The main objective of this study was to design gluten free rice cakes containing different gums and an emulsifier for baking in infrared (IR)-microwave combination oven. In the first part of the study, the effects of different gums (xanthan, guar, xanthan-guar blend, &amp / #954 / -carrageenan, locust bean, hydroxypropyl methylcellulose (HPMC) and xanthan-&amp / #954 / -carrageenan blend) and emulsifier blend (PurawaveTM) on physical properties of cake batters were investigated. In the second part of the study, weight loss, specific volume and texture of the cakes baked in different ovens were determined. Macro and micro-structures of the cakes were investigated both qualitatively and quantitatively by using image analysis and Scanning Electron Microscopy (SEM). In the last part of the study, Response Surface Methodology (RSM) was used to optimize IR-microwave baking conditions and formulation of the cakes. Power law and Casson models were suitable to explain the rheological properties. Xanthan and xanthan-guar gum blends resulted in higher apparent viscosities as compared to other gums. Gum types affected the dielectric properties and gelatinization enthalpies of cake batter. Emulsifier addition increased the volume and porosity but decreased the firmness of the cakes baked in IR-microwave combination oven. More porous cakes were obtained when xanthan and xanthan-guar gum blend were used. Baking method was found to be important in affecting porosity, pore size distribution and microstructure of the cakes. The highest quality gluten-free rice cakes were obtained when the formulation contained xanthan gum and 5.38% emulsifier and baked using 40% microwave power, 60% halogen lamp power for 7 min in IR-microwave combination oven. In addition, baking time was reduced by 76.7% as compared to conventional baking.

Staphylococcus aureus is one of the major causes of food-borne pathogenesis. Antibiotic consumption for these pathogens has been increasing year by year world-wide. In order to decrease the use of synthetic antibiotics, fresh fruits and dry herbs consumed as beverages in regular diets were examined as potential natural antibiotics for the treatment of food based infections against Staphylococcus aureus. Herbs consumed as tea infusions including Pimpinella anisum L. (anise), Anthemis arvensis L. (camomile), Rosa canina L. (rosehip), Salvia fruticosa Mill (sage) and fresh fruit juices including Vitis vinifera L. (grape), Citrus sinensis L. (orange), Prunus persica L. (peach) and Punica granatum L. (pomegranate) were selected as samples of hot or cold consumed beverages in our daily diets. Extracts of fresh fruit juices were prepared in methanol, on the other hand, tea infusions of herbs were filtered and lyophilized. Antioxidant capacities of the plant samples were investigated by radical scavenging methods, namely 2&rsquo / 2-azinobis-(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) and 2,2-diphenyl-1-picrylhydrazyl (DPPH) as well as determination of total phenolic and flavonoid contents. Furthermore, antimicrobial activities of plant samples were determined by minimum inhibitory concentration and minimum bactericidal concentration methods along with disc diffusion method. Trolox equivalent antioxidant capacities (TEAC) of the herbal tea infusions obtained by ABTS radical scavenging method were ranged between 48.38 &plusmn / 1.242 and 715.73 &plusmn / 4.265 (&mu / mol Trolox equivalent (TE)/g of extract) while, TEAC values of fresh fruits juices were between 26.86 &plusmn / 0.217 and 73.55 &plusmn / 0.973 (&mu / mol Trolox equivalent (TE)/g of extract). Moreover, EC50 values of the tea infusions obtained by DPPH radical scavenging method were ranged between 0.05 &plusmn / 0.001 and 1.53 &plusmn / 0.004 (mg/mL) while, EC50 values of the fruit juices were 1.6 &plusmn / 0.014 and 2 &plusmn / 0.093 (mg/mL). Total phenolic content of the plant samples tested in this study were varied from 1.383 (&mu / g gallic acid equivalent (GAE)/mg of extract) to 159.167 (&mu / g gallic acid equivalent (GAE)/mg of extract) and total flavonoid content varied from 0.111 (&mu / g quercetin equivalent (QE)/mg of extract) to 201.15 (&mu / g quercetin equivalent (QE)/mg of extract). Sage, orange and grape displayed higher antimicrobial activities with values of 1.5, 6 and 6 mg/mL minimum inhibitory concentrations and 1.5, 24 and 24 mg/mL minimum bactericidal concentrations, respectively. Inhibition zone diameters of sage, orange and grape were found to be 9, 9 and 11 mm.

