Ufuk Bakir | Middle East Technical University (original) (raw)

Papers by Ufuk Bakir

Research paper thumbnail of Crystallization and preliminary X-ray analysis of a bifunctional catalase-phenol oxidase from Scytalidium thermophilum

Acta Crystallographica Section F-structural Biology and Crystallization Communications, 2009

Research paper thumbnail of Preparation of cross-linked tyrosinase aggregates

Process Biochemistry, 2008

Tyrosinase from mushroom was immobilized as a cross-linked enzyme aggregate (CLEA) via precipitat... more Tyrosinase from mushroom was immobilized as a cross-linked enzyme aggregate (CLEA) via precipitation with ammonium sulfate and crosslinking with glutaraldehyde. The effects of precipitation and cross-linking on CLEA activity were investigated and the immobilized tyrosinase was characterized. Sixty percent ammonium sulfate saturation and 2% glutaraldehyde were used; a 3-h cross-linking reaction at room temperature, at pH 7.0 was performed; particle sizes of the aggregates were reduced; consequently, 100% activity recovery was achieved in CLEAs with enhanced thermal and storage stabilities. Slight changes in optimum pH and temperature values of the enzyme were recorded after immobilization. Although immobilization did not affect V max , substrate affinity of the enzyme increased. Highly stable CLEAs were also prepared from crude mushroom tyrosinase with 100% activity recovery. #

Research paper thumbnail of Production and characterization of xylanases of a Bacillus strain isolated from soil

World Journal of Microbiology and Biotechnology, 2005

Xylanase production was performed by growing a Bacillus isolate on agricultural by-products, whea... more Xylanase production was performed by growing a Bacillus isolate on agricultural by-products, wheat straw, wheat bran, corn cobs and cotton bagasse. A maximum xylanase activity of 180 U/ml was obtained together with a cellulase activity of 0.03 U/ml on 4 (w/v) ...

Research paper thumbnail of Screening of tree leaves as annual renewable green biomass for phenol oxidase production and biochemical characterization of mulberry (Morus alba) leaf phenol oxidases

World Journal of Microbiology and Biotechnology, 2011

... of mulberry (Morus alba) leaf phenol oxidases Didem Sutay Kocabas • Zumrut Begum Ogel • Ufuk ... more ... of mulberry (Morus alba) leaf phenol oxidases Didem Sutay Kocabas • Zumrut Begum Ogel • Ufuk Bakir ... References Akpinar O, Ak O, Kavas A, Bakir U, Yilmaz L (2007) Enzymatic production of xylooligosaccharides from cotton stalks. ...

Research paper thumbnail of Xylanase from a soil isolate, Bacillus pumilus: gene isolation, enzyme production, purification, characterization and one-step separation by aqueous-two-phase system

World Journal of Microbiology and Biotechnology, 2010

Page 1. ORIGINAL PAPER Xylanase from a soil isolate, Bacillus pumilus: gene isolation, enzyme pro... more Page 1. ORIGINAL PAPER Xylanase from a soil isolate, Bacillus pumilus: gene isolation, enzyme production, purification, characterization and one-step separation by aqueous-two-phase system Aysegul Ersayin Yasinok • Suzan Biran • Aytac Kocabas • Ufuk Bakir ...

Research paper thumbnail of Immobilization of invertase in functionalized copolymer matrices

Reactive and Functional Polymers, 2000

In this study, immobilization of invertase on functionalized polymer electrodes constructed with ... more In this study, immobilization of invertase on functionalized polymer electrodes constructed with pyrrole-capped polyazotetrahydrofuran and polytetrahydrofuran-block-polystyrene copolymer matrices was performed. Immobilization in these enzyme electrodes was carried out by the entrapment of the enzyme in conducting polymer matrices during electrochemical polymerization of pyrrole. Sodium dodecyl sulphate was used as the supporting electrolyte in the preparation of enzyme electrodes. The effects of temperature and pH on the activity of the enzyme electrodes were examined, and re-use number studies were performed. The changes in the maximum reaction rate and the variations of the Michaelis-Menten constant were investigated.

Research paper thumbnail of Antimicrobial properties of TiO2–SiO2 thin films

Research paper thumbnail of The effects of microbial lignocellulose pretreatments on xylooligosaccharide production

New Biotechnology, 2009

gases. The processing and utilization of lignocellulosic substrate is complex, differing in many ... more gases. The processing and utilization of lignocellulosic substrate is complex, differing in many aspects from crop-based ethanol production. One important requirement is an efficient microorganism able to ferment a variety of sugars (pentoses and hexoses) as well as to tolerate stress conditions. The study aims to extend the range of sources from which ethanol may be made beyond sugar cane bagasse which is used for the preparation of pulp and paper. Therefore, one fungal strain isolated from pulp and paper mill effluent identified as Cryptococcus albidus by 18S rDNA, internal transcribed spacer (ITS) together with Saccharomyces cerevisiae was used for the production of ethanol. The cellulose, lignin and xylan-degrading potency of fungus was evaluated by the production of sugar and enzymes, endoglucanase, exoglucanase, lignin peroxidase, manganese peroxidase, laccase, glucose oxidase and xylanase. The optimization of process parameters like pH, temperature, carbon and nitrogen source, phosphorus, agitation, inoculum size and duration using Taguchi approach indicated increase in 2-fold sugar production by fungus. The sugar cane bagasse treated by fungus subsequently treated by S. cerevisiae indicated the production of ethanol (36 g/L). The fermentation process was further improved by Taguchi approach where carbon, nitrogen, temperature, osmotic tolerance, inorganic compounds, stirring and pH were used. The result of the study indicated an increase in 1.5-fold production of ethanol. The method was tested in 15-L sequential bioreactor in which sugar cane bagasse was initially degraded by fungus and subsequently fermented by yeast for the production of ethanol for scale up of the method for huge production of bioethanol from sugar cane bagasse.

