Biyoinformatik ve Genetik Bölümü Koleksiyonu

Permanent URI for this collectionhttps://hdl.handle.net/20.500.12469/46

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Citation - WoS: 5
Citation - Scopus: 5
Temperature Dependence of Oxygen Diffusion Into Clay-Doped Ps Films
(John Wiley & Sons Inc, 2010) Uğur, Şaziye; Yargı, Önder; Pekcan, Önder
Fluorescence technique was employed for the measurement of the diffusion coefficient of oxygen into polystyrene (PS) latex/modified Na-activated bentonite (MNaLB) clay composite films. Three different MNaLB content (0 5 and 20 wt%) composite films were prepared from PS/MNaLB mixtures by annealing them at 200 degrees C above the glass transition temperature of PS for 10 min. To determine the diffusivity of oxygen in PS/MNaLB composite films diffusion measurements were performed over the temperature range from 25 to 70 degrees C. Pyrene (P) was used as the fluorescent agent. The diffusion coefficients (D) of oxygen were determined by combining the fluorescence quenching method with Fickian transport model and were found as a function of temperature for each MNaLB content film. The results showed that D values are strongly dependent on both temperature and clay content in composite film. It was also observed that D coefficients obey Arrhenius behavior from where diffusion activation energies were measured. POLYM. COMPOS. 31:77-82 2010. (C) 2009 Society of Plastics Engineers
Citation - WoS: 7
Citation - Scopus: 12
Design, Synthesis and Hmao Inhibitory Screening of Novel 2-Pyrazoline Analogues
(Bentham Science Publ Ltd, 2017) Evranos-Aksöz, Begüm; Uçar, Gülberk; Yelekçi, Kemal
Aim and Objective: MAO inhibitors have a significant effect on the nervous system since they act in regulation of neurotransmitter concentrations. Neurotransmitter levels are critical for a healthy nervous system. MAO inhibitors can be used in the treatment of neurological disorders such as depression, Parkinson's disease and Alzheimer's disease, as the increase or decrease of some neurotransmitter concentrations is associated with these neurological disorders. This study was conducted to discover new and active MAO inhibitor drug candidates. Materials and Methods: New pyrazoline derivatives have been designed with the molecular docking approach and interactions of our compounds with the MAO enzyme have been investigated using the Autodock 4.2 program. The designed pyrazoline derivative compounds were synthesized by the reaction of the chalcones and hydrazides in ethanol. hMAO inhibitory activities of the newly synthesized compounds were investigated by fluorimetric method. In vitro cytotoxicity of five most potent inhibitors were tested in HepG2 cells. Results: (3-(5-bromo-2-hydroxyphenyl)-5-(4-methoxyphenyl)-4,5-dihydropyrazol-1-yl)(phenyl) methanone (5i) and (3-(2-hydroxy-4-methoxy phenyl)-5-p-tolyl-4,5-dihydropyrazol-1-yl)(phenyl) methanone (5l) inhibited hMAO-A more potently than moclobemide (Ki values are 0.004 +/- 0.001 and 0.005 +/- 0.001, respectively). The same two compounds, 5i and 5l, inhibited hMAO-A more selectively than moclobemide (SI values are 5.55x10(-5) and 0.003, respectively). Both of these compounds were found non toxic at 1 mu M, 5 mu M and 25 mu M concentrations. Conclusion: Two of the newly synthesized compounds, (3-(5-bromo-2-hydroxyphenyl)-5-(4-methoxyphenyl)- 4,5-dihydropyrazol-1-yl)(phenyl) methanone and (3-(2-hydroxy-4-methoxy phenyl)5- p-tolyl-4,5-dihydropyrazol-1-yl)(phenyl) methanone were found to be promising MAO-A inhibitors due to their high inhibitory potency, high selectivity and low toxicity.
