PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7645
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Article Tc-99m Erythromycin Lactobionate Inhalation Scintigraphy in Parenchymal Lung Diseases(Elsevier Science inc, 1999) Durak, H; Aktogu, S; Degirmenci, B; Sayit, E; Ertay, T; Dereli, SWe have investigated Technetium 99m erythromycin lactobionate (Tc 99m EL) clearance from the lungs after inhalation, in the presence of an alveolitis. Eighteen patients (6 sarcoidosis, 7 idiopathic fibrosis, and 5 miliary tuberculosis) were imaged after the patients inhaled 1,110 MBq of Tc 99m EL. Clearance half time for the first 45 min, for 24 h, and retention at 24 h correlated with percentage of lymphocytes in bronchoalveolar lavage fluid (BAL) (r =.729, r =.883, and r =.826, respectively). There was a positive correlation between peripheral penetration (PP) and forced expiratory volume in 1 s (FEV1) (r =.806) and forced vital capacity (FVC) (r =.781). Retention was more marked in sarcoidosis compared with tuberculosis (0.025 < p less than or equal to 0.05). Radioaerosol lung imaging may reflect the pulmonary function impairment in parenchymal lung diseases. Retention of Tc 99m EL may be related to number of BAL cells or presence of a lymphocytic alveolitis. Long residency time of Tc 99m EL in the lungs implies that erythromycin can also be administered by inhalation for therapeutic purposes. NUCL MED BIOL 26;6:695-698, 1999. (C) 1999 Elsevier Science Inc. All rights reserved.Article Citation - WoS: 1Effect of Ultraviolet B Radiation on the Absorption Characteristics of Various Intraocular Lenses(S. Karger AG, 2006) Koçak, Nilüfer; Kaynak, Süleyman; İlknur, Turna; Özkan, Şebnem; Erdoğan, Gökhan; Çıngıl, GürayBackground: The aim of this study was to determine the effect of ultraviolet B (UVB) exposure on UV filters of various intraocular lenses (IOLs). Methods: Eight samples each of the hydrophobic acrylic, hydrophilic acrylic and silicone IOLs were used. Four IOLs of each type was selected randomly as the control group while the remaining four IOLs of each type were exposed to a UVB dose of 1.4 J/cm2 (2.40 mW/cm2) for 9.45 min, two times with a 4-week interval. IOLs were evaluated for any sign of opacification under microscope weekly. After a follow-up period of 16 weeks, spectrometry for UV filter absorption rates, scanning electron microscopy for deposit formation and energy dispersive X-ray analysis for elemental composition were performed for all IOLs, and findings of the control group IOLs were compared with those of the UVB-exposed IOLs. All these procedures were done at the Department of Ophthalmology, Faculty of Medicine, Dokuz Eylul University. Results: All the IOLs were free of any opacification during the follow-up period. Spectrometric analysis of their UV filters revealed a change in absorption rates in the hydrophilic acrylic and silicone IOLs compared to the control IOLs of the same type. Only the hydrophobic acrylic IOLs preserved the same UV absorption curve after UVB exposure. Conclusion: The pathogenesis of IOL opacification is still undetermined. Some reports claimed that the UV light was the responsible factor. Our experimental study revealed that high doses of UVB did not cause any opacification though they impaired the function of UV filters of the hydrophilic acrylic and silicone IOLs. Copyright © 2007 S. Karger AG.Article Citation - WoS: 73Citation - Scopus: 78Functional 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: 106Citation - Scopus: 114Msrb1 (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: 36Citation - Scopus: 38Antimicrobial Activity of Lactoperoxidase System Incorporated Into Cross-Linked Alginate Films(John Wiley and Sons Inc., 2009) Yener, Fatih Yalçın Güneş; Korel, Figen; Yemenicioğlu, AhmetIn this study, the antimicrobial effect of lactoperoxidase (LPS) incorporated alginate films was investigated on Escherichia coli (NRRL B-3008), Listeria innocua (NRRL B-33314), and Pseudomonas fluorescens (NRRL B-253) in presence of different concentrations of H2O2 (0.2, 0.4, and 0.8 mM) and KSCN (1, 2, and 4 mM). The incorporation of 