Proper bridge design is based on consideration of structural, hydraulic, and geotechnical conformities at an optimum level. The objective of this study is to develop an optimization-based methodology to select appropriate dimensions for components of a river bridge such that the aforementioned design aspects can be satisfied jointly. The structural and geotechnical design parts uses a statisticallybased technique, artificial neural network (ANN) models. Therefore, relevant data of many bridge projects were collected and analyzed from different aspects to put them into a matrix form. ANN architectures are used in the objective function of the optimization problem, which is modeled using Genetic Algorithms with penalty functions as constraint handling method. Bridge scouring reliability comprises one of the constraints, which is performed using Monte-Carlo Simulation technique. All these mechanisms are assembled in a software framework, named as AIROB. Finally, an application built on AIROB is presented to assess the outputs of the software by focusing on the evaluations of hydraulic &ndash / structure interactions.

Wheat diseases such as rusts and powdery mildews are among the most important and ancient diseases that affect wheat cultivation worldwide. The pathogen race specific resistance genes cannot maintain long lasting resistance. On the other hand, the presence of genes confers the non-race specific resistance last much longer. The durable resistance phenotypes in wheat against various rust and powdery mildew diseases were reported as Lr34, Yr18, and Pm38 separately / nevertheless, they were known to locate very close to each other based on linkage analysis. Recently, it was shown that all of these resistance phenotypes are indeed conferred by the same gene, encoding Adenosine triphosphate&ndash / binding cassette transporter (ABC-transporter) type protein. The way with which this transporter is functioning to maintain the durable resistance against different types of pathogens is still unknown. v The presence of LR34 (or ABC-transporter) gene resistant allele can be detected by specially designed markers. In spite of the few DNA sequence differences between the resistant and the susceptible alleles, the easily applicable PCR based markers allow the detection of the presence of this durable resistant allele on any given variety or cultivar. In our study, 62 different Turkish bread wheat varieties were screened by the gene specific molecular markers, developed from those LR34 gene mutation sites. The 11 cultivars determined to contain the resistant allele. This study is the first screening of Turkish cultivars for the presence of LR34 gene.

In this study, possible involvement of the small heat shock proteins (sHsps) from a thermoacidophilic archaeon, Thermoplasma (Tp) volcanium in the stress response was investigated. Our results showed that heterologous, high level expression of TVN0775/sHsp gene in E.coli increased its thermotolerance at 53&deg / C for two hours. But, the second sHsp of the Tp. volcanium, TVN0984/sHsp was not effective in improvement of the thermal resistance of the mesophilic bacterium (i. e., E.coli). The expression of the TVN0775/sHsp and TVN0984/sHsp genes increased about 3 fold after heat-shock at 65&deg / C, as revealed by Real-Time PCR analysis. Although expression of the both genes was induced at 70&deg / C, TVN0984/sHsp gene expression was increased higher (about 5 fold) than that of the TVN0775/sHsp gene expression (about 1.5 fold). Tp. volcanium cells were exposed to high pH (pH: 3.5, pH: 4.0, pH: 4.5, pH: 5.0), and the change in the sHsp genes&rsquo / expression profile were analyzed. The results showed that TVN0775/sHsp gene expression was more sensitive to increased pH than TVN0984/sHsp gene expression. The TVN0775/sHsp gene transcription induced at most 2.5 fold at pH 4.0 and the gene expression either reduced or did not change at higher pH values (i.e., pH 4.5 and 5.0). On the other hand, TVN0984/sHsp gene expression did not change at pH 4.0 but significantly reduced at higher pH values. The effect of oxidative stress on the expression of TVN0775 and TVN0984 genes was investigated by treatment of Tp. volcanium cells with 0.01 mM, 0.02 mM, 0,03 mM and 0.05 mM H2O2. For both sHsp genes, transcription was induced at lower concentrations of H2O2 (0.01 mM and 0.02 mM). At higher concentrations of H2O2 expression of both genes&rsquo / transcription either did not changed or down regulated. Lastly, in this study we have purified the recombinant TVN0775/sHsp, as an Nterminal 6x his-tag fusion to homogeneity on Ni-NTA affinity column. Purified protein samples were used in the chaperone activity assays using bovine glutamate dehydrogenase enzyme (boGDH) as substrate. We have found that the recovery of glutamate dehydrogenase activity at 45&deg / C, 50&deg / C and 53&deg / C in the presence of the Tp. volcanium sHsps was higher than that of spontaneous refolding. Also, TVN0775/sHsp increased the recovery of the boGDH enzyme that was denatured at 2.5 M GdnHCl concentrations for 30 min.

