Biyoinformatik ve Genetik Bölümü Koleksiyonu
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Article Citation - WoS: 17Citation - Scopus: 20In Silico Design of Novel and Highly Selective Lysine-Specific Histone Demethylase Inhibitors(Scientific Technical Research Council Turkey-Tubitak, 2011) Akdoğan, Ebru Demet; Erman, Burak; Yelekçi, KemalHistone lysine-specific demethylase (LSD1) is involved in a wide range of epigenetic processes and plays important roles in gene silencing DNA transcription DNA replication DNA repair and heterochromatin formation. Its active site shows a resemblance to those of 2 homologous enzymes monamine oxidase A and B (MAO-A and MAO-B.) In the present work starting from suitable scaffolds and generating thousands of structures from them 10 potential inhibitors were obtained with structural and physicochemical properties selectively suitable for inhibiting LSD1. iLib Diverse software was used to generate the diverse structures and 3 docking tools CDOCKER GOLD and AutoDock were used to find the most probable potential inhibitor based on its binding affinity. The dispositions of the candidate molecules within the organism were checked by ADMET_PSA_2D (polar surface area) versus ADMET_AlogP98 (the logarithm of the partition coefficient between n-octanol and water) and their suitability is discussed. The LSD1 inhibition activities of the candidates were compared with the properties of trans-2-phenylcyclopropylamine (tranylcypromine) and 2-(4-methoxy-phenyl) cyclopropylamine which are the 2 known inhibitors of LSD1.Article Citation - WoS: 145Citation - Scopus: 145Psychological Correlates of Covid-19 Conspiracy Beliefs and Preventive Measures: Evidence From Turkey(Springer, 2020) Alper, Sinan; Bayrak, Fatih; Yılmaz, OnurcanCOVID-19 pandemic has led to popular conspiracy theories regarding its origins and widespread concern over the level of compliance with preventive measures. In the current preregistered research, we recruited 1088 Turkish participants and investigated (a) individual differences associated with COVID-19 conspiracy beliefs; (2) whether such conspiracy beliefs are related to the level of preventive measures; and (3) other individual differences that might be related to the preventive measures. Higher faith in intuition, uncertainty avoidance, impulsivity, generic conspiracy beliefs, religiosity, and right-wing ideology, and a lower level of cognitive reflection were associated with a higher level of belief in COVID-19 conspiracy theories. There was no association between COVID-19 conspiracy beliefs and preventive measures while perceived risk was positively and impulsivity negatively correlated with preventive measures. We discuss the implications and directions for future research.Article Citation - WoS: 7Citation - Scopus: 6Investigation of Pst-Mwcnt Concentration on Epoxyacrylate Photopolymerization and Conductivity of Polymer Films(Elsevier Science SA, 2013) Doğruyol, Zekeriya; Temel, Gökhan; Doğruyol, Sevnur Keskin; Pekcan, Önder; Arsu, NergisPhotopolymerization kinetics and conductivity changes of epoxyacrylate composites for various loading modified PSt-MWCNT weight fractions changing from 0.0025 to 0.2 wt.% were evaluated by performing photo differential scanning calorimetry (photo-DSC) and four point conductivity measurements. 0.2% PSt-MWCNT additive polymeric films had their electrical conductivity boosted by 6% more than non-additive polymeric films. (C) 2012 Elsevier B.V. All rights reserved.Article Citation - WoS: 1Citation - Scopus: 1The Role of Pyranine in Characterization of Paam-Kappa C Composites by Using Fluorescence Technique(Springer/Plenum Publishers, 2011) Evingür, Gülşen Akın; Pekcan, ÖnderPolyacrylamide (PAAm) doped by kappa-carrageenan (kappa C) gels were prepared with various amounts of kappa C varying in the range between 0 wt.% and 3 wt.