Biyoinformatik ve Genetik Bölümü Koleksiyonu

Permanent URI for this collectionhttps://gcris.khas.edu.tr/handle/20.500.12469/46

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Citation Count: 16
Cation Effect on Slow Release from Alginate Beads: A Fluorescence Study
(Springer/Plenum Publishers, 2014) Kaygusuz, Hakan; Erim, F. Bedia; Pekcan, Önder; Evingür, Gülşen Akin
In 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.
Citation Count: 21
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 Count: 2
Corrected Panel-Reactive Antibody Positivity Rates for Hypersensitized Patients in Turkish Population With Calculated Panel-Reactive Antibody Software
(Elsevier Science Inc, 2017) Yelekçi, Kemal; 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 Count: 19
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 Count: 15
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 Count: 2
Critical Exponents of Thermal Phase Transitions of kappa-Carrageenan in Various Salt Solutions
(Wiley-VCH Verlag GmbH, 2009) Tarı, Özlem; Pekcan, Önder
The steady state fluorescence (SSF) technique was employed to study the phase transitions Of kappa-carrageenan in NaCl and KCl solutions. Pyranine was used as a fluorescence probe for monitoring these transitions. Scattered light I(sc) and fluorescence intensity 1 was monitored against temperature to determine transition temperatures and exponents. It was observed that transition temperatures are strongly correlated with the NaCl and KCl contents. The weight-average degree of polymerization DP(w) and gel fraction G exponents (gamma and beta) were measured and found to be in accord with the classical Flory-Stockmayer model.
Citation Count: 5
Design, Synthesis and hMAO Inhibitory Screening of Novel 2-Pyrazoline Analogues
(Bentham Science Publ Ltd, 2017) Yelekçi, Kemal; 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 Count: 3
Design, Synthesis and In Vitro Cytotoxic Activity of New 6,9-Disubstituted Purine Analogues
(Slovensko Kemijsko Drustvo, 2020) Kuçükdumlu, Aslıgül; Tunçbilek, Meral; Bilget Güven, Ebru; Atalay, Rengül Çetin
A series of new 6,9-disubstituted purine analogs with 4-substituted piperazine at C-6 and 4-substituted benzyl at N-9 were designed and synthesized in four steps. All synthesized compounds (7-26) were screened initially for their in vitro anticancer activity on Huh7 liver, HCT116 colon and MCF7 breast carcinoma cell lines. Cytotoxic bioactivity studies revealed that all compounds screened, with compound 19 being the exception, were found to have promising cytotoxic activities at IC50 range of 0.05-21.8 mu M against cancer cells Huh7, HCT116 and MCF7. Among the prepared purine analogs, two of them (12 and 22) exhibited excellent cytotoxic activities, with IC50 0.08-0.13 mu M, on Huh7 cells comparable to camptothecin (CPT) and better than cladribine, fludarabine and 5-FU. Afterwards, the evaluation of cytotoxicity of the most potent purine analogs was screened against further hepatocellular cancer (HCC) cell lines. The 6-(4-(4-trifluoromethylphenyl)piperazine (12) and 6-(4-(3,4-dichlorophenyl)piperazine analogs (25) displayed a significant IC50 values (IC50 < 0.1-0.13 mu M) comparable to CPT and better cytotoxic bioactivity when compared with 5-FU, cladribine and fludarabine on HCC cells (Huh7 and HepG2).
Citation Count: 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 Count: 6
The Effect Of Surfaces On The Orientational Properties and Phase Transitions Peculiarities Of A Nonpolar Smectogen
(World Scientific Publ Co Pte Ltd, 2010) Yıldız, Sevtap; Zayim, Esra Ozkan; Pekcan, Önder; Özbek, Haluk
The effect of thin films on the orientational and optical properties of nonpolar monolayer smectogen 4-butoxyphenyl-4'-decyloxybenzoate ((10) over barO (4) over bar) liquid crystal has been studied by polarizing microscopy and high-resolution photon transmission method. The uniform planar textures of (10) over barO (4) over bar on the surfaces coated with WO3 VO2 and WO3-VO2 mixture thin films have been obtained. No significant shifts in the phase transition temperatures to lower values under the influence of the surfaces have been observed. We have also presented the new experimental data on the critical behavior of the layer compression modulus B near the nematic-smectic A transition. It was observed that the data in the vicinity of the transition can be described by a power law expression after the introduction of a first-order correction-to-scaling term within the limit of experimental error. The resulting critical exponent was found to be 0.34 -/+ 0.01 which is good agreement with the previously reported values for other investigated compounds in literature.
Citation Count: 15
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.
Citation Count: 4
Electrical optical and fluorescence percolations in P(VAc-co-BuA)/MWCNT composite films
(Taylor & Francis Ltd, 2013) Arda, Ertan; Kara, Selim; Pekcan, Önder
Effects of multiwall carbon nanotube (MWCNT) addition on the electrical conductivities optical transparencies and fluorescence emissions of poly(vinyl acetate-co-butyl acrylate) (P(VAc-co-BuA))/MWCNT composite films were studied. Optical transmission fluorescence emission and two point probe resistivity techniques were used to determine the variations of the optical fluorescence and electrical properties of the composites respectively. Transmitted photon intensity (I-tr) fluorescence emission intensity (I-fl) and surface resistivity ((s)) of the composite films were monitored as a function of MWCNT mass fraction (M) at room temperature. All these measured quantities of the composites were decreased by increasing the content of MWCNT in the composite. The conductivity and the optical results were attributed to the classical and site percolation theories respectively. The fluorescence results however possessed both the site and classical percolation theories at low and high MWCNT content regions respectively.
Citation Count: 5
Epidemic models for phase transitions: application to a physical gel
(Taylor & Francis Ltd, 2017) Bilge, Ayşe Hümeyra; Pekcan, Önder; Kara, Selim; Öğrenci, Arif Selçuk
