ABSTRACT CORNEA ENGINEERING ON BIODEGRADABLE POLYESTERS Zorlutuna, Pinar M. Sc., Department of Biotechnology Supervisor: Prof. Vasif Hasirci Co-Supervisor: Asst. Prof. AySen Tezcaner January 2005, 66 pages Cornea is the outermost layer of the eye and has an important role in vision. Damage of cornea due to injuries or infections could lead to blindness lowering the quality of life of the patient severely. In such cases, transplantation or artificial corneas have been used for treatment but both had drawbacks. The novel approach for corneal replacements is the tissue engineering of the cornea, a promising method which would be free of these drawbacks, if successful. In this study, carriers for tissue engineering of the cornea were designed and tested in vitro. Blends of biodegradable and biocompatible polyesters of natural (PHBV8) and synthetic (PLLA) origin were used to construct these carriers. For the epithelial layer of the cornea, PLLA-PHBV8 micropatterned films were prepared with solvent casting and seeded with D407 (retinal pigment epithelial) cells. In order to achieve proper cell growth, the films were coated with fibronectin. For the stromal layer of the cornea, highly porous foams of PLLA-PHBV8 were prepared by lyophilization and seeded with 3T3 cells (fibroblasts). A new approach was developed to create a combination of the film and the foam to obtain a surface patterned, 3 dimensional cell carrier. These carriers were seeded with Saos-2 cells (osteosarcoma cells) in the preliminary optimization studies and with D407 and 3T3 cells in further studies. The cell numbers on the carriers were quantified by using MTS assay (non-radioactive cell proliferation assay) and the cell proliferation on polymeric carriers was significantly higher than that of control (Tissue culture polystyrene) by the day 14. Characterization of these cells and the carrier was done using a variety of microscopic methods. The micrographs showed that the foam had a highly porous structure and the pores were interconnected. 3T3 cells were found to be distributed quite homogeneously at the seeding site, but due to the high thickness of the foam, the cells could not sufficiently populate the core (central parts of the foam) during the given incubation time. The micropatterned film allowed multilayer formation of D407 cells. The functionality of the cells seeded on the carriers was examined by immunohistochemistry. These analyses proved that the cells retained their phenotype during culturing. D407 cells formed tight junctions characteristic of epithelial cells, and 3T3 cells deposited collagen type I into the foams. Based on the results, it can be concluded that the 3-D PLLA-PHBV8 construct with surface patterns have a serious potential for use as a tissue engineering carrier for the reconstruction of the cornea. Key words: Tissue engineering, cornea, polymeric carrier, biodegradable, polyester.

The objective of this study was to optimize an efficient selection system and Agrobacterium mediated transformation of chickpea (Cicer arietinum L.). Cotyledonary node explants of Turkish chickpea cultivar G&ouml / k&ccedil / e were used to determine the effects of selective agents, two antibiotics (Kanamycin, Hygromycin) and two herbicides (PPT, Glyphosate) as well as four antibiotics (Augmentin, Carbenicillin, Cefotaxime, Timentin) for eliminating Agrobacterium on multiple shoot and root induction. Selective agents and antibiotics were applied to explants at different concentrations for one month and numbers of regenerated shoots and roots were recorded. Kanamycin at 100 mg/L, Hygromycin at 20 mg/L, PPT at 3 mg/L and Glyphosate at 5 mg/L were found to be appropriate to select chickpea transformants. Lowest concentrations of all selective agents (50 mg/L Kanamycin, 10 mg/L Hygromycin, 3 mg/L PPT, 1 mg/L Glyphosate) totally inhibited rooting of the regenerated shoots. Among the Agrobacterium-eliminating antibiotics, Cefotaxime and Augmentin each up to 600 mg/L had no adverse effect on shoot induction, whereas Timentin (300 mg/L) significantly increased and Carbenicillin (300 mg/L) significantly decreased shoot induction after four weeks of culture. Augmentin was determined to have no effect on rooting capacities of chickpea shoots. However Cefotaxime at all concentrations significantly decreased root induction. On the other hand only high concentrations of Carbenicillin (300 mg/L) and Timentin (200 mg/L) significantly decreased rooting. Sulbactam in combination with Carbenicillin and Cefotaxime displayed effective inhibition of bacterial growth. Furthermore, Agrobacterium mediated transformation procedure for cotyledonary node explants of G&ouml / k&ccedil / e, was also optimized by monitoring transient uidA expression on 4th, 9th, and 16th days after transformation. Transformation procedure was improved via mechanical injury of axillary region of explants and application of vacuum infiltration at 200 mmHg for 40 minutes.