ANALYSIS OF CYTOCHROME P4501A1 GENETIC POLYMORPHISMS IN PATIENTS WITH ISCHEMIC STROKE Adali, Ayse &Ccedil / inar M.Sc., Department of Biochemistry Supervisor: Prof. Dr. Orhan Adali Co-Supervisor: Dr. Birsen Can Demird&ouml / gen January 2011, 179 pages Stroke is the third leading cause of death worldwide and results in serious disabilities. Cytochrome P450 1A1 gene (CYP1A1) is a highly polymorphic gene encoding its corresponding xenobiotic metabolizing enzyme which is responsible from the metabolism of carcinogenic polycyclic aromatic hydrocarbons (PAHs) that are engaged with the formation of free radicals. Atherosclerosis is a major cause of ischemic stroke and this pathology may be associated with the disruption of vascular homeostasis due to the formation of these chemicals. The main objective of this study was to investigate the coding region (A4889G) and non-coding region (T6235C) polymorphisms of the CYP1A1 gene as a risk factor for ischemic stroke. The study group in Turkish population consisted of 226 unrelated ischemic stroke patients and 113 control subjects. There was no statistically significant difference between the groups with respect to age and gender. Total blood samples were obtained from G&uuml / lhane Military Medical Academy Hospital, Neurology Department, Ankara. In stroke patients, hypertension, diabetes mellitus, smoking and obesity were at least 2 times more common and high density lipoprotein cholesterol (HDL-C) was significantly lower than controls. The frequency of mutant allele 4889G was 0.445 in patients and was nearly the same with controls. The frequency of mutant allele 6235C was 0.151 in patients and was significantly higher in controls (0.226, P=0.015). The risk of diabetic, smoker and obese individuals having ischemic stroke was significantly higher in 4889G allele carriers (AG+GG / Odds ratio / OR= 2.1, 2.4 and 3, respectively). The risk of hypertensive and diabetic individuals having ischemic stroke was higher in 6235TT genotypic people (OR= 3 and 2.2, respectively). On the contrary, the risk of smoker and obese individuals having ischemic stroke was significantly higher in 6235 C allele carriers (OR=5.3 and 3.7, respectively). Logistic regression analysis revealed that hypertension, smoking, levels of low density lipoprotein cholesterol (LDL-C) and HDL-C and 6235C allele were significant predictors of stroke. In this analysis, high level of LDL-C was found to be associated with almost 1.5-fold risk of ischemic stroke. On the other hand, HDL-C and having mutant 6235C allele decreased the risk of ischemic stroke 2.5 and 2-fold, respectively. This is the first study investigating the relation between A4889G polymorphism and stroke risk. Additionally, in Turkish population A4889G and T6235C polymorphisms were analyzed for the first time in terms of its relation to ischemic stroke. The present study demonstrated that the frequency of mutant 4889G allele was nearly the same in stroke patients and control subjects / whereas the frequency of mutant 6235 C allele was higher in control subjects than in stroke patients. Consequently, we decided that carrying mutant 4889 G allele does not constitute a risk for ischemic stroke and carrying mutant 6235C allele may have a protective effect against stroke.

The main aim of this study was to investigate biological hydrogen production from sucrose and molasses by purple non-sulphur bacteria (PNS). The hydrogen production capacities of four different PNS bacteria (Rhodobacter capsulatus (DSM 1710), Rhodobacter capsulatus YO3 (Hup-), Rhodopseudomonas palustris (DSM 127) and Rhodobacter sphaeroides O.U.001 (DSM 5864)) were tested on sucrose and molasses. The photobiological hydrogen production were performed in 50 ml and 150 ml small scale photobioreactors, in batch mode. The produced hydrogen quantities, bacterial growth profiles and pH of the media were recorded through the photobiological hydrogen production processes. Organic acids and sucrose consumption rates were determined by HPLC during the experiments. The maximum hydrogen productivitiy of 0.78 (mmol/lc.h) and 0.55 (mmol/lc.h) was obtained by R. palustris (DSM 127) on sucrose and molasses, respectively. Secondly, co-cultivation of these bacterial strains was studied. The maximum hydrogen productivity by co-cultivation of R. sphaeroides O.U.001 (DSM 5864) and R. palustris (DSM 127) was found as 1.0 (mmol/lc.h).

By mixing different stoichiometric ratios of chitosan with alginic acid (AA) and chitosan with p(toluenesulfonicacid) (PTSA), two new polymer networks were prepared. FT-IR spectroscopy results show the protonation of chitosan by AA and PTSA. Elemental analysis (EA) results show the composition of the networks. Thermal gravimetry analysis (TGA) and differential scanning calorimetry (DSC) results were used to characterize the thermal stability of the networks. Then, cholesterol oxidase (ChOx) enzyme were immobilized in these networks and checked for potential use of these enzyme entrapped polymer networks (EEPN) for enzyme immobilization. Additionally, the maximum reaction rate (Vmax) and Michaelis-Menten constant (Km) were evaluated for immobilized ChOx in these two polymer networks. Also, temperature and pH optimization, operational stability, shelf-life and the proton conductivity of these networks were investigated.