Citation - WoS: 52
Citation - Scopus: 59
Surfactant and Metal Ion Effects on the Mechanical Properties of Alginate Hydrogels
(Elsevier Science Bv, 2016) Kaygusuz, Hakan; Evingür, Gülşen Akin; Pekcan, Önder; von Klitzing, Regine; Erim, F. Bedia
This paper addresses the controlled variation of the mechanical properties of alginate gel beads by changing the alginate concentration or by adding different surfactants or cross-linking cations. Alginate beads containing nonionic Brij 35 or anionic sodium dodecyl sulfate (SDS) surfactants were prepared with two different types of cations (Ca2+ Ba2+) as crosslinkers. Compression measurements were performed to investigate the effect of the surfactant and cation types and their concentrations on the Young's modulus of alginate beads. The Young's modulus was determined by using Hertz theory. For all types of alginate gel beads the Young's modulus showed an increasing value for increasing alginate contents. Addition of the anionic surfactant SDS increases the Young's modulus of the alginate beads while the addition of non-ionic surfactant Brij 35 leads to a decrease in Young's modulus. This opposite behavior is related to the contrary effect of both surfactants on the charge of the alginate beads. When Ba2+ ions were used as crosslinker cation the Young's modulus of the beads with the surfactant SDS was found to be approximately two times higher than the modulus of beads with the surfactant Brij 35. An ion specific effect was found for the crosslinking ability of divalent cations. (C) 2016 Elsevier B.V. All rights reserved.
Citation - WoS: 4
Citation - Scopus: 4
The Modifier Effects of Chymotrypsin and Trypsin Enzymes on Fluorescence Lifetime Distribution of "n-(1 Serum Albumin" Complex
(Pergamon-Elsevier Science LTD, 2016) Özyiğit, İbrahim Ethem; Karakuş, Emine; Pekcan, Önder
Chymotrypsin and trypsin are the well known proteolytic enzymes, both of which are synthesized in the pancreas as their precursors the inactive forms; chymotrypsinogen and trypsinogen and then are released into the duodenum to cut proteins into smaller peptides. In this paper, the effects of activities of chymotrypsin and trypsin enzymes on fluorescence lifetime distributions of the substrat bovine serum albumin (BSA) modified with N-(1-pyrenyl)maleimide (PM) were examined. In the labeling study of BSA with PM, it is aimed to attach PM to the single free thiol (Cys34) and to all the free amine groups in accessible positions in order to produce excimers of pyrene planes of the possible highest amount to form the lifetime distributions in the widest range, that may show specifically distinguishing changes resulting from the activities of the proteases. The time resolved spectrofluorometer was used to monitor fluorescence decays, which were analyzed by using the exponential series method (ESM) to obtain the changes of lifetime distributions. After the exposure of the synthesized substrat PM-BSA to the enzymes, the fluorescence lifetime distributions exhibited different structures which were attributed to the different activities of the proteases. (C) 2015 Elsevier B.V. All rights reserved.
Fluorescence Technique for Monitoring Swelling of Paam-Kappa Gel Composites
(Shaker Publishing, 2009) Evingür, Gülşen Akin; Aktaş, Demet Kaya; Pekcan, Önder
Steady-state fluorescence (SSF) technique was employed for studying swelling of polyacrylamide (PAAm) gels with various content of kappa- carrageenan. Disc shaped composite gels were prepared by free-radical cross/inking copolymerization of acrylamide (AAm) with various amounts of kappa-carrageenan (kappa C) using N N'- methylenebis (acrylamide) (BIS) as crosslinker in the presence of ammonium persulfate (APS) initiator. Pyranine was introduced as a fluorescence probe. Fluorescence intensity of pyranine was monitored during in situ swelling processes of composite gels. It was observed that fluorescence intensity values decreased as swelling is proceeded. The Li-Tanaka equation was used to determine the swelling time constants tau and cooperative diffusion coefficients D from intensity variations during the swelling processes. It was shown that tau decreased and D increased as the kappa C content in the composites are increased.