Research paper thumbnail of Preparation of conducting thin film surfaces for amperometric biosensor applications

New Biotechnology, 2009

late was cultivated at pH condition of 5, thus, the goal of this work was to evaluate their catal... more late was cultivated at pH condition of 5, thus, the goal of this work was to evaluate their catalytic capacity of whole-cell by assay of para-nitrophenyl palmitate (pNPP). Bacterial cells were cultivated during 48 hours. Samples of different times were taken and cells were separated by centrifugation, washed three times and air dried at 40 • C. The reaction mixture consisted in 20 mg of cells, 0.5 ml of stock solution of pNPP (10 mM in n-heptane). To start the reaction 30 l of methanol or ethanol were added to the mixture an incubated at 40 • C and 160 rpm from 0.5 to 120 min. Then, 25 l of mixture were taken and mixed with 1 ml of 0.1 M of NaOH. Additionally, the reaction mixtures were incubated with no alcohol. The pNPP liberated was extracted by aqueous alkali phase and detected at 405 nm. The kinetics curves of samples demonstrated that the whole-cells cultivated at 12 hours and 24 hours presented the highest production of pNP with methanol during the first 10 min of reaction. After the lipase activity decreased and remains practically constant until the end of the experiment. The reaction with ethanol shows a maximal activity in samples of 24 hours of culture in 10 min of reaction. The lipase activity observed with no alcohol in the reaction was at a value of one third of that obtained in cells with methanol. The results presented here, using a whole-cell biocatalyst is considered promising for biodiesel production in industrial applications.

Research paper thumbnail of Enzyme immobilization to modified and patterned surfaces for biocatalytically active surface preparation

New Biotechnology, 2009

late was cultivated at pH condition of 5, thus, the goal of this work was to evaluate their catal... more late was cultivated at pH condition of 5, thus, the goal of this work was to evaluate their catalytic capacity of whole-cell by assay of para-nitrophenyl palmitate (pNPP). Bacterial cells were cultivated during 48 hours. Samples of different times were taken and cells were separated by centrifugation, washed three times and air dried at 40 • C. The reaction mixture consisted in 20 mg of cells, 0.5 ml of stock solution of pNPP (10 mM in n-heptane). To start the reaction 30 l of methanol or ethanol were added to the mixture an incubated at 40 • C and 160 rpm from 0.5 to 120 min. Then, 25 l of mixture were taken and mixed with 1 ml of 0.1 M of NaOH. Additionally, the reaction mixtures were incubated with no alcohol. The pNPP liberated was extracted by aqueous alkali phase and detected at 405 nm. The kinetics curves of samples demonstrated that the whole-cells cultivated at 12 hours and 24 hours presented the highest production of pNP with methanol during the first 10 min of reaction. After the lipase activity decreased and remains practically constant until the end of the experiment. The reaction with ethanol shows a maximal activity in samples of 24 hours of culture in 10 min of reaction. The lipase activity observed with no alcohol in the reaction was at a value of one third of that obtained in cells with methanol. The results presented here, using a whole-cell biocatalyst is considered promising for biodiesel production in industrial applications.

Research paper thumbnail of Optimization of xylanase production from Aspergillus terreus by using renewable agricultural lignocellulosic residues

Research paper thumbnail of Comparison of acid and enzymatic hydrolysis of tobacco stalk xylan for preparation of xylooligosaccharides

LWT - Food Science and Technology, 2010

... Like autohydrolysis, the main disadvantage of this method is the production of monomeric suga... more ... Like autohydrolysis, the main disadvantage of this method is the production of monomeric sugars and undesirable by-products. Food and other industries spend considerable amounts of time and/or money to obtain XOs. The ...

Research paper thumbnail of Photocatalytic microbial inactivation over Pd doped SnO2 and TiO2 thin films

Journal of Photochemistry and Photobiology A: Chemistry, 2006

The photocatalytic antimicrobial activity over TiO2, SnO2 and their Pd doped thin film samples we... more The photocatalytic antimicrobial activity over TiO2, SnO2 and their Pd doped thin film samples were determined against Escherichia coli, Staphylococcus aereus, Saccharomyces cerevisiae and Aspergilus niger spores. Higher antimicrobial activity was observed with TiO2 than SnO2 thin films and, Pd addition contributes to an increase in the activity of both semiconductor oxides. The highest microbial inactivation was achieved with 1% PdO/TiO2 against E. coli with a 98% decrease in survival after 2h illumination. SnO2 was found to show lower photocatalytic efficiency against E. coli with a 56% decrease in survival after 2h illumination and a 68% decrease in survival of E. coli after palladium addition. E. coli showed the least and S. cerevisiae showed the highest resistance against photocatalytic inactivation and, A. niger spores could not be inactivated up to 8h illumination over all the surfaces. The antimicrobial efficiencies against different microorganisms and fungal spores were found to decrease in the following order: E. coli>S. aereus>S. cerevisiae>A. niger spores for which, complexity and strength of the cell walls increased in the same order.

