Biyoinformatik ve Genetik Bölümü Koleksiyonu

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

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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.
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.
Citation - WoS: 21
Citation - Scopus: 20
Critical Exponents of Kappa Carrageenan in the Coil-Helix and Helix-Coil Hysteresis Loops
(Taylor & Francis Inc, 2009) Tarı, Özlem; Kara, Selim; Pekcan, Önder
The steady-state fluorescence technique was used to study coil-helix (sol-gel) and helix-coil (gel-sol) transitions of the kappa carrageenan-water system with various carrageenan contents. Fluorescence (I) and scattered light (I-sc) intensities were measured against temperature to determine critical phase transition temperatures and exponents. It was observed that the coil-helix transition temperatures T-ch were much lower than the helix-coil (T-hc) transition temperatures due to the hysteresis of the phase transition loops. The gel fraction exponent (beta) was measured and found to be in accord with the classical Flory-Stockmayer model.
Citation - WoS: 16
Citation - Scopus: 16
Critical Exponents of Photoinitiated Gelation at Different Light Intensities
(Taylor & Francis Inc, 2009) Doğruyol, Zekeriya; Arsu, Nergis; Pekcan, Önder
A photo-differential scanning calorimetric (Photo-DSC) technique was used to study the photoinitiated radical polymerization of a 75% epoxy diacrylate (EA) and 25% tripropyleneglycoldiacrylate (TPGDA) mixture with 2-mercaptothioxanthone (TX-SH) as photoinitiator by using different light intensities. Photopolymerization reactions were carried out under identical conditions of temperature and initiator concentration. It was observed that all conversion curves during gelation at various Might intensities present good sigmoidal behavior as predicted by the percolation model. Observations around the critical time called the glass transition point (t(g)) taken for polymerization to reach the maximum rate (R-pmax) show that the gel fraction exponents beta obeyed the universal percolation picture. On the other hand R-pmax t(g) and final conversion values were found to be dependent on the UV light intensity.
Citation - Scopus: 1
Determination of Growth Kinetics and Size Dependent Structural Morphological Optical Characteristics of Sol-Gel Derived Silica Nanoparticles in Silica Matrix
(De Gruyter Poland Sp Zoo, 2019) Uysal, Bengü Özuğur; Tepehan, Fatma Zehra
Nanocomposite silica thin films made using the sol-gel method were studied. The nano-silica films were prepared using a mixture of tetraethyl orthosilicate (TEOS) deionized water ethanol and ammonia solution. To control the growth of the particles inside the film the nanocomposite silica film was prepared using a mixture of the nano-silica sol and the silica sol. The change in the particle size with the heat treatment temperature ranging from 450 degrees C to 1100 degrees C was investigated. X-ray diffraction (XRD) atomic force microscopy (AFM) scanning electron microscopy (SEM) NKD (refractive index-N extinction coefficient-K and thickness-D) and ultraviolet-visible (UV-Vis) spectrophotometry were used for characterization purposes. The XRD studies showed that the nano-silica thin films were amorphous at all annealing temperatures except for 1100 degrees C. The alpha-cristobalite crystal structure formed at the annealing temperature of 1100 degrees C. Optical parameters such as refractive indices and extinction coefficients were obtained using the NKD analyzer with respect to the annealing temperature of the films. The activation energy and enthalpy of the nanocomposite silica film were evaluated as 22.3 kJ/mol and 14.7 kJ/mol respectively. The cut-off wavelength values were calculated by means of extrapolation of the absorbance spectra estimated using the UV-Vis spectroscopy measurements. A red shift in the absorption threshold of the nanocomposite silica films indicated that the size of the silica nanoparticles increased with an increase of the annealing temperatures from 450 degrees C to 900 degrees C and this confirms the quantum confinement effect in the nanoparticles.
Citation - WoS: 6
Citation - Scopus: 6
Effect of Calcium Ion Concentration on Small Molecule Desorption From Alginate Beads
(Taylor & Francis Inc, 2014) Evingür, Gülşen Akin; Kaygusuz, Hakan; Erim, F. Bedia; Pekcan, Önder
Spherical alginate beads were prepared by ionotropic gelation of sodium alginate through the use of calcium ions. Pyranine (Py) was added to the alginate solution as a small molecule probe for fluorescence studies. Desorption of Py in water from the alginate beads cross-linked with calcium ions was studied by using the steady state fluorescence technique. The fluorescence emission intensity (I) from Py was monitored during the desorption process at 512 nm using the time drive mode of the spectrofluorometer. The increase in I was attributed to Py release from the beads. The Fickian diffusion model was used to calculate the desorption coefficients D which were found to be increased up to 3% (w/v) CaCl2 concentration in the beads and then decreased with a further increase of CaCl2 content. On the other hand the encapsulation efficiency of Py in the calcium alginate beads presented the reverse behavior compared to D. It was observed that when the content of CaCl2 was increased the incubation time t(0) for the start of desorption increased.