Citation - WoS: 5
Citation - Scopus: 7
Thermal Phase Transitions of Agarose in Various Compositions: a Fluorescence Study
(Springer/Plenum Publishers, 2011) Kara, Selim; Arda, Ertan; Dolastir, Fahrettin; Pekcan, Önder
The effect of agarose content on thermal phase transitions of the agarose gels was investigated by using Steady State Fluorescence (SSF) method. Scattered light I(sc) and fluorescence intensity I(fl) were monitored against temperature during heating and cooling processes to investigate phase transitions. Two regions were observed during the heating and cooling processes. At the high temperature region double helix to coil (h-c) transition took place. However during the cooling process coil to double helix (c-h) transitions occurred at low temperature region. Transition energies were determined using the Arrhenius treatment and found to be strongly correlated with the agarose content in the gel system. Transition temperatures were determined from the derivative of the sigmoidal transition paths and found to be increased by increasing agarose content in both cases.
Measurement of Oxygen Diffusion in Ps/Pnipam Films Using Fluorescence Quenching
(Taylor & Francis Ltd, 2015) Yargı, Önder; Pekcan, Önder; Uğur, Şaziye
The diffusion of oxygen into pyrene labelled polystyrene (PS) latex/poly(N-isopropylacrylamide) (PNIPAM) composite films (PS/PNIPAM) was studied based on PS content with the use of fluorescence quenching method. Fluorescence experiments were carried out on composite films containing pyrene as a sensor dye. The Stern-Volmer equation for fluorescence quenching is combined with Fick's law for diffusion to derive mathematical expressions. Diffusion coefficients (D) were produced and found to be decreased with increasing PS content. This decrease was explained with the formation of a tortuous path for diffusing gas molecules which extends the diffusion path of oxygen in the films. In addition at high PS content two different D values were obtained which were attributed to the existence of two different areas in the composite films.
Citation - WoS: 10
Citation - Scopus: 11
Synthesis, Anticancer Activity on Prostate Cancer Cell Lines and Molecular Modeling Studies of Flurbiprofen-Thioether Derivatives as Potential Target of Metap (type Ii)
(Bentham Science PUBL LTD, 2020) Yılmaz, Özgür; Bayer, Burak; Bekçi, Hatice; Uba, Abdullahi, I; Cumaoğlu, Ahmet; Yelekçi, Kemal; Küçükgüzel, S. Guniz
Background: Prostate cancer is still one of the serious causes of mortality and morbidity in men. Despite recent advances in anticancer therapy, there is a still need of novel agents with more efficacy and specificity in the treatment of prostate cancer. Because of its function on angiogenesis and overexpression in the prostate cancer, methionine aminopeptidase-2 (MetAP-2) has been a potential target for novel drug design recently. Objective: A novel series of Flurbiprofen derivatives N-(substituted)-2-(2-(2-fluoro-[1,1'-biphenyl]-4-il)propanoyl)hydrazinocarbothioamide (3a-c), 4-substituted-3 -(1 -(2-fluoro-[1,1'-biphenyl]-4-yl)ethyl)-1H-1,2,4-triazole-5(4H)-thione (4a-d), 3-(substitutedthio)-4-(substituted-pheny1)5-(1-(2-fluoro-[1,1'-biphenyt]-4-yl)ethyl)-411-1,2,4-triazole (5a-y) were synthesized. The purpose of the research was to evaluate these derivatives against MetAP-2 in vitro and in silico to obtain novel specific and effective anticancer agents against prostate cancer. Methods: The chemical structures and purities of the compounds were defined by spectral methods (H-1-NMR, C-13-NMR, HR-MS and FT-IR) and elemental analysis. Anticancer activities of the compounds were evaluated in vitro by using MTS method against PC-3 and DU-143 (androgenindependent human prostate cancer cell lines) and LNCaP (androgen-sensitive human prostate adenocarcinoma) prostate cancer cell lines. Cisplatin was used as a positive sensitivity reference standard. Results: Compounds 5b and 5u; 3c, 5b and 5y; 4d and 5o showed the most potent biological activity against PC3 cancer cell line (IC50 = 27.1 mu M, and 5.12 mu M, respectively), DU-145 cancer cell line (IC50 - 11.55 mu M, 6.9 mu M and 9.54 mu M, respectively) and LNCaP cancer cell line (IC50 - 11.45 mu M and 26.91 mu M, respectively). Some compounds were evaluated for their apoptotic caspases protein expression (EGFR/PI31C/AKT pathway) by Western blot analysis in androgen independent-PC3 cells. BAX, caspase 9, caspsase 3 and anti-apoptotic BcL-2 mRNA levels of some compounds were also investigated. In addition, molecular modeling studies of the compounds on MetAP-2 enzyme active site were evaluated in order to get insight into binding mode and energy. Conclusion: A series of Flurbiprofen-thioether derivatives were synthesized. This study presented that some of the synthesized compounds have remarkable anticancer and apoptotic activities against prostate cancer cells. Also, molecular modeling studies exhibited that there is a correlation between molecular modeling and anticancer activity results.