Research paper thumbnail of Hydrothermal Synthesis of Nanostructured TiO<SUB>2</SUB> Particles and Characterization of Their Photocatalytic Antimicrobial Activity

Journal of Nanoscience and Nanotechnology, 2008

Nanostructured titania particles were synthesized by using hydrothermal processing and the photoc... more Nanostructured titania particles were synthesized by using hydrothermal processing and the photocatalytic antimicrobial activities were characterized. Both sol-gel synthesized and commercial TiO2 (anatase) samples were processed with two step hydrothermal treatments, under alkaline and neutral conditions. Scanning Electron Microscope (SEM) images showed that alkaline treatment yields nanofibers and lamellar structured particles from the commercial anatase and sol-gel synthesized samples respectively. Further treatment of nanofibers and nanostructured lamellar particles with distilled water results with crystal growth and the formation of nano structured bipyramidal crystalline particles. The photocatalytic antimicrobial activities of the samples were determined against Escherichia coil under irradiation. It was observed that the samples treated under alkaline conditions have improved activity than the original anatase samples. Limited activity and resulting time lag in bacterial inactivation were observed for hydrothermally treated samples with distilled water. However, a post treatment comprising the UV irradiation in aqueous conditions enhanced the photocatalytic activity.

Research paper thumbnail of IMMOBILIZATION OF YEAST CELLS IN SEVERAL CONDUCTING POLYMER MATRICES

Journal of Macromolecular Science, Part A, 2002

... Zeynep Balci,1 Ural Akbulut,1 Levent Toppare,1,* Selmiye Alkan,1 Ufuk Bakir,2 and Yusuf Yagci... more ... Zeynep Balci,1 Ural Akbulut,1 Levent Toppare,1,* Selmiye Alkan,1 Ufuk Bakir,2 and Yusuf Yagci3 ... Copyright © 2002 by Marcel Dekker, Inc. ... 12. Alkan, S.; Toppare, L.; Hepuzer, Y.; Yagci, Y. Block Copolymers of Thio-phene-Capped Poly(methyl methacrylate) with Pyrrole. ...

Research paper thumbnail of Production and Characterization of Films from Cotton Stalk Xylan

Journal of Agricultural and Food Chemistry, 2007

Composite film production based on cotton stalk xylan was studied, and the mechanical and physica... more Composite film production based on cotton stalk xylan was studied, and the mechanical and physical properties of the films formed were investigated. Xylan and lignin were separated from cellulose by alkali extraction and, then, lignin was removed using ethanol washing. Self-supporting continuous films could not be produced using pure cotton stalk xylan. However, film formation was achieved using 8-14% (w/w) xylan without complete removal of lignin during xylan isolation. Keeping about 1% lignin in xylan (w/w) was determined to be sufficient for film formation. Films were produced by casting the film-forming solutions, followed by solvent evaporation in a temperature (20 degrees C) and relative humidity (40%) controlled environment. The elastic modulus and hypothetical coating strength of the films obtained by using 8% xylan were significantly different from the ones containing 10-14% xylan. The water vapor transfer rates (WVTR) decreased with increasing xylan concentration, which made the films thicker. The glycerol addition as an additional plasticizer resulting in more stretchable films having higher WVTR and lower water solubility values. As a result, film production was successfully achieved from xylan, which was extracted from an agricultural waste (cotton stalk), and the film-forming effect of lignin on pure xylan has been demonstrated.

Research paper thumbnail of Enzymatic Production of Xylooligosaccharides from Cotton Stalks

Journal of Agricultural and Food Chemistry, 2007

Xylooligosaccharide (XO) production was performed from xylan, which was obtained by alkali extrac... more Xylooligosaccharide (XO) production was performed from xylan, which was obtained by alkali extraction from cotton stalk, a major agricultural waste in Turkey. Enzymatic hydrolysis was selected to prevent byproduct formation such as xylose and furfural. Xylan was hydrolyzed using a commercial xylanase preparation, and the effects of pH, temperature, hydrolysis period, and substrate and enzyme concentrations on the XO yield and degree of polymerization (DP) were investigated. Cotton stalk contains about 21% xylan, the composition of which was determined as 84% xylose, 7% glucose, and 9% uronic acid after complete acid hydrolysis. XOs in the DP range of 2-7 (X6 ≈ X5 > X2 > X3) were obtained with minor quantities of xylose in all of the hydrolysis conditions used. Although after 24 h of hydrolysis at 40°C, the yield was about 53%, the XO production rate leveled off after 8-24 h of hydrolysis. XO yield was affected by all of the parameters investigated; however, none of them affected the DP of the end product significantly, except the hydrolysis period. Enzyme hydrolysis was maintained by the addition of fresh substrate after 72 h of hydrolysis, indicating the persistence of enzyme activity. The optimal hydrolysis conditions were determined as 40°C, pH 5.4, and 2% xylan. The obtained product was fractionated via ultrafiltration by using 10, 3, and 1 kDa membranes. Complete removal of xylanase and unhydrolyzed xylan was achieved without losing any oligosaccharides having DP 5 or smaller by 10 kDa membrane. After a two-step membrane processing, a permeate containing mostly oligosaccharides was obtained.

