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Öğe Characterization of thermostable beta-amylase isozymes from Lactobacillus fermentum(ELSEVIER SCIENCE BV, 2016) Kocabay, Samet; Cetinkaya, Serap; Akkaya, Birnur; Yenidunya, Ali FazilA strain of Lactobacillus fermentum producing two isozymes of a 20 kDa beta-amylase was isolated from the faecal sample of a newborn. The starin was identified by sequencing its 16S rRNA gene. The two beta-amylase isozymes were resolved and visualized by two dimensional protein gel electrophoresis (2-D gel electrophoresis). Some of the physical and biochemical properties of the enzymes were characterized. The beta-amylase displayed two optimum pH s, 5.0 and 10.0 and two optimum temperatures, 45 degrees C and 37 degrees C, respectively. The isozymes hydrolyzed different substrates: glycogen at pH 5.0, and corn starch at pH 10.0. The activity did not require Ca2+, though the activity at pH 10.0 was enhanced in the presence of 5.0 mM and 10.0 mM CaCl2, 110% and 130%, respectively. (C) 2016 Elsevier B.V. All rights reserved.Öğe Cytotoxicity of three maleic anhydride copolymers and common solvents used for polymer solvation(SPRINGER, 2013) Karakus, Gulderen; Zengin, Haci Bayram; Polat, Zubeyde Akin; Yenidunya, Ali Fazil; Aydin, SemihaThree maleic anhydride copolymers were synthesized by free-radical copolymerization. The synthesized products were named as follows: maleic anhydride-styrene (MAST); maleic anhydride-vinyl acetate (MAVA), and maleic anhydride-methyl methacrylate (MAMMA). Initiators used in the reactions were azobisisobutyronitrile (AIBN, 70 A degrees C, benzene) for MAST and benzoyl-peroxide [BPO, 80 A degrees C, methyl ethyl ketone (MEK)] for MAVA and MAMMA. Structural characterizations were carried out by Fourier transform infrared (FTIR) and nuclear magnetic resonance [H-1 NMR, C-13 NMR, and C-13-APT (attached-proton test)] spectrometry. Surface morphology was studied by scanning electron microscopy (SEM). Solubility of the copolymers was examined in water and in twelve different organic solvents. Cytotoxicity of the copolymers and the solvents was evaluated by using a mouse fibroblast cell line (L929), copolymers had almost no toxicity. Of the twelve organic solvents, acetone, MEK, and tetrahydrofuran (THF) produced the least toxicity. MEK was found to be the best solvent and used for the solvation of the copolymers.Öğe D-Glucose-fatty Acid Ester Synthesis with or without a Biocatalyst in the Same Organic Media(Japan Oil Chemists Soc, 2020) Cetinkaya, Serap; Yenidunya, Ali Fazil; Basoglu, Faika; Sarac, KamuranEsterification of D-glucose with oleic- and palmitic acids were carried out in the absence and presence of a biocatalyst, Candida antarctica lipase. The reaction medium was a mixture of dimethyl sulphoxide and tert-butanol (1:4, v/v). The reaction products were analysed by FTIR, H-1-NMR and C-13-NMR, HSQC, and by ESI-MS. Results indicated that the ester products formed were 6-O-glucose oleate and 6-O-glucose palmitate both in the absence and in the presence of the biocatalyst, with yields above 90%.Öğe Esterification of Fructose-oleic Acid by tert-Butanol/Dimethyl Sulfoxide and by 2-Methyl-2-butanol/Dimethyl Sulfoxide(Japan Oil Chemists Soc, 2020) Cetinkaya, Serap; Yenidunya, Ali Fazil; Basoglu, Faika; Polat, Zubeyda Akin; Savas, SumeyraIn this study two different strategy were followed to obtain a D-fructose-oleic acid ester. One of the strategies has been well established enzymatic synthesis of an ester bond. The other strategy excluded the biocatalyst and only used a mixture of two organic solvents as the reaction media, 2-methyl-2-butanol / dimethyl sulfoxide or tert-butanol / dimethyl sulfoxide for the production of D-fructose-oleic acid ester. Ester products obtained were characterised by using FT-IR, NMR, by MS. Product yield was also assessed by HPLC. Results of structural analyses and yield measurement indicated that two approaches produced almost identical ester products.