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Publication Open Access To chemotaxonomy of willow species(İstanbul Kültür Üniversitesi, 2007-09) Kefeli, Valentine; Lininger, Chris; Shultz, RattyWillows could be good objects for water cleaning and landscape rehabilitation. Their reaction on auxin and phenolic quality could be used as chemo-taxonomic factors. In comparison with morphological properties they could be applied for willow species identification. The quality of phenolics may help to identify different plant species.Publication Open Access 39 spatial arrangement of the animal male germ cell genome: II. 2d-3d Simulation and visualization of spatial configuration of major chromosome 2 in Drosophila sperm(İstanbul Kültür Üniversitesi, 2007-09) Alexandrov, Igor D.; Stepanenko, Victor A.; Alexandrova, Margarita V.Data on the non-random distribution of radiationinduced inversion breakpoints were used as genetic markers for 2D and 3D modeling of the largescale architecture of the chromosome 2 in Drosophila sperm genome at the time of irradiation. During modeling, Gmax program with application of splines, the additional objects and operations as well as the methods of visualization of macromolecular biostructures were employed. A specific megarosette-loop model of spatial arrangement of chromatin fiber in the haploid sperm nucleus can account well for the experimental data.Publication Open Access The role of free radicals in ethiopathogenesis of diseases(İstanbul Kültür Üniversitesi, 2008) Gürkan, HakanFree radicals can be defined as atoms or molecules containing one or more unpaired electrons in their orbitals. Their formation occurs continuously in the cells as a consequence of both enzymatic and nonenzymatic reactions. It has been estimated that the average person has around 10000–20000 free radicals attacking each body cell each day. Some free radicals are good in that they enable your body to fight inflammation, kill bacteria, and control the tone of smooth muscles, which regulate the working of internal organs and blood vessels. On the other hand increased or uncontrolled free radical activity might combine with other factors to cause some diseases such as neurodegenerative diseases, heart disease, cancers etc. The balance between the production of free radicals and the antioxidant defences in the body has important health implications. Under the normal conditions the antioxidant defense system within the body can easily handle free radicals that are produced. If there are too many free radicals produced and too few antioxidants, this may cause chronic damage. The aim of this study is review the data on diseases which may be linked to free radicals in order to clarify the role of them in ethiopathogenesis of these diseases.Publication Open Access Identification of clinic uropathogen Escherichia coli isolates by antibiotic susceptibility, plasmid and whole cell protein profiles(İstanbul Kültür Üniversitesi, 2007-03) Çelebi, Ayten; Duran, Nizam; Öztürk, Fatma; Açık, Leyla; Aslan, Gönül; Aslantaş, ÖzkanThe aim of this research was to evaluate the protein, plasmid and antibiotic resistance patterns among 118 uropathogen E. coli strains from infected urinary systems. Plasmids were detected 113 strains (97%). Some isolates harboured up to 10 plasmids, ranging from 1 to 19 kb in size. The total whole cell protein profiles of the strains were obtained using the sodium dodecyl sulfatepolyacrylamide gel electrophoresis (SDS-PAGE) method. The protein bands were stained with Coomassie-blue and analyzed by statistics package POPGEN. The 118 E. coli were also analyzed for their resistance to antimicrobial agents. The highest rates of resistance were against ampicillin (61 %) and amoxicillin-clavulanic acid (46.6 %). The most common antimicrobial resistance of these isolates was ampicillin, amoxicillin-clavulanic acid, trimethoprimsulfamethoxazole, gentamicin, ciprofloxacin, amikacin, cefoxitin, and ceftriaxone. Multiple resistance to all antibiotics except imipenem was observed in 5 isolates. Similarity matrix and dendrograms were generated by using UPGMA algorithm which made it possible to evaluate the similarity or intra-specific polymorphism degrees based on whole-cell protein fingerprinting, plasmid profiles and antibiotic resistance pattern. It was determined that the SDS-PAGE method may provide better criteria than plasmid and antimicrobial susceptibility for the taxonomic and epidemiological studies of E. coli isolates.Publication Open Access Spatial arrangement