Bioengineering / Biyomühendislik
Permanent URI for this collectionhttps://hdl.handle.net/11147/4529
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Article Citation - WoS: 4A Src/Abl Kinase Inhibitor, Bosutinib, Downregulates and Inhibits Parp Enzyme and Sensitizes Cells To the DNA Damaging Agents(Türk Biyokimya Derneği, 2018) Kırmızıbayrak, Petek Ballar; İlhan, Recep; Yılmaz, Sinem; Günal, Selin; Tepedelen, Burcu ErbaykentBackground: Poly(ADP-ribosyl)ation (PARylation) catalyzed mainly by PARP1 is a highly regulated posttranslational modification associated with several pathways in cellular physiology and genotoxic deoxyribonucleic acid (DNA) damage response. PAR polymers and PARP enzyme function in DNA integrity maintenance and several PARP inhibitors have entered clinical phase studies for cancer therapies. Material and methods: The effect of bosutinib, a dual Src/Abl kinase inhibitor, on PARylation was fluorometrically measured. The cytotoxic and chemosensitizing effects were assessed by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. The levels of DNA repair proteins and PARP enzyme were examined by immunoblotting. Results: In this study, bosutinib is characterized as a novel PARP inhibitor. Bosutinib inhibited oxidative stress-induced cellular PARylation and nuclear foci formation by downregulating PARP1 levels. Bosutinib was found to be more cytotoxic on Capan1 cells with BRCA2 mutation. Furthermore by acting as a chemosensitizer, bosutinib enhanced the cytotoxicity of doxorubicin (DOXO) and etoposide (ETP) by decreasing phosphorylation of DNA repair enzymes checkpoint kinase 1 (Chk1) and ataxia-telangiectasia mutated (ATM). Conclusion: By inhibition of both PARP and DNA damage checkpoint kinases, bosutinib increased the phospho-H2AX levels, an early indicator of DNA double strand breaks.Article Citation - Scopus: 21Determination of Superoxide Dismutase Activities in Different Cyanobacteria for Scavenging of Reactive Oxygen Species(Taylor and Francis Ltd., 2015) Güneş, Seda; Tamburacı, Sedef; İmamoğlu, Esra; Dalay, Meltem ConkThere is considerable interest in cyanobacteria as sources of antioxidant pigments, antiinflammatory substances, enzymes such as superoxide dismutase (SOD) and vitamins. Antioxidant enzymes have significant role in the removal of reactive oxygen species produced during visible and ultraviolet irradiance stress in cyanobacteria. One of the most ubiquitous protective enzyme is superoxide dismutase (SOD). Most of cyanobacteria are known to have both FeSOD and MnSOD which are associated with photosystem I and II. These enzymes are responsible for scavenging superoxide radicals.Spirulina platensis and Synechococcus nidulans are widely used cyanobacteria as food supplement and cosmetic due to their bioactive compounds. Although the chemical composition of S.platensis has been investigated by many researchers, research on the relationship between protein content and comparison of SOD activity with other cyanobacteria is limited.Among several SOD producing cyanobacteria, the most promising organisms were investigate in terms of SOD activities in this study. The aim of the present work was to investigate and compare the SOD activities of different cyanobacteria including S. platensis, Pseudanabeana sp., S. nidulans and associate with protein contents. SOD activities of these cyanobacteria were determined by xanthine/xanthineoxidase method.Modified Lowry method was used for protein determination. The analysis results showed that the maximum specific SOD activity obtained was 50.4 U/mg from S.nidulans and the minimum specific SOD activity was 18.4 U/mg from Pseudanabeana sp. Total protein amount of S. nidulans, S. platensis, Pseudanabeana sp. was determined as 0.25 mg/ml, 0.27 mg/ml and 0.43 mg/ml respectively. As a result, Synechococcus nidulans was more efficient at scavenging peroxide radicals than Pseudanabeana sp. © 2015, © 2015 Har Krishan Bhalla & Sons.Article Citation - WoS: 14Citation - Scopus: 12Determination of the Chemical Composition and Antimicrobial Activity of Frankenia Hirsuta(Bangladesh Pharmacological Society, 2017) Canlı, Kerem; Şimşek, Özcan; Yetgin, Ali; Altuner, Ergin MuratFrankenia hirsuta is widely located in Turkey, but the antimicrobial potential and biochemical composition analysis of it weren't determined yet. By using the disk diffusion method, the susceptibility of 17 bacteria and 1 fungi were analyzed, which included Bacillus, Candida, Enterobacter, Enterococcus, Escherichia, Klebsiella, Listeria, Pseudomonas, Salmonella and Staphylococcus genera. 