70 nmol ABTS/min/cm2 LPS into alginate films gave 0.66 to 0.85 nmol ABTS/min/cm2 enzyme activity at 0.2 to 0.8 mM H2O 2 concentration range. The antimicrobial activity of LPS system on target bacteria changed according to the concentrations of KSCN and H 2O2. The growth of all tested bacteria was prevented for a 6-h period by applying LPS system in presence of 0.4 or 0.8 mM H 2O2 and 4 mM KSCN. At 0.8 mM H2O2 and 4 mM KSCN, the LPS system also inhibited growth of L. innocua and P. fluorescens for a 24-h incubation period, whereas E. coli growth could not be inhibited for 24 h under these conditions. At 0.2 mM H2O2 and 1 to 4 mM KSCN, a considerable inhibitory effect was obtained only on P. fluorescens. The decreasing order of the resistance of studied bacteria to LPS system is as follows: E. coli, L. innocua, and P. fluorescens. The developed antimicrobial system has a good potential for use in meat, poultry, and seafood since alginate coatings are already used in these products. Further studies are needed to test the LPS incorporated edible films in real food systems.Article Citation - WoS: 6Citation - Scopus: 8Segment 10 Based Molecular Epidemiology of Bluetongue Virus (btv) Isolates From Turkey: 1999-2001(Elsevier Ltd., 2009) Özkul, Aykut; Ertürk, Arife; Çalışkan, Elvin; Saraç, Fahriye; Ceylan, Çağatay; Mertens, Peter; Kabaklı, Özden; Dinçer, Ender; Çizmeci, Şirin G.Bluetongue is a significant arbovirus infection that has a negative impact on ruminant productivity in Turkey. Twenty-one Turkish BTV isolates were analyzed phylogenetically, based on genome segment 10 (Seg-10) nucleotide sequences. These analyses were used to explore the epidemiological background of individual isolates from both a regional and global perspective. In the regional analysis, the different BTV strains fell into two groups (Group 1 and Group 2). The Turkish virus isolates were localized in Group 1 which contains two sub-groups. The neighbor-joining analysis revealed that Seg-10 of majority of the Turkish viruses was closely related to certain other virus strains allocated in the eastern lineage. The Seg-10's of two viruses (TR25 and TR26) were more closely related to strains isolated in the Asia-Australia region. These strains belong to the 'eastern' topotype identified by [Maan, S., Maan, N.S., Ross-Smith, N., Batten, C.A., Shaw, A.E., Anthony, S.J., Samuel, A.R., Darpel, K.E., Veronesi, E., Oura, C.A.L., Singh,K.P., Nomikou, K., Potgieter, A.C., Attoui, H., van Rooij, E., van Rijn, P., De Clercq, K., Vandenbussche, F., Zientara, S., Bréard, E., Sailleau, C., Beer, M., Hoffman, B., Mellor, P.S., Mertens, P.P.C., 2008. Sequence analysis of bluetongue virus serotype 8 from the Netherlands 2006 and comparison to other European strains. Virology 377, 308-318]. Comparisons of amino acid sequences deduced from the Seg-10 genes showed a high level of conservation in the NS3/3A proteins from the Turkish viruses. The more frequent amino acid substitutions were identified by multiple alignment analysis, and one of the isolates (TR23) was remarkably found to be genetically quite distinct from the other isolates.Article Citation - WoS: 8Citation - Scopus: 9Modeling of Polygalacturonase Enzyme Activity and Biomass Production by Aspergillus Sojae Atcc 20235(Springer Verlag, 2009) Tokatlı, Figen; Tarı, Canan; Ünlütürk, Mehmet; Göğüş, NihanAspergillus sojae, which is used in the making of koji, a characteristic Japanese food, is a potential candidate for the production of polygalacturonase (PG) enzyme, which of a major industrial significance. In this study, fermentation data of an A. sojae system were modeled by multiple linear regression (MLR) and artificial neural network (ANN) approaches to estimate PG activity and biomass. Nutrient concentrations, agitation speed, inoculum ratio and final pH of the fermentation medium were used as the inputs of the system. In addition to nutrient conditions, the final pH of the fermentation medium was also shown to be an effective parameter in the estimation of biomass concentration. The ANN parameters, such as number of hidden neurons, epochs and learning rate, were