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Öğe A Novel Isolate (S15) of Streptomyces griseobrunneus Produces 1-Dodecanol(Springer, 2021) Cetinkaya, SerapOne-dodecanol was identified to be the predominant secondary metabolite of a novel isolate (S15) of Streptomyces griseobrunneus. For its demonstration, secondary metabolite extracts were electrophoresed by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE). A yellowish unique band was then cut out from the gel and its metabolite content was eluted in n-butanol. GC-MS analysis indicated that more than 93% of the of the elution material were 1-dodecanol. The compound was further characterized by FTIR and C-13 NMR analyses. Dendrogram built on the basis of 16S rRNA gene sequence indicated that the isolate S15 was a member of Streptomyces griseobrunneus.Öğe Biosorption of dye crystal violet on Tragopogon sp. leaf powder: Equilibrium, kinetics, thermodynamics, and DFT calculations(Elsevier, 2024) Eyupoglu, Volkan; Aksu, Aysun; Cetinkaya, Huseyin Fatih; Cetintas, Halil Ibrahim; Cetinkaya, Serap; Tuzun, BurakCrystal violet, CV, was adsorbed on dead mass of Tragopogon sp. in aqueous solutions and the adsorption process was evaluated by analytical, visual, and theoretical means. The functional groups on the biosorbent surface were detected by FT-IR (Fourier Transform Infrared Spectrophotometry), and the surface morphology was visualized by SEM (Scanning Electron Microscopy), and EDX (Energy Dispersive X-Ray Analysis). Some of the biosorption conditions, pH, time, adsorbent mass, and temperature, were optimized. Three isotherm models, Langmuir, Freundlich, and Dubinin-Radushkevich, employed for the understanding of the reaction kinetics, suggested a spontaneous endothermic reaction that took place on the surface of Tragopogon sp cells. Iterative usability experiments, involving four biosorption-desorption rounds, showed that Tragopogon sp. biomass retained approximately 42% of its sorbent activity. Calculations, using the Gaussian software packages B3LYP, HF, and M06-2x, indicated a very high biosorption capacity of Tragopogon sp. for crystal violet. Crystal violet had -7.2067 HOMO and 0.1921 LUMO values.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 Chemical composition, cytotoxicity, and molecular docking analyses of Thuja orientalis extracts(Elsevier, 2024) Kapancik, Serkan; Celik, Muhammed Safa; Demiralp, Mustafa; Unal, Kagan; Cetinkaya, Serap; Tuzun, BurakThere has been an increasing interest in the biologically active plant extracts. Studies still continue in order to discover novel components especially with antimicrobial activities to overcome the challenge of drug resistance and to ameliorate existing antibiotics. Three extract preparations, methanol, water, and chloroform, were made. Their chemical compositions were determined and compared. Extraction with water proved most fruitful as it contained forty-two active compounds. Cytotoxicity of these compounds was tested on MCF-7 and HT-29 cell lines and it was demonstrated that ethanol extracts were toxic. Molecular docking computations hinted that some of the compounds could target breast cancer proteins PDB ID, 1A52, and 1JNX and colorectal cancer proteins PDB ID, 1UWH, and 3RQ7). ADME/T calculations were made to examine the effects of Thuja orientalis extracts on human metabolism.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 Illumination of biosorption of Allura Red on Rhus coriaria L. (sumac) plant: equilibrium, kinetic, thermodynamic, and density functional theory-based analyses(Springer Heidelberg, 2024) Caylak, Osman; Cetintas, Halil Ibrahim; Celik, Muhammed Safa; Kaya, Nurevsan; Cetinkaya, Serap; Maslov, Mikhail M.; Kaya, SavasIn the present paper, the biosorption capability of Rhus coriaria L. (sumac) plant for the effective removal of Allura Red (AR) dye from wastewater was tested in the light of theoretical and experimental tools. The reactive functional groups in the structure of the studied biosorbent and the surface morphology of the mentioned biosorbent were highlighted with the help of FTIR spectrophotometer, SEM (scanning electron