Gebze Technical UniversityKocaeli

Gebze, Turkey

Gebze Technical UniversityKocaeli

Gebze, Turkey

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Kocak A.,Gebze Technical UniversityKocaeli | Yildiz M.,Gebze Technical UniversityKocaeli
Journal of Molecular Graphics and Modelling | Year: 2017

The disruption of aspartoacylase enzyme's catalytic activity causes fatal neurodegenerative Canavan disease. By molecular dynamics and docking methods, here we studied two deleterious mutations that have been identified in the Canavan patients’ genotype E285A, F295S, and revealed the possible cause for the enzyme inhibition due to the drastic changes in active site dynamics, loss of interactions among Arg 71, Arg 168 and the substrate and pKa value of critical Glu178 residue. In addition to changes in the enzyme dynamics, free energy calculations show that the binding energy of substrate decreases dramatically up on mutations. © 2017 Elsevier Inc.

Aydin M.,Gebze Technical UniversityKocaeli | Aydin M.,Namik Kemal University | Gorur M.,Istanbul Medeniyet University | Yilmaz F.,Gebze Technical UniversityKocaeli
Reactive and Functional Polymers | Year: 2016

A new hexa-armed star polymer bearing 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO)-pending polymer chains emanating from a phosphazene core (P2) was prepared and used as the cathode material in Li-ion battery assembly. The properties of the assembled battery (BP2) were compared with those of BL2 assembled using its linear counterpart (L2). Their spin concentrations investigated via solution electron spin resonance (ESR) measurements were found to be almost the same. The charge/discharge capacities and energy densities of BP2 were considerably higher than those of BL2. However, they exhibited comparable charge/discharge efficiencies and their discharge capacities dropped to similar percentages of their initial values. © 2016 Elsevier B.V. All rights reserved.

Chu M.,Grupo de Biotecnologia de Frutales | Quinonero C.,Grupo de Biotecnologia de Frutales | Akdemir H.,Gebze Technical UniversityKocaeli | Alburquerque N.,Grupo de Biotecnologia de Frutales | And 2 more authors.
Biotechnology Progress | Year: 2016

Although some works have explored the transformation of differentiated, embryogenic suspension-cultured cells (SCC) to produce transgenic grapevine plants, to our knowledge this is one of the first reports on the efficient transformation of dedifferentiated Vitis vinifera cv Monastrell SCC. This protocol has been developed using the sonication-assisted Agrobacterium-mediated transformation (SAAT) method. A construct harboring the selectable nptII and the eyfp/IV2 marker genes was used in the study and transformation efficiencies reached over 50 independent transformed SCC per gram of infected cells. Best results were obtained when cells were infected at the exponential phase. A high density plating (500 mg/dish) gave significantly better results. As selective agent, kanamycin was inefficient for the selection of Monastrell transformed SCC since wild type cells were almost insensitive to this antibiotic whereas application of paromomycin resulted in very effective selection. Selected eyfp-expressing microcalli were grown until enough tissue was available to scale up a new transgenic SCC. These transgenic SCC lines were evaluated molecularly and phenotypically demonstrating the presence and integration of both transgenes, the absence of Agrobacterium contamination and the ability of the transformed SCC to grow in highly selective liquid medium. The methodology described here opens the possibility of improving the production of valuable metabolites. © 2016 American Institute of Chemical Engineers.

Uludag Y.,Scientific and Technological Research Council of Turkey | Esen E.,Scientific and Technological Research Council of Turkey | Kokturk G.,Scientific and Technological Research Council of Turkey | Ozer H.,Scientific and Technological Research Council of Turkey | And 10 more authors.
Talanta | Year: 2016

