WoS İndeksli Yayınlar Koleksiyonu / WoS Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7150
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Article Citation - WoS: 4Citation - Scopus: 5Antioxidant and Antimicrobial Activities of Plants Grown in the Mediterranean Region(John Wiley and Sons Inc., 2022) Kaçar, D.; Bayraktar, Oğuz; Erdem, C.; Alamri, A.S.; Galanakis, C.M.Background: The main objective of this research was to identify plant species with possible bioactivities based on their total phenol content, antioxidant, and antimicrobial properties. Therefore, different parts of 42 plant species grown in the Mediterranean region were extracted with aqueous ethanol solutions to prepare extracts with antioxidant and antimicrobial activities, mainly resulting from their total phenol contents. No detailed laboratory data on the flora of this area exists regarding their total phenol contents and total antioxidant activities. Results: Yields of extraction for each plant material were determined. Extracts were characterized based on their total phenol contents, total antioxidant (both hydrophilic and lipophilic), and antimicrobial activities using Folin–Ciocalteu, Photochemiluminescence, disc diffusion, and microdilution methods, respectively. The extract of Hypericum empetrifolium had the relatively highest total water-soluble and lipid-soluble antioxidant activities. Sarcopoterium spinosum extract had relatively high total phenol content. Preliminary screening study was conducted with the disc diffusion method to evaluate the extracts' antimicrobial activities. 26 out of 42 plant species showed significant antimicrobial activities against the growth of microorganisms. Microdilution assays were performed to evaluate the most active plant species with their minimum inhibition concentrations. H. empetrifolium, Pistacia terebinthus, Arbutus unedo, and Cistus parviflorus were the most antimicrobial plant species among those investigated. CONCLUSION: The new potential sources for the isolation of bioactive natural compounds from specific plant species could be possible with the help of this present screening study. Isolated bioactive natural compounds can be utilized as raw materials in cosmetics, nutraceuticals, food supplements, and pharmaceutical industries. © 2022 Society of Chemical Industry.Article Citation - WoS: 27Citation - Scopus: 28Biocomposite Scaffolds for 3d Cell Culture: Propolis Enriched Polyvinyl Alcohol Nanofibers Favoring Cell Adhesion(John Wiley and Sons Inc., 2021) Bilginer, Rumeysa; Özkendir İnanç, Dilce; Yıldız, Ümit Hakan; Arslan Yıldız, AhuThe 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.Article Citation - WoS: 22Citation - Scopus: 24Scaffold-Free Biofabrication of Adipocyte Structures With Magnetic Levitation(John Wiley and Sons Inc., 2021) Sarıgil, Öykü; Yalçın Özuysal, Özden; Anıl İnevi, Müge; Meşe Özçivici, Gülistan; Fıratlıgil Yıldırır, Burcu; Fıratlıgil Yıldırır, Burcu; Ünal, Yağmur Ceren; Ünal, Yağmur Ceren; Yalçın Özuysal, Özden; Özçivici, Engin; Meşe, Gülistan; Sarıgil, Öykü; Özçivici, Engin; Anıl İnevi, Müge; Meşe Özçivici, GülistanTissue engineering research aims to repair the form and/or function of impaired tissues. Tissue engineering studies mostly rely on scaffold-based techniques. However, these techniques have certain challenges, such as the selection of proper scaffold material, including mechanical properties, sterilization, and fabrication processes. As an alternative, we propose a novel scaffold-free adipose tissue biofabrication technique based on magnetic levitation. In this study, a label-free magnetic levitation technique was used to form three-dimensional (3D) scaffold-free adipocyte structures with various fabrication strategies in a microcapillary-based setup. Adipogenic-differentiated 7F2 cells and growth D1 ORL UVA stem cells were used as model cells. The morphological properties of the 3D structures of single and cocultured cells were analyzed. The developed procedure leads to the formation of different patterns of single and cocultured adipocytes without a scaffold. Our results indicated that adipocytes formed loose structures while growth cells were tightly packed during 3D culture in the magnetic levitation platform. This system has potential for ex vivo modeling of adipose tissue for drug testing and transplantation applications for cell therapy in soft tissue damage. Also, it will be possible to extend this technique to other cell and tissue types.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: 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: 1Citation - Scopus: 1Triploid Induction of Green Tiger Shrimp, Penaeus Semisulcatus (de Haan, 1844) Using Temperature and Chemical Shock(John Wiley and Sons Inc., 2015) Kır, Mehmet; Tarhan, Gökhan; Okur, ÖzgürTriploidy in fertilized eggs of Penaeus semisulcatus was induced by temperature and chemical shocks. The eggs, which were obtained from the shrimp broodstock maintained at 29C, were exposed to cold temperature (8, 10, 12, and 14 C) and 6-dimetiloaminopurine (6-DMAP) concentrations (100, 150, 200, and 250 μM) for different durations (4, 6, and 8min) 9min after spawning was detected. While the highest triploidy rate of 49.7±4.5% was obtained with a 200μM 6-DMAP concentration for a duration of 8min, the best mean triploidy rate of 45.5±2.8% for cold shock was obtained at a temperature of 10 C for a duration of 8min. Temperature and 6-DMAP concentration did not have significant effect on triploidy rate (P>0.05) but shock duration had significant effect on triploidy rate for individual cold temperature shock or 6-DMAP chemical shock (P<0.05). Although longer durations of shock agent increased the rates of triploid induction, they generally had an adverse effect on hatching rates in the study.Article Citation - WoS: 1Citation - Scopus: 2Induction of