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- PublicationOpen Access39 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.
- PublicationOpen AccessAluminum 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.
- PublicationOpen AccessAntioxidant enzyme profile in chronic pelvic pain syndrome patients(İstanbul Kültür Üniversitesi Yayınları, 2007-03) Arısan, Elif Damla; Arısan, Serdar; Kiremit, Murat Can; Palavan-Ünsal, Narçin; Ergenekon, ErbilChronic pelvic pain syndrome (CPPS) is a common and serious health problem affecting the quality of life in men. According to National Institute of Health classification system abacterial chronic pelvic pain has two sub category which are defined as 3a and 3b. The major difference between these two groups inflammation status. In this study we aim to investigate the antioxidant enzyme levels such as Glutathion peroxidase (Gsh-Px), superoxide dismutase (SOD), catalase (CAT) and lipid peroxidation products in CPPS patients. All enzyme levels were determined in patients and disease free control group blood samples by spectrophotometrically. In our study, the enzyme levels were not a good indicator for comparison of 3a or 3b type CPPS patients. However, Gsh-Px, SOD and lipid peroxidation products were significantly different from disease free control samples. Although high generation of H202 due to SOD activity, we did not detect any change in CAT activity in patients blood samples compare to control group.
- PublicationOpen AccessCharacteristics 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.
- PublicationOpen AccessCytological evidences of the role of Meta-topolin and Benzyladenin in barley root tips(İstanbul Kültür Üniversitesi, 2008) Huyluoğlu, Zekiye; Ünal, Meral; Palavan-Ünsal, NarçinThe responses of mitotic activity affecting root growth to benzyladenine (BA) and meta-topolin (mT) which is thought to be alternative of BA were studied with time and dose dependent experiments in Hordeum vulgare Tarm-92. The all concentrations of mT caused an induction on mitotic index. 10-5 mT was the most effective stimulator, increasing division frequency from 16 to 26 BA treatment exhibited variations; the low concentrations (10-5 M and 10-6 M) increased the mitotic index but the higher concentration (10-4 M) decreased. The values of mitotic index reflected to the elongation of roots, coordinately. BA and mT are both affected chromosomal behavior and caused abnormalities such as unoriented metaphase, chromosome bridges, 2 nucleate cells, micronuclei formation.
- PublicationOpen AccessDetermination of HER2/NEU gene amplification and protein overexpression ib bladder transitional cell carcinoma(İstanbul Kültür Üniversitesi, 2007-09) Atış, Gökhan; Arısan, Serdar; Ayhan, DalkılınçHER2/neu 185 kDa is a transmembrane receptor tyrosine kinase being a part of epidermal growth factor receptor family. Especially overexpression was shown in breast cancer and treatment procedures targeting this protein are in clinical use. The aim of this study is to show the overexpression of HER2/neu in bladder TCC patients by using immunohistochemical methods. 46 TCC and 15 healthy bladder tissues as a control group were used in the study. Deparafinized tumor specimens were marked by using monoclonal antihuman HER2 protein antibody and the protein was shown by using peroxidase secondary antibody. Non-staining or membrane staining less than 10% were classified as 0, while membrane staining partly more than 10% were 1, poor complete membrane staining or moderate staining more than 10% were 2 and complete membrane strongly staining were classified as 3. Classification 2 and 3 were evaluated as over staining of HER2/neu. Overexpression of HER2/Neu protein were shown in 12/46 (24.5%) of TCC specimens. Overexpression of HER2/neu were detected in 2 (12.5%) of Grade 1, 1 (16.6%) of Grade 2 and 12 (50%) of Grade 3 patients. Overexpression of HER2/Neu protein were positive in 5 (17.8%) of 28 superficial (Ta-T1) tumor specimens and 7 (38.8%) of 18 invasive (T2-T3) tumor specimens. Overexpression of HER2/neu in Grade III tumors were statistically significant when compared with Grade I and Grade II (p=0.012). Overexpression of HER2/neu detected in bladder TCC will be used in clinical setting as a treatment option targeting this protein as in the breast cancer in the future.
- PublicationOpen AccessDetermination of IL-10 levels in chronic pelvic pain syndrome patients(İstanbul Kültür Üniversitesi, 2008) Arısan, Serdar; Kiremit, Murat Can; Ergenekon, Erbil; Çaşkurlu, TurhanChronic pelvic pain syndrome (CPPS) is very common pathology that is characterized by pain in the perineum, pelvis, supra pubic area, or the external genitalia, with variable degrees of voiding or ejaculatory disturbance. The etiology of disorder is controversial with groups postulating infections, autoimmune, inflammatory and neuromascular mechanism. CPPS is the most commonurologic diagnosisin men younger than 50 years and the third most common urologic diagnosis in men older than 50 years after benign prostate hyperplasia and prostate cancer. Although high incidence rate, the etiology and pathophysiology of the disease are still poor.
