The interactions of the non steroidal anti-inflammatory drug celecoxib with pure and cholesterol containing distearoyl phosphatidylcholine multilamellar vesicles were studied using Fourier transform infrared spectroscopy, differential scanning calorimetry and turbidity technique at 440 nm. The results reveal that celecoxib exerts opposing effects on membrane order in a concentration dependent manner while cholesterol disorders and orders the membrane in the gel and liquid crystalline phase, respectively. Ternary mixtures of DSPC/Cholesterol/celecoxib behave similar to cholesterol with a small effect of celecoxib. While celecoxib decreases fluidity of the DSPC membranes, cholesterol shows an opposite effect, and in ternary mixtures, a dominant effect of cholesterol is observed. Celecoxib induces opposite effects on the hydration status of the carbonyl groups in the binary system whereas / cholesterol induces hydrogen bonding around this group. An evidence of phase separation has also been observed for all three systems (DSPC/celecoxib, DSPC/Chol, and DSPC/Chol/celecoxib). In addition, a possible location of celecoxib in the interfacial region of the membrane has been proposed. Finally, penetration of celecoxib into the hydrophobic core of the ternary system at high cholesterol concentrations and formation of a new phase has also been suggested. Thus, depending on the concentration used, celecoxib induces significant changes in the biophysical properties of membranes that may aid in understanding its mechanism of action. Furthermore, highly complex interactions take place in ternary membrane systems and further investigations are needed to explore them in detail.

TAXONOMIC STUDIES ON THE GENUS SALVIA L. (LABIATAE) IN CENTRAL ANATOLIA, TURKEY SAFI BAGHERPOUR Ph.D., Department of Biological Sciences Supervisor: Prof. Dr. Musa Dogan June 2010, 203 pages This research study is a revision of the genus Salvia (Labiatae) in Central Anatolia. The author has carried out extensive research studies conducted in a 3 year period starting from June 2005 by collecting specimens from all the localities in Central Anatolia, Turkey. Specimens collected from Turkey by the other researchers and kept either in Turkey or abroad were also examined. The samples were studied using their root, stem and leaf morphology including essential characteristics of flowers. Using this information dendograms were obtained and taxa cut off lines were drawn. The cross sectional preparations of stem and leaf were observed for taxonomical evaluation. Salvia taxa leaf surface, flower organs and seed surface were studied for understanding the diagnostic value of their micro morphological characteristics. Anatomical sections of the specimens were analyzed under light microscope and the data was used for further taxa separations. The Salvia species were further investigated for their pollen characteristics such as surface view and dimensions. Numeric taxonomic methods were used for constructing a natural infrageneric grouping in the genus as far as the species allows. Using software and computer grouping each sample was ranked and placed into specific taxa. First the samples were identified by using the species key given in Turkish Flora. According to the Turkish Flora there were two ways to identify samples. One way based on the stamen features and the other based on the leaves and flowers. For nomenclatural reasons the specimens were cross checked with the existing type specimens known from Turkey and kept in some international herbaria. This thesis is formed by two sections. The first section is comprised of introduction, materials and methods and basic findings. Basic finding are the result of morphological, anatomical, palynological and ecological investigations. In the second section of the thesis, a revision of Salvia in Central Anatolia, Turkey is given. This includes results of numeric studies and infrageneric grouping. Soil types and habitat characteristics were also studied. Soil samples were taken from the various locations and analyzed for their content. The populations were revisited to determine the sustainability and vulnerability of each taxon. IUCN threat categories were determined based on habitat information and species limitations. The phenological data and relevant field observations were all recorded. In Central Anatolia 43 Salvia species were found. Among the specimens collected from the area one taxon was re-discovered after 116 years.