Research paper thumbnail of Immobilization of glucose oxidase in polypyrrole/polytetrahydrofuran graft copolymers

International Journal of Biological Macromolecules, 2002

Glucose oxidase (GOD) was immobilized in four different conducting polymer matrices, namely: poly... more Glucose oxidase (GOD) was immobilized in four different conducting polymer matrices, namely: polypyrrole, (PPy), poly(pyrrole-graft-polytetrahydrofuran), (1) and (3); and poly(pyrrole-graft-polystyrene/polytetrahydrofuran), (2). The kinetic parameters V(max) and K(m), and the optimum temperature were determined for both immobilized and native enzymes. The effect of electrolysis time and several supporting electrolytes, p-toluenesulfonic acid, p-toluene sulfonic acid (PTSA), sodium p-toluene sulfonate, sodium p-toluene sulfonate (NaPTS), and sodium dodecyl sulfate, sodium dodecyl sulfate (SDS), on enzyme immobilization were investigated. The high K(m) value (59.9 mM) of enzyme immobilized in PPy was decreased via immobilization in graft copolymer matrices of pyrrole. V(max), which was 2.25 mM/min for pure PPy, was found as 4.71 mM/min for compound (3).

Research paper thumbnail of Improvement of enzymatic xylooligosaccharides production by the co-utilization of xylans from different origins

Food and Bioproducts Processing, 2013

ABSTRACT This study aimed to improve XOs production by enzymatic hydrolysis of xylans from variou... more ABSTRACT This study aimed to improve XOs production by enzymatic hydrolysis of xylans from various lignocellulosic waste biomasses namely corn cob, cotton and sunflower stalks, rice hull, wheat straw by using two commercial xylanase preparations, Shearzyme 500L and Veron 191. Shearzyme 500L showed better xylan hydrolysis capacity with high amount of xylose liberation. Xylobiose was the main hydrolysis product in each case. Even though the enzymatic hydrolyses using Shearzyme 500L resulted higher reducing sugar production compared to those of Veron 191, the hydrolysis of complex xylan structures was improved and the production of undesirable xylose was lowered by the co-utilization of xylanase preparations. By the co-utilization of xylanase preparations, the reducing sugar production from wheat straw, corn cob and sunflower stalk originated xylans was increased by 36%, 33% and 13%, respectively, compared to the expected reducing sugar yields. The highest reducing sugar production was obtained from complex corn cob xylan. The depolymerization of cotton and sunflower stalk xylan was poorest even though they have simple structures. Poor utilization of these xylans might be related to their high residual lignin content which might hinder the accessibility of xylan by the xylanases. However, the utilization of sunflower and cotton stalk xylan was improved when they were hydrolyzed within a xylan mixture containing equal amounts of each of five different xylans. In short, XOs production efficiency from agricultural waste materials was improved by the co-utilization of suitable xylanase and/or xylan mixtures considering the heterogeneous structures of xylan and different substrate specificities of xylanases.

Research paper thumbnail of An endo-β-1,4-xylanase from Rhizopus oryzae: production, partial purification and biochemical characterization

Enzyme and Microbial Technology, 2001

An endoxylanase (1,4-␤-D-xylan xylanohydrolase, EC 3.2.1.8) was produced by Rhizopus oryzae ferme... more An endoxylanase (1,4-␤-D-xylan xylanohydrolase, EC 3.2.1.8) was produced by Rhizopus oryzae fermentation. Different xylancontaining agricultural byproducts such as wheat straw, wheat stems, cotton bagasse, hazelnut shells, corn cobs and oat sawdust were used as the carbon source, while soybean bagasse was used as both the nitrogen and carbon source in the enzyme production medium. Partial steam hydrolysis of the agricultural byproducts increased the enzyme yield of the microorganism. The highest xylanase activity, 260 IU/ml fermentation medium, was obtained by using a medium containing 3% hydrolyzed corn cobs, 1% hydrolyzed soybean bagasse, 1% ammonium sulfate and 0.5% sodium chloride at 35°C, pH 5, 350 rpm and under aerobic conditions in a 2-1 fermenter. A maximal cellulose activity of 0.06 IU/ml was observed. The enzyme was partially purified from the culture medium by ammonium sulfate precipitation and cation exchange filtration. A 55-fold purification was achieved, with the purified xylanase having a specific activity of about 50 IU/mg protein. The molecular weight of the enzyme is about 22 kDa by SDS-PAGE. The optimal pH and temperature values of the enzyme were about 4.5 and 55°C, respectively. The enzyme obeys Michaelis-Menten kinetics with K m and V max values being 18.5 mg xylan/ml and 90 IU/mg protein, respectively.