Stroke is characterized with loss of one or more functions of the body resulted by inadequate blood supply to the brain. Most of the cases result from a blood clot forms on an atherosclerotic plaque in the brain which is called as ischemic stroke. Structure of the arteries and vascular tone are listed in major determinants in the development of the disorder. Soluble epoxide hydrolase (sEH, EPHX2) catalyzes conversion of epoxyeicosatrienoic acids to inactive diol metabolites. EETs are potent vasodilators that participate in the regulation of vascular tone and cerebral blood flow. Microsomal epoxide hydrolase (mEH, EPHX1) is a critical phase I enzyme that catalyzes the conversion of various xenobiotic epoxide substrates and polycyclic aromatic hydrocarbons (PAHs). Animal studies show that tobacco smoke mutagens such as PAHs and heterocyclic amines directly increase the development of atherosclerotic lesions. The main purpose of this study is evaluation of effect of Arg287Gln single nucleotide polymorphism of EPHX2 gene and Tyr113His and His139Arg single nucleotide polymorphisms of EPHX1 gene as a risk factor for ischemic stroke in Turkish population. Blood samples of 237 ischemic stroke patients and 120 controls were collected and all polymorphisms were determined by PCR-RFLP method. Mutant allele frequencies in terms of Arg287Gln polymorphism of EPHX2 gene (A) were found as 0.08 for patient group and 0.09 for controls. Tyr113His polymorphism of EPHX1 gene (C) were found as 0.27 for patient group and 0.31 for controls when, His139Arg polymorphism of EPHX1 gene (G) were 0.820 and 0.814 for patient and control groups, respectively. The differences between mutant allele frequencies of patients and controls were not found to be statistically significant. Subgroup analysis was used to investigate the effects of conventional vascular factors according to the genotypes in the stroke susceptibility. Smoking, diabetes, obesity and hypertension were found to significantly increase the risk of having stroke. More detailed analysis on these factors with respect to genotypes showed that the risk of hypertensive individuals having ischemic stroke was higher in wild type homozygous genotype groups of Tyr113His (TT) and His139Arg (AA) polymorphisms and heterozygous and mutant homozygous genotypes of Arg287Gln (GA+AA) polymorphism than their counterparts (OR= 3.21, 3.15 and 4.69, respectively). Smoker people within the heterozygous and mutant homozygous genotypes group of Arg287His (GA+AA) polymorphism and wild type homozygous group of His139Arg (AA) polymorphism were found to be more susceptible to have stroke (OR= 11.81 and 4.78 respectively). Finally, diabetes mellitus was found to double the risk of having stroke regardless of the genetic background. Logistic regression analyses were used to ascertain the effects of vascular factors, lipid parameters and genotypes in the stroke susceptibility. LDL-cholesterol (OR=1.46 / 95%CI, 1.12-1.89, P=0.00), smoking (OR=3.46 / 95%CI, 1.66-7.21, P=0.00) and hypertension (OR=3.19 / 95%CI, 1.92-5.30, P=0.00) were found to be significant risk factors for ischemic stroke, whereas HDL (OR=0.27 / 95%CI, 0.12-0.65, P=0.02) was found to be a protective factor in general population. In this study, the relation of Tyr113His and His139Arg polymorphisms of EPHX1 gene and risk of ischemic stroke is investigated for the first time in literature while, Arg287Gln polymorphism and ischemic stroke risk in Turkish population was studied for the first time.

The genus Picea is located from temperate to Taiga (boreal) regions of northern hemisphere from subtropical to high altitude with 34 species. Picea orientalis is endemic to Eastern Black Sea Mountainous region of Turkey and Western Caucasus. To determine the genetic relatedness within Picea orientalis populations, as well as the relationship between other Pinaceae species from database, populations were sampled from 15 different locations within the natural range of species and grouped into 5 depending on several criteria. In order to evaluate the genetic structure of the taxon, non-coding trn and matK regions of choloroplast DNA (cpDNA) were sequenced. According to genetic diversity analysis of 15 Picea orientalis populations with respect to trn and matK regions, there is not much variation among populations. Among 3 non-coding trn and the matK region, there is only one variable site which was parsimony informative. The results indicated that the populations from Artvin had the highest divergence. In this study, the genetic divergence of Picea orientalis from other Pinaceae species were also observed. According to the results obtained from trnV region the studied Picea orientalis observed to display a close relationship with Larix and distinct from other Pinaceae especially Pinus genus. This result is unrepresentative due to the results of other studies. Moreover, as a result of analysis with trncd-ef region, the studied Picea orientalis populations possessed close relationship with species from clade Picea. Moreover, based on molecular clock estimations the studied Picea orientalis populations had close relationships with the species form Asia. Finally, the relationship of Picea orientalis with other Picea species were analyzed with respect to matK region. The result is consistent with the results of trncd-ef region and also with other studies.

