Molecular Biology and Genetics / Moleküler Biyoloji ve Genetik
Permanent URI for this collectionhttps://hdl.handle.net/11147/9
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Conference Object Citation - WoS: 1A Study of Multiple Drug Resistance Mechanisms Improved Against Bortezomib on Multiple Myeloma Cell Lines in Vitro(American Society of Hematology, 2007) Uyuklu, Tolga; Ural, A. Uğur; Sarper, Metal; Avcu, Ferit; Baran, Yusuf; Elçi, Pınar; Akar, NejatThe most important problem in the treatment of Multiple Myeloma (MM) is the multi drug resistance (MDR) observed before and after the treatment. For this reason in MM cases an early resistance to treatment can be developed or the disease can relapsed in early period. Yet, there has been no improved drug resistance against proteazom inhibitor Bortezomib (Bor), which is used alone or with other chemotherapeutic agents in resistant or relapsed MM casesOther Erratum: Protective Effect of Zinc on Cyclophosphamide-Induced Hematoxicity and Urotoxicity: (biol Trace Elem Res (2008) 126 (186-193) Doi 10.1007/S12011-008-8189-5)(Humana Press, 2009) Ayhancı, Adnan; Uyar, Ruhi; Aral, Erinç; Kabadere, Selda; Appak, SılaThe original version of this article unfortunately contained a mistake. The Materials and Methods section should include last paragraph. Section “Materials and Methods”, inclusion of the last paragraph should read: Only the groups which had CY treatment alone were killed 3 days after the CY injection. For the groups having Cy+ZnCl2 , ZnCl2 administration was started three days earlier than the CY administration and continued till the end of the experiment (6 days). On the fourth day the animals were weighed again, relative doses of CY were estimated and CY+ZnCl2 was administered together. On the seventh day blood samples were collected, bone marrow and the urinary bladders of the animals were resected under anesthesia. Also, the first three affiliations were incorrect. The correct information is given below.Article Citation - WoS: 86Citation - Scopus: 102Total Antioxidant Activity and Total Phenolic Contents in Different Turkish Eggplant (solanum Melongena L.) Cultivars(Taylor and Francis Ltd., 2009) Ökmen, Bilal; Şığva, Hasan Özgür; Mutlu, Sevgi; Doğanlar, Sami; Yemenicioğlu, Ahmet; Frary, AnneIn this study, total water soluble antioxidant activity and phenolic content of 26 eggplant (Solanum melongena L.) cultivars were investigated. Total water soluble antioxidant activity of the cultivars varied from 2664 to 8247 molTrolox/kg, which is a 3.1-fold difference. Cultivars also showed significant variation for total phenolic contents ranging from 615 to 1376 mg/kg, a 2.2-fold difference. The two traits were significantly correlated and results of this study suggested that breeders can use the information to develop eggplant cultivars with high antioxidant activity.Article Citation - WoS: 16Citation - Scopus: 17Protective Effect of Zinc on Cyclophosphamide-Induced Hematoxicity and Urotoxicity(Humana Press, 2008) Ayhancı, Adnan; Uyar, Ruhi; Aral, Erinç; Kabadere, Selda; Appak, SılaCyclophosphamide (CP) is widely used for the treatment of neoplastic diseases; however, its toxicity causes dose-limiting side effects. Zinc (Zn) is an essential trace element and has important biological functions that control many cell processes including DNA synthesis, normal growth, reproduction, fetal development, bone formation, and wound healing. Therefore, the toxicity of CP and the possible protective effect of Zn on blood cells, bone marrow, and bladder of rat were investigated in this study. Intraperitoneal administration of 50, 100, or 150 mg/kg CP for 3 days caused, in a dose-dependent manner, reductions in the number of leukocytes, thrombocytes, and bone marrow nucleated cells and a serious urotoxicity. To explore whether CP-induced damages could be prevented by Zn, other groups of rats were pretreated with 4 or 8 mg/kg ZnCl2 intraperitoneally for 3 days then challenged with respective doses of CP plus ZnCl2 on day 4 for three more days. The results indicated that treatment of rats with Zn could dose-dependently alleviate CP-induced toxicities on blood cells, bone marrow cells, and urinary bladder. We suggest that Zn could be a potentially effective drug in the prevention of CP-related hematoxicity and urotoxicity.Article Citation - WoS: 125Citation - Scopus: 156Antimicrobial and Antioxidant Activity of Edible Zein Films Incorporated With Lysozyme, Albumin Proteins and Disodium Edta(Elsevier Ltd., 2007) Mecitoğlu Güçbilmez, Çiğdem; Yemenicioğlu, Ahmet; Arslanoğlu, AlperIn this study, partially purified lysozyme was incorporated into zein films in combination with chickpea albumin extract (CPAE), bovine serum albumin (BSA) and disodium EDTA. The zein films showed an inherent free radical scavenging activity. Incorporation of lysozyme did not contribute to soluble free radical scavenging activity of zein films. However, the incorporation of lysozyme in combination with CPAE increased the soluble and immobilized free radical scavenging activity