- PublicationOpen AccessEffective Treatment in Amyotrophic Lateral Sclerosis? Invest in Each Player(İstanbul Kültür Üniversitesi, 2007-09) Chandawrkar, Akash; Özdinler, P. HandeALS (Amyotrophic lateral sclerosis) is a complex neurodegenerative disorder that affects corticospinal motor neurons in the cortex, corticobrainstem neurons and the spinal motor neurons in the spinal cord. ALS can develop both due to genetic or sporatic causes. The genetic causes of the disease are largerly unknown, but the cellular interactions between motor neurons and their environment are beginning to elicudate insights into the cellular pathogenesis of the disease. Even though cognition, memory and other brain functions are left intact in patient, the severed motor neuron circuitry leaves them paralyzed. To develop therapeutic approaches in ALS, there is a growing need to understand each and every component of the motor neuron circuitry, and their interaction in detail. In this rewiew, we will introduce cellular components of the complex neurocircuitry and discuss their possible contribution for therapeutic approaches in ALS.
- PublicationOpen AccessFatty 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.
- PublicationOpen AccessFree radicals: Our enemies or friends ?(İstanbul Kültür Üniversitesi, 2007-09) Pala, Funda Sibel; Tabakçıoğlu, KıymetFree radicals are atoms or groups of atoms containing at least one unpaired electron in their orbitals and can be formed when oxygen interacts with certain molecules. Once formed these highly reactive radicals can start a chain reaction, like dominoes. Their main danger comes from the damage they can do when they react with important cellular components such as DNA, or the cell membrane. Cells may function poorly or die if this occurs. On the other hand they are playing an important role in natural processes involved in cytotoxicity, defense against microorganisms and neurotransmission etc. There are several enzyme systems within the body that neutralize free radicals. The defense system that prevents the body from free radicals’ damage is called as antioxidants. Antioxidants are molecules which can safely interact with free radicals and terminate the chain reaction before vital molecules are damaged. Nowadays most people are under the impression that the field of investigation into antioxidants and free radicals is a brand new phenomenon. The aim of this review is to clarify what is the role of free radicals in our metabolism.
- PublicationOpen AccessGenetic differentiation of Turkish Althaea L. and Alcea L. species(İstanbul Kültür Üniversitesi, 2009) Öztürk, Fatma; Babaoğlu, Selcen; Uzunhisarcıklı, M. Erkan; Açık, Leyla; Vural, Mecit; Gürcan, I. SefaRandom amplified polymorphic DNA (RAPD) analysis and SDS-PAGE analysis of total seed proteins were used to estimate genetic differences between/within four Althaea (Malvaceae) and eighteen Alcea species. The 4 Althaea and 18 Alcea species were found to have species-specific protein profiles. The total of 223 different RAPD bands for Althaea species were generated by the 11 primers and total of 116 different RAPD bands by the 8 random primers for Alcea species. The results of the POPGENE cluster analysis were in broad agreement with previous morphological classifications of these four species. Statistical significance within Alcea and Althaea population was tested using of molecular variance (AMOVA) approach used in Arlequin. According to the results, there is a large genetic differentiation between species A. hirsuta with A. armeniaca, A. officinalis with A. hirsuta, FST 0.24 and FST 0.21, respectively. There is also wide differentiation between Alcea species. FST statistics range from 0,126 (A. guestii between A. striata ssp. striata) to 0,685 (A. biennis between A. acaulis). The results suggest that RAPD and SDS-PAGE markers can be used to reveal genetic differentiation between species and genus.