Ubiquitylation is an important post-translational modification and can be reversed by the action of deubiquitinating (DUB) enzymes. The ubiquitylation and deubiquitylation of target proteins are significant in terms of regulating cellular events such as protein degradation, signal transduction, vesicle trafficking, DNA repair and apoptosis. Chromosomal band 17q23 is frequently amplified in breast cancers and harbors a predicted ubiquitin specific protease gene, USP32 (ubiquitin specific protease 32). Given its potential role in breast cancer, we aimed to characterize USP32 for its potential DUB activity. Bioinformatic analysis of USP32 and known yeast and mouse DUBs suggested presence of Cys-His domains which are common in active DUBs of the USP superfamily. Our in vivo and in vitro DUB activity assays revealed that USP32 was indeed an active deubiquitinating enzyme. To investigate its substrate specificity and kinetic properties, USP32 was expressed in insect cell culture to be isolated and purified. Using isolated USP32 protein, diubiquitin assay was performed with all seven types of diubiquitin (K6, K11, K27, K29, K33, K48 and K63) as well as linear diubiquitin. Results showed that USP32 was able to cleave all seven types of ubiquitin linkages with higher cleavage efficiency for K6, K11, K48 and K63-linked diubiquitin. Moreover, kinetic parameters, Km, kcat and kcat/ Km, suggested that full length protein had lower affinity for potential substrates and lower catalytic activity compared to the catalytic domain alone. These data suggested the importance of USP32 tertiary structure and possible role of other non DUB domains (e.g. EF hand domain) which may be regulated by an as of unknown mechanism in cells. Further investigations are underway to understand the functions of USP32 in cells and how it may contribute to breast tumorigenesis.

Synthetic CpG containing oligodeoxynucleotides (ODNs) are recognized by Toll like Receptor 9 (TLR9) and induce a strong pro-inflamatory immune response. To date, four different CpG ODN classes have been described. K-Class ODNs (also known as B-ODN) are potent B cell activators and stimulate TNF

Bacteria, nanoflagellates and ciliates constitute the microbial loop and it is a model of the pathways of carbon and nutrient cycling through microbial components of pelagic aquatic communities. The current study comprised of a comparative study of the microbial food web community along north to south latitudinal gradient using space for time susbtitute, monitoring and mesocosms experiments with contrasting nutrient and predation states. We investigated effect of fish predation through different zooplankton taxa on microbial loop community with in situ food web experiments in 14 lakes along north to south latitudinal gradient. The effect of seasonality was also determined by monitoring in Lakes Eymir and Mogan between 2010 and 2011. Effects of hydrology and fish through microbial community was studied in mesocosms in Lake Eymir. An implication of global warming along with eutrophication on microbial community was further explored in warmed and nutrient enriched artificial ponds during 4 months in Silkeborg, Denmark. Our results revealed that temperature, hydrology, fish, macrophytes and seasonality affected the top down control of zooplankton and bottom up control of nutrients on microbial loop and interactions between controls and increase in these controls had a strong negative impact on the contribution and biomass of microbial loop and change the interactions within microbial community. Global warming may also effect the impact of top down and bottom up controls through increasing eutrophication, temperature, change in hydrology and zooplankton composition and in a consequence of that efficiency of microbial loop may decrease in the future warmer, drier and eutrophic conditions.

In an earlier project completed in our laboratory a seasonal fluctuation in Phosphoglucomutase (PGM) phenotype frequencies was found, so that the winter bees were almost all heterozygotes and long lived than the summer bees among which homozygotes were significantly at high frequencies at Pgm locus. Same results were obtained in populations of three subspecies, A. m. meda, A. m. caucasica, and A. m. carnica from different climatic regions. In the current study environmental cues related with seasonal change in PGM phenotype frequency was examined along with the correlation between PGM heterozygosity and overwintering success. Cessation of food influx was found to be effective by itself as an environmental cue that causes a sudden and sharp increase in PGM heterozygosity. In addition to that, PGM heterozygosity of the colonies with greater overwintering success was found to be significantly higher than the ones with intermediate or low overwintering success. Benefiting from the previous studies and the results of current study, ethyl oleate was suggested as a chemical signal that functions in the regulation of PGM heterozygosity.