Research paper thumbnail of Crystallization and preliminary X-ray analysis of a bifunctional catalase-phenol oxidase from Scytalidium thermophilum

Acta Crystallographica Section F-structural Biology and Crystallization Communications, 2009

Research paper thumbnail of Preparation of cross-linked tyrosinase aggregates

Process Biochemistry, 2008

Tyrosinase from mushroom was immobilized as a cross-linked enzyme aggregate (CLEA) via precipitat... more Tyrosinase from mushroom was immobilized as a cross-linked enzyme aggregate (CLEA) via precipitation with ammonium sulfate and crosslinking with glutaraldehyde. The effects of precipitation and cross-linking on CLEA activity were investigated and the immobilized tyrosinase was characterized. Sixty percent ammonium sulfate saturation and 2% glutaraldehyde were used; a 3-h cross-linking reaction at room temperature, at pH 7.0 was performed; particle sizes of the aggregates were reduced; consequently, 100% activity recovery was achieved in CLEAs with enhanced thermal and storage stabilities. Slight changes in optimum pH and temperature values of the enzyme were recorded after immobilization. Although immobilization did not affect V max , substrate affinity of the enzyme increased. Highly stable CLEAs were also prepared from crude mushroom tyrosinase with 100% activity recovery. #

Research paper thumbnail of Production and characterization of xylanases of a Bacillus strain isolated from soil

World Journal of Microbiology and Biotechnology, 2005

Xylanase production was performed by growing a Bacillus isolate on agricultural by-products, whea... more Xylanase production was performed by growing a Bacillus isolate on agricultural by-products, wheat straw, wheat bran, corn cobs and cotton bagasse. A maximum xylanase activity of 180 U/ml was obtained together with a cellulase activity of 0.03 U/ml on 4 (w/v) ...

Research paper thumbnail of Screening of tree leaves as annual renewable green biomass for phenol oxidase production and biochemical characterization of mulberry (Morus alba) leaf phenol oxidases

World Journal of Microbiology and Biotechnology, 2011

... of mulberry (Morus alba) leaf phenol oxidases Didem Sutay Kocabas • Zumrut Begum Ogel • Ufuk ... more ... of mulberry (Morus alba) leaf phenol oxidases Didem Sutay Kocabas • Zumrut Begum Ogel • Ufuk Bakir ... References Akpinar O, Ak O, Kavas A, Bakir U, Yilmaz L (2007) Enzymatic production of xylooligosaccharides from cotton stalks. ...

Research paper thumbnail of Xylanase from a soil isolate, Bacillus pumilus: gene isolation, enzyme production, purification, characterization and one-step separation by aqueous-two-phase system

World Journal of Microbiology and Biotechnology, 2010

Page 1. ORIGINAL PAPER Xylanase from a soil isolate, Bacillus pumilus: gene isolation, enzyme pro... more Page 1. ORIGINAL PAPER Xylanase from a soil isolate, Bacillus pumilus: gene isolation, enzyme production, purification, characterization and one-step separation by aqueous-two-phase system Aysegul Ersayin Yasinok • Suzan Biran • Aytac Kocabas • Ufuk Bakir ...

Research paper thumbnail of Immobilization of invertase in functionalized copolymer matrices

Reactive and Functional Polymers, 2000

In this study, immobilization of invertase on functionalized polymer electrodes constructed with ... more In this study, immobilization of invertase on functionalized polymer electrodes constructed with pyrrole-capped polyazotetrahydrofuran and polytetrahydrofuran-block-polystyrene copolymer matrices was performed. Immobilization in these enzyme electrodes was carried out by the entrapment of the enzyme in conducting polymer matrices during electrochemical polymerization of pyrrole. Sodium dodecyl sulphate was used as the supporting electrolyte in the preparation of enzyme electrodes. The effects of temperature and pH on the activity of the enzyme electrodes were examined, and re-use number studies were performed. The changes in the maximum reaction rate and the variations of the Michaelis-Menten constant were investigated.

Research paper thumbnail of Antimicrobial properties of TiO2–SiO2 thin films

Research paper thumbnail of The effects of microbial lignocellulose pretreatments on xylooligosaccharide production

New Biotechnology, 2009

gases. The processing and utilization of lignocellulosic substrate is complex, differing in many ... more gases. The processing and utilization of lignocellulosic substrate is complex, differing in many aspects from crop-based ethanol production. One important requirement is an efficient microorganism able to ferment a variety of sugars (pentoses and hexoses) as well as to tolerate stress conditions. The study aims to extend the range of sources from which ethanol may be made beyond sugar cane bagasse which is used for the preparation of pulp and paper. Therefore, one fungal strain isolated from pulp and paper mill effluent identified as Cryptococcus albidus by 18S rDNA, internal transcribed spacer (ITS) together with Saccharomyces cerevisiae was used for the production of ethanol. The cellulose, lignin and xylan-degrading potency of fungus was evaluated by the production of sugar and enzymes, endoglucanase, exoglucanase, lignin peroxidase, manganese peroxidase, laccase, glucose oxidase and xylanase. The optimization of process parameters like pH, temperature, carbon and nitrogen source, phosphorus, agitation, inoculum size and duration using Taguchi approach indicated increase in 2-fold sugar production by fungus. The sugar cane bagasse treated by fungus subsequently treated by S. cerevisiae indicated the production of ethanol (36 g/L). The fermentation process was further improved by Taguchi approach where carbon, nitrogen, temperature, osmotic tolerance, inorganic compounds, stirring and pH were used. The result of the study indicated an increase in 1.5-fold production of ethanol. The method was tested in 15-L sequential bioreactor in which sugar cane bagasse was initially degraded by fungus and subsequently fermented by yeast for the production of ethanol for scale up of the method for huge production of bioethanol from sugar cane bagasse.