of zein films 17% to 25% and almost 84%, respectively. The incorporation of CPAE also improved the distribution of partially purified lysozyme preparation in zein films and enabled the controlled release of lysozyme by reducing its release rate from zein films between 1.5- and 3.5-fold, depending on the concentration of incorporated CPAE. In contrast, the BSA incorporation made distribution of lysozyme more heterogeneous and it did not contribute to the free radical scavenging activity of films significantly. The combinational incorporation of partially purified lysozyme with disodium EDTA · 2H2O or CPAE and disodium EDTA · 2H2O gave zein films effective on Escherichia coli and Bacillus subtilis. This study clearly showed the benefits of using functional protein extracts to control lysozyme distribution and release rate and to improve antioxidant activity in zein films.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: 119Citation - Scopus: 121Structure of Halothiobacillus Neapolitanus Carboxysomes by Cryo-Electron Tomography(Academic Press Inc., 2006) Schmid, Michael F.; Paredes, Angel M.; Khant, Htet A.; Soyer Dönmez, Ferda; Aldrich, Henry C.; Chiu, Wah; Shively, Jessup M.Carboxysomes are polyhedral bodies consisting of a proteinaceous shell filled with ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO). They are found in the cytoplasm of all cyanobacteria and some chemoautotrophic bacteria. Previous studies of Halothiobacillus neapolitanus and Nitrobacter agilis carboxysomes suggest that the structures are either icosahedral or dodecahedral. To determine the protein shell structure more definitively, purified H. neapolitanus carboxysomes were re-examined by cryo-electron tomography and scanning transmission electron microscopy (STEM). Due to the limited tilt angles in the electron microscope, the tomographic reconstructions are distorted. Corrections were made in the 3D orientation searching and averaging of the computationally extracted carboxysomes to minimize the missing data effects. It was found that H. neapolitanus carboxysomes vary widely in size and mass as shown by cryo-electron tomography and STEM mass measurements, respectively. We have aligned and averaged carboxysomes in several size classes from the 3D tomographic reconstruction by methods that are not model-biased. The averages reveal icosahedral symmetry of the shell, but not of the density inside it, for all the size classesLetter 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: 115Citation - Scopus: 142Development of a Set of Pcr-Based Anchor Markers Encompassing the Tomato Genome and Evaluation of Their Usefulness for Genetics and Breeding Experiments(Springer Verlag, 2005) Farry, Anne; Xu, Yimin; Liu, Jiping; Mitchell, Sharon E.; Tedeschi, Eloisa; Tanksley, Steven D.Tomato and potato expressed sequence tag (EST) sequences contained in the solanaceae genomics network (SGN) database were screened for simple sequence repeat (SSR) motifs. A total of 609 SSRs were identified and assayed on Solanum lycopersicum LA925 (formerly Lycopersicon esculentum) and S. pennellii LA716 (formerly L. pennellii). The SSRs that did not amplify, gave multiple band products, or did not exhibit a polymorphism that could be readily detected on standard agarose gels in either of these species were eliminated. A set of 76 SSRs meeting these criteria was then placed on the S. lycopersicum (LA925) × S. pennellii (LA716) high-density map. A set of 76 selected cleaved amplified polymorphism (CAP) markers was also developed and mapped onto the same population. These 152 PCR-based anchor markers are uniformly distributed and encompass 95% of the genome with an average spacing of 10.0 cM. These PCR-based markers were further used to characterize S. pennellii introgression lines (Eshed and Zamir, Genetics 141:1147-1162, 1995) and should prove helpful in utilizing these stocks for high-resolution mapping experiments. The majority of these anchor markers also exhibit polymorphism between S. lycopersicum and two wild species commonly used as parents for mapping experiments, S. pimpinellifolium (formerly L. pimpinellifolium) and S. habrochaites (formerly L. hirsutum), indicating that they will be useful for mapping in other interspecific populations. Sixty of the mapped SSRs plus another 49 microsatellites were tested for polymorphism in seven tomato cultivars, four S. lycopersicum var. cerasiforme accessions and eight accessions of five different wild tomato species. Polymorphism information content values were highest among the wild accessions, with as many as 13 alleles detected per locus over all accessions. Most of the SSRs (90%) had accession-specific alleles, with the most unique alleles and heterozygotes usually found in accessions of self-incompatible species. The markers should be a useful resource for qualitative and quantitative trait mapping, marker-assisted selection, germplasm identification, and genetic diversity studies in tomato. The genetic map and marker information can be found on SGN ( http://www.sgn.cornell.edu ).