Molecular Biology and Genetics / Moleküler Biyoloji ve Genetik

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    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, Sıla
    The 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: 23
    Citation - Scopus: 29
    Physical 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, Ferda
    Antifungal 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: 73
    Citation - Scopus: 78
    Functional Analysis of Free Methionine-R Reductase From Saccharomyces Cerevisiae
    (American Society for Biochemistry and Molecular Biology, 2009) Le, Dung Tien; Lee, Byung Cheon; Marino, Stefano M.; Zhang, Yan; Fomenko, Dmitri E.; Kaya, Alaattin; Hacıoğlu, Elise; Kwak, Geun-Hee; Koç, Ahmet; Kim, Hwa-Young; Gladyshev, Vadim N.
    Methionine sulfoxide reductases (Msrs) are oxidoreductases that catalyze thiol-dependent reduction of oxidized methionines. MsrA and MsrB are the best known Msrs that repair methionine S-sulfoxide (Met-S-SO) and methionine-R-sulfoxide (Met-R-SO) residues in proteins, respectively. In addition, an Escherichia coli enzyme specific for free Met-R-SO, designated fRMsr, was recently discovered. In this work, we carried out comparative genomic and experimental analyses to examine occurrence, evolution, and function of fRMsr. This protein is present in single copies and two mutually exclusive subtypes in about half of prokaryotes and unicellular eukaryotes but is missing in higher plants and animals. A Saccharomyces cerevisiae fRMsr homolog was found to reduce free Met-R-SO but not free Met-S-SO or dabsyl-Met-R-SO. fRMsr was responsible for growth of yeast cells on Met-R-SO, and the double fRMsr/MsrA mutant could not grow on a mixture of methionine sulfoxides. However, in the presence of methionine, even the triple fRMsr/MsrA/MsrB mutant was viable. In addition, fRMsr deletion strain showed an increased sensitivity to oxidative stress and a decreased life span, whereas overexpression of fRMsr conferred higher resistance to oxidants. Molecular modeling and cysteine residue targeting by thioredoxin pointed to Cys101 as catalytic and Cys125 as resolving residues in yeast fRMsr. These residues as well as a third Cys, resolving Cys91, clustered in the structure, and each was required for the catalytic activity of the enzyme. The data show that fRMsr is the main enzyme responsible for the reduction of free Met-R-SO in S. cerevisiae.
  • Article
    Citation - WoS: 106
    Citation - Scopus: 114
    Msrb1 (methionine-R Reductase 1) Knock-Out Mice: Roles of Msrb1 in Redox Regulation and Identification of a Novel Selenoprotein Form
    (American Society for Biochemistry and Molecular Biology, 2009) Fomenko, Dmitri E.; Novoselov, Sergey V.; Natarajan, Sathish Kumar; Lee, Byung Cheon; Koç, Ahmet; Carlson, Bradley A.; Lee, Tae- Hyung; Kim, Hwa-Young; Hatfield, Dolph L.; Gladyshev, Vadim N.
    Protein oxidation has been linked to accelerated aging and is a contributing factor to many diseases. Methionine residues are particularly susceptible to oxidation, but the resulting mixture of methionine R-sulfoxide (Met-RO) and methionine S-sulfoxide (Met-SO) can be repaired by thioredoxin-dependent enzymes MsrB and MsrA, respectively. Here, we describe a knock-out mouse deficient in selenoprotein MsrB1, the main mammalian MsrB located in the cytosol and nucleus. In these mice, in addition to the deletion of 14-kDa MsrB1, a 5-kDa selenoprotein form was specifically removed. Further studies revealed that the 5-kDa protein occurred in both mouse tissues and human HEK 293 cells; was down-regulated by MsrB1 small interfering RNA, selenium deficiency, and selenocysteine tRNA mutations; and was immunoprecipitated and recognized by MsrB1 antibodies. Specific labeling with 75Se and mass spectrometry analyses revealed that the 5-kDa selenoprotein corresponded to the C-terminal sequence of MsrB1. The MsrB1 knock-out mice lacked both 5- and 14-kDa MsrB1 forms and showed reduced MsrB activity, with the strongest effect seen in liver and kidney. In addition, MsrA activity was decreased by MsrB1 deficiency. Liver and kidney of the MsrB1 knock-out mice also showed increased levels of malondialdehyde, protein carbonyls, protein methionine sulfoxide, and oxidized glutathione as well as reduced levels of free and protein thiols, whereas these parameters were little changed in other organs examined. Overall, this study established an important contribution of MsrB1 to the redox control in mouse liver and kidney and identified a novel form of this protein.
