Molecular Biology and Genetics / Moleküler Biyoloji ve Genetik
Permanent URI for this collectionhttps://hdl.handle.net/11147/9
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Article Citation - WoS: 38Citation - Scopus: 47Docetaxel/Zoledronic Acid Combination Triggers Apoptosis Synergistically Through Downregulating Antiapoptotic Bcl-2 Protein Level in Hormone-Refractory Prostate Cancer Cells(John Wiley and Sons Inc., 2009) Karabulut, B.; Erten, C.; Gül, M. K.; Cengiz, E.; Karaca, B.; Küçükzeybek, Y.; Görümlü, G.; Atmaca, H.; Uzunoğlu, S.; Şanlı, U. A.; Baran, Yusuf; Uslu, R.Docetaxel, a semi-synthetic taxane analogue, is used effectively in the treatment of metastatic prostate cancer. Zoledronic acid, the most potent member of bisphosphonates, has shown pleiotropic anti-tumoral effects on prostate cancer cells. We have explored the possible additive/synergistic effects and the apoptotic pathways induced by combination treatment of docetaxel and zoledronic acid in hormone and drug refractory, PC-3 and DU-145 prostate cancer cells. Combination of docetaxel and zoledronic acid synergistically inhibits cell growth in PC-3 and DU-145 cells. Moreover, this effect was due to downregulation of antiapoptotic protein Bcl-2 in PC-3 and DU-145 cells. In conclusion, docetaxel/zoledronic acid combination is potentially a novel and effective approach for the treatment of prostate cancer.Article Citation - WoS: 23Citation - Scopus: 29Physical Properties of Biopolymers Containing Natamycin and Rosemary Extract(John Wiley and Sons Inc., 2009) Türe, Hasan; Özen, Fatma Banu; Eroğlu, Erdal; Soyer, Ferda; Özen, Banu; Soyer, FerdaAntifungal biopolymers were prepared by incorporating natamycin (NA) and NA + rosemary extract (RE) into wheat gluten (WG) and methyl cellulose (MC) films. Interaction between antimicrobial agents and biopolymers was determined with mid-infrared spectroscopy and scanning electron microscopy (SEM). Water vapour permeability and mechanical properties of these films were also measured. Mid-infrared spectroscopy did not indicate any interaction. SEM observations showed that NA crystallises at high concentrations in biopolymers. There were no significant changes in water vapour permeabilities of biopolymers containing active agents at P < 0.05. While NA incorporation did not result in any changes in mechanical properties of WG films a reduction in tensile strength was observed for MC films containing high concentration of NA. In general, active agent incorporation into WG and MC films did not result in any considerable changes in their physical properties that could affect their application.Article Citation - WoS: 29Citation - Scopus: 29Methionine Sulfoxide Reduction and the Aging Process(John Wiley and Sons Inc., 2007) Koç, Ahmet; Gladyshev, Vadim N.Aging has been described for multicellular and asymmetrically dividing organisms, but the mechanisms are poorly understood. Oxidation of proteins is considered to be one of the major factors that leads to aging. Oxidative damage to proteins results in the oxidation of certain amino acid residues, among which oxidation of sulfur-containing amino acids, methionine and cysteine, is notable because of the susceptibility of these residues to damage, and occurrence of repair mechanisms. Methionine sulfoxide reductases, MsrA and MsrB, are thioredoxin-dependent oxidoreductases that reduce oxidized forms of methionine, methionine sulfoxides, in a stereospecific manner. These enzymes are present in all cell types and have shown to be regulating life spans in mammals, insects, and yeast. Here, their roles in modulating yeast life span are discussed.Article Citation - WoS: 59Citation - Scopus: 60Effects of Deleting Mitochondrial Antioxidant Genes on Life Span(John Wiley and Sons Inc., 2007) Ünlü, Ercan Selçuk; Koç, AhmetReactive oxygen species (ROS) damage biomolecules, accelerate aging, and shorten life span, whereas antioxidant enzymes mitigate these effects. Because mitochondria are a primary site of ROS generation and also a primary target of ROS attack, they have become a major focus area of aging studies. Here, we employed yeast genetics to identify mitochondrial antioxidant genes that are important for replicative life span. In our studies, it was found that among the known mitochondrial antioxidant genes (TTR1, CCD1, SOD1, GLO4, TRR2, TRX3, CCS1, SOD2, GRX5, PRX1), deletion of only three genes, SOD1 (Cu, Zn superoxide dismutase), SOD2 (Manganese-containing superoxide dismutase), and CCS1 (Copper chaperone), shortened the life span enormously. The life span decreased 40% for Δsod1 mutant, 72% for