Research paper thumbnail of Preparation of conducting thin film surfaces for amperometric biosensor applications

New Biotechnology, 2009

late was cultivated at pH condition of 5, thus, the goal of this work was to evaluate their catal... more late was cultivated at pH condition of 5, thus, the goal of this work was to evaluate their catalytic capacity of whole-cell by assay of para-nitrophenyl palmitate (pNPP). Bacterial cells were cultivated during 48 hours. Samples of different times were taken and cells were separated by centrifugation, washed three times and air dried at 40 • C. The reaction mixture consisted in 20 mg of cells, 0.5 ml of stock solution of pNPP (10 mM in n-heptane). To start the reaction 30 l of methanol or ethanol were added to the mixture an incubated at 40 • C and 160 rpm from 0.5 to 120 min. Then, 25 l of mixture were taken and mixed with 1 ml of 0.1 M of NaOH. Additionally, the reaction mixtures were incubated with no alcohol. The pNPP liberated was extracted by aqueous alkali phase and detected at 405 nm. The kinetics curves of samples demonstrated that the whole-cells cultivated at 12 hours and 24 hours presented the highest production of pNP with methanol during the first 10 min of reaction. After the lipase activity decreased and remains practically constant until the end of the experiment. The reaction with ethanol shows a maximal activity in samples of 24 hours of culture in 10 min of reaction. The lipase activity observed with no alcohol in the reaction was at a value of one third of that obtained in cells with methanol. The results presented here, using a whole-cell biocatalyst is considered promising for biodiesel production in industrial applications.

Research paper thumbnail of Enzyme immobilization to modified and patterned surfaces for biocatalytically active surface preparation

New Biotechnology, 2009

late was cultivated at pH condition of 5, thus, the goal of this work was to evaluate their catal... more late was cultivated at pH condition of 5, thus, the goal of this work was to evaluate their catalytic capacity of whole-cell by assay of para-nitrophenyl palmitate (pNPP). Bacterial cells were cultivated during 48 hours. Samples of different times were taken and cells were separated by centrifugation, washed three times and air dried at 40 • C. The reaction mixture consisted in 20 mg of cells, 0.5 ml of stock solution of pNPP (10 mM in n-heptane). To start the reaction 30 l of methanol or ethanol were added to the mixture an incubated at 40 • C and 160 rpm from 0.5 to 120 min. Then, 25 l of mixture were taken and mixed with 1 ml of 0.1 M of NaOH. Additionally, the reaction mixtures were incubated with no alcohol. The pNPP liberated was extracted by aqueous alkali phase and detected at 405 nm. The kinetics curves of samples demonstrated that the whole-cells cultivated at 12 hours and 24 hours presented the highest production of pNP with methanol during the first 10 min of reaction. After the lipase activity decreased and remains practically constant until the end of the experiment. The reaction with ethanol shows a maximal activity in samples of 24 hours of culture in 10 min of reaction. The lipase activity observed with no alcohol in the reaction was at a value of one third of that obtained in cells with methanol. The results presented here, using a whole-cell biocatalyst is considered promising for biodiesel production in industrial applications.

Research paper thumbnail of Optimization of xylanase production from Aspergillus terreus by using renewable agricultural lignocellulosic residues

Research paper thumbnail of Comparison of acid and enzymatic hydrolysis of tobacco stalk xylan for preparation of xylooligosaccharides

LWT - Food Science and Technology, 2010

... Like autohydrolysis, the main disadvantage of this method is the production of monomeric suga... more ... Like autohydrolysis, the main disadvantage of this method is the production of monomeric sugars and undesirable by-products. Food and other industries spend considerable amounts of time and/or money to obtain XOs. The ...

Research paper thumbnail of Photocatalytic microbial inactivation over Pd doped SnO2 and TiO2 thin films

Journal of Photochemistry and Photobiology A: Chemistry, 2006

The photocatalytic antimicrobial activity over TiO2, SnO2 and their Pd doped thin film samples we... more The photocatalytic antimicrobial activity over TiO2, SnO2 and their Pd doped thin film samples were determined against Escherichia coli, Staphylococcus aereus, Saccharomyces cerevisiae and Aspergilus niger spores. Higher antimicrobial activity was observed with TiO2 than SnO2 thin films and, Pd addition contributes to an increase in the activity of both semiconductor oxides. The highest microbial inactivation was achieved with 1% PdO/TiO2 against E. coli with a 98% decrease in survival after 2h illumination. SnO2 was found to show lower photocatalytic efficiency against E. coli with a 56% decrease in survival after 2h illumination and a 68% decrease in survival of E. coli after palladium addition. E. coli showed the least and S. cerevisiae showed the highest resistance against photocatalytic inactivation and, A. niger spores could not be inactivated up to 8h illumination over all the surfaces. The antimicrobial efficiencies against different microorganisms and fungal spores were found to decrease in the following order: E. coli>S. aereus>S. cerevisiae>A. niger spores for which, complexity and strength of the cell walls increased in the same order.

