The aim of the present study was to elucidate the possible relationship between the levels of various brain fatty acids and learning indices in aged and young mice classified as &ldquo / good&rdquo / or &ldquo / poor&rdquo / learners basing on their performance in a spatial learning task, the Morris Water Maze. The levels of several fatty acids including palmitic, stearic, oleic, linoleic, arachidonic acid (AA) and docosahexaenoic acid (DHA) were measured using gas chromatography separately in samples from four different brain areas: hippocampus, cortex, striatum and hypothalamus. The level of oleic acid in the cerebral cortex was significantly higher in young-good learners as compared to young-poor learners and higher in young-poor learners than in old-poor learners, with no significant difference in the concentration of this acid between old-good and old-poor learners. The most consistent correlation between animals&rsquo / learning capacity and brain fatty acid&rsquo / level was found for the arachidonic acid in the hippocampal region: AA level was significantly lower in young-good learners as compared to both young-poor learners&rdquo / and old-good learners&rdquo / with young-good learners showing significantly better performance than the two other groups. Interestingly, except hypothalamus, no significant between-group differences were recorded for the remaining fatty acids including DHA, in none of the four brain regions examined.

Amplification of target DNA in vitro via polymerase chain reaction (PCR) is a widely used scientific technique in molecular biology. This method relies on repeated heating and cooling cycles of the DNA and enzyme mixture, resulting with the enzymatic replication of the DNA. A heat stable Taq DNA polymerase and a thermal cycler that enables repeated heating/cooling cycles are the two key components of the PCR. In this study we have produced a high activity Taq DNA polymerase and used this enzyme to validate and optimize two newly developed thermal cyclers- a conventional and a capillary thermal cycler. Taq DNA polymerase gene was amplified from Thermus aquaticus DNA, was cloned and overexpressed using Gateway&reg / recombination cloning technology. Highly active Taq DNA polymerase enzyme was purified from E.coli and its activity was tested by PCR, using different sources of DNA. Our results showed that the enzyme activity of the produced Taq DNA polymerase was not significantly different from the commercial available Taq DNA polymerase. To further characterize the purified enzyme, endonuclease and nicking activities were also tested to be absent. The fidelity of the purified Taq DNA polymerase was also tested and found to be the same as the commercially available Taq polymerases. In this study, in addition to the production of a Taq polymerase, optimization studies for two new thermal cyclers, a conventional and a capillary, was also carried out. The conventional thermal cycler was found to be as efficient as the commercially available thermal cyclers in the 95% confidence interval. The capillary thermal cycler was tested as a proof of concept and our results showed that it works less efficiently due to the insufficient insulation and capillary tubes being longer than the capillary tube holder.

The eastern Mediterranean has been known as the most oligotrophic water body among the worlds oceans and as a result of limited nutrient inputs from terrestrial sources primary productivity and plankton succession are restricted by lack of nutrients especially by phosphorus and nitrogen. Within this domain, Mersin bay forms a so called hot spot (highly sensitive) area where a sharp contrast exists between the coastal area supplied by land-based nutrient sources and the nutrient limited open sea. Excess nutrient enrichment lead for eutrophication in the inner Mersin bay while altering the quality and quantity of flora from shore to offshore. Microorganisms are highly sensitive and profoundly affected by environmental disturbances and are widely used to assess the impact of environmental changes on ecosystem functioning. With this study, it is aimed to investigate responses of the smaller fractions of phytoplankton composed of heterotrophic bacteria, Synechococcus and flagellates to rapidly changing ambient biological, chemical and physical properties of shelf waters over an extended period between 2008 and 2010. Epiflourescence microscopy and image analysis setup were used to enumerate and measure size of cells for biomass estimates.