The objective of the present study was to examine the effects of prenatal exposure to alcohol on sensorimotor coordination, emotionality, learning and memory in young adult Wistar rats. Most of the recent reports concerning behavioral effects of fetal alcohol exposure refer to the juvenile period of life and very few studies investigated different aspects of behavior simultaneously in the same subjects. In the current study, alcohol was delivered to the pregnant dams by intragastric infusions, throughout gestation days (GD) 7-20, at the dose of 6g /kg maternal body weight /day. This dose resulted in relatively high peak blood alcohol concentration (340 mg/dl) as assessed on GD 20. A pair-fed isocaloric and untreated control groups were included. Prenatal alcohol administration retarded dams&rsquo / weight gain significantly, and had an adverse effect on pups&rsquo / weight at birth but not in adulthood. No between-group differences were observed in the litter size and in the pups&rsquo / mortality. The adult brain weight was neither affected. Pups were subjected to a series of behavioural tests as young adults (at 2.5 months of age). In adulthood, rats prenatally treated with alcohol were not impaired in sensorimotor coordination and/or did not show muscle weakness as assessed by rotarod/accelerod tests. Their behavior in the open field and plus maze suggested alcohol-induced increase in iv anxiety level and some decrease in behavioral flexibility, but hyperactivity was not observed. In cognitive tasks, alcohol treated rats showed slightly slower rate of initial place learning in the water maze. However, memory retention tested after 1 and 10-day delay, reversal learning, rate of extinction of place preference, as well as working memory capacity appeared to be the same in alcohol exposed and control rats. The possible reasons of this negative result are discussed.

iv The objective of this study was to optimize tissue culture and regeneration parameters of immature inflorescence culture of Triticum aestivum cv. Bezostaja- 01 and Triticum durum cv. Kiziltan-91. The effects of callus age and vernalisation time of explants on regeneration success were evaluated. For determination of optimum vernalisation time of immature inflorescence, plants subjected to 4 &deg / C for 1, 2, 3, 4, and 5 weeks, respectively. Tillers containing immature inflorescences were collected at the same time. Percentage of inflorescence formed tillers over total explants were reached the highest value, 79 %, at 4 weeks cold treated Kiziltan cultivar and, 73 %, at 5 weeks cold treated Bezostaja cultivar. Isolated immature inflorescences were put onto 2mg /L 2,4-dichlorophenoxyacetic acid and picloram containing callus induction medium for Kiziltan and Bezostaja cultures, respectively. Callus induction rate were found to be 100 % for Kiziltan and Bezostaja. These explants were taken to regeneration after 6, 9, 12 and 15 weeks of dark incubation period. The regeneration capacities of calli were determined as shooting percentage and data were collected after 4, 8, 12, and 15 week regeneration period. The highest shooting percentage of 69 %, were obtained from 6 weeks old calli produced from 4 weeks vernalised explants in Kiziltan cultures at the end of 15 weeks regeneration period. However, shooting percentage was 57.2 % for 9 weeks old calli while it decreases to 37.6 % in 12 weeks old calli and 44.2 % in 15 weeks old calli at the end of 15 weeks regeneration period. This showed that prolonged dark incubation period decreased regeneration capacity of the callus. However, there was no significant difference in regeneration capacities of calli produced from Bezostaja immature inflorescence and the highest shooting percentage was obtained from 9 weeks old calli produced from 5 weeks vernalised explants, 27.4 %. Besides regeneration studies, optimization of transformation parameters for winter wheat cultivars Kiziltan and Bezostaja by using Agrobacterium tumefaciens AGLI containing binary vector pALl56 was performed. Transformation efficiencies were determined by monitoring the transient expression of uidA gene via histochemical GUS assay. Three to four weeks old calli were found to be more responsive to Agrobacterium-mediated transformation in Kiziltan cultures. However, four to five weeks old calli were found to be more responsive to Agrobacterium-mediated transformation in Bezostaja cultures. Different transformation protocols were used. It was found that MGL based and MMA based protocols could be used for Bezostaja and Kiziltan transformation, respectively. The highest GUS expression, 84%, was obtained from 28 weeks old calli produced from 5 weeks vernalised explants in Bezostaja cultures.

