Bioengineering / Biyomühendislik

Permanent URI for this collectionhttps://hdl.handle.net/11147/4529

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  • Conference Object
    Citation - WoS: 1
    Kinetic and Thermodynamic Properties of Crude and Three-Phase Partitioned Polygalacturonase From Aspergillus Sojae
    (Elsevier, 2007) Doğan, Nergiz; Tari, Canan; Göğüş, Nihan
    Commercial preparations of pectinolytic enzymes derived from fungi are well known to have high biotechnological value in the industry. Since potential applications of pectinases in vari- ous fields of food, paper, textile and waste water treatment are increasing, it is important to understand the properties of these enzymes for efficient and effective usage.
  • Conference Object
    Effect of Symbiotic Relationship of Lactobacillus Butgaricus 77 and Streptococcus Thermophilus 9512 on Betagalactosidase and Lactic Acid Production
    (Elsevier, 2007) Üstok, Fatma Işık; Tari, Canan; Harsa, Şebnem
    Enzyme production which is a growing field of biotechnology has an annual world sale close to billion dollars. Therefore isolation of new strains producing novel enzymes is important for industrial enzyme production.
  • Conference Object
    Citation - WoS: 1
    Optimization of Exo-Polygalacturonase Production From Orange Peel by Aspergillus Sojae
    (Elsevier, 2010) Büyükkileci, Ali Oğuz; Tarı, Canan; Fernandez-Lahore, H. M.; Gençkal Demir, Hande; Göğüş, Nihan
    Pectinases catalyze the degradation of pectic substances, thus they are used extensively in fruit juice and wine industry to facil-itate extraction and clarification. Aspergillus species, in particular Aspergillus niger, have long been utilized for production of pectinases. Previous studies of our group showed that A. sojae has a potential to produce enhanced amount of polygalacturonase, which is one of the pectic enzymes, in both submerged and solid-state cultures (Gogus et al., 2006; Tari et al., 2007). In this study, several agricultural products were screened in an effort to find a cheap and abundant substrate for submerged polygalacturonase production using a UV-mutated A. sojae strain. Medium composition was optimized to further enhance the enzyme level. Experiments were designed and analyzed statistically using the trial version of the statistical software, Design Expert.
  • Article
    Citation - WoS: 13
    Citation - Scopus: 15
    Cytotoxic Tolerance of Healthy and Cancerous Bone Cells To Anti-Microbial Phenolic Compounds Depend on Culture Conditions
    (Humana Press, 2019) Karadaş, Özge; Meşe, Gülistan; Özçivici, Engin
    Carnosol and carnosic acid are polyphenolic compounds found in rosemary and sage with known anti-oxidant, anti-inflammatory, and anti-microbial properties. Here, we addressed the potential use of carnosol and carnosic acid for in vitro bone tissue engineering applications, specifically depending on their cytotoxic effects on bone marrow stromal and stem cells, and osteosarcoma cells in monolayer and 3D cultures. Carnosol and carnosic acid displayed a bacteriostatic effect on Gram-positive bacteria, especially on S. aureus. The viability results indicated that bone marrow stromal cells and bone marrow stem cells were more tolerant to the presence of carnosol compared to osteosarcoma cells. 3D culture conditions increased this tolerance further for healthy cells, while not affecting the cytotoxic potential of carnosol for osteosarcoma cells. Carnosic acid was found to be more cytotoxic for all cell types used in the study. Results suggest that phenolic compounds might have potential use as anti-microbial and anti-carcinogenic agents for bone tissue engineering with further optimization for controlled release.
  • Article
    Citation - WoS: 79
    Citation - Scopus: 93
    Magnetic Force-Based Micro Fluidic Techniques for Cellular and Tissue Bioengineering
    (Frontiers Media S.A., 2018) Yaman, Sena; Anıl İnevi, Müge; Özçivici, Engin; Tekin, Hüseyin Cumhur
    Live cell manipulation is an important biotechnological tool for cellular and tissue level bioengineering applications due to its capacity for guiding cells for separation, isolation, concentration, and patterning. Magnetic force-based cell manipulation methods offer several advantages, such as low adverse effects on cell viability and low interference with the cellular environment. Furthermore, magnetic-based operations can be readily combined with microfluidic principles by precisely allowing control over the spatiotemporal distribution of physical and chemical factors for cell manipulation. In this review, we present recent applications of magnetic force-based cell manipulation in cellular and tissue bioengineering with an emphasis on applications with microfluidic components. Following an introduction of the theoretical background of magnetic manipulation, components of magnetic force-based cell manipulation systems are described. Thereafter, different applications, including separation of certain cell fractions, enrichment of rare cells, and guidance of cells into specific macro- or micro-arrangements to mimic natural cell organization and function, are explained. Finally, we discuss the current challenges and limitations of magnetic cell manipulation technologies in microfluidic devices with an outlook on future developments in the field.
  • 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
    Evaluation of Anti-Inflammatory Potential and Lc-ms/Ms Analysis of Different Standards
    (Wiley, 2018) Sözmen, Alper Baran; Canbay, E.; Yıldırım Sözmen, Eser; Övez, Bikem
    Standardization 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: 6
    Antioxidant, Antimicrobial and Cytotoxic Activities of Extracts From Some Selected Mediterranean Shrub Species (maquis)
    (Biointerface Research Applied Chemistry, 2016) Bayraktar, Oğuz; Altıok, Evren; Yılmazer, Özgür; Rusçuklu, Dane; Büyüköz, Melda
    In this study in vitro antioxidant, antimicrobial and cytotoxic activities of ethanol extracts of some plants from Urla region in Turkey were investigated. Plant material samples of Pistacia lentiscus, Vitex agnus-castus, Cistus creticus and Nerium oleander were collected in October, November and December. The harvesting time significantly affected their antioxidant, antimicrobial and cytotoxic activities of these plant extracts. The highest biological activities in terms of antioxidant, antimicrobial and cytotoxic activities were observed for the leaf extract of C. creticus. The applied doses of leaf extracts of C. creticus, P. lentiscus, and N. oleander resulted in higher Bax and GAPDH expressions than those for control cells. These plant extracts may trigger apoptosis and may be a promising natural source for prostate cancer treatment.
  • Article
    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.
  • Article
    Citation - WoS: 5
    Citation - Scopus: 10
    Performance Evaluation of Webrtc-Based Online Consultation Platform
    (Türkiye Klinikleri Journal of Medical Sciences, 2019) Tarım, Ergün Alperay; Tekin, Hüseyin Cumhur
    Information 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.