0.8, 1.5 and 3.1 mg of samples were prepared by using absolute ethanol. The bioactive composition of the plant extract was determined by gas chromatography-mass spectroscopy, and National Institute of Standards and Technology library was used for the mass spectra analysis. The results showed that F. hirsuta had antimicrobial activity against all of the studied micro-organisms except E. aerogenes and E. coli. Several active metabolites were identified, but some composition of this sample didn't match with the library. These results are the first report for the antimicrobial potential and biochemical composition of F. hirsuta.Article Citation - WoS: 18Citation - Scopus: 17Cnt Incorporated Polyacrilonitrile/Polypyrrole Nanofibers as Keratinocytes Scaffold(Trans Tech Publications, 2019) İnce Yardımcı, Atike; Aypek, Hande; Öztürk, Özgür; Yılmaz, Selahattin; Özçivici, Engin; Meşe, Gülistan; Selamet, YusufPolypyrrole (PPy) is an attractive scaffold material for tissue engineering with its non-toxic and electrically conductive properties. There has not been enough information about PPy usage in skin tissue engineering. The aim of this study is to investigate biocompatibility of polyacrilonitrile (PAN)/PPy nanofibrous scaffold for human keratinocytes. PAN/PPy bicomponent nanofibers were prepared by electrospinning, in various PPy concentrations and with carbon nanotube (CNT) incorporation. The average diameter of electrospun nanofibers decreased with increasing PPy concentration. Further, agglomerated CNTs caused beads and disordered parts on the surface of nanofibers. Biocompatibility of these PAN/PPy and PAN/PPy/CNT scaffolds were analyzed in vitro. Both scaffolds provided adhesion and proliferation of keratinocytes. Nanofiber diameter did not significantly influence the morphology of cells. However, with increasing number of cells, cells stayed among nanofibers and this affected their shape and size. In this study, we demonstrated that PAN/PPy and PAN/PPy/CNT scaffolds enabled the growth of keratinocytes, showing their biocompatibility.Article Citation - WoS: 26Citation - Scopus: 32Low-Intensity Vibrations Normalize Adipogenesis-Induced Morphological and Molecular Changes of Adult Mesenchymal Stem Cells(SAGE Publications Inc., 2017) Baskan, Öznur; Meşe, Gülistan; Özçivici, EnginBone marrow mesenchymal stem cells that are committed to adipogenesis were exposed daily to high-frequency low-intensity mechanical vibrations to understand molecular, morphological and ultrastructural adaptations to mechanical signals during adipogenesis. D1-ORL-UVA mouse bone marrow mesenchymal stem cells were cultured with either growth or adipogenic medium for 1 week. Low-intensity vibration signals (15 min/day, 90 Hz, 0.1 g) were applied to one group of adipogenic cells, while the other adipogenic group served as a sham control. Cellular viability, lipid accumulation, ultrastructure and morphology were determined with MTT, Oil-Red-O staining, phalloidin staining and atomic force microscopy. Semiquantitative reverse transcription polymerase chain reaction showed expression profile of the genes responsible for adipogenesis and ultrastructure of cells. Low-intensity vibration signals increased viability of the cells in adipogenic culture that was reduced significantly compared to quiescent controls. Low-intensity vibration signals also normalized the effects of adipogenic condition on cell morphology, including area, perimeter, circularization and actin cytoskeleton. Furthermore, low-intensity vibration signals reduced the expression of some adipogenic markers significantly. Mesenchymal stem cells are sensitive and responsive to mechanical loads, but debilitating conditions such as aging or obesity may steer mesenchymal stem cells toward adipogenesis. Here, daily application of low-intensity vibration signals partially neutralized the effects of adipogenic induction on mesenchymal stem cells, suggesting that these signals may provide an alternative and/or complementary option to reduce fat deposition.Article Citation - WoS: 4Citation - Scopus: 5Adsorption/Desorption and Biofunctional Properties of Oleuropein Loaded on Different Types of Silk Fibroin Matrices(The Society of Chemists and Techonogists of Macedonia, 2017) Bayraktar, Oğuz; Balta, Ali Bora; Başal Bayraktar, GüldemetThe objective of this study was to investigate the adsorption/desorption behavior of oleuropein on different types of silk fibroin matrices including silk fibroin microfibers (MF), regenerated silk fibroin (RSF), and silk fibroin nanofibers (NF). Nanofibers with an average diameter of ranging between 24 and 326 nm were successfully prepared using the electrospinning technique. The effects of the silk fibroin concentration, the voltage applied and the distance between needle tip and collector plate on the morphol-ogy of the NF were investigated. The adsorption capacities of MF, RSF and NF were determined as 104.92, 163.07 and 228.34 mg oleuropein per gram of material, respectively. The percentage of initially adsorbed oleuropein that was desorbed was 86.08, 91.29 and 96.67% for MF, RSF and NF, respectively. NF and RSF discs loaded with oleuropein were subjected to disc diffusion assays