Citation - WoS: 4
Citation - Scopus: 4
Modelling of Swelling by the Fluorescence Technique in Kappa Carrageenan Gels
(Amer Inst Physics, 2011) Tari, Özlem; Pekcan, Önder
Kappa (-kappa) carrageenan gels prepared with various carrageenan concentrations in pure water were completely dried and then swelled in water vapor. Steady state fluorescence measurements were performed using a spectrometer equipped with temperature controller. Pyranine was embedded in kappa-carrageenan gels as a fluorescence probe during gel preparation. The fluorescence intensity I increased exponentially as swelling time is increased for all gel samples. The increase in I was modelled using Li-Tanaka equation from which swelling time constants tau(c) and cooperative diffusion coefficients D-c were determined. It was observed that D-c increased as the swelling temperature was increased. On the other hand at each temperature it was seen that D-c decreased as kappa carrageenan concentration was increased. Activation energies for swelling were obtained and found to be 57.4 58.3 and 62.73kJ mol(-1) for the gels with increasing amount of kappa-carrageenan content.
Citation - WoS: 45
Citation - Scopus: 46
Optical Energy Band Gap of Paam-Go Composites
(Elsevier Science, 2018) Evingür, Gülşen Akin; Pekcan, Önder
Graphene oxide (GO) can be used as an electron acceptor for polymers. The generation of the exciton in such materials is intimately related to the optical band gap. Polyacrylamide (PAAm) - graphene oxide (GO) composites were prepared via free radical crosslinking copolymerization with GO content varying in the range between 5 and 40 mu l of GO. The influence of the GO content on the optical properties of the composites is characterized by ultraviolet visible spectrophotometer. The optical band gap of the composite has been calculated by using Tauc's model. The tail width of the localized states has been calculated by using Urbach's relation and the values of Urbach's energy with the variation of GO have been found from 289 to 296 eV. The results demonstrated that GO can be well dispersed in the PAAm-GO composites and consequently the optical band gap has been correlated with the various amounts of GO. (C) 2017 Elsevier Ltd. All rights reserved.
Citation - WoS: 2
Citation - Scopus: 3
Corrected Panel-Reactive Antibody Positivity Rates for Hypersensitized Patients in Turkish Population With Calculated Panel-Reactive Antibody Software
(Elsevier Science Inc, 2017) Karadeniz, Sedat Tanju; Akgül, Sebahat Usta; Öğret, Yeliz; Çiftçi, Hayriye Şentürk; Bayraktar, Adem; Bakkaloğlu, Hüseyin; Çalışkan, Yaşar Kerem; Yelekçi, Kemal; Türkmen, Aydin; Aydın, Ali Emin; Oğuz, Fatma Savran; Çarin, Mahmut Nezih; Aydın, Filiz
however the rate was 86.2% using the cPRA. Discussion. cPRA shows the rate of the rejected donors according to all unacceptable antigens. The need for a list of unacceptable antigens in place of the PRA positivity rate is a real change in the sensitization-dependent calculation as cPRA positivity rate. Conclusion. In principal implementation of cPRA will encourage many centers and laboratories to adopt a standard measurement of sensitization in Turkey. It will increase the chances of better donor match particularly for hypersensitized patients by the creation of an unacceptable mismatch program using cPRA software.