Here, we provide results of mid/late Holocene fresh water Ostracoda analyses from coastal modern lake basins in the Thrace region of Istanbul and Sarikum Lake, on the Black Sea coast near Sinop. While neither diatoms nor Cladocera are abundant in the sediments, Podocopian (fresh water) ostracods preserved well, but with discontinuous occurences during the mid/late Holocene. Un-noded forms of Cyprideis torosa, along with other Podocopian ostracods, dominated the sediments of all three lakes. Studying these three lagoonal basins along the Black Sea and Thracian coasts of Turkey allows reconstruction of long term, regional environmental histories, using the following methods. Loss-on-ignition (LOI) analyses at 1 cm intervals of short and long cores provide stratigraphic cross-correlation and calculations of organic matter, carbonate and mineral weight. At 5 cm intervals, spectrally-inferred chlorophyll-a contents by visible reflectance spectroscopy (Michelutti et al., 2010), provide estimates of algal production. Trace element analysis (Mg/Ca and Sr/Ca) using ICP-AES (coupled plasma atomic emission spectroscopy) is applied to fully calcified adult specimens of un-noded forms of Cyprideis torosa shells (which dominate the uppermost 145 cm of Terkos Lake). 210Pb and 137Cs dating of short cores, and AMS 14C dating of long cores, are used to infer sediment accumulation rates and to place specific ages on inferred environmental changes. Benthic foraminifers, gastropods, bivalves, single valves of fossil Glochidia, and Charophyte seeds are the other biological indicators observed within the sediment archive. Based on these data: 1. Terkos Lake sediments contain records of multiple, sub-millennial scale marine incursion events, over the last 2.8 ka, inferred to be the result of severe storms or tsunami on the Black Sea, including the tsunami in AD 1598 and AD 557-543 / 2. short core sediments from Sarikum Lake reveal sharp decreases in organic matter, carbonate, and increases in algal production and sand amount that suggest a storm or more recent earthquake / such as the Great Erzincan Earthquake (26 December, 1939) or the Bartin earthquake (3 September, 1968) while four more such events appear in the undated sediments of the Sarikum Lake long core / and 3. a large earthquake in AD 447 that affected the entire Sea of Marmara (Leroy et al., 2002) does not appear in the B&uuml / y&uuml / k&ccedil / ekmece Lake sediment record, but there is evidence for a significant hiatus in these deposits before the development of the dam (AD 1989) and after the youngest AMS date (2400 cal yrs BP). This suggests that B&uuml / y&uuml / k&ccedil / ekmece Lagoon was an environment of net erosion prior to its artificial impoundment, either from gradual processes or from scouring by one or more tsunami.

Whooping cough (pertussis) is a highly contagious respiratory infection caused by Bordetella pertussis. It becomes widespread among adolescent and adults as well as infants. Although availability of effective pertussis vaccines seems to decrease the incidence of the disease, B. pertussis circulation in population has not been eliminated. It is thought that the antigenic drifts in major protective antigens and continued circulation of B. pertussis strains will result in gradual loss of the efficacy of the current pertussis vaccines. Therefore, development of more effective acellular pertussis vaccines with conserved protective proteins is a convenient strategy to provide a better protection against whooping cough. In this study, immune responses against putative peptidyl-prolyl cis-trans isomerase (PPIase) which was shown to be immunogenic in B. pertussis for the first time by our immunoproteome group and FimX whose expression was found higher in our local Saadet strain were determined in mice. The genes encoding FimX and putative PPIase were amplified by PCR, cloned into pGEM&reg / -T Easy vector and sequenced. The genes were then introduced into pET-28a (+) vector and they were expressed in Escherichia coli BL21(DE3) cells. The recombinant proteins were purified by His-tag affinity chromatography and dialyzed. After Western blot analyses, 20 &micro / g and 80 &micro / g recombinant FimX and 80 &micro / g recombinant putative PPIase were used to immunize BALB/c mice (16-18 g) at day 0 and 21. The mice were challenged intranasally with 2.5 x 109 live B. pertussis Saadet cells. Before second immunization and challenge, the sera were collected to carry out ELISA for measurement of serum-specific IgG levels. According to ELISA results, IgG levels in the mice immunized with 20 &micro / g and 80 &micro / g recombinant FimX were found significantly higher than in control groups at both first and second vaccinations (p&lt / 0.01). On the other hand, immunization with 160 &micro / g recombinant putative PPIase provided a significant increase in IgG level (p&lt / 0.05) only at second vaccination. The lungs of the mice were removed at day 2, 5, 8 after challenge and bacterial colonization was determined. No significant decrease in bacterial colonization was observed in the lungs of the mice immunized with 20 &micro / g and 80 &micro / g recombinant FimX and 80 &micro / g recombinant putative PPIase with respect to control groups. After respiratory challenge and second immunization (at day 30) with 20 &micro / g and 80 &micro / g recombinant FimX, the spleens of the mice were removed and a spleen cell culture was obtained. Supernatants were collected after induction of the cells with the recombinant protein and cytokine ELISA was carried out to measure IFN-&gamma / level. No significant difference was observed between control and vaccinated mice in terms of IFN-&gamma / production.