microscopy), and EDX (energy-dispersive X-ray analysis). The effect of important parameters such as pH, time, adsorbent mass, and temperature on the biosorption process was checked and discussed in detail. pH 2 was determined as the optimum value for the highest biosorption. Maximum effectiveness was reached at a biosorbent mass of 200 mg. The biosorption process adhered to the Langmuir isotherm and PSO kinetic models, and the process was determined to have a spontaneous and exothermic nature. Through the recovery experiments, it was noted that the studied plant retained approximately 30% of its biosorption capacity after three cycles. To prove the power of the interaction between Allura Red dye and dominant components of Rhus coriaria L. (sumac), density functional theory calculations were performed. Theoretically obtained conceptual DFT-based descriptors, the comments made within the framework of popular electronic structure rules, and calculated adsorption energies were in good agreement with the experimentally obtained data. As a result, it was reported that Rhus coriaria L. can be used as an effective and useful biosorbent for the removal of AR from wastewater.Öğe Metal Concentrations of Wild Edible Mushrooms from Turkey(TAYLOR & FRANCIS INC, 2012) Sarikurkcu, Cengiz; Tepe, Bektas; Solak, Mehmet Halil; Cetinkaya, SerapIn the present study, the contents of Zn, Fe, Cu, Mn, Co, Ni, Pb, Cd, Cr, Al, Ca, Mg, and K in Agaricus campestris, Agrocybe cylindracea, Collybia dryophila, Helvella leucopus, Russula delica, Tricholoma auratum, Amanita ovoidea, Melanoleuca excissa, Rhizopogon roseolus, Russula chloroides, Volvoriella gloiocephala, Lyophyllum decastes, Morcella angusticeps, Morchella esculenta and Morcella eximia collected from Isparta, Mugla, and Osmaniye provinces (Turkey) were determined by inductively coupled plasma optical emission spectrometry (ICP-OES) after microwave digestion. The intake of heavy metals (Pb, Cd) and other metals (Fe, Cu, Zn) by consumption of 30 g dry weight of mushrooms daily poses no risk at all except in A. cylindracea and H. leucopus (for Cd) for the consumer.Öğe Molecular Typing of Different Salmonella Serotypes by Multiple-Locus Analysis of Tandem Repeats(Japan Oil Chemists Soc, 2020) Savas, Sumeyra; Cetinkaya, SerapSalmonella enterica subspecies enterica causes salmonellosis in humans and animals and is an important cause of food infections worldwide. In recent years, the multiple-locus variable-number of tandem repeat (VNTR) analysis (MLVA), a fast molecular typing method with strong epidemiological discrimination, has facilitated the effective control of diverse infections. This study aimed at the typing of 28 human origined Salmonella enteritidis, Salmonella infantis, and Salmonella typhimurium strains by using a single MLVA protocol. Previously these strains have been identified by pulsed field gel electrophoresis (PFGE) method and it has been shown that each strain produced a distinct PFGE banding profile. One MLVA protocol was tested on 3 serotypes simultaneously and it produced three banding patterns specific to each of the three common Salmonella serotypes. MLVA also constitute a relatively more cost-effective and faster method than PFGE.Öğe Novel imidazo[2,1-b]thiazole-based anticancer agents as potential focal adhesion kinase inhibitors: Synthesis, in silico and in vitro evaluation(Wiley, 2021) Basoglu, Faika; Ulusoy-Guzeldemirci, Nuray; Akalin-Ciftci, Gulsen; Cetinkaya, Serap; Ece, AbdulilahThe purpose of this study was to synthesize imidazo[2,1-b]thiazole derivatives, characterize them with spectroscopical techniques and investigate for cytotoxic and apoptotic effects on glioma C6 cancer cell line. The in vitro anticancer activities were also investigated against focal adhesion kinase. Most of the compounds, particularly the derivatives carrying 3-oxo-1-tiya-4-azaspiro[4.5]decane moiety, exhibited higher or comparable activities in comparison with the reference drug, cisplatin. Compounds with methyl, propyl, phenyl moieties at the eighth and second position of the spirothiazolidinone ring showed high FAK inhibitory activities. In addition, molecular docking studies shed light on the binding modes of the synthesized compounds. The critical interactions with amino acid residues located in the active site were revealed. The results obtained from both biological assay data and computational results might provide insight into developing new inhibitors against focal adhesion kinase.