Triploidy in Melicertus Kerathurus (forskal, 1775) With Temperature Shock(John Wiley and Sons Inc., 2016) Kır, Mehmet; Şahan, Ali Kemal; Okur, ÖzgürTriploidy in fertilized eggs of Melicertus kerathurus was induced by cold (8, 10, 12°C) and heat (34, 36, 38°C) shock for different duration times (2, 4 and 8 min) after 10 min of post spawning. The best individual treatment produced 64.5% triploid nauplii in cold shock application at a temperature of 10°C for a duration of 8 min. Temperature did not have significant effect (P > 0.05) on triploid rate but duration time had a significant effect (P < 0.05) for individual cold or heat shock. This study demonstrates that because of a wide variety of effective parameters, it is essential to optimize shock conditions for each species strain at each location. © 2016 John Wiley & Sons Ltd.Article Citation - WoS: 30Citation - Scopus: 35Bioactive Sheath/Core Nanofibers Containing Olive Leaf Extract(John Wiley and Sons Inc., 2016) Doğan, Gamze; Başal, Güldemet; Bayraktar, Oğuz; Özyıldız, Figen; Uzel, Ataç; Erdoğan, İpekThis study aimed at producing silk fibroin (SF)/hyaluronic acid (HA) and olive leaf extract (OLE) nanofibers with sheath/core morphology by coaxial electrospinning method, determining their antimicrobial properties, and examining release profiles of OLE from these coaxial nanofibers. Optimum electrospinning process and solution parameters were determined to obtain uniform and bead-free coaxial nanofibers. Scanning electron microscopy and transmission electron microscopy (TEM) were used to characterize the morphology of the nanofibers. The antimicrobial activities of nanofibers were tested according to AATCC test method 100. Total phenolic content and total antioxidant activity were tested using in vitro batch release system. The quality and quantity of released components of OLE were determined by high-performance liquid chromatography. The changes in nanofibers were examined by Fourier-transform infrared spectroscopy. Uniform and bead-free nanofibers were produced successfully. TEM images confirmed the coaxial structure. OLE-loaded nanofibers demonstrated almost perfect antibacterial activities against both of gram-negative and gram-positive bacteria. Antifungal activity against C. albicans was rather poor. After a release period of 1 month, it was observed that ∼70-95% of the OLE was released from nanofibers and it was still bioactive. Overall results indicate that the resultant shell/core nanofibers have a great potential to be used as biomaterials.Article Citation - WoS: 3Citation - Scopus: 3Effects of Different Lipopolysaccharide Preparations on Neutrophil Function in the Fathead Minnow, Pimephales Promelas Rafinesque(John Wiley and Sons Inc., 2011) Jovanovic, B.; Baran, Ezgi; Goetz, F. W.; Palic, D.The fish innate immune response to pathogensrelies on the adequate function of neu trophilicgranulocytes (Palic´, Andreasen, Herolt, Menzel &Roth 2006). The ability of neutrophils to phago-cytose microor ganisms and cellular debris is essen-tial for normal development an d survival of animalpopulations (Segal 2005). The evaluation of neu-trophil function is valuable for assessing the healthstatus of individuals and fish populations (Smith &Lumsden 1983). Resistance of fishes to septic shockand tolerance to high concentrations of lipopoly-saccharide (LPS) was observed as a major differencebetween mammalian and fish innate immuneresponses (Berczi, Bertok & Bereznai 1966). Thisfunctional difference could be attri buted to severalcostimulatory molecules and intracellular mediatorsbeing absent in fish, but active in mammals duringresponse to LPS stimulation (Iliev, Roach, Mac-kenzie, Planas & Goetz 2005). Most fish do notpossess a Toll-like receptor (TLR) with sequencesimilarity to mammalian TLR4 (Leulier & Lemai-tre 2008) and the ones that do have no ability forTLR4 downstream signalling (Sepulcre, Alcaraz-Perez, Lopez-Munoz, Roca, Meseguer, Cayuela &Mulero 2009). Regardless of the absence andfunctionality of TLR4 and costimulatory molecules,bacterial LPS can induce a robus t inflammatorygene response in innate immune fish cells, but atconcentrations 1000-fold higher than is commonlyobserved in mammalian species ( lgmL)1vs.ng mL)1) (Palic´, Ostojic, Andreasen & Roth2007; Mackenzie, Roher, Boltan˜a & Goetz 2010).In contrast, ultrapure LPS preparations are rela-tively inactive in fish (Iliev et al. 2005).Article Citation - WoS: 22Citation - Scopus: 21A Novel Silk Fibroin-Supported Iron Catalyst for Hydroxylation of Phenol(John Wiley and Sons Inc., 2006) Pekşen, Bahar Başak; Üzelakçil, Caner; Güneş, Alev; Malay, Özge; Bayraktar, OğuzThe aim of this study was to explore the potential use of silk fibroin (SF) as a catalyst support material for phenol hydroxylation reactions. Iron-substituted silk fibroin fibers were prepared using formic acid at room temperature and characterized using inductively coupled plasma atomic-emission spectrometry, scanning electron microscopy, Fourier transform infrared spectroscopy (FTIR) and optical microscopy. Measurement of an FTIR spectrum showed that the secondary structure was β-structure before and after iron substitution. To evaluate the catalytic properties of prepared catalyst, phenol hydroxylation reaction was carried out using aqueous hydrogen peroxide as an oxidant. An excellent transformation of phenol into dihydroxybenzenes (catechol and hydroquinone) was achieved. Phenol conversions of 3.3%, 61.2%, and 80.3% were obtained at room temperature, 40°C and 60°C respectively. It was found that no further phenol conversion proceeded because catalysts became separated from the reaction system during the reaction. No significant leaching of the iron was detected. Catalyst could be reused several times without a significant change in activity. Parent silk fibroin fibers without iron were inactive.