Polymers were synthesized and utilized for aflatoxin detection coupled with a novel lab-on-a-chip biosensor: MiSens and high performance liquid chromatography (HPLC). Non-imprinted polymers (NIPs) were preferred to be designed and used due to the toxic nature of aflatoxin template and also to avoid difficult clean-up protocols. Towards an innovative miniaturized automated system, a novel biochip has been designed that consists of 6 working electrodes (1 mm diameter) with shared reference and counter electrodes. The aflatoxin detection has been achieved by a competition immunoassay that has been performed using the new biochips and the automated MiSens electrochemical biosensor device. For the assay, aflatoxin antibody has been captured on the Protein A immobilized electrode. Subsequently the sample and the enzyme-aflatoxin conjugate mixture has been injected to the electrode surfaces. The final injection of the enzyme substrate results in an amperometric signal. The sensor assays for aflatoxin B1 (AFB1) in different matrices were also performed using enzyme link immunosorbent assay (ELISA) and HPLC for confirmation. High recovery was successfully achieved in spiked wheat samples using NIP coupled HPLC and NIP coupled MiSens biosensor [2 ppb of aflatoxin was determined as 1.86 ppb (93% recovery), 1.73 ppb (86.5% recovery), 1.96 ppb (98% recovery) and 1.88 ppb (94.0% recovery) for immunoaffinity column (IAC)-HPLC, NIP-HPLC, Supel™ Tox SPE Cartridges (SUP)-HPLC and NIP-MiSens, respectively]. Aflatoxin detection in fig samples were also investigated with MiSens biosensor and the results were compared with HPLC method. The new biosensor allows real-time and on-site detection of AFB1 in foods with a rapid, sensitive, fully automated and miniaturized system and expected to have an immense economic impact for food industry. © 2016 Elsevier B.V.

Ertekin O.,Scientific and Technological Research Council of Turkey | Ertekin O.,Gebze Technical UniversityKocaeli | Ozturk S.,Scientific and Technological Research Council of Turkey | Ozturk Z.Z.,Gebze Technical UniversityKocaeli
Sensors (Switzerland) | Year: 2016

This study introduces the use of an IgA isotype aflatoxin (AF) specific monoclonal antibody for the development of a highly sensitive Quartz Crystal Microbalance (QCM) immunobiosensor for the detection of AF in inhibitory immunoassay format. The higher molecular weight of IgA antibodies proved an advantage over commonly used IgG antibodies in label free immunobiosensor measurements. IgA and IgG antibodies with similar affinity for AF were used in the comparative studies. Sensor surface was prepared by covalent immobilization of AFB1, using self assembled monolayer (SAM) formed on gold coated Quartz Crystal, with 1-Ethyl-3-(3-dimethylaminopropyl) carbodiimide/N-hydroxy succinimide (EDC/NHS) method using a diamine linker. Nonspecific binding to the surface was decreased by minimizing the duration of EDC/NHS activation. Sensor surface was chemically blocked after AF immobilization without any need for protein blocking. This protein free sensor chip endured harsh solutions with strong ionic detergent at high pH, which is required for the regeneration of the high affinity antibody-antigen interaction. According to the obtained results, the detection range with IgA antibodies was higher than IgG antibodies in QCM immunosensor developed for AFB1. © 2016 by the authors; licensee MDPI, Basel, Switzerland.

Aksakal F.,Gebze Technical UniversityKocaeli | Shvets N.,Gebze Technical UniversityKocaeli | Dimoglo A.,Kocaeli University
Journal of Molecular Graphics and Modelling | Year: 2015

Abstract Structural and electronic factors influencing selective inhibition of cyclooxygenase-2 and 5-lipoxygenase (COX-2/5-LOX) were studied by using Electronic-Topological Method combined with Neural Networks (ETM-NN), molecular docking, and Density Functional Theory (DFT) in a large set of molecules. The results of the ETM-NN calculations allowed for the selection of pharmacophoric molecular fragments, which could be taken as a basis for a system capable of predicting the COX-2/5-LOX inhibitory activity. For the more effective extraction of the pharmacophoric molecular fragments, docking of molecules into the active sites of the two enzymes was carried out to get data on the ligand-receptor interaction. To make an assessment of these interactions, stabilization energies were calculated by using Natural Bond Orbital (NBO) analysis. Docking and data on the electronic structures of active sites of enzymes helped to reveal effectively the peculiarities of the ligand-receptor binding. The system for the selective COX-2/5-LOX inhibitory activity prediction that has been developed as the result of the ETM-NN study recognized correctly 93% of compounds as highly active ones. Thus, this system can be successfully used for carrying out computer screening and synthesis of potent inhibitors of COX-2/5-LOX with diverse molecular skeletons. © 2015 Elsevier Inc.

