approximately $ 200. Developed system was tested on an optical table in lab conditions. It is measured that system can provide rates up to 0.05 mL/ h, when used on a 0.5 mL syringe whereas the maximum volume 60 mL injector can provide a flow rate of 5.8 mL/ h. Mean flow rate error of the system is calculated as 1.33%. Time-distance plots reveal a high degree of linearity and negligible hysteresis. Thus, the manufactured syringe pump is an excellent candidate as a high-precision liquid delivery system for low-resource settings.Öğe Insights into a type III cohesin-dockerin recognition interface from the cellulose-degrading bacterium Ruminococcus flavefaciens(Wiley, 2015) Weinstein, Jonathan Y.; Slutzki, Michal; Karpol, Alon; Barak, Yoav; Gul, Ozgur; Lamed, Raphael; Bayer, Edward A.Cellulosomes are large multicomponent cellulose-degrading assemblies found on the surfaces of cellulolytic microorganisms. Often containing hundreds of components, the self-assembly of cellulosomes is mediated by the ultra-high-affinity cohesin-dockerin interaction, which allows them to adopt the complex architectures necessary for degrading recalcitrant cellulose. Better understanding of how the cellulosome assembles and functions and what kinds of structures it adopts will further effort to develop industrial applications of cellulosome components, including their use in bioenergy production. Ruminococcus flavefaciens is a well-studied anaerobic cellulolytic bacteria found in the intestinal tracts of ruminants and other herbivores. Key to cellulosomal self-assembly in this bacterium is the dockerin ScaADoc, found on the non-catalytic structural subunit scaffoldin ScaA, which is responsible for assembling arrays of cellulose-degrading enzymes. This work expands on previous efforts by conducting a series of binding studies on ScaADoc constructs that contain mutations in their cohesin recognition interface, in order to identify which residues play important roles in binding. Molecular dynamics simulations were employed to gain insight into the structural basis for our findings. A specific residue pair in the first helix of ScaADoc, as well as a glutamate near the C-terminus, was identified to be essential for cohesin binding. By advancing our understanding of the cohesin binding of ScaADoc, this study serves as a foundation for future work to more fully understand the structural basis of cellulosome assembly in R. flavefaciens. Copyright (c) 2015 John Wiley & Sons, Ltd.Öğe Kinome-wide RNAi screening for mediators of ABT-199 resistance in breast cancer cells identifies Wee1 as a novel therapeutic target(Pergamon-Elsevier Science Ltd, 2021) Aka, Yeliz; Karakas, Bahriye; Acikbas, Ufuk; Basaga, Huveyda; Gul, Ozgur; Kutuk, OzgurAntiapoptotic and proapoptotic BCL-2 protein family members regulate mitochondrial apoptotic pathway. Small molecule inhibitors of antiapoptotic BCL-2 proteins including BCL-2-specific inhibitor ABT-199 (Venetoclax) are in clinical development. However, the efficiency of ABT-199 as a single agent in solid tumors is limited. We performed a high-throughput RNAi kinome screen targeting 691 kinases to identify potentially targetable kinases to enhance ABT-199 response in breast cancer cells. Our studies identified Wee1 as the primary target kinase to overcome resistance to ABT-199. Depletion of Wee1 by siRNA-mediated knockdown or inhibition of Wee1 by the small molecule Wee1 inhibitor AZD1775 sensitized SKBR3, MDA-MB-468, T47D and CAMA-1 breast cancer cells to ABT-199 along with decreased MCL1. BH3-only proteins PUMA and BIM functionally contribute to apoptosis signaling following co-targeting BCL-2 and Wee1. Suppression of Wee1 function increased mitochondrial cell death priming. Furthermore, we found that Wee1 inhibition altered MCL1 phosphorylation and protein stability, which led to HUWE1-mediated MCL1 degradation. Our findings suggest that Wee1 inhibition can overcome resistance to ABT-199 and provide a rationale for further translational investigation of BCL-2 inhibitor/Wee1 inhibitor combination in breast cancer.