- PublicationOpen AccessHeat stress and wounding response in expression and RNAi impact on Arabidopsis thaliana soluble pyrophosphatase isoforms(İstanbul Kültür Üniversitesi, 2009) Ergen, Z. Neslihan; greiner, Steffen; Rausch, ThomasMature plants are assumed to lack cytoplasmic soluble pyrophosphatase activity and vacuolar membrane-bound proton-pumping pyrophosphatase is generally accepted as the sole enzyme responsible for the removal of pyrophosphate accumulated in the cytosol as a by-product of several biosynthetic pathways. On the contrary, Arabidopsis thaliana genome encodes six soluble pyrophosphatase isoforms, which were shown to be highly conserved both in nucleic and in amino acid sequences. There is only one isoform that is shown to be localized in plastids and there is no data available on the localization and/or possible expressional regulation of other isoforms. The analyses of the change in transcription of all A. thaliana soluble pyrophosphatases showed isoform-specific regulation, indicating the role of these isoforms during stress response. Furthermore, we have selected two isoforms through Digital Northern analysis derived from UniGene database and specifically knockdown these isoforms by RNAi approach. The results indicated that A. thaliana soluble pyrophosphatases have specific function in vivo and the loss of function of one or more isoforms can not be compensated by the function of others. Data obtained from this study indicates the possible critical role of soluble pyrophosphatases during plant development and stress response.
- PublicationOpen AccessHuman growth hormone(İstanbul Kültür Üniversitesi, 2009) Çoker, Ajda; Arman, AhmetGrowth hormone (GH), is expressed from anterior pituitary gland as a 191 amino acid long polypeptide hormone, has essential role on postnatal growth. In addition to longitudinal growth, GH has various effects on carbohydrate, lipid, protein and mineral metabolisms. GH is expressed from GH-N gene which is located within the GH gene cluster consisting three chorionic somatomammotropin (CS) and GH-V genes on chromosome 17q22-24. Secretion of GH is under control of hypothalamic hormones; somatostatin (SRIF) and growth hormone releasing hormone (GHRH). GH shows it’s biological activities by binding to growth hormone receptor (GHR). After dimerization of GHR, JAK2 is associated with GHR and activated, and JAK2 phosphorylates itself, GHR, signal transducer and activator of transcription (STAT) and intracellular proteins. Activated STAT dimers enter into nucleus, bind to promoter of the target genes such as Spi and activate transcription. Also, RAS/MAPK and PKC signal transduction pathways are known to take role in GH signaling. GH signaling is negatively controlled by SHP via the reduction of intracellular Ca++ levels and also suppressors of cytokine signaling (SOC) with dephosphorilation of JAK2.
- PublicationOpen AccessIdentification 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.
- PublicationOpen AccessIn vitro antisense activity of chitosan/AsODN complexes(İstanbul Kültür Üniversitesi, 2009) Enneli, Burcu; Özabaş Turan, S.; Uslu, B.; Akbuğa, J.In this study, the complex forms of AsODNs (phosphodiester and phosphorothioate forms) were prepared by using a cationic polymer called chitosan. The effect of chitosan mol wts and chitosan/AsODN ratio on the complex properties was studied. Afterwards, the physicochemical properties such as zeta-potential and particle size of complexes were measured and the in vitro antisense activities of the appropriate formulations were investigated. Full complexation was observed with phosphorothioate AsODN at the ratio of 10:1 (+/-), however phosphodiester AsODN could not be formed full complex with chitosan. The antisense activity of 100:1 (chitosan/AsODN) complexes which have approximately 200 nm particle size, was measured based on the inhibition of β-galactosidase by the antisense containing formulations into the b-Gal transfected HeLa cell lines. Eventually, both of these complex forms protected AsODNs from potential enzymatic degradations. In 100:1 (+/-) complex formulations, high antisense activity (88- 90%) was observed. As a result, chitosan can be considered as a suitable carrier especially for phosphorothioate modified AsODNs. Molecular weight of chitosan and chitosan/AsODN mass ratio had no importance in in vitro inhibition. This study can form the basis for the forthcoming studies related with carrier systems of AsODNs that will be done with chitosan polymer
- PublicationOpen AccessPhysiological taxonomy of willow species - dormancy, rooting of cuttings, reaction on auxins(İstanbul Kültür Üniversitesi, 2007-09) Kefeli, Valentine; Lininger, Chris; Shultz, RattyCuttings of six willow species were rooted in water (control) and after auxin (indole-3-acetic acid 150 mg/l) treatment. The intensity of the dormancy was determined by the following data: Root formation, shoot development, and reaction on auxin. Silky, weeping, and pussy willows do not have deep dormancy and were sensitive to auxin. The cuttings of purple, autumn and white willows were less active in the rooting process and less sensitive to auxin. These species do not open their buds in favorite laboratory conditions. These physiological characteristics – rooting, bud opening, and reaction to auxin could be used as taxonomic features for willow identification. The rooting of poplar was connected with the position of cutting on the mother plant. The highest intensity of rooting was specific for the basal part of the twig of poplar (Populus nigra).