%. Steady-state fluorescence (SSF) technique was employed for studying sol-gel transition and swelling of PAAm-kappa C composite gels which were prepared by free-radical crosslinking copolymerization. Pyranine was introduced as a fluorescence probe. Pyranine molecules start to bind to acrylamide polymer chains upon the initiation of the polymerization thus the spectra of the bonded pyranines shift to the shorter wavelengths. Fluorescence spectra from the bonded pyranines allow one to monitor the sol-gel transition and to test the universality of the sol-gel transition as a function of some kinetic parameters like polymer concentration. Observations around the gel point t (c) for PAAm-kappa C composite gels showed that the gel fraction exponent beta obeyed the percolation result for low kappa C (< 2.0 wt. %) however classical results were produced at higher kappa C (> 2.0 wt.%). On the other hand fluorescence intensity of pyranine was measured during in situ swelling process at various amounts of kappa C and it was observed that fluorescence intensity values decreased as swelling is proceeded. Li-Tanaka equation was used to determine the swelling time constants tau and cooperative diffusion coefficients D.Book Part Citation - WoS: 4Conductivity Percolation of Carbon Nanotubes in Polyacrylamide Gels(Intech Europe, 2011) Pekcan, Önder; Evingür, Gülşen Akın[Abstract Not Available]Article Citation - WoS: 13Citation - Scopus: 13In Situ Steady State Fluorescence (ssf) Technique To Study Drying of Paam Hydrogels Made of Various Cross-Linker Contents(Elsevier Science, 2009) Evingür, Gülşen Akın; Aktas, Demet Kaya; Pekcan, ÖnderDrying experiments of polyacrylamide (PAAm) gels were performed using steady-state fluorescence (SSF) spectrometer. Pyranine (P) was introduced as a fluorescence probe and intensity of P from various crosslinker content gel samples was monitored. It was observed that the intensity of P increased during the in situ drying processes. Gravimetrical and volumetric experiments were also performed. An empirical model was derived and introduced to determine the desorption coefficient D of water molecules from the drying PAAm gels. It is observed that D increased as the cross-linker content was increased. (c) 2008 Elsevier B.V. All rights reserved.Article Citation - WoS: 6Citation - Scopus: 7Drying of Polyacrylamide Composite Gels Formed With Various Kappa- Carrageenan Content(Springer/Plenum Publishers, 2011) Evingür, Gülşen Akın; Pekcan, ÖnderDrying of polyacrylamide (PAAm)-kappa-carrageenan (kappa C) composite gels were monitored by using steady-state fluorescence technique. Disc shaped gels were formed from acrylamide (AAm) and N N'- methylenebisacrylamide(Bis) with various kappa- carrageenan (kappa C) contents by free radical crosslinking copolymerization in water. Pyranine (P) was doped as a fluorescence probe and scattered light I (sc) and fluorescence intensities I were monitored during drying of these gels. It is observed that fluorescence intensity of pyranine increased as drying time is increased for all samples. The increase in I was modeled using Stern- Volmer equation and diffusion with moving boundary. It is found that desorption coefficient D decreased as kappa C contents were increased. Supporting gravimetrical and volumetric experiments were also carried out during drying of PAAm- kappa C composite gels.Article Citation - WoS: 54Citation - Scopus: 66Synthesis Molecular Modeling in Vivo Study and Anticancer Activity of 124-Triazole Containing Hydrazide-Hydrazones Derived From (s)-Naproxen(Wiley-VCH Verlag GmbH, 2019) Han, Muhammed İhsan; Bekçi, Hatice; Uba, Abdullahi İbrahim; Yıldırım, Yeliz; Karasulu, Ercüment; Cumaoğlu, Ahmet; Karasulu, Hatice Y.; Yelekçi, Kemal; Yılmaz, Ozguer; Küçükgüzel, Şükriye GünizA new series of 124-triazole containing hydrazide-hydrazones derived from (S)-naproxen (7a-m) was synthesized in this study. The structures of these compounds were characterized by spectral (Fourier-transform infrared spectroscopy H-1-nuclear magnetic resonance (NMR) C-13-NMR and high-resolution electron ionization mass spectrometry) methods. Furthermore molecular modeling of these compounds was studied on human methionine aminopeptidase-2. All synthesized compounds were screened for anticancer activity