Δsod2 mutant, and 50% for Δccs1 mutant. Deletion of the other genes had little or no effect on life span.Article Citation - WoS: 46Citation - Scopus: 52Antifungal Activity of Biopolymers Containing Natamycin and Rosemary Extract Against Aspergillus Niger and Penicillium Roquefortii(John Wiley and Sons Inc., 2008) Türe, Hasan; Eroğlu, Erdal; Soyer, Ferda; Özen, Fatma BanuAntimicrobial agent-releasing films have been proposed as an effective way of inhibiting chiefly surface spoilage of food products. Antifungal activities of natamycin (NA), rosemary extract (RE) and NA + RE were tested against Aspergillus niger and Penicillium roquefortii with agar disc diffusion assay. NA, RE and NA + RE were also included into biopolymers made from gluten and methyl cellulose. Minimum inhibitory concentrations (MIC) of NA in both films were 2 and 1 mg NA per 10 g film solution against A. niger and P. roquefortii, respectively. RE did not show any inhibitory antifungal activity alone. Although NA incorporated into both films at a concentration of 1.5 mg NA per 10 g film solution was not effective against A. niger, combination of NA at the same concentration with RE in the films inhibited the growth of this mould. NA in solution or in biopolymers is very effective in inhibiting the growth of selected organisms, and RE acted synergistically with NA to prevent the growth of A. niger when incorporated into both films. © 2008 Institute of Food Science and TechnologyArticle Citation - WoS: 19Citation - Scopus: 19Biofilm Formation by Staphylococcus Epidermidis on Nitrogen Ion Implanted Cocrmo Alloy Material(John Wiley and Sons Inc., 2007) Öztürk, Orhan; Sudağıdan, Mert; Türkan, UğurStaphylococcus epidermidis is the primary cause of medical device-related infections due to its adhesion and biofilm forming abilities on biomaterial surfaces. For this reason development of new materials and surfaces to prevent bacterial adhesion is inevitable. In this study, the adhesion of biofilm forming S. epidermidis strain YT-169a on nitrogen (N) ion implanted as well as on as-polished CoCrMo alloy materials were investigated. A medical grade CoCrMo alloy was ion implanted with 60 keV N ions to a high dose of 1.9 × 10 18 ions/cm2 at substrate temperatures of 200 and 400°C. The near-surface implanted layer crystal structures, implanted layer thicknesses, and roughnesses were characterized by XRD, SEM and AFM. The number of adherent bacteria on the surfaces of N implanted specimens was found to be 191 × 106 CFU/cm2 for the 200°C and 70 × 106 CFU/cm2 for the 400°C specimens compared to the as-polished specimen (3 × 106 CFU/cm2). The adhesion test results showed that S. epidermidis strain YT-169a adhere much more efficiently to the N implanted surfaces than to the as-polished CoCrMo alloy surface. This was attributed mainly to the rougher surfaces associated with the N implanted specimens in comparison with the relatively smooth surface of the as-polished specimen.Letter Citation - WoS: 2Citation - Scopus: 3Rates of Myocardial Infarction and Coronary Artery Disease and Risk Factors in Patients Treated With Radiation Therapy for Early-Stage Breast Cancer(John Wiley and Sons Inc., 2007) Ural, Ali Uğur; Avcu, Ferit; Baran, YusufWe read the interesting article by Jagsi et al on the increased rates of coronary artery disease in patients treated with radiation therapy for early-stage breast cancer.1 In their study, those authors concluded that the findings support further assessment of clinical outcomes when newer techniques of chemotherapy planning are employed as well as investigation of the potential role of innovative techniques. However, there was no mention of the novel radiosensitizing and chemosensitizing effects of bisphosphonates (BPs), which inhibit tumor cell adhesion to bone, and tumor growth in breast cancer.Article Citation - WoS: 7Citation - Scopus: 8Identification of Extracellular Enzyme Producing Alkalophilic Bacilli From Izmir Province by 16s-Its Rdna Rflp(John Wiley and Sons Inc., 2004) Akbalık, Güney; Güneş, Hatice; Yavuz, Elif; Yaşa, İhsan; Harsa, Hayriye Şebnem; Elmacı, Zehra Seda; Yenidünya, Ali FazılAims: To screen industrially important extracellular enzymes from the newly isolated alkalophilic bacilli and to characterize them by phenotypic and 16S-internal transcribed spacer (ITS) rDNA restriction pattern analysis. Methods and Results: Three different environmental samples, soil, leather and horse faeces, were collected within the province of Izmir. Isolates grown on Horikoshi-I medium for 24 h at 37°C were screened for extracellular enzyme activity by using eight