- PublicationOpen AccessRas oncogenes polymorphism in Turkish thyroid cancer patients(İstanbul Kültür Üniversitesi, 2008) Öztürk, Fatma; Daloğlu, Cihan; Açık, Leyla; Kılıç, Mehmet; Koç, MahmutMolecula r mutations to proto - oncogene sequences may be involved in the pathogenesis of human thyroid neoplasm. Problems on oncogenes and tumor supressor genes activation in cell circle could cause tumor. Many oncogenes and tumor suppressing genes exist in varying percentages in various types of thyroid cancers. Ras, Gsp, Ret or Trk oncogenes can be involve in thyroid tumors . Members of t h e Ras gene family (H-ras, K-ras, and N-ras) are signal transferring proteins. These genes codes for 21 kDa GTP binding proteins. We studied 24 thyroid cancer and 77 control for ras gene point mutations in two different codons (12 and 13) using a restriction fragment length polymorphism technique. According to enzyme digesting, no c-K-ras gene codon 12/13 and N-ras gene codon 12 point mutation were observed in any of the samples we studied .
- PublicationOpen AccessResveratrol: Chemoprevention with red wine(İstanbul Kültür Üniversitesi, 2007-03) Arısan, Elif Damla; Palavan-Ünsal, NarçinAccording to epidemiological studies, western diet has disadvantages because of cancer prevalence more than Mediterranean or Asia people who consume more vegetables and fruits. Resveratrol (trans-3,4,5-trihydroxystilbene) which is highly found in grapes, berries has received attention for its potential chemopreventive and antitumor effects in experimental systems. Because of high resveratrol content, researchers noted that red wine has multidimensional benefits for cardiovascular health. Resveratrol also protects neuron cells from other well known chemotherapeutics. The molecular function of resveratrol in chemoprevention and carcinogenesis are reviewed by experimental cancer cell models. Resveratrol is going to be a promising molecule in future cancer prevention and therapy models.
- PublicationOpen AccessSome molecular studies related to leaf rolling in Ctenanthe Setosa(İstanbul Kültür Üniversitesi, 2008) Terzi, Rabiye; Sağlam, AykutThe changes in total RNA content under drought stress condition that eventually causes leaf rolling was investigated in Ctenanthe setosa, a member of Marantaceae family in Zingiberales. Degree of leaf rolling (%) and total RNA content were measured under drought stress condition. It was determined that total RNA content decreased while degree of leaf rolling was increasing. In addition, partial sequence of small subunit ribosomal DNA (18S rDNA) of Ctenanthe setosa was determined to use as a control marker in polymerase chain reactions (PCR) during molecular studies. When compared with presumably functional sequences, 18S rDNA partial sequence of Ctenanthe setosa shows greater complete sequence similarity of 18S small subunits of Marantochloa atropurpurea, Maranta bicolor and Calathea loeseneri which are the members of same family. Obtained sequence also resembled Strelitzia nicolai and Phenakospermum guyannense belonging another family, Strelitziaceae from Zingiberales order. In addition, it seemed like to Ravenala madagascariensis, Musa acuminate, Heliconia indica, Orchidantha fimbriata and Orchidantha siamensis from same order. These results have been pointed out that obtained 18S rDNA partial sequence is true for Ctenanthe setosa.
- PublicationOpen AccessSpatial arrangement of the animal male germ cell genome: I. Non-random pattern of radiation-induced inversions involving the vestigial region in autosome 2 of Drosophila melanogaster(İstanbul Kültür Üniversitesi, 2007-03) Alexandrov, Igor; Alexandrova, Margarita V.; Korablinova, Svetlana V.; Korovina, Larisa N.At present, given a bulk of models for higher-order chromatin structure in interphase nuclei of animal somatic cells, little is known about the spatial chromosome organization in animal male germ cells mainly due to the lack suitable methods for detailed observation and analysis without disruption of the existing organization. We pioneered in the study of this issue via analysis of radiation-induced inversion patterns in Drosophila male germ cell genome taking into account the fact that the formation of inversion requires the spatial proximity and contact of its ends. Analysis of 72 γ- ray- or neutron-induced vg inversions in which the first break is invariantly associated with the vestigial (vg) gene in the middle of 2R autosome shows the second inversion breakpoints that highly non-randomly distributed over the entire second chromosome clustering at the three autosome 2 “hot” chromosome areas. These findings show that the polar Rabl-configuration of interphase chromosomes in various somatic cells is not typical for the haploid genome of Drosophila mature sperms. The specific megarosetteloopstructure of haploid chromosome in the mature animal sperms is proposed and justified.