Colorectal carcinoma (CRC) is often lethal when invasion and/or metastasis occur. 15-lipoxygenase-1 (15-LO-1), an enzyme of the inflammatory eicosanoid pathway, oxidatively metabolizes linoleic acid and its expression is repressed in CRC. In the present study, the hypothesis that the lack of 15-LO-1 expression in CRC cells may contribute to the tumorigenesis was investigated. Therefore 15-LO-1 was introduced to colon cancer cell line HT-29 that does not have detectable levels of the 15-LO-1. The HT-29 cells were transiently transfected with the eukaryotic expression vector pcDNA3.1-15-LO-1 and the effects of 15-LO-1 expression on the proliferation, apoptosis as wells as metastatic potential of the cells were investigated. Cellular proliferation was analyzed by MTT assay and the apoptotic potential of 15-LO-1 was evaluated by acridine orange, floating cell ratio and caspase-3 assays as well as expression levels of the antiapoptotic protein XIAP. Cellular migration and invasion were investigated by Boyden chamber migration and Matrigel invasion assay.The data indicates that 15-LO-1 expression significantly decreased cell proliferation and increased apoptosis. In addition, a significant reduction was observed in migratory and invasive capacity 15-LO-1 expression also significantly reduced the expression of metastasis associated 1 protein (MTA-1). Taken together we propose that 15-LO-1 expression in CRC can inhibit colon cancer cell growth through induction of apoptotic cell death and may contribute to the inhibition of metastatic capacity in vitro which may be exploited for therapeutic purposes.

The main aim of this study is to determine genetic diversity of milk protein genes associated with milk traits, namely beta-casein, kappa-casein and betalactoglobulin, in native Turkish cattle breeds (Turkish Grey, Eastern Anatolian Red, Anatolian Black, and Southern Anatolian Red) and Turkish Holstein. Only 11% deviation from the Hardy-Weinberg equilibrium and insignificant Fis values for the populations were observed, indicating that samples are free of inbreeding. B alleles of these genes, which are positively related with cheese yield and quality, seem to be relatively high in native Turkish breeds. Therefore, the results suggest that milk of Turkish native breeds is advantageous for producing high-quality and -yield cheese. A1 allele of beta-casein, which releases a bioactive peptide called BCM-7 after successive gastrointestinal proteolytic digestions, has been claimed to have adverse health effects on humans. Another aim of this study is to develop a protocol and assess the potential detrimental effects of BCM-7 on human peripheral blood cells. Despite the fact that the results are inconclusive, the optimized experimental protocol will guide further researchers while judging the effect of BCM-7 on human health. Even though A1 beta-casein, which has a low frequency in native Turkish breeds, and hence BCM-7 have no adverse health effects on humans, this probability should be enough to keep its frequency low in native cattle breeds. Bulls must be screened for A1 allele of beta-casein as well as E allele of kappa-casein, which is absent in native breeds and known to have detrimental effects on cheese quality.

In this study, three subspecies of Apis mellifera L. (A. m. caucasica, A. m. carnica, and A. m. syriaca) from different climatic regions were evaluated electrophoretically at ontogenetic level by means of four enzymes, namely Phosphoglucomutase (PGM), Hexokinase (HK), Phosphoglucose isomerase (PGI) and Glukose-6-phosphate dehydrogenase (G6PD). It is determined that only Pgm and Hk loci were polymorphic. Allele and genotype frequencies at Pgm locus changes seasonally whereas Hk locus does not exhibit seasonal variation. Within the scope of this study we investigated at which developmental stage shifting to heterozygotes prior to winter occurs. It is found that there is a seasonal fluctuation throughout the year in Pgm genotype frequencies at each developmental stage studied and correlated with enzyme activity and glycogen content. As the studied enzymes have crucial v roles in insect energy metabolism, results of this study provided further information about the relationship between carbohydrate metabolism and enzyme polymorphism of honey bees.