Chemical communication in aquatic organisms has been topic of a large number of studies focusing interactions between organisms via info chemicals. Diel Vertical Migration (DVM) is commonly observed among zooplankton and consists of a single daily ascent with minimum depth reached between sunset and sunrise and a descent with maximum depth attained during the day. DVM was absent or reduced when predators were absent and well developed in their presence. Species of the Daphnia are one of the well investigated group in freshwater environments. Variation in DVM of Daphnia in response to fish kairomone is one of the best studied behavioral strategies. Kairomone, as a term, is described interspecific chemical messengers, the adaptive benefit of which falls on the recipient rather than the emitter. As a result, nature and origin of kairomone is still unclear and needs to be investigated. It was decided that FT-IR technique would be favorable tool for this aim. In this frame, it was conceived that the occurrence of migration adaptation relevant to the seasonal changes in the presence of fish kairomone could be proved and characterized by FT-IR technique. Results of the present study indicate that non-aromatic, secondary amine compound has significant contribution to fish cue. Since other sources other than fish can contribute the natural amine compounds level in fresh water environment, origin and concentration of amines are needed further investigation to determine ecological function of amine.

Arylamine N-acetyltransferases (NATs) were partially purified from human breast tumor tissues with complete separation of the isoforms in DEAE-Cellulose ion-exchange step. NAT with activity towards p-aminobenzoic acid (PABA) was isolated and purified from human breast tumor with 77 % yield and a purification factor of 5-fold. NAT with activity towards sulfamethazine (SMZ) was isolated and purified from human breast tumor with 21 % yield and a purification factor of 3-fold. Further purification attempts by Blue Sepharose affinity column chromatography resulted in the complete loss of both enzyme activities. The NAT1 purified from human breast tumor tissues had a molecular weight (Mr) value of about 27600 and an isoelectric point (pI) around 4.8, as confirmed by SDS-PAGE, IEF and Western blotting analysis. With immunohistochemical analysis, level of intensity of NAT1 immunostaining was observed to be going from weak in reduction mammoplasty samples to strongest in malignant breast tissue. The interindividual variation in the conjugation of p-aminobenzoic acid (PABA) and of sulfamethazine (SMZ) by cytosolic arylamine N-acetyltransferases (NATs) were investigated in 30 human breast tumor and matched samples. The average specific activity against PABA was calculated as 13&amp / #61617 / 2 pmole/min/mg protein for breast control NATs, and 20&amp / #61617 / 3 pmole/min/mg protein for breast tumor NATs. The average specific activity against SMZ was calculated as 12&amp / #61617 / 2 pmole/min/mg protein for breast control NATs, and 34&amp / #61617 / 6 pmole/min/mg protein for breast tumor NATs. Wilcoxon test revealed that the difference between the control and tumor groups is statistically significant with respect to the NAT1 activities as well as NAT2 activities. In three (3/30, 10%) patients tumor and tumor-free breast tissue NAT1 activity was not detectable. Among control tissues, the percentage of measurable NAT2 activity was 77% (23/30), while in tumor tissues it increased to 91%. Chemotherapy treatment was observed to have a slight inhibitory effect on mean NAT1 and NAT2 activities. There was an indication of a possible negative association with mean NAT1 activity and estrogen receptor status, while mean tumor NAT2 activity was observed to increase among estrogen receptor positive patients. Grade of malignancy seems to be positively associated with NAT1, but no such association could be suggested for NAT2 enzyme. Menopausal state of the patient was suggested to have a significant effect on NAT2 activity. Genotype determination of NATs revealed that NAT1*4 and NAT2*5A allele being most common among 10 breast cancer patients. NAT1*11 allele was prevalent among postmenopausal women. The putative rapid NAT1 genotypes was found to display lower control and tumor mean NAT1 activities compared to normal NAT1 genotypes. Among slow NAT2 acetylators, mean tumor NAT2 activities was found to be significantly higher than respective controls.