Öğe Probiotic Properties of a Lactobacillus fermentum Isolated from New-born Faeces(Japan Oil Chemists Soc, 2020) Kocabay, Samet; Cetinkaya, SerapLactic acid bacteria (LAB) have been demonstrated to have roles in many applications, ranging from lowering of cholesterol to immunological development. In this study, Lactobacillus fermentum was isolated from a new-born's faeces and its genotypic and probiotic characterizations were performed. Our results showed that the survival rate of isolated Lactobacillus fermentum was 39.39% at pH 2 and 81.34% in the stimulated gastric juice at pH 3. It also digested bile salts. Its surface hydrophobicity was found to be 57.59% in n-hexane. These findings indicated that the isolate can be a good probiotic candidate.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 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 Selective and single step adsorption of a-lactalbumin from whole cow's milk on hydroxyapatite microbeads(ELSEVIER SCIENCE BV, 2016) Cetinkaya, Serap; Akkaya, BirnurIn this study, newly modified hydroxyapatite microbeads were used to isolate alpha-lactalbumin (alpha-LA) from cow's milk by a single step. Inorganic material, pure hydroxyapatite was embedded in ethylene glycol dimethacrylate (EGDMA) in the presence of pore maker. Newly synthesized hydroxyapatite microbeads were used firstly for adsorption of alpha-LA from aqueous solution. The maximum adsorption capacity of alpha-LA from aqueous solution was observed at pH 7.0 (10.0 mM phosphate buffer) at 25 degrees C in a batch system, in which parallel separate experiments were performed independently. Synthesized hydroxyapatite microbeads and pure hydroxyapatite were used for adsorption studies from whole milk (without pre-treatment such as fat and caseins removal). Our method is cheap, simple, efficient and rapid. The results showed that modified hydroxyapatite microbeads had selective affinity to alpha-LA because of good adsorption properties. (C) 2016 Elsevier B.V. All rights reserved.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 Theoretically supported experimental analyses on Safranin O biosorption from textile wastewater via dead biomass of Spirogyra porticalis(Springer Heidelberg, 2024) Aksu, Aysun; Kutuk, Nursah; Caylak, Osman; Kasaka, Erguen; Cetinkaya, Serap; Maslov, Mikhail M.; Kaya, SavasHigh-performance chemical systems designed to eliminate pollution caused by dyestuffs are still among the focuses of interest of chemists. Non-toxic biological materials especially have begun to be widely used in this field. Fourier transform infrared spectrometry, SEM (scanning electron microscopy), EDS (energy-dispersive X-ray analysis), and TGA (thermogravimetric analysis) were performed. Adsorption was performed in batch-adsorption experiments. Optimization processes involved pH, amounts of the sorbent and Safranin O, adsorption kinetics, desorption, and reusability. To highlight the mechanism of the interaction between Safranin O and S. porticalis and to predict the power and nature interactions, density functional theory computations were performed. Optimization processes included pH, amounts of sorbent and Safranin O, adsorption kinetics, desorption, and reusability. Experimental results were re-evaluated using Langmuir and Freundlich isotherm models and the biosorption process followed Freundlich isotherm kinetics. The biosorption mechanism was understood by pseudo-first-order (PFO), intraparticle diffusion (IPD), and Elovich models. Adsorption was determined to follow PFO kinetics: physical, endothermic, and spontaneous. The highest recovery was obtained in NaOH. Density functional theory (DFT) finding calculations were also performed to prove the high adsorption capacity for Safranin O of the material used.