Öğe Experimental and Theoretical Evidence on the Amoebicidal Activity of Synthesized tRNA-Palmitic Acid Esters(Jihad Daneshgahi, 2024) Aksu, Aysun; Celik, Muhammed Safa; Polat, Zubeyde Akin; Yenidunya, Ali Fazil; Cetinkaya, Serap; Tuzun, BurakSynthesis of tRNA-palmitic acid esters was carried out in dimethyl sulfoxide (DMSO) and tert-butanol, %20 and %80 (v/v), respectively, for 24h at 55oC. These conditions have been to be optimal in the synthesis of monosaccharide-fatty acid esters in previous studies. The majority of the ester product (89.19%) was phthalic acid, butyl undecyl ester, as identified by GC-MS. This finding hinted that the ester bond took place between tRNA ribose unit(s) and carboxyl group of the palmitic acid. NMR (Nuclear Magnetic Resonance) was also used for the characterization of the ester product (data not shown). The ester product (O1) exerted remarkable amoebicidal activity, at 4mg/ml, on the trophozoites and cysts of Acanthamoeba castellanii. No live trophozoites or cysts could be detected after the 24th and 72th of incubation, respectively. The study included all the necessary control experiments. Interactions between the substrate molecules were scrutinized by molecular docking calculations. Activities of the studied molecules against various Acanthamoeba castellanii proteins (PDB ID: 1PRQ and 6UX0), in crystal form, were compared, and finally, ADME/T analyses were carried out.Öğe Modification of Maleic Anhydride-Styrene Copolymer with Noradrenaline by Chemical and Enzymatic Methods(WILEY-BLACKWELL, 2011) Karakus, Gulderen; Yenidunya, Ali Fazil; Zengin, Haci Bayram; Polat, Zubeyde AkinMaleic anhydride copolymer was modified with another biologically active agent, noradrenaline (NA), using both chemical and enzymatic methods. The modification and synthesized products were named as follows: chemical modification, MASTNAc; enzymatic modification, MASTNAe; enzymatically synthesized MASTNA from individual monomers, MASTNAem. Chemical and enzymatic reactions were performed at 70 degrees C and 38 degrees C, respectively. In the chemical reactions azobisisobutyronitrile was used as the initiator. In the enzymatic reactions, an extracellular extract, including an enzyme with peroxidase-like activity, was used. All the reactions were performed in an organic medium, methyl ethyl ketone. Structural characterization of the copolymer and modified copolymer were carried out by Fourier transform infrared (FTIR) and nuclear magnetic resonance ((1)H NMR). FTIR and (1)H NMR spectra confirmed that NA was successfully covalently bound onto the MAST copolymer backbone by both chemical and enzymatic methods. Surface morphology of the samples was studied by scanning electron microscopy. Results obtained indicated that chemical and enzymatic addition of NA to MAST backbone yielded products having quite similar physical and chemical properties. On the other hand, MASTNA-modified copolymer synthesized by individual monomers appeared to be different in its chemical structure. Furthermore, enzymatic modification and synthesis appeared to provide a good alternative method because it required much milder conditions such as low temperature, and better product qualities: higher solubility in water, higher yield and purity. (C) 2011 Wiley Periodicals, Inc. J Appl Polym Sci 122: 2821-2828, 2011Öğe Production and immobilization of a novel thermoalkalophilic extracellular amylase from bacilli isolate(ELSEVIER SCIENCE BV, 2012) Akkaya, Birnur; Yenidunya, Ali Fazil; Akkaya, RecepA Thermoalkalophilic amylase was produced from an environmental bacterial isolate. The enzyme was then immobilized through its amino groups onto the epoxy rings of magnetic poly glycidyl methacrylate [m-poly (GMA)] beads. The free enzyme was active within a large pH range, between 7 and 12 and displayed the optimum activity at 95 degrees C and pH 10. The immobilization appeared to increase the stability of the enzyme as its bound form showed optimum activity at 105 degrees C and pH 11.0. Kinetic studies demonstrated that immobilized enzyme had higher K-m and lower V-max values. The activity of the free and bound enzyme was determined, at 37 degrees C and pH 10.0 and pH 11.0, respectively, in the presence of various organic solvents and detergents (5%, v/v). Results obtained indicated that detergents, sodium dodecyl sulfate (SDS) and TritonX-100, caused six fold increase and that various organic solvents also increased the activity of the amylase. (C) 2012 Elsevier B.V. All rights reserved.