against three prostate cancer cell lines (PC3 DU-145 and LNCaP) using the 3-(45-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium colorimetric method. Compound 7a showed the best activity against the PC3 DU-145 and LNCaP cancer cell lines with IC50 values of 26.0 34.5 and 48.8 mu M respectively. Compounds 7b 7k and 7m showed anticancer activity against cancer cell lines PC3 and DU-145 with IC50 values of 43.0 36.5 29.3 mu M and 49.8 49.1 31.6 mu M respectively. Compounds 7f and 7g showed anticancer activity against PC3 cells with IC50 values of 43.4 and 34.5 mu M respectively. To assess the biodistribution in mice of IRDye800 dye-labeled compound 7a or 100 mu M of free dye was injected intravenously into the mice's tail. In vivo images were taken with in vivo imaging system spectrum device at 60 120 180 240 300 and 360 min after injection. At the end of 360 min ex vivo studies were carried out to determine in which organs the dye was accumulated in the urogenital system. Ex vivo studies showed that the accumulation of compound 7a in the prostate is greater than that of the free dye and it is concluded that compound 7a may be promising for the treatment of prostate cancer..Article Citation - WoS: 8Citation - Scopus: 8Elastic Properties of a Swollen Paam-Nipa Copolymer With Various Nipa Contents(Taylor & Francis, 2014) Evingür, Gülşen Akin; Pekcan, ÖnderCopolymer based on cross-linked polyacrylamide (PAAm) having N-isopropylacrylamide (NIPA) was prepared and their elastic properties were studied as a function of NIPA contents. NIPA content dependency of the shear modulus S of the PAAm-NIPA copolymers due to volume phase transition was measured using tensile testing technique at 30 degrees C. It was observed that its shear modulus and toughness were found to be strongly dependent on NIPA content. It is understood that the shear modulus was found to increase with NIPA contents keeping constant temperature at 30 degrees C. Elastic properties of the PAAm-NIPA copolymers show compositional dependence.Article Citation - WoS: 4Citation - Scopus: 3Drying of Polyacrylamide-Multiwalled Carbon Nanotube (mwnt) Composites With Various Mwnts Contents: a Fluorescence Study(Walter De Gruyter Gmbh, 2013) Evingür, Gülşen Akin; Pekcan, ÖnderWe studied the drying of polyacrylamide (PAAm)-multiwalled carbon nanotube (MWNT) composites prepared by free radical crosslinking copolymerization in water with a steady state fluorescence technique. Composite gels were prepared at room temperature with pyranine (Py) doped as a fluorescence probe. Drying experiments were performed in air at various MWNT contents by real time monitoring of the Py fluorescence intensity (I) which increased as the drying proceeded. The Stern-Volmer equation combined with the moving boundary diffusion model was used to explain the behavior of I during drying. It was observed that the desorption coefficient (D) increased as the temperature increased. Drying energies (Delta E) were measured for the drying processes for each MWNT content gel by using fluorescence gravimetrical and volumetric methods. It is understood that Delta E values decrease by increasing MWNT content until 1 wt % MWNT and then increase above the level of this threshold value. The energy of drying is strongly correlated with the MWNT content in the composite. Delta E drops to its lowest value at which conducting cluster starts to appear.Article Citation - WoS: 25Citation - Scopus: 26How an Inhibitor Bound To Subunit Interface Alters Triosephosphate Isomerase Dynamics(Cell Press, 2015) Kürkçüoğlu, Zeynep; Fındık, Doğa; Akdoğan, Ebru Demet; Doruker, PemraThe tunnel region at triosephosphate isomerase (TIM)'s dimer interface distant from its catalytic site is a target site for certain benzothiazole derivatives that inhibit TIM's catalytic activity in Trypanosoma cruzi the parasite that causes Chagas disease. We performed multiple 100-ns molecular-dynamics (MD) simulations and elastic network modeling (ENM) on both apo and complex structures to shed light on the still unclear inhibitory mechanism of one