In this study, the effects of bioprocess operation parameters on aromatic amino acid synthesis performance of Bacillus acidocaldarius were investigated. Firstly, in laboratory scale shake-bioreactors, a defined medium was designed in terms of its carbon and nitrogen sources, to achieve the highest cell concentration. Thereafter, the effects of bioprocess operation parameters, i.e., pH and temperature were investigated / and the optimum medium contained (kg m-3): fructose, 8 / (NH4)2HPO4, 5 / CaCl2, 0.2 / KH2PO4, 2 / NaH2PO4.2H2O, 7.318 / Na2HPO4, 0.0438 / Mg(CH3COO)2.4H2O, 87&times / 10-3 / 1 , MgSO4.7H2O / 2&times / 10-3, FeSO4.7H2O / 2&times / 10-3, ZnSO4.7H2O / 15 &times / 10-5, MnSO4.H2O / 2&times / 10-5, CuSO4.5H2O with pH0 =5, T=55&amp / #61616 / C, N=175 min-1. In this medium, the bacteria produced L-tryptophan at the highest concentration of 0.204 kg m-3 and L-phenylalanine at a maximum concentration of 0.0106 kg m-3 with no L-tyrosine production. Finally the fermentation and oxygen transfer characteristics of the bioprocess were investigated in 3.0 dm3 pilot scale bioreactors. The effects of oxygen transfer were investigated at four different conditions at the parameters air inlet rates of QO/VR =0.2, and 0.5 vvm, and agitation rates of N= 250, 500, 750 min-1. The effect of pH was investigated at pH=5 uncontrolled and controlled operations. The variations in cell, fructose, amino acid and organic acid concentrations with the cultivation time / and using the dynamic method, the oxygen uptake rate and the liquid phase mass transfer coefficient values throughout the growth phase of the bioprocess / the yield and maintenance coefficients were determined. The aromatic amino acids produced at the highest and the least amount and frequency were L-tryptophan and L-tyrosine, respectively. The highest L-tryptophan production, 0.32 kg m-3 in 17 hour was at 0.2 vvm and 500 min-1. Among all operations, the highest L-tryptophan was produced at the lowest oxygen transfer condition. Controlled-pH conditions produced more L-tryptophan.

Free radicals are the compounds having one or more unpaired electrons in their outer orbital and this unpaired electron make these compounds very reactive. Especially as their concentration increases, they initiate a chain oxidation reaction of lipids, proteins and nucleic acids. The condition, in which the production of free radicals exceeds their elimination or tissue defense mechanism decrease against them or both occur together, is called oxidative stress. In diabetes mellitus which is a glucose metabolism disorder, there occurs excessive non-enzymatic protein oxidation, glucose autoxidation and enhanced activity of polyol pathway enzymes, which are the possible sources of the oxidative stress in this disease. In this study, the conditions of the activity measurements of major antioxidant enzymes, namely superoxide dismutase (SOD, EC 1.15.1.1), catalase (CAT, EC 1.11.1.6), glutathione peroxidase (GPx, 1.11.1.9) and glutathione S-transferase (GST, EC 2.5.1.18) were studied and the optimum conditions (pH, temperature and substrate concentrations) for each assay were determined. Further objectives of the study were to characterize the enzymatic antioxidant systems (catalase, superoxide dismutase, glutathione peroxidase and glutathione S-transferase), tissue oxidation status (concentrations of TBARS, protein carbonylation, and lipid/protein ratios) and nonenzymatic antioxidant (reduced glutathione) levels of the diabetic rat liver tissues. According to our results, the hepatic SOD and GPx activities significantly increased whereas CAT activity markedly decreased in diabetic rats compared to control group. Also, GST activities did not change in diabetes. As a result of oxidative stress, TBARS concentration, lipid/protein ratios and protein carbonylation increased and GSH levels decreased in diabetic rats compared to control rats. This increase in tissue damage, in spite of the increase in antioxidant enzyme activities, could have been due to the overproduction of reactive oxygen species that exceeded the capacity of the antioxidant enzymes during the eight week of diabetes.