Öğe Production, purification, and characterization of metalloprotease from Candida kefyr 41 PSB(ELSEVIER SCIENCE BV, 2017) Yavuz, Sevgi; Kocabay, Samet; Cetinkaya, Serap; Akkaya, Birnur; Akkaya, Recep; Yenidunya, Ali Fazil; Bakici, Mustafa ZahirA thermostable metalloprotease, produced from an environmental strain of Candida kefyr 41 PSB, was purified 16 fold with a 60% yield by cold ethanol precipitation and affinity chromatography (bentoniteacrylamide-cysteine microcomposite). The purified enzyme appeared as a single protein band at 43 kDa. Its optimum pH and temperature points were found to be 7.0 and 105 degrees C, respectively. K-m and V-max values of the enzyme were determined to be 3.5 mg/mL and 4.4 mu mol mL(-1) min(-1), 1.65 mg/mL and 6.1 mu mol mL(-1) min(-1), using casein and gelatine as the substrates, respectively. The activity was inhibited by using ethylenediamine tetraacetic acid (EDTA), indicating that the enzyme was a metalloprotease. Stability of the enzyme was investigated by using thermodynamic and kinetic parameters. The thermal inactivation profile of the enzyme conformed to the first order kinetics. The half life of the enzyme at 95, 105, 115, 125 and 135 degrees C was 1310, 610, 220, 150, and 86 min, respectively. (C) 2016 Elsevier B.V. All rights reserved.Öğe Properties of an extracellular lipase from a traditional yoghurt yeast(WALTER DE GRUYTER GMBH, 2012) Akkaya, Birnur; Yenidunya, Ali FazilPurpose: To produce an organic solvent tolerant extracellular lipase from a traditional yoghurt Saccharomyces cerevisiae isolate and to characterize this enzyme activity. Material and Methods: A traditional yoghurt sample collected from a farm (Sivas-Turkey) was diluted and mixed with de Man, Rogosa and Sharp Medium (MRS) and poured into Petri dishes. One hundred colonies were selected and transferred onto MRS agar plates including Tween 80 as a lipase substrate. Only four colonies with lipase activity were incubated in MRS broth for 3 days at 37 degrees C and the extracellular proteins were precipitated with ethanol (95% v/v) from the supernatant. The precipitate with the highest lipase activity was selected for further analysis. Results: The optimum pH and temperature were 7.0 and 37 degrees C, respectively. While (1 mM) Mn2+ caused a slight increase (similar to 8%) Hg2+ or Zn2+ caused a substantial activity loss (similar to 70%). Organic solvents (5% chloroform or n-butanol, v/v) increased activity similar to 2.5 fold. Five percent SDS or Triton X-100 increased activity by 8% and 14%, respectively. The enzyme could hydrolyse hydroxyethyl methacrylate (HEMA) and 2,3-epoxy propyl methacrylate (GMA), retained similar to 83% of its activity after 1 hour at 37 degrees C, lost no activity when stored at pH 7.0 and at 4 degree C for 60 days. Conclusion: The properties of the extracellular yeast lipase was investigated using a number of physiological parameters. The results obtained indicated that it was an organic solvent-and detergent tolerant enzyme having the optimum activity at mild reaction conditions.Öğe Purification and characterisation of 1-dodecanol from an isolate of Streptomyces viridodiastaticus(Elsevier, 2021) Cetinkaya, Serap; Yenidunya, Ali Fazil; Aksu, Aysun; Celik, Muhammed SafaOne-dodecanol was identified as the predominant secondary metabolite produced by a novel isolate of Streptomyces viridodiastaticus. A total secondary metabolite extract was electrophoresed, along with a prestained protein ladder (from 10 to 180 kDa), in a 10% SDS-polyacrylamide gel. Two prominent bands obtained were aligned with 25 and 10 kDa bands of the protein marker. These two secondary metabolite bands were also visualized by thin layer chromatography. The two bands, lower band (C1) and upper band (C2), in the polyacrylamide gel were sliced off and their metabolite content was eluted in n-butanol. Elution samples were analysed by GC-MS. Results indicated that the lower C1 band mostly contained 1-dodecanol, approximately 93%. The lower band also contained a 1-dodecanol-like metabolite, approximately 55%. The elution samples were also analysed by FTIR and the results were in accordance with those of the GC-MS.