Citation - WoS: 3
Citation - Scopus: 4
Elasticity Study of Paam-Kappa C Composite Prepared in Various Kappa C Content and Measured at Several Temperatures
(Polish Acad Sciences Inst Physics, 2015) Evingür, Gülşen Akin; Pekcan, Önder
Polyacrylamide (PAAm)-kappa carrageenan (kappa C) composite gels were prepared via free radical crosslinking copolymerization with various (w/v) percentages of kappa C in the range between 0.5 and 3 (w/v)% of kappa C . Elasticity properties such as stress strain and compressive elastic modulus S of these composite gels were studied in various kappa C content and at several temperatures. The content and temperature dependence of the compressive elastic modulus S of the swollen PAAm-kappa C composite gels due to volume phase transition were produced by using tensile testing technique. It is understood that the compressive elastic modulus was found to decrease up to 1 (w/v)% of kappa C and then increase by increasing kappa C contents at constant temperatures. The composite preserves the ability to undergo the volume phase transition and its compressive elastic modulus is found to be strongly dependent on the kappa C content and temperature. It is observed that the compressive elastic modulus increased when temperature is increased up to 40 degrees C and then decreases below this temperature for all composite gels. However PAAm-kappa C composite gel presented lower values for the compressive elastic modulus showing a minima at 40 degrees C for 1 (w/v)% of kappa C content gel.
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
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: 2
Citation - Scopus: 2
Fractal Features and Structural Morphological Optical Characteristics of Sol-Gel Derived Silica Nanoparticled Thin Films
(Polish Acad Sciences Inst Physics, 2018) Uysal, Bengü Özuğur; Pekcan, Önder
Nanostructured silica films using a simple and effective sol-gel spin coating technique were synthesized and the influence of ammonia/sol ratios on the particle size and thickness of this film was investigated. In addition fractal dimensions of the prepared films were determined using the scattering response technique. The samples were characterized by atomic force microscopy and UV-vis spectroscopy. Comparing optical method and image analysis of atomic force microscopy micrographs the fractal dimension of silica nanoparticled thin films was determined. The fractal dimensions of the films verified by atomic force microscopy analysis were found to be around 2.03 which is very close to the values (2.0358 2.0325 and 2.0335) obtained using optical method. As a result of these findings precise determination of the nanoparticled silica thin films fractal dimension using both optical and surface analysis methods was realized.
Citation - WoS: 10
Citation - Scopus: 9
Mathematical Characterization of Thermo-Reversible Phase Transitions of Agarose Gels
(Taylor & Francis Inc, 2018) Öğrenci, Arif Selçuk; Pekcan, Önder; Kara, Selim; Bilge, Ayşe Hümeyra
The thermal phase transition temperatures of high (HMP) and low melting point (LMP) agarose gels were investigated by using UV-vis spectroscopy techniques. Transmitted light intensities from the gel samples with different agarose concentrations were monitored during the heating (gel-sol) and cooling (sol-gel) processes. It was observed that the transition temperatures T-m defined as the location of the maximum of the first derivative of the sigmoidal transition paths obtained from the UV-vis technique slightly increased by increasing the agarose concentration in both the HMP and LMP samples. Here we express the phase transitions of the agar-water system as a representative of reversible physical gels in terms of a modified Susceptible-Infected-Susceptible epidemic model whose solutions are the well-known 5-point sigmoidal curves. The gel point is hard to determine experimentally and various computational techniques are used for its characterization. Based on previous work we locate the gel point T-0 of sol-gel and gel-sol transitions in terms of the horizontal shift in the sigmoidal transition curve. For the gel-sol transition (heating) T-0 is greater than T-m i.e. later in time and the difference between T-0 and T-m is reduced as the agarose content increases. For the sol-gel transition (cooling) T-0 is again greater than T-m but it is earlier in time for all agarose contents and moves forward in time and gets closer to T-m as the agarose content increases.