Fluorescence Study of Effect of Particle Size in Ps Latex/Al2o3 Nanocomposite Films
(MANEY PUBLISHING, 2015) Uğur, Şaziye; Sunay, M. Selin; Pekcan, Önder
Steady state fluorescence and BioUV-Visible techniques were used to study film formation of polystyrene (PS) latex and Al2O3 composites depending on PS particles size and Al2O3 content. Two film series (SmPS/Al2O3 and LgPS/Al2O3) were prepared covering PS sphere (SmPS: 203 nm
Effect of Content and Temperature on the Phase Transitions of Polymer Composites Doped by Kappa Carrageenan and Alginate
(Elsevier Academic Press Inc, 2016) Evingür, Gülşen Akın; Pekcan, Önder
[Abstract Not Available]
Citation - WoS: 8
Citation - Scopus: 7
Fractal Dimensions of Kappa-Carrageenan Gels During Gelation and Swelling
(Taylor & Francis Inc, 2018) Kara, Selim; Arda, Ertan; Pekcan, Önder
A photon scattering technique for research on the sol-gel and gel-sol transitions in kappa-carrageenan-water systems with various carrageenan contents (CC) was utilized for characterizing the fractal dimensions during gelation and swelling. It was observed that the scattered photon intensity I-sc increased at all temperatures with an increase in the CC when I-sc was monitored against temperature. Additionally the sol-gel transition temperatures were found to be much lower than the gel-sol transition temperatures causing hysteresis of the phase transition loops. I-sc increased with an increase in CC at all test temperatures which is attributed to the formation of a fractal-like carrageenan gel. After drying the gels were used in swelling experiments where the gels were immersed in water at room temperature reswelling to the original structure. It was observed that I-sc from the carrageenan gels increased as the CC was increased. The fractal dimension d during gelation was found to increase as the gelation temperature was increased. On the other hand the d values during swelling decreased as the swelling time was increased.
Citation - WoS: 17
Citation - Scopus: 18
Electrical and Optical Percolations in Pmma/Gnp Composite Films
(Taylor & Francis Ltd, 2018) Arda, Ertan; Mergen, Omer Bahadir; Pekcan, Önder
Effects of graphene nanoplatelet (GNP) addition on the electrical conductivity and optical absorbance of poly(methyl methacrylate)/graphene nanoplatelet (PMMA/GNP) composite films were studied. Optical absorbance and two point probe resistivity techniques were used to determine the variations of the optical and electrical properties of the composites respectively. Absorbance intensity A and surface resistivity R-s of the composite films were monitored as a function of GNP mass fraction (M) at room temperature. Absorbance intensity values of the composites were increased and surface resistivity values were decreased by increasing the content of GNP in the composite. Electrical and optical percolation thresholds of composite films were determined as M-sigma = 27.5 wt.% and M-op = 26.6 wt.% respectively. The conductivity and the optical results were attributed to the classical and site percolation theories respectively. Optical ((op)) and electrical ((sigma)) critical exponents were calculated as 0.40 and 1.71 respectively.