In this study, dynamic effects on high speed railway bridges under moving traffic are investigated. Within this context, the clear definition of the possible dynamic effects is provided and the related studies that exist in literature are investigated. In the light of those studies, analytical procedures that are defined to find the critical dynamic responses such as deflections, accelerations and resonance conditions are examined and a MatLab programming language is written to obtain the responses for different train loading and velocity values. The reliability of the written program is conformed by comparing the results with the related studies in literature. In addition to the analytical procedures, the approaches in the European standards concerning the dynamic effects of railway traffic are defined. A case study is investigated for a bridge that is in the scope of the Ankara-Sivas High Speed Railway Project. The related bridge is modeled by using finite element program, SAP2000 according to the definitions that are stated in European standards. The related high speed railway bridge is analysed with a real train which is French TGV together with the HSLM trains that are defined in Eurocode and the results obtained are compared with each other. This study also includes the analysis of the bridges performed for 7 different stiffness and 3 different mass values to determine the parameters affecting dynamic behaviour.

Genetically modified organisms are entering the human diet in all over the world. In order to have transparency in the foods that are being consumed, there is a need to trace the genetically modified organisms (GMOs) in the market and consequently this need brings the necessity of analytical methods that are capable of detecting, identifying and quantifying the transgenic events. These analytical methods also form the basis of the labeling regulations that are tried to be formed regarding GMOs. The main aim of this study is to develop and apply the detection methods for the two of the tomato events, delayed ripening and insect resistant. Currently the only validated detection methods are mainly for the corn, soybean, and cotton. There is no validated detection method for tomato. Tomato is one of the most consumed food products in Turkey and it is also among the controversial organisms in terms of genetic modifications and labeling, therefore the analysis of the genetic modifications in tomato is crucial. In this study, DNA-based detection is performed, with PCR being the chosen method of study. In order to detect the GMO-derived DNA, the method of analysis includes the following studies: species-specific, screening, gene-specific, construct-specific and inverse PCR. In addition, the quantification method is developed using the real-time PCR. In order to develop the procedure of identification method, the reference samples are used and the unknown varieties that are to be analyzed using this method are expected to have similarities with the authorized transgenic events.

This study describes development of methods for screening, identification and quantification of genetic modifications in maize samples. Totally 88 maize samples were collected randomly throughout Turkey in three years from 2006 to 2008 and were analyzed. Two maize samples that were detected as GM positive in previous studies were selected as positive controls. Following the DNA extraction by manual CTAB method, conventional PCR methods were employed for screening of genetic modifications in samples by detecting of P-35S and T-NOS. Qualitative PCR methods were conducted for target specific detection of cry and pat genes. Construct-specific and event-specific PCR assays were designed for detection of Bt11, Bt10 and Mon810 maize events. Specific primers and corresponding probes labeled with reporter and quencher dyes were designed for both absolute and relative quantification of Bt11 and Mon810 in samples by using TaqMan probe method. Comparing the absolute and relative quantification results indicates that there is correlation between them. In order to verify the accuracy of the quantification methods, three parallel applications were conducted according to the CRL validated protocol. The statistical analyses were performed to check the precision and repeatability of the quantification experiments by in-house validation methods. Regarding the Repeatability Relative Standard Deviation (RSDr) values of absolute and relative quantifications of Bt11 and Mon810 systems majority of the validation results accomplish the ENGL requirements for quantification of GMOs. According to screening assays, the overall results indicate that five samples (H3, H48, H73, 4M, 4G) were detected as GM positive. While the samples H3 and H48 were identified as Bt11, it was shown that the sample 4M and 4G contains both of the Bt11 and Mon810 maize events. Bt11 quantification results show samples H3 and 4G respectively with 1.06% and 5.36% exceed the 0.9% threshold level. Amount of Mon810 in samples was determined as 1.33 % for 4M and 17.32% for 4G which is higher than 0.9% threshold level. Sample H73 which was detected as GM positive did not contain Bt11 and Mon810 maize events. Since the methods developed in this study reduce dependence on commercial kits they would contribute to expansion of GMO testing in Turkey with lower cost. However the methods developed in this work should be extended to other maize events and their validation procedure should be completed.