Carrageenan gels are characterized by reversible sol-gel and gel-sol transitions under cooling and heating processes and these transitions are approximated by generalized logistic growth curves. We express the transitions of carrageenan-water system as a representative of reversible physical gels in terms of a modified Susceptible-Infected-Susceptible epidemic model as opposed to the Susceptible-Infected-Removed model used to represent the (irreversible) chemical gel formation in the previous work. We locate the gel point T-c of sol-gel and gel-sol transitions and we find that for the sol-gel transition (cooling) T-c > T-sg (transition temperature) i.e. T-c is earlier in time for all carrageenan contents and moves forward in time and gets closer to T-sg as the carrageenan content increases. For the gel-sol transition (heating) T-c is relatively closer to T-gs
Citation Count: 0
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 Count: 5
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 Count: 14
GELATION MECHANISMS
(World Scientific Publ Co Pte Ltd, 2012) Pekcan, Önder; Kara, Selim
In this paper, we survey the gelation mechanisms for various polymeric systems which are classified by the type and the strength of the cross-linkages. These are the "irreversible" gels that are cross-linked chemically by covalent bonds and the "reversible" gels that are cross-linked physically by hydrogen or ionic bonds and by the physical entanglement of polymer chains. Some of the natural polymer gels fall into the class of physical gels, among which the red algae that has attracted attention for various applications is discussed in detail. Various composite gels, formed from mixture of physical and chemical gels are also discussed in the last section of the article. Theoretical models describe the gelation as a process of random linking of subunits to larger and larger molecules by formation of an infinite network, where no matter what type of objects are linked, there is always a critical "gel point" at which the system behaves neither as a liquid nor as a solid on any length scale. The Flory-Stockmayer theory and percolation theory provide bases for modeling this sol-gel phase transition. The experimental techniques for measuring the critical exponents for sol-gel phase transitions in different polymeric systems are introduced and the validation of various theoretical predictions are surveyed.
Citation Count: 2
Gelation of PAAm-PVP composites: A fluorescence study
(World Scientific, 2014) Evingür, Gülşen Akin; Kaygusuz, Hakan; Erim, F. Bedia; Pekcan, Önder
Hybrid hydrogels are a new class of composite materials. Polyacrylamide (PAAm) hydrogels are mainly produced by free radical crosslinking copolymerization (FCC) of AAm in the presence of N N'-methylene bis (acrylamide) (BIS) as the crosslinker. Pyranine doped PAAm-poly (N-vinyl pyrrolidone) (PVP) composite were prepared with different amounts of PVP varying in the range between 0.0015 and 0.1 gr. It was observed that pyranine molecules as a fluoroprobe bind to AAm and PVP chains upon the initiation of the polymerization causing the fluorescence spectra of the bonded pyranines shift to the shorter wavelengths. The sol-gel phase transition and its universality were monitored and tested as a function of PVP contents. Observations around the critical point show that the gel fraction exponent beta agreed with the percolation result for below 0.025 gr PVP contents. However classical result was observed above 0.0125 gr PVP content.
Citation Count: 3
Kinetic models for the dynamical behavior of polyacrylamide (PAAm)-kappa-carrageenan (kappa C) composite gels
(Springer, 2015) Evingür, Gülşen Akın; Pekcan, Önder
A fluorescence method was employed for studying the drying and swelling of PAAm-kappa C composite gels which were formed from acrylamide (AAm) and N N'- methylenebisacrylamide (BIS) with various kappa-carrageenan (kappa C) contents by free radical crosslinking copolymerization in water. Composite gels were prepared at 80 A degrees C with pyranine (Py) as a fluorescence probe. Scattered light I (sc) and fluorescence emission intensities I (em) were monitored during drying and swelling of these gels. The fluorescence intensity of pyranine increased and decreased as drying and swelling time are increased respectively for all gel samples. The Stern-Volmer equation combined with moving boundary and Li-Tanaka models were used to explain the behavior of I (em) during drying and swelling processes respectively. It is found that the desorption coefficient D (d) decreased as kappa C contents were increased for a given temperature during drying. However the cooperative diffusion coefficient D (s) presented exactly the opposite case. Conventional gravimetrical and volumetric experiments were also carried out during drying and swelling of PAAm-kappa C composite gels. It was observed that D (d) and D (s) values measured with the fluorescence method were found to be much larger than they were measured with the conventional methods.
Citation Count: 2
Mapping the two-component atomic Fermi gas to the nuclear shell-model
(Springer, 2014) Özen, Cem; Zinner, Nikolaj Thomas
The physics of a two-component cold Fermi gas is now frequently addressed in laboratories. Usually this is done for large samples of tens to hundreds of thousands of particles. However it is now possible to produce few-body systems (1-100 particles) in very tight traps where the shell structure of the external potential becomes important. A system of two-species fermionic cold atoms with an attractive zero-range interaction is analogous to a simple model of nucleus in which neutrons and protons interact only through a residual pairing interaction. In this article we discuss how the problem of a two-component atomic Fermi gas in a tight external trap can be mapped to the nuclear shell-model so that readily available many-body techniques in nuclear physics such as the Shell-Model Monte Carlo (SMMC) method can be directly applied to the study of these systems. We demonstrate an application of the SMMC method by estimating the pairing correlations in a small two-component Fermi system with moderate-to-strong short-range two-body interactions in a three-dimensional harmonic external trapping potential.
Citation Count: 8
Mathematical Characterization of Thermo-reversible Phase Transitions of Agarose Gels
(Taylor & Francis Inc, 2018) Bilge, Ayşe Hümeyra; 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.

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