to determine their antibacterial activity against test microorganisms Staphylococcus epidermidis (Gram +) and Esche-richia coli (Gram -). The results showed that both biomaterials possessed antibacterial properties after loading with oleuropein. Wound scratch assays using oleuropein released from NF revealed an enhance-ment of cell migration, indicating a wound healing property of the material. In conclusion, the NF can be utilized as a biofunctional polymeric material with better perfor-mance for the adsorption and desorption of oleuropein compared with MF and RSF.Article Citation - WoS: 6Citation - Scopus: 9Secondary Metabolites From Astragalus Lycius and Their Cytotoxic Activities(SAGE Publications Inc., 2016) Horo, İbrahim; Kocabaş, Fatma; Alankuş Çalışkan, Özgen; Özgökçe, Fevzi; Khan, İhlas A.; Bedir, ErdalEight known secondary metabolites were isolated from the methanolic extract of the whole plant of Astragalus lycius Boiss. They were identified as 5,5'-dihydroxy-3'-methoxy-isoflavone-7-O-β-D-glucoside (1), genistin (2), sissotrin (3), 5,4'-dimethoxy-isoflavone-7-O-β-D-glucopyranoside (4), (7S,8R)-5-methoxydehydrodiconiferyl alcohol-4-O-β-D-glucopyranoside (5), 4-O-lariciresinol-glucoside (6), 2-phenylethyl-β-D-glucopyranoside (7) and β-sitosterol-3-O-β-D-glucopyranoside (8) by spectroscopic methods including 1H- and 13C-NMR and HR-MS experiments, and by comparison with literature values. Compounds 1-7 are reported for the first time from Astragalus taxa. All of the compounds were tested for their cytotoxic activities against a number of cancer cell lines. Among them, only 6 exhibited significant activity against human colon carcinoma (HT-29) at 2.69 μM concentration.Article Citation - WoS: 13Citation - Scopus: 13Genetic and Tissue Level Muscle-Bone Interactions During Unloading and Reambulation(International Society of Musculoskeletal and Neuronal Interactions, 2016) Judex, Stefan; Zhang, Weidong; Donahue, Leah Rae; Özçivici, EnginLittle is known about interactions between muscle and bone during the removal and application of mechanical signals. Here, we applied 3wk of hindlimb unloading followed by 3wk of reambulation to a genetically heterogeneous population of 352 adult mice and tested the hypothesis that changes in muscle are associated with changes in bone at the level of the tissue and the genome. During unloading and relative to normally ambulating control mice, most mice lost muscle and cortical bone with large variability across the population. During reambulation, individual mice regained bone and muscle at different rates. Across mice, changes in muscle and trabecular/cortical bone were not correlated to each other during unloading or reambulation. For unloading, we found one significant quantitative trait locus (QTL) for muscle area and five QTLs for cortical bone without overlap between mechano-sensitive muscle and cortical bone QTLs (but some overlap between muscle and trabecular QTLs). The low correlations between morphological changes in muscle and bone, together with the largely distinct genetic regulation of the response indicate that the premise of a muscle-bone unit that co-adjusts its size during (un)loading may need to be reassessed. © 2016, International Society of Musculoskeletal and Neuronal Interactions. All rights reserved.Article Kinetic and Structural Characterization of Interaction Between Trypsin and Equisetum Arvense Extract(Türk Biyokimya Derneği, 2014) Uslu, Mehmet Emin; Bayraktar, Oğuz; Ceylan, ÇağatayObjective: In this study the inhibitory effect of E. arvense extract on trypsin activity and the effect of trypsin on E. arvense extract were studied. In addition the nature of the interaction between the extract and trypsin was investigated. Methods: The inhibitory effect ethanol extract of E. arvense on trypsin activity was determined using trypsin enzyme assay. The structural effects of the extract-trypsin interaction for the extract were analyzed by FTIR. Finally, the HPLC analyses were carried out to analyze the individual components of the extract and the supernatant and soluble precipitate phases. Results: E. arvense extract was found to decrease total percent activity of trypsin to 5% in 24 hour at 24 °C. FTIR analyses indicated that the interaction between trypsin and E. arvense extract caused changes in the structure and hydrogen bonding behavior and composition of the extract proteins. These interactions also caused the extract lipids to accumulate in the insoluble precipitate phase. Most of the phenolics remained in the supernatant phase enhancing the inactivation of trypsin. However, the precipitated compounds were shown to be of apolar in nature as shown in the HPLC chromatograms. Conclusion: The methods that were used showed that the high phenolic content of E. arvense was the main reason for the inhibition of trypsin enzyme activity by denaturing the enzyme.