Streptomyces clavuligerus is a gram-positive, filamentous bacterium which has a great ability to produce secondary metabolites including isopenicillin N, cephamycin C and a beta-lactamase inhibitor clavulanic acid. Clavulanic acid (CA) which is a bicyclic beta-lactam, inhibits most of class A beta-lactamases by binding irreversibly to the serine hydroxyl group at the active center of beta-lactamases and resulting in the stable acyl-enzyme complexes. Clavaminate synthase (CAS) is one of the best characterized enzymes in the CA biosynthesis pathway regarding its mechanism, activity and structure. It exists as two isoenzymes, CAS1 and CAS2. cas1 gene is located in clavam biosynthetic gene cluster and its expression is nutritionally regulated. cas2 gene encodes for the rate limiting CAS2 isoenzyme which catalyzes the three distinct oxidative transformations. Conversion of deoxyguanidinoproclavaminic acid into guadinoproclavaminic acid takes part in early steps of CA biosynthesis and is catalysed by CAS2. Similarly, proclaviminic acid is converted into claviminic acid by a two-step reaction and also catalysed by CAS2. Integration of an extra copy of the cas2 gene into the chromosome of a clavulanic acid over-producer industrial strain of Streptomyces clavuligerus by means of an integration vector to improve CA production capacity of the industrial strain is the main goal of this study. Via comperative CA analysis based on HPLC, it was estimated that the recombinant strains produced higher amount of CA in comparison to the parental industrial S. clavuligerus strain. The highest CA production achieved by the recombinant strain, namely S. clavuligerus GV61 (1583.3 &mu / g/g) corresponded to more than 2 fold increase in the maximal CA titer of the parental strain.

In the present study, within and among breed genetic diversity in thirteen Turkish sheep breeds (Sakiz, Karag&uuml / l, Hemsin, &Ccedil / ine &Ccedil / apari, Norduz, Herik, Akkaraman, Dagli&ccedil / , G&ouml / k&ccedil / eada, Ivesi, Karayaka, Kivircik and Morkaraman / in total represented by 628 individuals) were analyzed based on 20 microsatellite loci. Loci were amplified by Polymerase Chain Reactions and products were electronically recorded and converted into [628 x 20] matrix representing genotypes of individuals. Reliability of the genotyping and genetic diversity analyses were done by means of various bioinformatics tools. For the analyses, various statistical methods (Fisher&#039 / s Exact Test, Neighbor-Joining tree construction, Factorial Correspondence Analysis (FCA), Analysis of Molecular Variation, Structure Analysis and Delaunay Analysis) were used. Since, inputs of some software were not compatible with the outputs of other software some Java classes were written whenever necessary. Analyses revealed that among the major breeds Dagli&ccedil / , Karayaka and Morkaraman breeds are highly admixed but Kivircik, Akkaraman and Ivesi are relatively distinct. Among the minor breeds, distinctness of Hemsin, Sakiz, &Ccedil / ine &Ccedil / apari, G&ouml / k&ccedil / eada and Karag&uuml / l are more pronounced compared to all of the examined breeds. Since highly admixed individuals can be identified by Structure and FCA tests, results of the present study, which is part of a national project with the acronym TURKHAYGEN-I (www.turkhaygen.gov.tr), were found to be promising in establishing and managing relatively pure conservation flocks for the Turkish native sheep breeds which are believed to be the reservoirs of genetic variability.

