Bioengineering / Biyomühendislik
Permanent URI for this collectionhttps://hdl.handle.net/11147/4529
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Article 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: 8Citation - Scopus: 11Application of Low Intensity Mechanical Vibrations for Bone Tissue Maintenance and Regeneration(TÜBİTAK, 2016) Ölçüm, Melis; Baskan, Öznur; Karadaş, Özge; Özçivici, EnginPhysical exercise is beneficial for bone tissue health, yet its usage is limited for preventing osteoporosis. Even though natural for the bone tissue from development to homeostasis, mechanical loads present with a multitude of physical parameters, including amplitude, duration, frequency, and distribution. Utilizing the most beneficial parameters of mechanical loads may potentiate a nonpharmaceutical tool for biotechnology to prevent and treat bone loss related to aging, bedrest, sedentary lifestyles, weightlessness, and other diseases. Low intensity vibrations (LIVs) consist of mechanical loads with amplitudes smaller than loads prescribed by habitual activity, with a higher frequency. In this review, literature covering LIV signal application on bone tissue and cellular and molecular level is presented. Studies indicate that LIV signals are safe, anabolic, and anticatabolic for skeletal tissue and are of great significance in regenerative medicine applications.Conference Object Role of Connexin 32 on Gap Junctions in Breast Cancer Cells With Varying Metastatic Potential.(American Society for Cell Biology, 2017) Uğur, Deniz; Özçivici, Engin; Meşe, Gülistan[No abstract available]Conference Object Investigating the Role of Connexin 32 in Cell Cycle, Cell Viability and Epithelial To Mesenchymal Transition of Normal Breast and Breast Cancer Cells(American Society for Cell Biology, 2017) Adak, Aslı; Özçivici, Engin; Meşe, Gülistan[No abstract available]Conference Object Role of Myelin Topography and Alignment on the Activation of Astrocytes(Mary Ann Liebert, Inc, 2017) Gürer, F.; Bulmuş Zareie, Volga; Bulmus Zareire, Esma Volga; Baskerville, K.; Özdemir, T.Myelin sheath is thick layers of neuronal plasma membrane that serves as a capacitor during neuronal signal transmission. Decay in myelin sheath is associated with several neurodegenerative diseases such as multiple sclerosis and Alzheimer disease. Although its primary purpose is to insulate and accelerate the neuronal impulse, very few studies focused on the geometrical aspect of myelination in neuronal function. Here, we developed a versatile platform to study the effect of myelin topography and alignment on the neuronal signal transmission.Conference Object The Ordering of Smokers' Criteria in Choosing Toothpaste With Fuzzy Dematel Model(European Publishing, 2018) Tarım, Ergün Alperay; Mevsim, Vildan; Kandemir, EmelSmokers give more harm to tooth and mouth flora than non-smokers. These conditions can affect the decision of smokers when buying toothpaste. Unlike non-smokers, expectations of toothpaste can vary. Regarding these, the aim of this study is to show which criteria are important to smokers in choosing toothpaste for dental health or related problems. These criteria are sorted according to their importance with the model to be applied.Conference Object Evaluation of Anti-Inflammatory Potential and Lc-ms/Ms Analysis of Different Standards(Wiley, 2018) Sözmen, Alper Baran; Canbay, E.; Yıldırım Sözmen, Eser; Övez, BikemStandardization of a LC-MS/MS method for phenolic compound content of biomass originated extracts was aimed in this study, Chlorella miniata extracts, which were cultivated solely for this study, were used for this purpose. The first step of the study was to compare external standard method, added standard method, and conventional standard method the qualitative identification of phenolic compounds of the extracts were performed by using LC-MS/MS system.Article Citation - WoS: 25Citation - Scopus: 33Novel Phytochemical Cissus Quadrangularis Extract-Loaded Chitosan/Na-carboxymethyl Cellulose-Based Scaffolds for Bone Regeneration(SAGE Publications, 2018) Tamburacı, Sedef; Kimna, Ceren; Tıhmınlıoğlu, FundaMedicinal plants are attracting considerable interest as a potential therapeutic agent for bone tissue regeneration. Cissus quadrangularis L. is also a medicinal plant known with its osteogenic activity. In this study, a phytochemical scaffold was produced by incorporating Cissus quadrangularis with chitosan/Na-carboxymethyl cellulose blend by lyophilization technique. The effect of Cissus quadrangularis loading on the mechanical, morphological, chemical, and degradation properties as well as in vitro cytotoxicity, cell proliferation, and differentiation of the composites was investigated. Scanning electron microscopy images showed that porous Cissus quadrangularis-loaded scaffolds were obtained with an average pore size of 148-209 mu m which is appropriate for bone regeneration. Cissus quadrangularis incorporation enhanced the compression modulus of scaffolds from 76 to 654 kPa. In vitro cell culture results indicated that Cissus quadrangularis/chitosan/Na-carboxymethyl cellulose scaffolds provided a favorable substrate for the osteoblast adhesion, proliferation, and mineralization. Results supported the osteoinductive property of the Cissus quadrangularis extract-incorporated scaffolds even without osteogenic media supplement. Cissus quadrangularis extract increased the alkaline phosphatase activity of the SaOS-2 cells on scaffolds on 7th and 14th days of incubation. The investigation of characterization and cell culture studies suggest that Cissus quadrangularis-loaded osteoinductive Cissus quadrangularis/chitosan/Na-carboxymethyl cellulose scaffold can serve as a potential biomaterial for bone tissue engineering applications.Article Citation - WoS: 15Citation - Scopus: 17Improved 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, Gülşahalpha-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.Article Citation - WoS: 5Citation - Scopus: 10Performance Evaluation of Webrtc-Based Online Consultation Platform(Türkiye Klinikleri Journal of Medical Sciences, 2019) Tarım, Ergün Alperay; Tekin, Hüseyin CumhurInformation technologies give patients the opportunity to communicate with medical professionals remotely. Telemedicine uses these technologies to provide advanced healthcare and medical services. We present a medical online consultation application based on Web Real-Time Communications (WebRTC) technology enabling chat, audio, and video calls. Communication architecture and protocols of the application are explained in detail. Additionally, the user interface of the application is shown via performed calls. The application is tested and evaluated on different network connections (3G, 4G, local, and DSL) and different browsers and mobile operating systems (Android, Chrome, Firefox, Internet Explorer, iOS, Opera, Safari). During calls, communication quality parameters such as round-trip time (RTT) and packet loss, obtained via the WebRTC application programming interface, are analyzed. 3G, 4G, and local connections show low packet losses (<1%). Packet losses are high (>1%) in Android, Chrome, iOS, Opera, and Safari for DSL connection, but RTT values are low (<100 ms) in all different conditions excluding iOS. In the presented application, RTT and packet loss remain lower than 100 ms and 1%, respectively, in various scenarios, indicating good communication quality. RTT and packet loss are related to total time and hang time parameters, which describe the necessary time to establish and to end a call. It is shown that communication quality of the application can simply be measured by analyzing the total time parameter. This enables predictable information for communication quality for WebRTC-based applications without continuously monitoring RTT and packet loss for the first time.