different substrates: birchwood xylan, carboxymethylcellulose, casein, citrus pectin, polygalacturonic acid, soluble starch, and Tween 20 and 80. In total, 115 extracellular enzyme-producing bacilli were obtained. Casein was hydrolysed by 78%, soluble starch by 67%, citrus pectin by 63%, polygalacturonic acid by 62%, Tween 20 by 34%, birchwood xylan by 16%, Tween 80 by 12%, and carboxymethylcellulose by 3% of the isolates. The isolates were differentiated into 19 distinct homology groups by the 16S-ITS rDNA restriction pattern analysis. Conclusions: Eight different extracellular enzyme activities were determined in 115 endospore forming bacilli. The largest 16S-ITS rDNA homology group (HT1) included 36% of the isolates, 98% of which degraded casein, polygalacturonic acid, pectin and starch. Significance and Impact of the Study: This study is the first report on the characterization of the industrial enzyme-producing alkalophilic bacilli by 16S-ITS rDNA restriction fragment length polymorphism (RFLP). Restriction profiles of 64% of the isolates were found to be different from those of five reference strains used.Article Citation - WoS: 24Citation - Scopus: 25Identification of Extracellular Enzyme Producing Thermophilic Bacilli From Balcova (agamemnon) Geothermal Site by Its Rdna Rflp(John Wiley and Sons Inc., 2004) Yavuz, Elif; Güneş, Hatice; Harsa, Hayriye Şebnem; Yenidünya, Ali FazılAims: Molecular characterization of extracellular enzyme producing thermophilic bacilli from Balcova geothermal site. Methods and Results: Three types of geothermal samples were collected: mud, re-injection water, and samples from uncontrolled hydrothermal vents. Isolates grown at 55°C in culture media prepared in sterilized re-injection water, were screened for extracellular enzyme activity by using eight different substrates: casein, carboxymethyl-cellulose, pectin, polygalacturonic acid (PGA), soluble starch, Tween 20 and 80, and xylan. In total, 109 thermoaerophilic isolates were selected. All of the isolates could hydrolyse Tween 20 (100%) but not Tween 80. Soluble starch was hydrolysed by 96%, casein by 55%, xylan and carboxymethylcellulose by 9%, and pectin and PGA by 2% of the isolates. The isolates were grouped into 14 different homology groups by the restriction pattern analysis of 16S-internal transcribed spacer (ITS) rDNA RFLP. Each of the RFLP groups was also studied by 16S rRNA gene partial sequence analysis. Plasmid DNA profiles revealed that 15 of the isolated strains contained small plasmid DNA molecules ranging in size from 12 000 to 35 000 bp. Conclusions: Combined analysis of 16S-ITS rDNA RFLP and 16S rRNA gene partial sequence results indicated the presence of novel or existing species of Anoxybacillus (nine species) and Geobacillus (three species). Significance and Impact of the Study: In this study 16S-ITS rDNA RFLP was applied for the first time to differentiate thermophilic bacilli. It was also the first study on thermophilic bacilli of Balcova geothermal site.Article Citation - WoS: 1Citation - Scopus: 1Identification of Differentially Expressed Genes in Isogenic Highly Metastatic and Poorly Metastatic Cell Lines of R3230ac Rat Mammary Adenocarcinoma(John Wiley and Sons Inc., 2003) Güneş, Hatice; Carlsen, S. A.Tumour metastasis occurs as a result of a cascade of events including alterations in the expression of various genes. The identification of such genes is essential to understanding formation of metastasis. In a previous study, highly metastatic (LN4.D6) and poorly metastatic (CAb.D5) cell lines were obtained from the rat mammary adenocarcinoma cell line R3230AC. Subtractive hybridization was used to identify differentially expressed genes between these two cell lines. We identified eight cDNA clones in CAb.D5 and six cDNA clones in LN4.D6 that were differentially expressed. One of the cDNA clones in each cell line had no homology with known sequences. Expression patterns of these differentially expressed genes were examined in a pair of rat mammary and prostate adenocarcinoma cell lines. Compared with cell lines examined, cDNA FF-10 was only expressed in CAb.D5; however, cDNA RB-8, RE-1, RF-5 were only expressed in the highly metastatic LN4.D6. No correlation was observed between expression patterns of the differentially expressed genes and metastatic potential of these cells. However, differential expression of genes, especially cytokeratins (CK8 and CK5) and collagens (III and IV) between highly metastatic and low metastatic rat mammary adenocarcinoma cell lines might initiate further investigation of these genes in metastatic process.