of the animal male germ cell genome: IV. Radiation-induced locus-specific translocations (2;3) and large-scale organization of Drosophila sperm nucleus(İstanbul Kültür Üniversitesi, 2009) Alexandrov, Igor D.; Stepanenko, Victor A.; Alexandrova, Margarita V.; Korablinova, Svetlana V.; Korovina, Larisa N.At the previous papers (Alexandrov et al., 2007b, 2008), the specific megarosette-loop organization (but not polar-linear Rabl-configuration) of major haploid autosome 2 in Drosophila sperm nucleus has been proposed and experimentally substantiated by analysis of radiation-induced locus-specific inversions showing highly nonrandomly distribution of the second inversion breakpoints over the entire autosome. We have speculated that spatial organization of the other major chromosomes in Drosophila sperm nucleus must be the same. To test this expectations, the nature and frequency of radiation-induced interchromosomal exchanges (reciprocal translocations) between autosomes 2 and 3 with the first breaks invariantly associated with the same genetic loci (black or vestigial) on the autosome 2 were studied and, at once, the distribution patterns of the second translocation breakpoints over the entire autosome 3 were detected. Analysis of 23 translocations scored has shown that both black and vestigial loci highly non-randomly interact with certain, including pericentromeric heterochromatin, “hot” areas of autosome 3. Surprisingly, positioning of these areas found to be co-linear with that of “hot” areas for inversion breakpoints on the autosome 2 if both euchromatic arms and pericentromeric heterochromatic regions of two major autosomes arrange in parallel to each other, showing thereby that spatial organization of both autosomes 2 and 3 goes on concurrently with space and time. Using these data, 2D and 3D models of spatial arrangement of autosome 3 in Drosophila haploid sperm nucleus were constructed the principle features of which found to be well consistent with the megarosette-loop configuration proposed for the second chromosome. Independent reciprocal translocations (2;3) scored in the genome of the eight radiation-induced “point” black or vestigial mutants turned out to have the breakpoints within the autosomes 2 and 3 areas proximity of which is predetermined by the megarosette-loop configuration of these major chromosomes. These results show that approaches of the classical radiation cytogenetics and genetics employed in our genomic investigations may be useful strategy to assist in the elucidation of the other conceptual point in the dynamics of sperm nucleus as a self-organizing system, namely, whether the chromatic protein remodeling (histon -to- protamine transition) in late spermatids is coupled with the structural reorganization of primary polar-linear Rabl’s state of chromosomes in the early post-meiotic spermatids into the compact megarosette-loop structures in the fully mature spermatozoa.Publication Open Access Aluminum toxicity and resistance in higher plants(İstanbul Kültür Üniversitesi, 2007-03) Vardar, Filiz; Ünal, MeralAluminum (Al) is the major element in the soil and exists as a stable complex with oxygen and silicate. When the soil pH is below 5, Al is solubilized in the soil water and absorbed by plant roots. Absorbed Al inhibits root elongation severely within hours. Al toxicity is a very important limitation to worldwide crop production, because 50% of the world’s potentially arable lands are acidic. Thus, many research has been conducted to understand the mechanism of Al toxicity and resistance which is important for stable food production in future. Al resistance can be achieved by mechanisms that facilitate Al exclusion from the root apex and/or by mechanisms that confer the ability of plants to tolerate Al in the plant symplasm. However, despite intense research efforts, there are many aspects of Al toxicity and resistance remain unclear. In this review, Al toxicity and resistance mechanisms are described with the physiological and molecular basis.Publication Open Access Spatial arrangement of the animal male germ cell genome: III. A new experimental evidences in support of the Megarosette-loop model of spatial organization of chromosomes in Drosophila sperm genome(İstanbul Kültür Üniversitesi, 2008) Alexandrov, Igor; Alexandrova, Margarita V.; Stepanenko, Victor A.; Korablinova, Svetlana V.; Korovina, Larisa N.; Stetsenko, Stanislav G.The data on the non-random pattern of induction of the black (b) inversions in autosome 2 after action