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: 7
Citation - Scopus: 8
Novel Mutants of the Aubergine Gene
(Taylor & Francis Inc, 2016) Şahin, H. Bahar; Karataş, Ömer Faruk; Specchia, Valeria; Di Tommaso, Silvia D.; Diebold, Celine; Bozzetti, Maria Pia; Giangrande, Angela
Aubergine is an RNA-binding protein of the Piwi clade functioning in germline in the piRNA pathway that silences transposons and repetitive sequences. Several mutations of this gene exist but they mostly result in truncated proteins or correspond to mutations that also affect neighboring genes. We have generated complete aubergine knock-out mutants that do not disrupt the neighboring genes. These novel mutants are characterized by PCR and sequencing. Their nature is confirmed by female sterility and by the presence of crystals in testes common to the aubergine loss of function mutations. These mutants provide novel and more appropriate tools for the study of the piRNA pathway that controls genome stability.
Citation - WoS: 4
Citation - Scopus: 4
Paam-Kappa Carrageenan Composites: Drying and Swelling With Various Kappa Carrageenan Contents
(Polish Acad Sciences Inst Physics, 2012) Akın-Evingür, Gülşen; Pekcan, Önder
The purpose of this study is to discuss the role of kappa-carrageenan (kappa-car) in the drying and swelling of polyacrylamide (PAAm)-kappa-car composite. The fluorescence intensity of pyranine increased and decreased as drying and swelling time were increased respectively for all samples. The desorption coefficient D-d decreased as kappa-car contents were increased for a given temperature during drying. However cooperative diffusion coefficient D-s increased as kappa-car contents were increased during swelling at a given temperature.
Citation - WoS: 1
Citation - Scopus: 1
Swelling Kinetics of Paam-Kappa Composites: a Fluorescence Technique
(Taylor & Francis Inc, 2011) Evingür, Gülşen Akın; Pekcan, Önder
The steady-state fluorescence (SSF) technique was introduced for studying swelling of disc-shaped polyacrylamide (PAAm) gels containing various amount of kappa-carrageenan (kappa C). They were prepared by free-radical cross-linking copolymerization. N N'-methylenebisacrylamide (BIS) and ammonium persulfate (APS) were added as a crosslinker and an initiator respectively. Composite gels were prepared at 80 degrees C with pyranine as a fluorescence probe. After drying of these gels swelling kinetics were performed in water at 60 degrees C by real-time monitoring of the pyranine fluorescence intensity I which decreased as swelling proceeded. 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 gels during the swelling processes in all cases. It was observed that tau(1) decreased and D(0) increased as the kappa C concentrations in the composites were increased indicating that high kappa C gels swell faster than low kappa C gels.
Citation - WoS: 6
Citation - Scopus: 6
Synthesis Molecular Modelling and Antibacterial Activity Against Helicobacter Pylori of Novel Diflunisal Derivatives as Urease Enzyme Inhibitors
(Bentham Science Publ Ltd, 2019) Coşkun, Göknil Pelin; Djikic, Teodora; Kalaycı, Sadık; Yelekçi, Kemal; Şahin, Fikrettin; Küçükgüzel, Şükriye Güniz
Background: The main factor for the prolongation of the ulcer treatment in the gastrointestinal system would be Helicobacter pylori infection which can possibly lead to gastrointestinal cancer. Triple therapy is the treatment of choice by today's standards. However observed resistance among the bacterial strains can make the situation even worse. Therefore there is a need to discover new targeted antibacterial therapy in order to make success in the eradication of H. pylori infections. Methods: The targeted therapy rule is to identify the related macromolecules that are responsible for the survival of the bacteria. Thus 2-[(2'4'-difluoro-4-hydroxybiphenyl-3-yl)carbonyl]-N-( substituted)hydrazinocarbothioamide (3-13) and 5-(2'4'-difluoro-4-hydroxybiphenyl-3-yl)-4-( substituted)-24-dihydro-3H-124-triazole-3-thiones (14-17) were synthesized and evaluated for antibacterial activity in vitro against H. pylori. Results: All of the tested compounds showed remarkable antibacterial activity compared to the standard drugs (Ornidazole Metronidazole Nitrimidazin and Clarithromycin). Compounds 4 and 13 showed activity as 2 mu g/ml MIC value. Conclusion: In addition we have investigated binding modes and energy of the compounds 4 and 13 on urease enzyme active by using the molecular docking tools.