Research paper thumbnail of Hydrothermal Synthesis of Nanostructured TiO<SUB>2</SUB> Particles and Characterization of Their Photocatalytic Antimicrobial Activity

Journal of Nanoscience and Nanotechnology, 2008

Nanostructured titania particles were synthesized by using hydrothermal processing and the photoc... more Nanostructured titania particles were synthesized by using hydrothermal processing and the photocatalytic antimicrobial activities were characterized. Both sol-gel synthesized and commercial TiO2 (anatase) samples were processed with two step hydrothermal treatments, under alkaline and neutral conditions. Scanning Electron Microscope (SEM) images showed that alkaline treatment yields nanofibers and lamellar structured particles from the commercial anatase and sol-gel synthesized samples respectively. Further treatment of nanofibers and nanostructured lamellar particles with distilled water results with crystal growth and the formation of nano structured bipyramidal crystalline particles. The photocatalytic antimicrobial activities of the samples were determined against Escherichia coil under irradiation. It was observed that the samples treated under alkaline conditions have improved activity than the original anatase samples. Limited activity and resulting time lag in bacterial inactivation were observed for hydrothermally treated samples with distilled water. However, a post treatment comprising the UV irradiation in aqueous conditions enhanced the photocatalytic activity.

Research paper thumbnail of IMMOBILIZATION OF YEAST CELLS IN SEVERAL CONDUCTING POLYMER MATRICES

Journal of Macromolecular Science, Part A, 2002

... Zeynep Balci,1 Ural Akbulut,1 Levent Toppare,1,* Selmiye Alkan,1 Ufuk Bakir,2 and Yusuf Yagci... more ... Zeynep Balci,1 Ural Akbulut,1 Levent Toppare,1,* Selmiye Alkan,1 Ufuk Bakir,2 and Yusuf Yagci3 ... Copyright © 2002 by Marcel Dekker, Inc. ... 12. Alkan, S.; Toppare, L.; Hepuzer, Y.; Yagci, Y. Block Copolymers of Thio-phene-Capped Poly(methyl methacrylate) with Pyrrole. ...

Research paper thumbnail of Production and Characterization of Films from Cotton Stalk Xylan

Journal of Agricultural and Food Chemistry, 2007

Composite film production based on cotton stalk xylan was studied, and the mechanical and physica... more Composite film production based on cotton stalk xylan was studied, and the mechanical and physical properties of the films formed were investigated. Xylan and lignin were separated from cellulose by alkali extraction and, then, lignin was removed using ethanol washing. Self-supporting continuous films could not be produced using pure cotton stalk xylan. However, film formation was achieved using 8-14% (w/w) xylan without complete removal of lignin during xylan isolation. Keeping about 1% lignin in xylan (w/w) was determined to be sufficient for film formation. Films were produced by casting the film-forming solutions, followed by solvent evaporation in a temperature (20 degrees C) and relative humidity (40%) controlled environment. The elastic modulus and hypothetical coating strength of the films obtained by using 8% xylan were significantly different from the ones containing 10-14% xylan. The water vapor transfer rates (WVTR) decreased with increasing xylan concentration, which made the films thicker. The glycerol addition as an additional plasticizer resulting in more stretchable films having higher WVTR and lower water solubility values. As a result, film production was successfully achieved from xylan, which was extracted from an agricultural waste (cotton stalk), and the film-forming effect of lignin on pure xylan has been demonstrated.

Research paper thumbnail of Enzymatic Production of Xylooligosaccharides from Cotton Stalks

Journal of Agricultural and Food Chemistry, 2007

Xylooligosaccharide (XO) production was performed from xylan, which was obtained by alkali extrac... more Xylooligosaccharide (XO) production was performed from xylan, which was obtained by alkali extraction from cotton stalk, a major agricultural waste in Turkey. Enzymatic hydrolysis was selected to prevent byproduct formation such as xylose and furfural. Xylan was hydrolyzed using a commercial xylanase preparation, and the effects of pH, temperature, hydrolysis period, and substrate and enzyme concentrations on the XO yield and degree of polymerization (DP) were investigated. Cotton stalk contains about 21% xylan, the composition of which was determined as 84% xylose, 7% glucose, and 9% uronic acid after complete acid hydrolysis. XOs in the DP range of 2-7 (X6 ≈ X5 > X2 > X3) were obtained with minor quantities of xylose in all of the hydrolysis conditions used. Although after 24 h of hydrolysis at 40°C, the yield was about 53%, the XO production rate leveled off after 8-24 h of hydrolysis. XO yield was affected by all of the parameters investigated; however, none of them affected the DP of the end product significantly, except the hydrolysis period. Enzyme hydrolysis was maintained by the addition of fresh substrate after 72 h of hydrolysis, indicating the persistence of enzyme activity. The optimal hydrolysis conditions were determined as 40°C, pH 5.4, and 2% xylan. The obtained product was fractionated via ultrafiltration by using 10, 3, and 1 kDa membranes. Complete removal of xylanase and unhydrolyzed xylan was achieved without losing any oligosaccharides having DP 5 or smaller by 10 kDa membrane. After a two-step membrane processing, a permeate containing mostly oligosaccharides was obtained.