of γ-rays of 60Co or 0.85 MeV fission neutrons on Drosophila mature spermatozoa were described and 2D model of spatial arrangement of this autosome in sperm nucleus at the time of irradiation based on these data was presented. The main features of this model found to be entirely consistent with the chromosome macroarchitecture proposed earlier on the basis of data for the vestigial (vg) inversions at the same autosome. A general 2D and 3D models for the specific megarosette-loop structure of autosome in question with both sets of the inversion data were constructed validity of which was independently confirmed by the induction patterns of inversions not associated with the locus-specific mutations under study. It is stated that there are all reasons to believe that all other chromosomes in sperm genome have the same spatial macroarchitecture as the most compact and suitable one to pass on the genetic information from one generation to another. It is particularly emphasized that large-scale chromosome geometry proposed is fundamentally unlike Rabl’s configuration of interphase chromosomes in animal somatic cells. The conversion of Rabl’s configuration to megarosetteloop structure is presumed to keep pace with protein remodeling of chromatin in late spermiogenesis.Publication Open Access Fatty acid and amino acid profiles in the fruits of Prunus spinosa L. subsp. dasyphylla (Schur) Domin from Europe-in- Turkey(İstanbul Kültür Üniversitesi, 2008) Özcan, Tamer; Bayçu, GülrizFatty acid and amino acid compositions were determined in the fruits of Prunus spinosa subsp. dasyphylla with GC and amino acid analyser. Total oil (0.22%) and total protein (1.35%) were quantified in lower levels. Major fatty acids were palmitic (34%), oleic (20.85%) and stearic acids (16.20%), respectively. Linoleic (6.07%), eicosatrioneic (3.17%), α-linolenic (1.95%), gamma-linolenic (1.76%), myristic (1.61%), arachidic (1.17%) and lauric acids (1.10%) exhibited the lower concentrations. The other fatty acids were examined below 1%. Total percentage of the saturated fatty acids were observed higher (56.56%) compare to the unsaturated fatty acids (35.68%). Total concentration of mono and polyunsaturated fatty acids were 22.73% and 12.95% respectively. Valuable ratio of linoleic: α-linolenic acid (3.103) were detected with respect to dietary reference for fatty acid intake. Amino acid concentrations ranged from 356.7 (aspartic acid) to 47.6 (threonin) (mg/100 g dry wt.). The highest values among essential amino acids were obtained in leucin (122.6), isoleucine (99.2), valine (87.8) and phenylalanin (84.7). Tyrosin (51.3) and lysine (50.6) were quantified at the lowest levels. All essential amino acids were observed in sufficient levels compared to FAO reference values for life stage groups. Investigated traits in the fruits of Prunus spinosa subsp. dasyphylla may be useful in explaining the natural product potential and taxonomical variations based on different populations.Publication Open Access Sustainability and Regeneration of Ecological Systems in Western Pennsylvania, USA: Research and Efforts(İstanbul Kültür Üniversitesi, 2007-03) Kefeli, V.; Leininger, C.Publication Open Access Characteristics of Fabricated Soil for Landscape Rehabilitation: The Four Crop Test for Biological Activity(İstanbul Kültür Üniversitesi, 2008) Kefeli, Valentine; Leininger, Christopher; Mastalski, Shari; Kimberly, PincinFabricated soil (FS) is a mixture of substrates containing balanced amounts of carbon, nitrogen, phosphorus, potassium and mineral elements that support plant growth . In our experiments, we use FS for the rehabilitatio n of land f r om mining soil pollutants. Characteristics of fabricated soil were determined including measurements of N, P, K; other nutritive elements including Mg, Ca, S, and Fe; and micro-elements and toxic elements including Mn, Zn, A l , Ni, and Pb. Also , microbial activity of the soil was tested to determine fungal and bacterial presence. After investigating these soil characteristics, we used a four - crop test to investigate fabricated soils and related substrates for biological activity. Soil health includes a balance of mineral and organic elements and healthy microbial activity. These characteristics play the key role in the soil ' s ability to support the growth of higher plants which complete the regenerative process of soil cycling. Healthy soils provide materials for food, energy, and shelter. Healthy soils are crucial to all biological, geological, and water cycles.