The purpose of the study is to purify human growth hormone from the fermentation broth by affinity chromatography. For this purpose, human growth hormone specific oligonucleotide aptamers are selected among an aptamer library / selected oligonucleotides were synthesized and used as ligands. Effect of pH on ligand-human growth hormone complex formation was investigated and the highest complex formation was obtained at pH= 7.0. Human growth hormone is separated from the fermentation broth with 99.8% purity and 41% overall yield. The equilibrium data obtained was described by Langmuir type isotherm where saturation constant (q0) and affinity constant (K) are calculated as 0.338 mg hGH/&micro / mol aptamer and 0.059 mg hGH/ml, respectively. Further, equilibrium data obtained using aptamer affinity column was described by Langmuir type isotherm where saturation constant (q0) and affinity constant (K) are 0.027 mg hGH/&micro / mol aptamer and 1.543 mg hGH/ml, respectively. It is possible that, selected aptamer can be used for purification of bulk amounts of recombinant human growth hormone by using aptamer affinity chromatography.

ABSTRACT PURIFICATION AND CHARACTERIZATION OF CYTOPLASMIC AND PROTEASOME ASSOCIATED CHYMOTRYPSIN-LIKE PROTEASES FROM THERMOPLASMA VOLCANIUM &Ouml / zdemir, F.inci Ph.D., Department of Biology Supervisor: Prof. Dr. Semra Kocabiyik September, 147 pages In this study, two novel cytoplasmic serine proteases were isolated and characterized from thermophilic archaea Thermoplasma volcanium. The first protease was purified by ion exchange and affinity chromatographies and identified as a chymotrypsin-like serine protease mainly based on its substrate profile and inhibition pattern. The presence of protease activity was analyzed by gelatin zymography which was detected as a single band (35 kDa). Optimum temperature was found to be 60oC for azocasein hydrolysis and 50oC for N-Suc-Phe-pNA hydrolysis. Optimum activity was observed in the pH range of 6.0-8.0 with a maximum value at pH 7.0. The Km and Vmax values for the purified protease were calculated to be 2.2 mM and 40 &micro / moles of p-nitroanilide released min-1.ml-1, respectively, for N-Suc-Phe-PNA as substrate. Ca2+ and Mg2+ at 4 mM concentrations were the most effective divalent cations in activating the enzyme. In the second stage of this study, 20S proteasome of Tp. volcanium with substantial chymotrypsin-like activity was purified and characterized. This enzyme complex was purified with 19.1 U/mg specific activities from cell free extract by a four-step procedure. SDS-PAGE analysis revealed two strong bands with relative molecular masses of 26 kDa (&amp / #945 / -subunit) and 21.9 kDa (&amp / #946 / -subunit). Tp. volcanium 20S proteasome predominantly catalyzed cleavage of peptide bonds carboxyl to the acidic residue Glu (postglutamyl activity) and the hydrophobic residue Phe (chymotrypsin-like activity) in short chromogenic peptides. Low-level hydrolyzing activity was also detected carboxyl to basic residue Arg (trypsin-like activity). Chymotrypsin-like activity of Tp. volcanium 20S proteasome was significantly inhibited by chymotrypsin specific serine protease inhibitor chymostatin. When N-CBZ-Arg was used which is a substrate for trypsin, 20S proteasome was strongly inhibited by TLCK. The optimum temperature for Ala-Ala-Phe-pNA hydrolysis by the Tp. volcanium 20S proteasome was 55oC and the optimum pH was 7.5. The chymotryptic activity was significantly enhanced by divalent cations such as Ca+2 and Mg2+ at high concentrations, i.e. 125-250 mM. Keywords:Serine protease, 20S proteasome, archaea, thermophilic protease, Thermoplasma volcanium, chymotrypsin-like serine protease.