such inhibitor named bt10. Within the time frame of our MD simulations we observed stabilization of aromatic clusters at the dimer interface and enhancement of intersubunit hydrogen bonds in the presence of bt10 which point to an allosteric effect rather than destabilization of the dimeric structure. The collective dynamics dictated by the topology of TIM is known to facilitate the closure of its catalytic loop over the active site that is critical for substrate entrance and product release. We incorporated the ligand's effect on vibrational dynamics by applying mixed coarse-grained ENM to each one of 54000 MD snapshots. Using this computationally efficient technique we observed altered collective modes and positive shifts in eigenvalues due to the constraining effect of bt10 binding. Accordingly we observed allosteric changes in the catalytic loop's dynamics flexibility and correlations as well as the solvent exposure of catalytic residues. A newly (to our knowledge) introduced technique that performs residue-based ENM scanning of TIM revealed the tunnel region as a key binding site that can alter global dynamics of the enzyme.Article Citation - WoS: 17Citation - Scopus: 16Cation Effect on Slow Release From Alginate Beads: a Fluorescence Study(Springer/Plenum Publishers, 2014) Kaygusuz, Hakan; Erim, F. Bedia; Pekcan, Önder; Evingür, Gülşen AkinIn this study spherical alginate beads containing pyranine (P-y) as a fluorescence probe were prepared by ionotropic gelation of a sodium alginate solution. The steady state fluorescence technique was used to study pyranine release from the alginate beads crosslinked with calcium barium and aluminum ions respectively. The slow release of P-y was observed with the time drive mode of the spectrophotometer at 512 nm. Fluorescence emission intensity (I-p) from P-y was monitored during the release process and the encapsulation efficiency (EE) of pyranine from the alginate beads was calculated. The Fickian Diffusion model was used to measure the release coefficients D-sl. It was seen that the slow release coefficients of pyranine from the alginate beads crosslinked with Ca2+ Ba2+ and Al3+ ions increased in the following order: D-sl (Al3+)> D-sl (Ca2+)> D-sl (Ba2+). In contrast the initial amount of pyranine and EE into the beads showed the reverse behavior.Book Part 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]Article Citation - WoS: 4Citation - Scopus: 4Temperature Dependence of Oxygen Diffusion Into Polymer/Carbon Nanotube Composite Films(Wiley-Blackwell, 2012) Yargı, Önder; Uğur, Şaziye; Pekcan, ÖnderThis study examines the transport properties of polystyrene (PS)/multiwalled carbon nanotube (MWNT) composite films taking into consideration both MWNT composition and temperature via fluorescence technique. Three different (3 15 and 40 wt%) MWNT content films were prepared from PS/MWNT mixtures by annealing them at 170 degrees C above the glass transition temperature of PS for 10 min. The diffusivity of the PS/MWNT composite was determined by performing oxygen (O2) diffusion measurements within a temperature range of 24 to 70 degrees C for each film and pyrene (P) was used as the fluorescent probe. The diffusion coefficients (D) of oxygen were determined by the fluorescence quenching method assuming Fickian transport. Results indicated that D values are strongly dependent on both temperature and the MWNT content in the film and it was also observed that D coefficients obey Arrhenius behavior from which diffusion energies were produced and increased along with increases of MWNT content. POLYM. ENG. SCI. 2012. (C) 2011 Society of Plastics EngineersArticle Citation - WoS: 13Citation - Scopus: 14Superelastic Percolation Network of Polyacrylamide (paam)-Kappa Carrageenan (kappa C) Composite(Springer, 2013) Evingür, Gülşen Akin; Pekcan, ÖnderThe elasticity of the polyacrylamide (PAAm)-kappa carrageenan (kappa C) composite was determined as a function of (w/v-%) kappa C content at 40 A degrees C. The gel composites studied contained various percentages (w/v-%) of kappa C. The