Research paper thumbnail of Immobilization of glucose oxidase in polypyrrole/polytetrahydrofuran graft copolymers

International Journal of Biological Macromolecules, 2002

Glucose oxidase (GOD) was immobilized in four different conducting polymer matrices, namely: poly... more Glucose oxidase (GOD) was immobilized in four different conducting polymer matrices, namely: polypyrrole, (PPy), poly(pyrrole-graft-polytetrahydrofuran), (1) and (3); and poly(pyrrole-graft-polystyrene/polytetrahydrofuran), (2). The kinetic parameters V(max) and K(m), and the optimum temperature were determined for both immobilized and native enzymes. The effect of electrolysis time and several supporting electrolytes, p-toluenesulfonic acid, p-toluene sulfonic acid (PTSA), sodium p-toluene sulfonate, sodium p-toluene sulfonate (NaPTS), and sodium dodecyl sulfate, sodium dodecyl sulfate (SDS), on enzyme immobilization were investigated. The high K(m) value (59.9 mM) of enzyme immobilized in PPy was decreased via immobilization in graft copolymer matrices of pyrrole. V(max), which was 2.25 mM/min for pure PPy, was found as 4.71 mM/min for compound (3).

Research paper thumbnail of Improvement of enzymatic xylooligosaccharides production by the co-utilization of xylans from different origins

Food and Bioproducts Processing, 2013

ABSTRACT This study aimed to improve XOs production by enzymatic hydrolysis of xylans from variou... more ABSTRACT This study aimed to improve XOs production by enzymatic hydrolysis of xylans from various lignocellulosic waste biomasses namely corn cob, cotton and sunflower stalks, rice hull, wheat straw by using two commercial xylanase preparations, Shearzyme 500L and Veron 191. Shearzyme 500L showed better xylan hydrolysis capacity with high amount of xylose liberation. Xylobiose was the main hydrolysis product in each case. Even though the enzymatic hydrolyses using Shearzyme 500L resulted higher reducing sugar production compared to those of Veron 191, the hydrolysis of complex xylan structures was improved and the production of undesirable xylose was lowered by the co-utilization of xylanase preparations. By the co-utilization of xylanase preparations, the reducing sugar production from wheat straw, corn cob and sunflower stalk originated xylans was increased by 36%, 33% and 13%, respectively, compared to the expected reducing sugar yields. The highest reducing sugar production was obtained from complex corn cob xylan. The depolymerization of cotton and sunflower stalk xylan was poorest even though they have simple structures. Poor utilization of these xylans might be related to their high residual lignin content which might hinder the accessibility of xylan by the xylanases. However, the utilization of sunflower and cotton stalk xylan was improved when they were hydrolyzed within a xylan mixture containing equal amounts of each of five different xylans. In short, XOs production efficiency from agricultural waste materials was improved by the co-utilization of suitable xylanase and/or xylan mixtures considering the heterogeneous structures of xylan and different substrate specificities of xylanases.

Research paper thumbnail of An endo-β-1,4-xylanase from Rhizopus oryzae: production, partial purification and biochemical characterization

Enzyme and Microbial Technology, 2001

An endoxylanase (1,4-␤-D-xylan xylanohydrolase, EC 3.2.1.8) was produced by Rhizopus oryzae ferme... more An endoxylanase (1,4-␤-D-xylan xylanohydrolase, EC 3.2.1.8) was produced by Rhizopus oryzae fermentation. Different xylancontaining agricultural byproducts such as wheat straw, wheat stems, cotton bagasse, hazelnut shells, corn cobs and oat sawdust were used as the carbon source, while soybean bagasse was used as both the nitrogen and carbon source in the enzyme production medium. Partial steam hydrolysis of the agricultural byproducts increased the enzyme yield of the microorganism. The highest xylanase activity, 260 IU/ml fermentation medium, was obtained by using a medium containing 3% hydrolyzed corn cobs, 1% hydrolyzed soybean bagasse, 1% ammonium sulfate and 0.5% sodium chloride at 35°C, pH 5, 350 rpm and under aerobic conditions in a 2-1 fermenter. A maximal cellulose activity of 0.06 IU/ml was observed. The enzyme was partially purified from the culture medium by ammonium sulfate precipitation and cation exchange filtration. A 55-fold purification was achieved, with the purified xylanase having a specific activity of about 50 IU/mg protein. The molecular weight of the enzyme is about 22 kDa by SDS-PAGE. The optimal pH and temperature values of the enzyme were about 4.5 and 55°C, respectively. The enzyme obeys Michaelis-Menten kinetics with K m and V max values being 18.5 mg xylan/ml and 90 IU/mg protein, respectively.