determined using a statistical approach. In the determination of network architecture, a cross-validation technique was used to test the ANN models. Goodness-of-fit of the regression and ANN models was measured by the R 2 of cross-validated data and squared error of prediction. The PG activity and biomass were modeled with a 5-2-1 and 5-9-1 network topology, respectively. The models predicted enzyme activity with an R 2 of 0.84 and biomass with an R 2 value of 0.83, whereas the regression models predicted enzyme activity with an R 2 of 0.84 and biomass with an R 2 of 0.69.Article Citation - WoS: 16Citation - Scopus: 14Isolation and Characterization of Bacillus Thuringiensis Strains From Olive-Related Habitats in Turkey(John Wiley and Sons Inc., 2008) Çınar, Çelenk; Apaydın, Özgür; Yenidünya, Ali Fazıl; Harsa, Hayriye Şebnem; Güneş, HaticeAims: To isolate Bacillus thuringiensis strains from different olive-related habitats (olive groves and olive oil factories) in Turkey and to characterize these strains by molecular methods. Methods and Results: A total of 150 samples, consisting of olive grove soil, green olive leaves, olive leaf residues, animal faeces, olive pomace and dust, were examined for the presence of B. thuringiensis. One hundred B. thuringiensis strains were isolated from 54 environmental samples (36%) and characterized in terms of crystal morphology, cry and cyt gene content by polymerase chain reaction, plasmid profiles and 16S-internal transcribed spacer ribosomal DNA restriction fragment length polymorphism (16S-ITS rDNA RFLP). The highest percentage of samples containing B. thuringiensis was found in 38 out of 54 total soil samples (70%). Of the 100 B. thuringiensis isolates, the most frequent crystal shapes were irregularly shaped (24%), spherical-irregular pointed (19%), cuboidal (17%) and spherical (16%). The cry1 plus cry4 genotype was the most abundant genotype in our collection (21%). RFLP analysis of the amplified 16S-ITS rDNA revealed 11 distinct patterns for the isolates and 10 reference strains. Conclusions: Bacillus thuringiensis isolates showed a great genetic diversity and crystal shape heterogeneity. Significance and Impact of the Study: This is the first study on the isolation and characterization of B. thuringiensis from olive-related habitats in Turkey. No correlation was observed between the cry genotypes and insecticidal crystal shapes of the isolates. Restriction profiles of 23% of the isolates were found to be different from those of the 10 reference strains used.Article Citation - WoS: 11Citation - Scopus: 16Bisphosphonate Treatment and Radiotherapy in Metastatic Breast Cancer(Humana Press, 2008) Ural, Ali Uğur; Avcu, Ferit; Baran, YusufPatients 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: 8Citation - Scopus: 8The Effects of Urease Immobilization on the Transport Characteristics and Protein Adsorption Capacity of Cellulose Acetate Based Hemodialysis Membranes(Springer Verlag, 2009) Yaşar Mahlıçlı, Filiz; Alsoy Altınkaya, SacideIn this study, cellulose acetate (CA) based hemodialysis membranes were prepared by a dry phase inversion method and the influences of urease immobilization on the clearing performance and protein adsorption capacity of the membranes were investigated. Permeation experiments have shown that modification of CA membranes with urease immobilization not only enhanced the transport rate of urea but also increased the permeation coefficients of uric acid and creatinine by changing the structure of the membrane. Furthermore, the protein adsorption capacity of the CA membranes decreased. On the other hand, the mechanical strength of the modified CA membrane did not change significantly compared with that of the unmodified one. A mathematical model was derived to determine the rate of mass transfer of urea through modified CA membranes. Model predictions along with the experimental data suggest that urease immobilization can be used as an alternative method in preparing CA based hemodialysis membranes with improved transport characteristics and biocompatibility through reduced protein adsorption capacities.