RNA-binding proteins (RBP) shuttle between cellular compartments either constitutively or in response to stress and regulate localization, translation and turn over of mRNAs. In our laboratory, cytosolic proteome map of Phanerochaete chrysosporium was established and upon Pb exposure, the changes in cytosolic protein expressions were determined. The identified RBPs were a newly induced polyadenylate-binding protein (RRM superfamily) as well as two up-regulated proteins, namely splicing factor RNPS1 and ATP-dependent RNA helicase, all being very important candidates of post-transcriptional control in response to stress. This finding inspired us to conduct Real Time PCR studies in order to have a better understanding of the changes in the expression of corresponding genes at mRNA level in response to Pb exposure, thus the present study aims at examining the effect of lead exposure on the transcript levels of the genes coding for ATP-dependent RNA helicase, splicing factor RNPS1 and polyadenylate binding protein. As shown via expression analysis based on Real Time PCR, the mRNA level of splicing factor RNPS1 showed 2.68, 2.62 and 4.86 fold increases in a dose-dependent manner when the cells were grown for 40 h in the presence of 25, 50 and 100 &micro / M Pb, repectively. ATP-dependent RNA helicase mRNA level showed no significant increase in response to 25 &micro / M Pb exposure while increased 2 and 1.84 fold in response to 50 and 100 &micro / M Pb, respectively. Polyadenylate binding protein mRNA levels revealed no significant increase when exposed to 25, 50 and 100 &micro / M Pb. As to the mRNA dynamics as a function of duration of lead exposure, the mRNA level of this protein showed 2.54-fold increase upon 1 h exposure to 100 &micro / M Pb. Splicing factor RNPS1 mRNA level showed a significant increase of 19.22 fold at 2nd h of 50 &micro / M Pb exposure. Expression level of ATP-dependent RNA helicase was not affected by the time of exposure to Pb.

This thesis was aimed to analyze phenol oxidation by the bifunctional catalase/phenol oxidase of the thermophilic fungus Scytalidium thermophilum. Several reactive oxygen species (ROS) are continuously produced in fungi under oxidative stress. Depending on the nature of the ROS species, some are highly toxic and are rapidly detoxified by various cellular enzymatic mechanisms, including the production of catalase. S. thermophilum produces a novel bifunctional catalase-phenol oxidase (CATPO) which is capable of oxidizing phenolics in the absence of hydrogen peroxide. Phenol oxidases convert phenolic compounds to quinones, which are then polymerized mainly by free- radical mediated reactions. In this study, 14 phenolic compounds were selected according to their different chemical structures and functional properties and were analyzed as substrates of CATPO. Among 14 phenolic compounds, only in catechol, chlorogenic acid, catechin and caffeic acid distinct oxidation products were observed by HPLC. The oxidation products of catechol, caffeic acid, chlorogenic acid and catechin were characterized by LC-ESI-MS. Dimer, trimer, tetramer and oligomer formations were detected. While the maximum conversion efficiency, at 1 hour of reaction, was observed with catechin, minimum conversion efficiency was attained by caffeic acid, under the specified conditions. The oxidation products observed after oxidation of catechol, chlorogenic acid, catechin and caffeic acid by CATPO was compared with the same phenolic compounds oxidation products oxidized by laccase and tyrosinase. CATPO was incapable of oxidizing tyrosinase and laccase-specific substrates tyrosine and ABTS respectively. However, the oxidizing spectrum of substrates indicates that the nature of phenol oxidation by CATPO appears to resemble mainly those of laccase.