Öğe Mitochondrial estrogen receptors alter mitochondrial priming and response to endocrine therapy in breast cancer cells(Springernature, 2021) Karakas, Bahriye; Aka, Yeliz; Giray, Asli; Temel, Sehime Gulsun; Acikbas, Ufuk; Basaga, Huveyda; Gul, OzgurBreast cancer is the most common cancer with a high rate of mortality and morbidity among women worldwide. Estrogen receptor status is an important prognostic factor and endocrine therapy is the choice of first-line treatment in ER-positive breast cancer. However, most tumors develop resistance to endocrine therapy. Here we demonstrate that BH3 profiling technology, in particular, dynamic BH3 profiling can predict the response to endocrine therapy agents as well as the development of acquired resistance in breast cancer cells independent of estrogen receptor status. Immunofluorescence analysis and subcellular fractionation experiments revealed distinct ER-alpha and ER-beta subcellular localization patterns in breast cancer cells, including mitochondrial localization of both receptor subtypes. shRNA-mediated depletion of ER-beta in breast cancer cells led to resistance to endocrine therapy agents and selective reconstitution of ER-beta in mitochondria restored sensitivity. Notably, mitochondria-targeted ER-alpha did not restore sensitivity, even conferred further resistance to endocrine therapy agents. In addition, expressing mitochondria-targeted ER-beta in breast cancer cells resulted in decreased mitochondrial respiration alongside increased total ROS and mitochondrial superoxide production. Furthermore, our data demonstrated that mitochondrial ER-beta can be successfully targeted by the selective ER-beta agonist Erteberel. Thus, our findings provide novel findings on mitochondrial estrogen signaling in breast cancer cells and suggest the implementation of the dynamic BH3 technique as a tool to predict acquired endocrine therapy resistance.Öğe Quantitative detection system for immunostrips in 180nm standard CMOS technology(Springer, 2021) Tekin, Engincan; Celikdemir, Caner; Ucar, Busra; Gul, Ozgur; Sarioglu, BaykalIn this work, a CMOS based optical read-out system for biomarker on immunostrips detection is presented. For the proposed system, a CMOS integrated circuit containing an on-chip photodiode is designed in standard 180 nm UMC CMOS Technology. The system also contains cost-effective 3D Printed structures for holding both IC and the sample immunostrip together. The proposed system can be operated in two modes (1) light reflectance and (2) light transmittance. In the system, a laser with a wavelength of 637 nm is applied to the CMOS IC through immunostrip. Photovoltaic and photoconductive measurements are carried out for each mode on a custom Gluten biomarker immunostrip. Sensing operation of the biomarker is successfully realized with optical powers from 5 mW to 8 mW. Biomaterial density on the immunostrip is sensed and images of the biomarker with varying intensities are constructed from the measurements. Feasibility of the system for low power biomarker sensing applications is demonstrated.Öğe Quantitative Measurement of Colorimetric Signals in 180nm Standard CMOS Technology(IEEE, 2019) Celikdemir, Caner; Tekin, Engincan; Ucar, Busra; Gul, Ozgur; Sarioglu, BaykalIn this work, a CMOS based optical read-out system for biomarker sensing is presented. An integrated circuit containing an on-chip photodiode is designed an manufactured in 180nm UMC CMOS Technology. A 3D Printed structure is designed for holding both IC and the marker paper together. Laser light with 637 nm wavelength is applied to the marker paper and the CMOS IC. Optical measurements carried-out are based on the light transmissivity of the marker paper. Both photovoltaic and photoconductive measurements are carried out. The markers are successfully detected with 5mW to 20mW optical power. Images of the marker lines with varying intensity are generated from the measurements. Lastly, theoretical equations are derived, and the feasibility of the system for low power biomarker sensing applications is shown.Öğe RAB25 confers resistance to chemotherapy by altering mitochondrial apoptosis signaling in ovarian cancer cells(Springer, 2020) Temel, Sehime Gulsun; Giray, Asli; Karakas, Bahriye; Gul, Ozgur; Kozanoglu, Ilknur; Celik, Husnu; Basaga, HuveydaOvarian cancer remains one of the most frequent causes of cancer-related death in women. Many patients with ovarian cancer suffer from de novo or acquired resistance to chemotherapy. Here, we report that RAB25 suppresses chemotherapy-induced mitochondrial apoptosis signaling in ovarian cancer cell lines and primary ovarian cancer cells. RAB25 blocks chemotherapy-induced apoptosis upstream of mitochondrial outer membrane permeabilization by either increasing antiapoptotic BCL-2 proteins or decreasing proapoptotic BCL-2 proteins. In particular, BAX expression negatively correlates with RAB25 expression in ovarian cancer cells. BH3 profiling assays corroborated that RAB25 decreases mitochondrial cell death priming. Suppressing RAB25 by means of RNAi or RFP14 inhibitory hydrocarbon-stapled peptide sensitizes ovarian cancer cells to chemotherapy as well as RAB25-mediated proliferation, invasion and migration. Our data suggest that RAB25 is a potential therapeutic target for ovarian cancer.