Cornea is the transparent outermost layer of the eye. It is a thin (500 &micro / m) multilayer tissue which performes around 75% of the total refraction in the eye. It also protects the inner layers against any type of damage. Since it is avascular, the three cellular layers of cornea always need transport of nutrients and other materials in and out of the tissue via diffusion. Any change in shape, transparency or thickness of cornea, or physical damages and infections, may cause serious defects. The conventional methods are satisfactory in the treatment of mild injuries but severe cases require the substitution of the tissue with an equivalent. Keratoprosthesis and donor corneas that are used as replacements do not completely meet requirements. Tissue engineering can be an alternative method for preparing a biocompatible and stable cornea equivalent. The ability to choose from a variety of materials and the ability to incorporate bioactive agents allow the researchers to tailor make the construct. The structure needs to be seeded with the patient&rsquo / s own cells and cultured in vitro to yield an optimal corneal replacement. In this study a novel, split thickness cornea replacement is proposed to substitute the two upper cellular layers (epithelium and stroma) of the native cornea. The design includes a chondroitin sulfate impregnated collagen type I (isolated from rat tail) foam (CSXLF) produced by lyophilization carrying electrospun fibers of the same polymer collected directly on top of the foam, forming the bilayer structure (Fo-Fi). The fiber layer was intended to separate the epithelium and the stroma of the reconstructed cornea yet to allow material transfer in between. The foam layer (bottom) was crosslinked by N-ethyl-N-[3-dimethylaminopropyl] carbodiimide (EDC), and N-hydroxy succinimide and after fiber deposition the bilayer was further stabilized with physical crosslinking (DHT method). The physical characterization of the foam showed that their pore sizes (10-200 &micro / m) and porosities (around 70%) were well within the desired range for typical tissue engineering applications. The cell free wet thicknesses of both single and bilayer constructs were close to that of the native stroma and light transmittance through these scaffolds was quite high (around 82% in the 500-700 nm range). The scaffolds were also tested for their stability and shown to be suitable for in vitro testing. In vitro studies were performed using retinal pigment epithelial cells (RPE, D407 cell line) and isolated human corneal keratocytes (HK) to reconstruct the epithelium and the stroma, respectively. Three types of constructs were prepared / only HK seeded Fo-Fi constructs, RPE-HK seeded CSXLFs, and RPE-HK seeded Fo-Fi constructs. All were shown to support cell attachment and promoted cell proliferation as was shown by the cells that covered the inner and outer spaces of the scaffolds. The fiber layer prevented the mixing of the two cell types, without hindering material exchange between them. Moreover, when co-cultured for 14 days, the keratocytes started to deposit collagen type I, a specific marker of these cells. In contrast, ECM deposition could not be observed in the single type cell seeded samples. The co-cultured bilayer construct was tested for suturability at the end of 31 days of in vitro incubation and it was shown that it could be successfully sutured without any major tears. Under the light of these results it was concluded that both the single layer and the bilayer constructs show promise for use as split thickness cornea replacements.

NMDA (N-methyl D-aspartate) Receptor is a ligand and voltage gated ion channel and involved in many processes such as synaptic plasticity, memory formation, behavioral responses and cell survival. In the sense of functional activity, cellular localization of NMDAR is important since this receptor shows its activity on the membrane. Although NMDA receptor is intensely studied there are no satisfying study showing its localization with microscobic methods. Besides, the effect of florescent protein labelling of NMDA receptor on its distribution is not shown. It is expected to provide basis for further interaction and distribution studies with this comparison. Contrary to literature, in this study it is shown that NMDA receptor does not localize only in ER and membrane instead has a cytosolic pattern and this pattern is compatible with the distribution of wild type NMDA receptor. In addition, florescent protein labelling of NMDA receptor does not interrupt cellular distribution of NMDAR. Moreover, this study shows that N-terminal domain of NR1 subunit is sufficient to prevent degradation of NR2B in the cell. In consideration of this study it can be concluded that EGFP and mCherry labelled NMDA receptors can be used in interaction studies such as FRET and other studies, making use of fluorescent labelling of NMDA receptors, in terms of cellular distribution.