Rhodobacter capsulatus DSM1710 is a purple non-sulfur bacterium capable of hydrogen production via photofermentation. Biohydrogen is a clean and renewable way of hydrogen production, which can be achieved by PNS bacteria in outdoor large scale photobioreactors using sun light. In outdoor conditions bacteria can be exposed to heat and cold stress. In this study in order to understand the effects of heat and cold stress on photofermentative hydrogen production and gene expression profile of R.capsulatus on acetate as the carbon source, microarray analysis was carried out. Since there is no commercially available microarray chip for R.capsulatus, an Affymetrix GeneChip&reg / was designed and it was manufactured by Affymetrix.The experiments were conducted at 30

Integral bridges (IBs) are defined as a class of rigid frame bridges with a single row of piles at the abutments cast monolithically with the superstructure. In the last decade, IBs have become very popular in North America and Europe as they provide many economical and functional advantages. However, standard design methods for IBs have not been established yet. Therefore, most bridge engineers depend on the knowledge acquired from performance of previously constructed IBs and the design codes developed for conventional jointed bridges to design these types of bridges. This include the live load distribution factors used to account for the effect of truck loads on bridge components in the design as well as issues related to the seismic design of such bridges. Accordingly in this study issues related to live load effects as well as seismic effects on IB components are addressed in two separate parts. In the first part of this study, live load distribution formulae for IB components are developed and verified. For this purpose, numerous there dimensional and corresponding two dimensional finite element models (FEMs) of IBs are built and analyzed under live load. The results from the analyses of two and three dimensional FEMs are then used to calculate the live load distribution factors (LLDFs) for the components of IBs (girders, abutments and piles) as a function of some substructure, superstructure and soil properties. Then, live load distribution formulae for the determination of LLDFs are developed to estimate to the live load moments and shears in the girders, abutments and piles of IBs. It is observed that the developed formulae yield a reasonably good estimate of live load effects in IB girders, abutments and piles. In the second part of this study, seismic performance of IBs in comparison to that of conventional bridges is studied. In addition, the effect of several structural and geotechnical parameters on the performance of IBs is assessed. For this purpose, three existing IBs and conventional bridges with similar properties are considered. FEMs of these IBs are built to perform nonlinear time history analyses of these bridges. The analyses results revealed that IBs have a better overall seismic performance compared to that of conventional bridges. Moreover, IBs with thick, stub abutments supported by steel H piles oriented to bend about their strong axis driven in loose to medium dense sand are observed to have better seismic performance. The level of backfill compaction is found to have no influence on the seismic performance of IBs.

Cancer may arise as a result of deregulation of oncogenes and/or tumor suppressors. Although much progress has been made for the identification of such cancer related genes, our understanding of the complex tumorigenesis pathways is still not complete. Therefore, to improve our understanding of how certain basic mechanisms work in normal and in cancer cells, we aimed to characterize two different breast cancer related genes. First part of the study focused on subcellular localization USP32 (Ubiquitin Specific Protease 32) to help understand the function of this uncharacterized gene. USP32 is a member of deubiquitinating enzymes (DUBs) and the gene maps to a gene rich region on 17q23. Genes on 17q23 are known to undergo amplification and overexpression in a subset of breast cancer cells and tumors. DUBs are known to be implicated in a variety of cellular functions including protein degradation, receptor endocytosis and vesicle trafficking. Therefore to elucidate the function of USP32, we localized the full length USP32 protein fused to GFP, in HeLa cells, using Fluorescence Protease Protection (FPP) assay and confocal microscopy. Results suggested a Golgi localization for USP32 as confirmed by co-localization study via BODIPY-TR, a Golgi specific marker. Additional investigations to find the role of USP32 in Golgi will further clarify the function of this candidate oncogene. Second part of the study focused on a potential tumor suppressor. For this purpose, we functionally characterized miR-125b, a microRNA gene as a potential tumor suppressor in breast cancer. microRNAs are regulators of gene expression and their deregulation is detected in cancer cells. miR-125b is reported as a down regulated microRNA in breast cancers. In this study, we investigated the expression, function and possible targets of miR-125b in breast cancer cell lines (BCCLs). Our results revealed a dramatic down regulation of miR-125b in a panel of BCCLs. Restoring the expression of miR-125b in low miR-125b expressing cells decreased the cell proliferation and migration as well as cytoplasmic protrusions, detected by staining of actin filaments. While connection of miR-125b and cell motility based on ERBB2 targeting has been reported earlier, here we present data on ERBB2 independent effects of miR-125b on cell migration in non-ERBB2 overexpressing breast cancer cells. Our results showed involvement of a miR-125b target, ARID3B, in cell motility and migration. Our findings showed miR-125b to be an important regulator of cell proliferation and migration in ERBB2 negative breast cancer cells, possibly through regulating multiple targets.