This thesis covers the combination of two seperate work accomplished during the throughout the study. In the first part of the study, xanthene based artificial enzymes were synthesized, and kinetic hydrolysis studies done. Artificial enzyme design is an active field of supramolecular chemistry and metalloenzymes are attractive targets in such studies. Enzymatic catalysis is essentially a &lsquo / multifuctional&rsquo / catalysis. As part of our work, we designed and synthesized three novel xanthene derivatives. All three model contain Zn(II) in their active sites. Using the model substrate p-nitrophenyl acetate, we showed that the bifunctional model is at least an order of magnitude more active in catalyzing the hydrolysis of the substrate. Compared to the uncatalyzed hydrolysis reaction of the p-nitrophenyl ester at pH 7.0, the bifunctional model complex showed a 5714-fold rate acceleration. The second part of the thesis involves the design of a dimeric calixpyrrole as a chromogenic chemosensor. Anions are involved in a large number of biological processes and there is an interest in developing molecular sensors for these charged species. The calixpyrroles are a class of old but new heterocalixarene analogues that show considerable promise in the area of anion sensing. In this work, we have designed, synthesized and characterized a calixpyrrole-dimer anion sensor for its anion binding strength. The dimer forms stable complexes with p-nitrophenolate ion. This formed complex is used as a colorimetric sensor by displacing the chromogenic anion with the addition of various anions. like fluoride and acetate. The receptor shows strong affinity and high selectivity for fluoride anion, and also show reasonable affinity toward acetate. Thus, effective optical sensing of biochemically relevant these anions is accomplished using the calixpyrrole dimer.

ABSTRACT UTILIZATION OF SCYTALIDIUM THERMOPHILUM PHENOL OXIDASE IN BIOORGANIC SYNTHESES Kaptan, Yelda M.S., Department of Biotechnology Supervisor: Prof. Dr. Z&uuml / mr&uuml / t B. &Ouml / gel Co-supervisor: Prof Dr. Ufuk Bakir September 2004, 90 pages In this study, the ultimate aim was to utilize phenol oxidases of Scytalidium thermophilum in bioorganic syntheses. For this purpose, studies were conducted towards enhancing the production of phenol oxidases by Scytalidium thermophilum, developing a suitable method for laccase activity assays, analyzing the effects of organic solvents on phenol oxidase activity and analysis of the biotransformation of a number of organic substrates by phenol oxidases of Scytalidium thermophilum. In order to enhance the production of phenol oxidases, induction experiments were carried out with gallic acid, syringaldazine and chlorogenic acid. Gallic acid was found as the most effective inducer for phenol oxidase production. Inductive effect of edible mushroom Agaricus bisporus was also assayed, however, the phenolic compounds released by mushroom did not represent any induction for phenol oxidase activity of Scytalidium thermophilum. Different substrates were tested and catechol was determined as the most suitable substrate rather than syringaldazine and ABTS. Molar extinction coefficient (e) of catechol was calculated as 3450 M-1 cm-1 and 3700 M-1 cm-1 by using &ldquo / substrate blank&rdquo / and &ldquo / enzyme blank&rdquo / respectively at 420 nm. Kinetic parameters, Km and Vmax for the enzymatic reactions in which catechol was used as substrate were calculated as 52.03 mM and 0.253 U/ml respectively from Lineweaver-Burk plot and as 41.25 mM and 0.2055 U/ml from Hanes-Woolf plot. Effect of some organic solvents on phenol oxidases of Scytalidium thermophilum was assayed and DMSO was found as an appropriate solvent for the organic substrates. Phenol oxidase containing culture supernatant could oxidize benzoin, hydrobenzoin and benzoyl benzoin.

Helicoverpa armigera is a polyphagous pest. Due to excessive use of insecticides, the field populations of H. armigera have become resistant to synthetic pyrethroids by one or combination of three mechanisms / reduced penetration through the cuticle, decreased nerve sensitivity and enhanced metabolism by the detoxification enzymes especially glutathione S-transferases. In this study, gut sections of H. armigera were obtained from Adana and Antalya field populations and susceptible populations from Israel. Each gut section was homogenized separately in 1.0 ml, 40 mM and pH 7.5 phosphate buffers. GST activity was determined using CDNB as substrate. Product formation linearly increased up to 29.5&micro / g proteins in 20mM, pH 7.5 phosphate buffers. Maximum reaction rate was reached at 30&amp / #9702 / C. The Vmax and Km values for GST towards CDNB and GSH were calculated with Lineweaver-Burk and Eadie-Scatchard plots as CDNB Vmax / 6.54&micro / mol/min/mg, 6.35&micro / mol/min/mg , Km / 0.29mM, 0.28mM ,respectively and as GSH Vmax / 6.42&micro / mol/min/mg, 6.65&micro / mol/min/mg, Km / 0.22mM, 0.23mM, respectively. Cytosolic GST activity of each individual from Adana, Antalya and susceptible populations were determined under optimized conditions. The mean of GST activity in Adana population (n=50) and Antalya population (n=50) were found 7.824&micro / mol/min/mg and 9.518&micro / mol/min/mg, respectively. The mean of GST activity in susceptible population (n=50) was determined as 3.272&micro / mol/min/mg. According to these results, GST activities of Adana and Antalya field populations&rsquo / showed statistically significant increase (p&lt / 0.05) than susceptible H. armigera populations with ANOVA method. In addition, Antalya population showed statistically increase (p&lt / 0.05) GST activity than Adana.