Ozyigit I.I.,Marmara University | Filiz E.,Duzce University | Vatansever R.,Marmara University | Kurtoglu K.Y.,Marmara University | And 5 more authors.
Frontiers in Plant Science | Year: 2016

Among major reactive oxygen species (ROS), hydrogen peroxide (H2O2) exhibits dual roles in plant metabolism. Low levels of H2O2 modulate many biological/physiological processes in plants; whereas, its high level can cause damage to cell structures, having severe consequences. Thus, steady-state level of cellular H2O2 must be tightly regulated. Glutathione peroxidases (GPX) and ascorbate peroxidase (APX) are two major ROS-scavenging enzymes which catalyze the reduction of H2O2 in order to prevent potential H2O2-derived cellular damage. Employing bioinformatics approaches, this study presents a comparative evaluation of both GPX and APX in 18 different plant species, and provides valuable insights into the nature and complex regulation of these enzymes. Herein, (a) potential GPX and APX genes/proteins from 18 different plant species were identified, (b) their exon/intron organization were analyzed, (c) detailed information about their physicochemical properties were provided, (d) conserved motif signatures of GPX and APX were identified, (e) their phylogenetic trees and 3D models were constructed, (f) protein-protein interaction networks were generated, and finally (g) GPX and APX gene expression profiles were analyzed. Study outcomes enlightened GPX and APX as major H2O2-scavenging enzymes at their structural and functional levels, which could be used in future studies in the current direction. © 2016 Ozyigit, Filiz, Vatansever, Kurtoglu, Koc, Öztürk and Anjum.

Bulut A.,Bogazici University | Zorlu Y.,Gebze Technical UniversityKocaeli | Topkaya R.,Gebze Technical UniversityKocaeli | Aktas B.,Gebze Technical UniversityKocaeli | And 3 more authors.
Dalton Transactions | Year: 2015

Engineering a copper coordination sphere with organoimine ligands and tuning the organophosphonate protonation states produced [{Cu(2,2′-bpy)}2(HO3P(CH2)8PO3H2)4] (1) and [{Cu(terpy)}2(2,7-FDA-H2)2]·(2,7-FDA-H4)(2H2O) (2) (2,7-FDA-H4 = 2,7-fluorenonediphosphonic acid) macrocyclic copper-organophosphonate building blocks. 1 exhibits high temperature magnetic ordering, while 2 is paramagnetic. The structures were characterized by single crystal X-ray diffraction. This journal is © The Royal Society of Chemistry.

Inan H.,Gebze Technical UniversityKocaeli | Turkay O.,Gebze Technical UniversityKocaeli | Akkiris C.,Gebze Technical UniversityKocaeli
Desalination and Water Treatment | Year: 2016

This study aimed to investigate the effect of microwave (MW) and microwave–chemical (MWC) pretreatment on barley straw and to identify the acidic, basic, or oxidative chemicals that provide the highest sugar conversion for subsequent enzymatic hydrolysis. The MW and MWC processes were applied as a pretreatment step before fermentation. MW radiation at 200 and 300 W and MW radiation plus a chemical (H2SO4 or NaOH or H2O2) as catalyst were applied, and total sugar, total phenol, and Klason and acid-soluble lignin were measured. Although the MWC pretreatment produced a higher total sugar concentration than the MW pretreatment, the addition of an NaOH solution produced the best results in terms of all parameters. Fourier transform infrared analysis was also performed to observe the deterioration of molecular structures after the application of MW and MWC. © 2015 Balaban Desalination Publications. All rights reserved.

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