  • Article
    Citation - WoS: 86
    Citation - Scopus: 102
    Total 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, Anne
    In 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: 14
    Citation - Scopus: 23
    Water-Soluble Antioxidant Potential of Turkish Pepper Cultivars
    (American Society for Horticultural Science, 2008) Frary, Anne; Keçeli, Mehmet Ali; Ökmen, Bilal; Şığva, Hasan Özgür; Yemenicioğlu, Ahmet; Doğanlar, Sami
    In this work, 29 pepper cultivars that represent the diversity of types and varieties grown in Turkey were analyzed for water-soluble antioxidant capacity and phenolic and vitamin C contents. In addition, 14 non-Turkish cultivars were tested for comparison. Significant diversity was observed in the different cultivars with the most variation (7.4-fold) seen for total antioxidant capacity, which ranged from 2.57 to 18.96 mmol Trolox/kg. Vitamin C content for the peppers ranged from 522 to 1631 mg·kg-1, a 3.1-fold difference, whereas total phenolic content for the pepper cultivars ranged from 607 to 2724 mg·kg-1, a 4.5-fold difference. When cultivars were grouped by morphology/ use, it was found that some types had significantly more variation and higher antioxidant activities than other types. Thus, for water-soluble antioxidant capacity, most variation was seen in long, blunt-ended Çarliston types, whereas long, pointed Sivri peppers had the highest mean capacity. Bell-shaped Dolmalik and Sivri peppers had the most variation for phenolic content, but fancy Süs and Sivri types had the highest means for this trait. Dolmalik types showed the most variation for vitamin C content, whereas Süs and Sivri peppers had the highest means for this character. All three parameters were significantly and positively correlated with the strongest correlation between total antioxidant capacity and phenolic content (r = 0.71). The presence of significant variation for antioxidant content in Turkish germplasm indicates that this material can be used for improvement and genetic mapping of nutritional content in pepper.
  • Article
    Citation - WoS: 11
    Citation - Scopus: 16
    Bisphosphonate Treatment and Radiotherapy in Metastatic Breast Cancer
    (Humana Press, 2008) Ural, Ali Uğur; Avcu, Ferit; Baran, Yusuf
    Patients with advanced breast cancer frequently develop metastasis to bone. Bone metastasis results in intractable pain and high risk of pathologic fractures due to osteolysis. The treatment of breast cancer patients with bone metastases requires a multidisciplinary approach. Radiotherapy is an established treatment for metastatic bone pain. It may be delivered either as a localized low dose treatment for localized bone pain or systemically for more widespread symptoms. Bisphosphonates have been shown to reduce morbidity and bone pain from bone metastases when given to patients with metastatic bone disease. In vivo studies indicate that early bisphosphonates administration in combination with radiotherapy improves remineralization and restabilization of osteolytic bone metastases in animal tumor models. This review focused on a brief discussion about biology of bone metastases, the effects of radiotherapy and bisphosphonate therapy, and possible mechanisms of combination therapy in metastatic breast cancer patients.
  • Article
    Citation - WoS: 16
    Citation - Scopus: 17
    Protective Effect of Zinc on Cyclophosphamide-Induced Hematoxicity and Urotoxicity
    (Humana Press, 2008) Ayhancı, Adnan; Uyar, Ruhi; Aral, Erinç; Kabadere, Selda; Appak, Sıla
    Cyclophosphamide (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: 3
    Citation - Scopus: 3
    Regulation of Mrna Stability Through a Pentobarbital-Responsive Element
    (Elsevier Ltd., 2007) Akgül, Bünyamin; Tu, Chen-Pei D.
    Pentobarbital, a general anesthetic and non-genotoxic carcinogen, can induce gene expression by activating transcription. In the Drosophila glutathione S-transferase D21 (gstD21) gene, pentobarbital's regulatory influence extends to the level of mRNA turnover. Transcribed from an intronless gene, gstD21 mRNA is intrinsically very labile. But exposure to pentobarbital renders it stabilized beyond what can be attributed to transcriptional activation. We aim here to identify cis-acting element(s) of gstD21 mRNA as contributors to the molecule's pentobarbital-mediated stabilization. In the context of hsp70 5′UTR and the 3′UTR of act5C, gstD21 mRNA, minus its native UTRs, is stable. Maintaining the same context of heterologous UTRs, we can reconstitute using the full-length gstD21 sequence the inherent instability of gstD21 mRNA and its stabilization by pentobarbital. Transgenic flies that express these chimeric gstD21 mRNA exhibit decay intermediates lacking 3′UTR, which are not stabilized by PB treatment. The 3′UTR sequence, when inserted downstream from a reporter transcript, stabilizes it 1.6-fold under PB treatment. The analysis of the decay intermediates suggests a polysome-associated decay pattern. We propose a regulatory model that features a 59-nucleotide pentobarbital-responsive element (PBRE) in the 3′UTR of gstD21 mRNA.
  • Article
    Citation - WoS: 36
    Citation - Scopus: 46
    Expression of Vitreoscilla Hemoglobin in Gordonia Amarae Enhances Biosurfactant Production
    (Springer Verlag, 2006) Doğan, İlhan; Pagilla, Krishna R.; Webster, Dale A.; Stark, Benjamin C.
    The gene (vgb) encoding Vitreoscilla (bacterial) hemoglobin (VHb) was electroporated into Gordonia amarae, where it was stably maintained, and expressed at about 4 nmol VHb g -1 of cells. The maximum cell mass (OD 600) of vgb-bearing G. amarae was greater than that of untransformed G. amarae for a variety of media and aeration conditions (2.8-fold under normal aeration and 3.4-fold under limited aeration in rich medium, and 3.5-fold under normal aeration and 3.2-fold under limited aeration in mineral salts medium). The maximum level of trehalose lipid from cultures grown in rich medium plus hexadecane was also increased for the recombinant strain, by 4.0-fold in broth and 1.8-fold in cells under normal aeration and 2.1-fold in broth and 1.4-fold in cells under limited aeration. Maximum overall biosurfactant production was also increased in the engineered strain, by 1.4-fold and 2.4-fold for limited and normal aeration, respectively. The engineered strain may be an improved source for producing purified biosurfactant or an aid to microorganisms bioremediating sparingly soluble contaminants in situ.