One of the main problems of current cancer chemotherapy is the lack of selectivity of anti-cancer drugs to tumor cells which leads to systemic toxicity and adverse side effects. In order to overcome these limitations, researches on controlled drug delivery systems have gained much attention. Nanoscale based drug delivery systems provide tumor targeting. Among many types of nanocarriers, superparamagnetic nanoparticles with their biocompatible polymer coatings can be targeted to an intented site by an external magnetic field. Thus, the drug can be carried to the targeted site safely. The aim of this study is to prepare poly(dl-lactic-co-glycolic acid) (PLGA) coated magnetic nanoparticles and load anti-cancer drug, doxorubicin to them. For this purpose, magnetite (Fe3O4) iron oxide nanoparticles were synthesized as a magnetic core material (MNP) and then coated with oleic acid. Oleic acid coated MNP (OA-MNP) was encapsulated into PLGA. Effects of different OA-MNP/PLGA ratios on magnetite entrapment efficiency were investigated. Doxorubicin loaded magnetic polymeric nanoparticles (DOX-PLGA-MNP) were prepared. After the characterization of prepared nanoparticles, their cytotoxic effects on MCF-7 cell line were studied. PLGA coated magnetic nanoparticles (PLGA-MNP) had a proper size and superparamagnetic character. The highest magnetite entrapment efficiency of PLGA-MNP was estimated as 63 % at 1:8 ratio. Cytotoxicity studies of PLGA-MNP did not indicate any notable cell death between the concentration ranges of 2 and 250 &mu / g ml-1. It was observed that DOX-PLGA-MNP showed significant cytotoxicity on MCF-7 cells compared to PLGA-MNP. The results showed that prepared nanoparticles have desired size and superparamagnetic characteristics without serious toxic effects on cells. These nanoparticles may be suitable for targeted drug delivery applications. The findings obtained from drug studies may contribute to further work.

Conventional cancer chemotherapies cannot differentiate between healthy and cancer cells, and lead to severe side effects and systemic toxicity. In the last decades, different kinds of controlled drug delivery systems have been developed to overcome these shortcomings of chemotherapeutics. Magnetic nanoparticles (MNP) are potentially important in cancer treatment since they can be targeted to tumor site by an externally applied magnetic field. In this study, it is aimed to synthesize folic acid conjugated / polyethylene glycol (PEG) coated magnetic nanoparticles with appropriate size, surface chemistry, magnetization and biocompatibility to be used in biomedical applications. First MNP were synthesized, then covered with oleic and PEG / and finally conjugated with folic acid. A detailed characterization of synthesized nanoparticles was done by TEM, XRD, FTIR, VSM and XTT analyses. MNP synthesized by the rapid addition of ammonium hydroxide exhibited more spherical nanoparticles with a narrower size distribution. Agglomeration tendency of naked nanoparticles was prevented by oleic acid addition during the synthesis. Both naked and surface treated MNP have been found to exhibit superparamagnetic behavior both at room temperature (23

The largest class of cell surface receptors in mammalian genomes is the superfamily of G protein-coupled receptors (GPCRs) which are activated by a wide range of extracellular responses such as hormones, pheromones, odorants, and neurotransmitters. Drugs which have therapeutic effects on a wide range of diseases are act on GPCRs. In contrast to traditional idea, it is recently getting accepted that G-protein coupled receptors can form homo- and hetero-dimers and this interaction could have important role on maturation, internalization, function or/and pharmacology. Bimolecular fluorescence complementation technique (BiFC) / is an innovative approach based on the reassembly of protein fragments which directly report interactions. In our study we implemented this technique for detecting and visualizing the GPCR interactions in yeast cells. The enhanced green fluorescent protein (EGFP) fractionated into two fragments at genetic level which does not possess fluorescent function. The target proteins which are going to be tested in terms of interaction are modified with the non-functional fragments, to produce the fusion proteins. The interaction between two target proteins, in this study Ste2p receptors which are alpha pheromone receptors from Saccharomyces cerevisiae, enable the fragments to come in a close proximity and reassemble. After reassembly, EGFP regains its fluorescent function which provides a direct read-out for the detection of interaction. Further studies are required to determine subcellular localization of the interaction. Moreover, by using the fusion protein partners constructed in this study, effects of agonist/antagonist binding and post-translational modifications such as glycosylation and phosphorylation can be examined. Apart from all, optimized conditions for BiFC technique will guide for revealing new protein-protein interactions.