Öğe Removal of lead ions (Pb2+) from aqueous solution using chitosan/starch composite material: Experimental and density functional theory findings(Springer Heidelberg, 2024) Celik, Muhammed Safa; Caylak, Osman; Kutuk, Nursah; Yenidunya, Ali Fazil; Cetinkaya, Serap; Maslov, Mikhail M.; Kaya, SavasTreatment of wastewater has become vital to prevent environmental pollution in recent years. Adsorption is an easily applicable, low-cost and efficient method and is the subject of this study. In this study, an adsorbent was synthesized to be used in heavy metal removal using chitosan and starch. The composite was characterized by Fourier transform infrared (FTIR) spectrophotometry, X-ray powder diffraction (XRD), thermogravimetric analysis (TGA), and scanning electron microscopy (SEM), energy-dispersive X-ray (EDX) analysis. It was determined that the composite had an amorphous and compact structure. Adsorption experiments were carried out under the optimized parameters such as solution pH, concentration, adsorbent amount, equilibrium time, and temperature. It shows that during adsorption, with the increase in pH, the adsorption efficiency and adsorption capacity first increase and then a fluctuation occurs. The highest adsorption efficiency and Q value were reached at pH 3.46 as 78% and 0.038 mol/kg, respectively. Moreover, the adsorption capacity (Q) reached its highest value with a value of 0.067 mol/kg in the presence of 30 mg adsorbent. Equilibrium experiments were validated by the Langmuir, Freundlich, Temkin and Dubinin-Radushkevich isotherm models. To investigate the adsorption mechanism, pseudo-first-order (PFO) and pseudo-second-order (PSO) kinetic models were used. It was determined that the adsorption process followed the D-R isotherm (R-2 = 0.99) and PSO (R-2 = 0.99). Therefore, the existence of chemical adsorption can be mentioned. Thermodynamic parameters enthalpy (triangle H), Gibbs free energy (triangle G) and entropy change (triangle S) were investigated. The adsorbate-adsorbent interactions were studied by density functional theory (DFT).Öğe Removal of safranin O from wastewater using Streptomyces griseobrunneus dead biomass and in silico calculations(Springer Heidelberg, 2023) Celik, Muhammed Safa; Kutuk, Nursah; Yenidunya, Ali Fazil; Cetinkaya, Serap; Tuzun, BurakEnvironmental pollution with the dye produced by the textile industry causes a serious problem worldwide. The aim of the study is to use the environmentally friendly and low-cost Streptomyces griseobrunneus (S. griseus S15) dead cells for the adsorption of safranin O from aqueous milieu. Optimum retention was achieved with 200 mg/L safranin O and 25 g/L adsorbent at pH 9. Biosorption was found to better fit the Langmuir isotherm and PSO kinetics. The maximum biosorption (q(max)) was 188.67 mg/g. The reaction between S. griseus S15 and safranin O was chemical, exothermic, and spontaneous. S. griseus S15 biomass was reusable. Molecules supposed to be involved in the process were investigated by using a Gaussian software program, calculations B3LYP, HF, and M06-2X, 6-31G, 6-31++G, and 6-31++G**. For molecular docking calculations, the affinity of safranin O molecule to various proteins was investigated. Finally, ADME/T was applied to gain an insight into the possible effects of safranin O on human health.Öğe Secondary Metabolites of an of Streptomyces griseorubens Isolate Are Predominantly Pyrrole- and Linoleic-acid like Compounds(Japan Oil Chemists Soc, 2020) Cetinkaya, Serap; Yenidunya, Ali Fazil; Arslan, Kubilay; Arslan, Donsel; Dogan, Ozgul; Dastan, TanerThe study involved the isolation and identification of a member of Streptomyces griseorubens and the identification of its secondary metabolite content. Two extract samples were prepared by using butanol and chloroform. In the analyses of the extracts TLC, FT-IR, and GC-MS were employed. Butanol extract appeared to be dominated by three different pyrrole compounds (43.59%), while two fatty acids, linoleic and erucic acids, were the most abundant secondary metabolites in the chloroform extract, 27.57% and 12.34%, respectively. Pyrrolo[1,2-alpyrazine-1,4-dione, hexahydro-compound was represented by a single and distinct band on the thin layer chromatography plate. In GC-MS spectra, it also constituted 13.50% of the butanol extract.