Medi 333-Histone Deacetylase Inhibition Activity of Resveratrol and Its Analogs
(Amer Chemical Soc, 2007) Dayangac-Erden, Didem; Ayhan, Peruze; Bora, Gamze; Yelekçi, Kemal; Dalkara, Sevim; Demir, Ayhan S.; Erdem-Yurter, Hayat
[Abstract Not Available]
Comp 297-Experimental and Molecular Docking Simulation Studies of Histone Deacetylases (hdacs) Enzyme Inhibitors
(Amer Chemical Soc, 2007) Yelekçi, Kemal; Bora, Gamze; Dayangaç-Erden, Didem; Ayhan, Peruze; Dalkara, Sevim; Demir, Ayhan S.; Erdem-Yurter, Hayat
[Abstract Not Available]
Citation - WoS: 15
Citation - Scopus: 21
Examining the Stability of Binding Modes of the Co-Crystallized Inhibitors of Human Hdac8 by Molecular Dynamics Simulation
(Taylor & Francis Inc, 2019) Uba, Abdullahi Ibrahim; Weako, Jackson; Keskin, Özlem; Gürsoy, Attila; Yelekçi, Kemal
Histone deacetylase (HDAC) 8 has been implicated as a potential therapeutic target in a variety of cancers neurodegenerative disorders metabolic dysregulation and autoimmune and inflammatory diseases. Several nonselective HDAC inhibitors have been co-crystallized with HDAC8. Molecular dynamics (MD) studies may yield valuable information on the structural stabilities of the complexes over time as determined by various pharmacophore features of the co-crystallized inhibitors. Here using 11 unmodified X-ray crystal structures of human HDAC8 (complexes) structure-based pharmacophore models were built and clustered based on distance - a function of the number of common pharmacophore features and the root-mean-squared displacement between the matching features. Based on this information a total of seven complexes (1T64 1W22 3RQD 3SFF 3F0R 5VI6 and 5FCW) were submitted to unrestrained 50 ns-MD simulations using nanoscale MD (NAMD) software. 1T64 (HDAC8 in complex with TSA) was found to show the highest stability over time presumably because of the TSA's ability to span HDAC8 catalytic channel and form a strong ionic interaction with zinc metal ion. Other stable complexes were 1W22 3SFF 3F0R and 5FCW. However 3RQD and 5VI6 showed relative instability over 50 ns time period. This may be attributed to bulkiness of the capping groups of both largazole thiol and trapoxin A making them unable to fit well into the active site of HDAC8. They rather formed steric clashes with residues on loop regions near the entrance to the channel. Thus 1T64 and similar crystal structures may be good candidates for HDAC8 structural dynamics studies and inhibitor design. Communicated by Ramaswamy H. Sarma
Epitope Based Hla Matching by Using Antibody Reactivity With High Resolution Allele Typing and Hlamatchmaker Algorithm Based Software
(Wiley, 2017) Karadeniz, Sedat Tanju; Akgül, Sebahat Usta; Çiftçi, Hayriye Şentürk; Öğret, Yeliz; Oğuz, Fatma; Yelekçi, Kemal; Aydın, Filiz
[Abstract Not Available]
Citation - WoS: 21
Citation - Scopus: 24
Conductivity Percolation of Carbon Nanotubes (cnt) in Polystyrene (ps) Latex Film
(Canadian Science Publishing Nrc Research Press, 2010) Uğur, Şaziye; Yargı, Önder; Pekcan, Önder
In this study the effect of multiwalled carbon nanotubes (MWNT) on film formation behaviour and electrical conductivity properties of polystrene (PS) latex film was investigated by using the photon transmission technique and electrical conductivity measurements. Films were prepared by mixing PS latex with different amounts of MWNTs varying in the range between 0 and 20 wt%. After drying MWNT content films were separately annealed above the glass transition temperature (T-g) of PS ranging from 100 to 270 degrees C for 10 min. To monitor film formation behavior of PS-MWNT composites transmitted light intensity I-tr was measured after each annealing step. The surface conductivity of annealed films at 170 degrees C was measured and found to increase dramatically above a certain fraction of MWNT (4 wt%) following the percolation theory. This fraction was defined as the percolation threshold of conductivity R-c. The conductivity scales with the mass fraction of MWNT as a power law with exponent 2.27 which is extremely close to the value of 2.0 predicted by percolation theory. In addition the increase in I-tr during annealing was explained by void closure and interdiffusion processes. Film formation stages were modeled and the corresponding activation energies were measured.

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