Some yeast strains secrete extracellular polypeptide toxins known to have potential growth inhibitory activity on other sensitive yeast genera but are immune to their own toxins. These yeast strains are termed as killer yeasts and their toxins are designated as killer proteins or killer toxins. Killer phenotypes are classified into 11 typical types (K1-K11). The toxic actions of yeast killer proteins on sensitive cells show differences and one of the most important toxic actions involves the selective functional damage by hydrolyzing major cell wall components. Because mammalian cells lack a cell wall, novel highly selective antifungals tend to be harmless to people by targeting important cell wall components specific to fungi. We have previously characterized the K9 type yeast killer protein isolated from Hansenula mrakii. This protein is stable at pH and temperature values appropriate for its medical usage. Antifungal activity of this protein was tested against 23 human pathogenic yeast and 9 dermathophyte strains. Pathogenic yeast strains found to be susceptible and both the MIC and MFC values ranged from 0.25 to 8 &micro / g/ml except C. parapsilosis and C guilliermondii isolates. 9 dermatophyte strains were not susceptible to this protein and MICs were &gt / 64 &micro / g/ml. According to the cell killing analysis toxin activity starts within the first 4 hours and complete cell death was observed for the 4, 8 and 16 times the MIC concentrations at 24 hour. The results obtained from this study might make the potential use of this protein possible as a selective antimycotic agent.

ABSTRACT Three different genotypes of sugar beet (diploid, triploid and tetraploid) / 4 varieties from diploid and triploid genotypes Soraya (KWS8123) and Leila (diploid), Visa (H68121) and Kassandra (triploid) and 2 lines from tetraploid genotype &Ccedil / BM315 and EA2075 (tetraploid) were used for investigating the effects of ploidy level on plant regeneration. Within three sugar beet genotypes, with respect to the treatments, triploids or tetraploids were found to respond to treatments significantly different when compared with diploids. The responses of polyploids were superior over the responses of diploids. Moreover, varieties from same genotype responded differently to treatments. Two types of calli were obtained / one white and friable with regenerative capacity and the other green and compact with no regenerative capacity. Concentration of sucrose on callus development was observed to be important. High concentration of sucrose (30 g/L) was found to cause discoloration and irresponsiveness of formed calli at callus enlargement and subsequent shoot regeneration stages. Therefore, low concentration (10 g/L) is advised to be used at these stages / although this caused less callus induction. Although initially used for the prevention of tissue discoloration, L-ascorbic acid inclusion into the medium was found to be positively affecting the regeneration capacity. When used at 20 mg/100 mL concentration, the only two spontaneous shoots from the tetraploid EA2075 line were obtained. Subsequently, these shoots were successfully rooted and whole plants were obtained. The effect of silver nitrate, in combination with L-ascorbic acid, on the prevention of sugar beet tissue discoloration was investigated. Unfortunately, the symptoms of discoloration did not diminish. Moreover, callus formation was reduced and the subsequent shoot recovery could not be achieved. Since a total of 3456 explants were used during this study, and only 2 whole plants were regenerated, the efficiency of plant recovery was calculated as a rather low value of 0.058 %.