Cornea is the most exterior, avascular and transparent layer of the eye and is about 500 &micro / m in thick. It protects the eye from external objects and it is the main optical element of the eye refracting 70 % of the incoming light. After cataract, corneal diseases and wounds are the second leading cause of the blindness that affects more than 4 million people worldwide. For the highly damaged corneas where the corrections with spectacles or contact lenses cannot be achieved, tissue replacement is the only choice, and is done by cornea transplantation or keratoprostheses. However, due to limited number of donor corneas and the risk of infections during transplantation, and development of glaucoma, necrosis and other complications caused by the keratoprostheses, prevent them from meeting expectations. Tissue engineering is a promising field which emerged from biomaterials science and aims to replace, restore or improve the function of the diseased or injured tissues. In this method, after the production of an ideal scaffold that mimics the natural human tissue, cells of the host are isolated, increased in number, and seeded on the scaffold developed to serve as the microenvironment of the cells. In the current study a 3D corneal stroma replacement was designed to mimic the native stroma. It consisted of 4 films of patterned collagen or collagen blended with Elastin Like Recombinamer (ELR) stacked on top of each other and then crosslinked by dehydrothermal (DHT) treatment. The characterization of the films showed that the pattern fidelity was good and they did not deteriorate after crosslinking. Enzymatic and in situ degradation studies showed that the DHT treatment at 150 oC for 24 h (DHT150) was the optimum condition. The transparency of all the films was quite high where uncrosslinked (UXL) films and DHT150 Col:ELR films yielded the best results. The individual films and 3D construct of 4 stacked films were seeded with isolated human corneal keratocytes (HK) and cultured for 21 days. Cells attached and proliferated well on the single Col and Col:ELR films. However, the proliferation was higher on Col multilayer constructs than their Col:ELR counterparts. Cells were aligned along the patterns of the films while no significant alignment was observed for the cells on unpatterned films. Ultimate tensile strength (UTS) and Young&rsquo / s Modulus (E) of Col and Col:ELR films were significantly lower after a 30 day culture than that of unseeded films of Day 1. Transparency of the seeded Col:ELR films was superior to Col films over a 30 days test and quite close to the transmittance of the native human cornea. It was concluded that the Col and Col:ELR patterned films and their 3D constructs have a significant potential for use as a corneal stroma equivalent.

In the current study, sub-fossil Cladocera collected from the surface sediment of 44 shallow lakes spanning over five latitudes from north to south of Turkey using snap-shot methodology revealed strong impact of salinity on cladoceran community structure. To see the whole picture, sediment cores collected from six of the lakes and long-term monitoring data from two of the lakes were also investigated. Contemporary cladocerans and sub-fossil assemblages were compared to reveal that their responses to salinity changes were highly similar. This lead us to use sub-fossil cladocerans and salinity data from water column together while generating the calibration data set using ordination techniques. Salinity transfer function models were developed utilising weighted averaging techniques. The developed salinity transfer function was applied to cladocera assemblages from dated sediment cores. Hindcasting of the salinity inference model was performed using monitoring data and the reconstructed salinities from two central Anatolian lakes and reflected good linear correlation with the known lake salinity history. This thesis has confirmed that sub-fossil Cladocera is a valuable indicator of historical salinity change and marker for the monitoring of lakes. For the first time, the lake environmental variables and sub-fossil cladoceran species composition from the surface sediments of Turkish shallow lakes were studied and a salinity transfer function was developed to elucidate past salinity change. The approach of the current study has been proven to be reliable while interpreting past salinity conditions. Since monitoring programmes are scarce in Turkey, paleolimnological analyses would be beneficial especially when defining effective restoration strategies.