Citation - WoS: 8
Citation - Scopus: 10
Synthesis, in Silico Studies and Cytotoxicity Evaluation of Novel 1,3,4-Oxadiazole Derivatives Designed as Potential Mpges-1 Inhibitors
(MARMARA UNIV, 2020) Erensoy, Gizem; Ding, Kai; Zhan, Chang-Guo; Elmezayen, Ammar D.; Yelekçi, Kemal; Duracık, Merve; Özakpınar, Özlem Bingol; Küçükgüzel, İlkay
A series of new 1,3,4-oxadizole derivatives containing thioether group, has been synthesized to investigate their mPGES-1 inhibitory activities. The synthesized compounds were also evaluated for their anticancer and COX-1/2 inhibitory activities. All compounds were checked for their purity using TLC and HPLC analyses. The melting points, elemental analysis, FT-IR, H-1-/C-13-NMR and LR-MS data were utilized for structural characterization. The most potent derivative was 2-[5-{[2-methyl-5-(propan-2-yl)phenoxy]methyl}-1,3,4-oxadiazol-2-yl)sulphanyl]-1-(phenyl)ethan-1-one 3a, which showed inhibitory activity against mPGES-1 with an IC50 of 4.95 mu M. Docking studies with mPGES-1 and COX-1/2 enzymes revealed their affinity and potential binding mechanism for the tested compounds.
Citation - WoS: 2
Citation - Scopus: 3
Tailoring the Electrical and Optical Properties of Carbon Nanotube Reinforced Transparent Tio 2 Composites by Varying Nanotube Concentrations
(World Scientific Publ Co Pte Ltd, 2019) Uysal, Bengü Özuğur; Akkaya Arier, Ümit Özlem; Pekcan, Önder
In the present work multi-walled carbon nanotube (MWCNT)-doped TiO 2 nanocomposite films were synthesized by sol-gel method. The influence of nanotube concentration on the structural electrical and optical properties of the films was investigated. The beneficial effects of the addition of carbon nanotubes into a TiO 2 film and titania-coated MWCNTs have much in common. On the other hand this work contributes to the previous studies in terms of the optical and electrical properties of MWCNT. For this reason MWCNT/rare brookite-phased TiO 2 matrix as simple sol-gel deposited composite films were investigated in our study. The XRD studies showed that the composite film has a brookite crystal structure at the annealing temperature of 450C. According to the surface morphology investigations SEM image of nanocomposite film shows that composite film has a granular and rod-like structure. The absorbance measurements of the films were carried out by the UV-Vis spectrophotometer to investigate transparency and to calculate the bandgap energy of composite films. The surface resistivity of the MWCNT-doped TiO 2 composites decreased from 2.50×1010 to 2.20×109 ohm/sq with increase in MWCNT content. © 2019 World Scientific Publishing Company.
Citation - WoS: 4
Citation - Scopus: 4
Temperature Effect on the Elasticity of Acrylamide-N Copolymers
(Taylor & Francis Inc, 2018) Evingür, Gülşen Akin; Pekcan, Önder
Acrylamide (AAm) - N-isopropylacrylamide (NIPA) copolymers were prepared via free radical crosslinking copolymerization with various weight percentages (wt%) of AAm and NIPA. The temperature dependence of the compressive elastic modulus G and toughness U-TU- of the PAAm- NIPA copolymers due to a volume phase transition was found using a compressive testing technique. It was observed that the compressive elastic modulus increased comprehensively when the temperature was increased between 30 degrees C and 60 degrees C. The PAAm- NIPA copolymers presented higher values of the compressive elastic modulus than pure NIPA above the lower critical solution temperature (LCST) (NIPA exhibits a volume phase transition from hydrophilic to hydrophobic in water at 31 degrees C) and their compressive elastic modulus and toughness had a strong temperature dependence.
Citation - WoS: 2
Citation - Scopus: 4
Thermal Phase Transitions of Iota Carrageenan in Cacl2 Solutions: a Fluorescence Study
(Taylor & Francis Inc, 2011) Tari, Ozlem; Kara, Selim; Pekcan, Önder
The fluorescence technique was employed to study thermal phase transitions of iota (-) carrageenan (IC) in CaCl2 solution. IC gels underwent coil to double helix (c-h) and double helix to dimer (h-d) transitions upon cooling. Upon heating IC gels presented dimer to double helix (d-h) and double helix to coil (h-c) transitions showing hysteresis types of transition paths. Scattered light Isc and fluorescence intensity I were monitored against temperature to determine phase transitions. Transition temperatures were determined from the derivative of the transition paths. The critical gel fraction exponent was measured and found to be in accord with the classic Flory-Stockmayer model.

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