Rhodobacter capsulatus is a photosynthetic, purple non-sulfur (PNS) bacterium that produces biohydrogen via photofermentation. Nitrogenase enzyme is responsible for hydrogen production / during fixation of molecular nitrogen into ammonium, hydrogen is produced. Since this process is an energetically expensive process for the cell, hydrogen production is strictly controlled at different levels. When ammonium is present in the environment, hydrogen production completely ceases. The key proteins in the regulation of nitrogenase by ammonium are two PII proteins / GlnB and GlnK. &lsquo / Hyvolution&rsquo / , 6th framework EU project, aims to achieve maximum hydrogen production by combining two hydrogen production processes / dark fermentation and photofermentation. In the first stage of the overall process, biomass is used for hydrogen production in dark fermentation process. Then, the effluent of dark fermentation is further utilized by photosynthetic bacteria to produce more hydrogen. However, the effluent of dark fermentation contains high amount of ammonium, which inhibits photofermentative hydrogen production. In order to achieve maximum hydrogen production, ammonium regulation of nitrogenase enzyme in R.capsulatus has to be released. For this purpose, all PII signal transduction proteins of R.capsulatus (GlnB and GlnK) were targeted to be inactivated by site-directed mutagenesis. The internal parts of glnB and glnK genes were deleted individually without using antibiotic cassette insertion. The successful glnB mutant was obtained at the end of mutagenesis studies. In the case of glnK mutation, the suicide vector was constructed and delivered into the cells. However, glnK mutant could not be obtained. The effect of ammonium on glnB mutant R.capsulatus was investigated and compared with wild type. Biomass of the bacterial cultures, pH of the medium and amount of produced hydrogen were periodically determined. Moreover, the concentrations of acetic, lactic, formic and propionic acids in the medium were periodically measured. Both wild type and glnB mutant grew on acetate and effectively utilized acetate. Ammonium negatively affected hydrogen production of glnB mutant and wild type. The ammonium inhibition of hydrogen production did not release in glnB mutant due to the presence of active GlnK protein in the cell / hence, inactivation of one of PII proteins was not enough to disrupt ammonium regulation of the cell. Moreover, kinetic analysis of bacterial growth and hydrogen production were done. Growth data fitted to the Logistic Model and hydrogen production data fitted to the Modified Gompertz Model.

In this study, the role of two DNA repair genes, X-ray repair cross complementing group 3 (XRCC3) Thr241Met and Rad51 G135C polymorphisms were investigated in the risk of development of childhood ALL in Turkish population among 193 healthy controls and 184 ALL patients, by using PCR-RFLP technique. For XRCC3 Thr241Met polymorphism, the frequencies of both heterozygous and homozygous mutant genotypes were found to be higher in the controls compared to ALL patients (OR: 0.59, p = 0.02 / OR: 0.48, p = 0.02, respectively). In addition, either heterozygous (Thr/Met) or homozygous mutant (Met/Met) genotypes were significantly more common in the controls than the ALL patients (OR: 0.55, p =0.005). In case of Rad51 G135C polymorphism, no significant associations have been found with the risk of childhood ALL. Combination of XRCC3 heterozygote and Rad51 heterozygote genotypes increased the protective effect for risk of childhood ALL. (OR=0.35 / p =0.02). Combination of homozygote mutant genotype of XRCC3 with homozygote wild type genotype of Rad51 gave a highly statistically proved protective effect for the development of disease (OR= 0.36 / p= 0.004). To our knowledge, this is the first study showing the protective role of XRCC3 Thr241Met polymorphism either alone or in combination with Rad51 G135C variant on the risk of development of childhood ALL. In addition, interactions of these polymorphisms with non-genetic risk factors were investigated. Only in terms of paternal exposure, the heterozygote (Thr/Met) genotype for XRCC3 gene in children whose father exposed to cigarette smoke demonstrated a significant risk of 3.0 fold (p=0.05). Moreover, the frequency of Rad51 135C allele was determined for the first time in Turkish population. The frequency of the mutant allele was found to be very similar to that observed in other Caucasian populations.