v It was found that most of the classical scrapie genotypes belong to R3 risk group, whereas atypical scrapie genotypes belonging to zero (0) and one (1) risk groups were frequently seen in sheep analyzed. In other words, Turkish sheep is found to have intermediate risk of classical scrapie and low atypical scrapie risk, in general. The data from the current study may help to establish a breeding program for classical scrapie control in Turkey and will be beneficial for both the animal and public health in the country. In addition, the outcomes of the study will fill the gap which is present in the geographic distribution data of PrP gene polymorphisms in Eurasia.Scrapie is an infectious fatal disease of sheep and goats which affects the central nervous system. In the present study, samples of 14 native Turkish sheep breeds (n=655) were analyzed with respect to their polymorphisms of PrP gene (at codons: 136, 141, 154 and 171) and their classical and atypical scrapie risk levels were identified. Turkish sheep are found to have the highest PrP genetic variability with 13 classical scrapie alleles and 14 atypical scrapie alleles compared to all previous studies. Classical scrapie-susceptible and wild-type ARQ allele was found as the most frequent allele in Turkish sheep examined. The most classical scrapie-susceptible allele, VRQ was detected at low frequencies in 5 of the breeds (&Ccedil / ine &Ccedil / apari, Dagli&ccedil / , Kivircik, Karayaka and G&ouml / k&ccedil / eada). One novel allele (TL141HQ) was observed in Sakiz breed for the first time in this study.

In the present study, history of domestic sheep were investigated by mitochondrial DNA (mtDNA) based haplogroups (HPG) of 628 samples and mtDNA control region (CR) sequences of 240 samples from 13 Turkish sheep breeds which were located in the hearth of the first domestication center. Also, 30 Anatolian wild sheep (Ovis gmelinii anatolica) mtDNA CR sequences were obtained to contribute to the scenarios on initial domestication stages of sheep. Haplogroup compositions of breeds were identified with SSCP method by using mtDNA ND2 region. The genetic diversity and relationship between haplogroups were calculated. Phylogenetic analyses of haplogroups such as median joining networks and neighbor joining trees were constructed for mtDNA CR, cytochrome B (cytB) and combined CR-cytB sequences with sequences from the present study together with sequences retrieved from NCBI (http://www.ncbi.nlm.nih.gov/). Results of the present study showed that all previously observed haplogroups (HPG A-E) were present in Turkish sheep breeds. Two individuals from rare HPG D and eleven individuals from rare HPG E were detected and sequenced. With increased sample size, for HPG E, past population expansion was observed as was the case of HPG A, B and C with mismatch distributions and neutrality tests. Spatial autocorrelation analyses and synthetic map with respect to mtDNA (maternal) pattern revealed that Turkey was separated into two regions which may be attributed to the imprints of third migration of sheep associated with the arrivals of nomadic Turks to Anatolia nearly 1000 years before present. Finally, Ovis gmelinii anatolica samples exhibited two haplotypes / one of them belongs to HPG A (possibly feral domesticate), and the other one shows a distinct haplotype (close to HPG E and C) that was not observed before. Observed, low mtDNA diversity might be the result of isolation, fragmentation, extinction of fragments and bottlenecks. Ovis gmelinii anatolica can be part of the evolved descendants of the wild sheep which gave birth to the domestic sheep.