Öğe Synthesis of Ribose - Oleic Acid Esters in the Presence- and Absence of Candida antarctica Lipase B(Japan Oil Chemists Soc, 2020) Cetinkaya, Serap; Yenidunya, Ali Fazil; Basoglu, Faika; Sarac, KamuranD-ribose-oleic acid esters were produced with or without a biocatalyst, using in the same organic media. dimethyl sulfoxide (DMSO): tort-butanol (TBU) or 2-methyl-2-butanol (2M2B). The yield of the ester product was above 90% in both of the reactions. The biocatalyst used was lipase B of Candida antarctica. Molecular characterization was performed by using all the analytical methods available: IR, H-1-NMR and C-13-NMR, HSQC, and ESI-MS.Öğe Synthesis, characterization and cytotoxicity of novel modified poly[(maleic anhydride)-co-(vinyl acetate)]/noradrenaline conjugate(WILEY-BLACKWELL, 2013) Karakus, Gulderen; Polat, Zubeyde Akin; Yenidunya, Ali Fazil; Zengin, Haci Bayram; Karakus, Can BulentPoly[(maleic anhydride)-co-(vinyl acetate)] (MAVA) copolymer was synthesized by free radical polymerization reaction, in methyl ethyl ketone at 80 degrees C, using benzoyl peroxide as the initiator. The copolymer was then modified with a biomolecule, noradrenaline (NA). The modification reaction was performed at 70 degrees C in dimethylformamide containing triethylamine as the catalyst. The modified polymer was named MAVA/NA. Structural characterization of the copolymer and the modified product was carried out by Fourier transform infrared (FTIR) and 1H NMR and 13C NMR spectroscopy. The FTIR, 1H NMR and 13C NMR spectra confirmed that NA was successfully covalently bound to the MAVA copolymer backbone. Surface morphology was visualized by atomic force microscopy. The cumulative release of NA from MAVA/NA was determined in phosphate buffered saline solution for 7 days at 37 degrees C and compared with MAVA. Cytotoxicity of the MAVA/NA was evaluated by using a mouse fibroblast cell line (L929). Results obtained indicated that MAVA/NA had almost no toxicity and no negative effect on cell viability at 250 mu g mL1 concentration. (c) 2012 Society of Chemical IndustryÖğe Synthesis, characterization, and assessment of cytotoxic, antiproliferative, and antiangiogenic effects of a novel procainamide hydrochloride-poly(maleic anhydride-co-styrene) conjugate(TAYLOR & FRANCIS LTD, 2013) Karakus, Gulderen; Polat, Zubeyde Akin; Yaglioglu, Ayse Sahin; Karahan, Mesut; Yenidunya, Ali FazilPoly(maleic anhydride-co-styrene) (MAST) was synthesized by a free-radical polymerization reaction. A bioactive molecule, procainamide hydrochloride (PH), was then conjugated to MAST. The conjugation product was named as MAST/PH. Structural characterization of MAST and MAST/PH was carried out by Fourier Transform Infrared and Nuclear Magnetic Resonance spectroscopy. Their molecular weights were determined by size-exclusion chromatography. A mechanism was then suggested for the conjugation reaction. The results of the cytotoxicity assay, employing a mouse fibroblast cell line (L929), indicated that MAST/PH had no cytotoxicity at concentrations 62gmL(1) (p>0.05). Antiproliferative activities of MAST/PH and PH were determined by the BrdU cell proliferation ELISA assay, using C6 and HeLa cell lines. In the experiment, two anticancer chemotherapy drugs, cisplatin and 5-fluorouracil, were included as positive control. Antiproliferative activity results demonstrated that MAST/PH yielded the highest suppression profile (approximately 42%) at 20g/ml, while free PH exerted the same activity at 100g/ml. Interestingly, both MAST/PH and PH suppressed the proliferation of only one of the cell lines, C6 cells. Both cisplatin and 5-fluorouracil yielded approximately 60% antiproliferative activity on C6 cells at 20 and 100g/ml concentrations. Antiangiogenic capacity of both MAST and MAST/PH was also investigated by using the chicken chorioallantoic membrane assay. Results obtained indicated that while MAST/PH could be included into the category of good antiangiogenic substances, the activity score of MAST was within the weak category.