elasticity of the swollen PAAm-kappa C composite was characterized by using the tensile testing technique. This study investigated the elasticity and the percolation threshold of PAAm-kappa C composite as a function of kappa C content. It is understood that the compressive elastic modulus decreases up to 1 (w/v-%) of kappa C and then increases at contents above 1(w/v-%) of kappa C. The critical exponent of elasticity y was determined between 1 and 1.6 (w/v-%) of kappa C and found to be 0.68. The observed elastic percolation threshold is consistent with the suggested values of the superelastic percolation network.Conference Object Design and Synthesis of Novel 2-Pyrazoline Analogues and Their Hmao Inhibitory Activities(Wiley-Blackwell, 2015) Uçar, Gülberk; Evranos-Aksoz, Begum; Yabanoglu-Çiftçi, Samiye; Yelekçi, Kemal[Abstract Not Available]Conference Object Citation - Scopus: 1Effect of Temperature and Graphene Oxide on the Swelling of Paam-Go Composite Gels(Avestia Publishing, 2019) Osma, Büşra; Akın Evingür, Gülşen; Pekcan, ÖnderGraphene oxide (GO) is a two dimensional carbon material with similar one-atom thickness, and is a light material having extremely high strength and thermal stability [1]. Thus, GO is an efficient filler for the enhancement of the electrical, mechanical and thermal properties of composite materials [2]. We focused on GO as a nanofiller in polyacrylamide hydrogels and PAAm-GO composites to investigate the effect of temperature and graphene oxide on the swelling. Polyacrylamide (PAAm) hydrogels have been proposed for use as promising biomaterials in biomedical and tissue engineering. The composite gels were prepared by free radical crosslinking copolymerization with GO content varying in the range between 8 and 50 μl of GO. The effects of temperature and graphene oxide on the swelling of the composites were studied. The swelling experiment was performed in the distilled water. Decreasing in pyranine (Py) as a fluorescence probe and emission light intensity (Iem) were monitored by steady state fluorescence spectroscopy. Since the increase in Isc corresponds to the increase in turbidity of the swelling composite gel, the corrected fluorescence intensity, I was introduced to analyze the swelling processes. The Stern-Volmer equation combined with Li-Tanaka models was used to explain the behaviour of I during swelling processes. The cooperative diffusion coefficients and time constants were calculated as a function of temperature and GO, respectively.Article Citation - WoS: 6Citation - Scopus: 6Temperature Effect on the Swelling of Paam-Kappa Composites(Wiley-Blackwell, 2012) Evingür, Gülşen Akin; Pekcan, ÖnderThe steady-state fluorescence (SSF) technique was used for studying swelling of disc-shaped polyacrylamide (PAAm)-kappa-carrageenan (kappa C) composites which were prepared by free-radical crosslinking copolymerization at 80 degrees C. Pyranine was introduced as a fluorescence probe during polymerization. Swelling experiments were performed in water at various temperatures by real-time monitoring of the pyranine (Py) fluorescence intensity I which decreased as swelling proceeded. Stern-Volmer equation is modified for low quenching efficiencies to interpret the behavior of Py intensity during the swelling of PAAm-kappa C composites. The Li-Tanaka equation was used to determine the swelling time constants tau(1) and cooperative diffusion coefficients D(0) from fluorescence intensity weight and volume variations of the composites at various temperatures. It was observed that tau(1) first decreased up to 40 degrees C and then increasedConference Object A New Thiadiazine Derivative Induces Oxidative Stress Dependent Cell Death in Hepatocellular Carcinoma Stem Cells(Wiley, 2019) Kahraman, Deniz Cansen; Bilget Güven, Ebru; Aytaç, Peri; Tozkoparan, Birsen; Çetin Atalay, Rengül[Abstract Not Available]Conference Object Thermal Rearrangement of 2-Acetoxy Trimethylbicyclo[3.1.0]hexane: Theoretical Elucidation of the Mechanism(Amer Chemical Soc, 2007) Yelekçi, Kemal; Erdem, Safiye Sağ[Abstract Not Available]
