PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7645
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Article Citation - WoS: 19Citation - Scopus: 18Biyomalzeme Yüzeylerinden İzole Edilen Metisiline Dirençli Staphylococcus Aureus Suşlarında Virülans Genlerinin Araştırılması(Ankara Microbiology Society, 2008) Sudağıdan, Mert; Çavuşoğlu, Cengiz; Bacakoğlu, FezaStafilokoklar, biyomalzeme kaynaklı nozokomiyal enfeksiyonların en önemli etkenlerindendir. Bu çalışmada, Göğüs Hastalıkları Yoğun Bakım Ünitesi (YBÜ)'nde yatan 48 hastada kullanılan polimerik biyomalzeme yüzeylerinden izole edilen metisiline dirençli 11 Staphylococcus aureus suşunda virülans genlerinin varlığının saptanması ve bunların bazılarının fenotipik ifadelerinin araştırılması amaçlanmıştır. Çalışmamızda polimeraz zincir reaksiyonu (PCR) ile özgül primerler kullanılarak, bağlanma ve biyofilm oluşumundan sorumlu genler (icaA, icaC, bap), metisilin direnç geni (mecA), enterotoksin A-E üretiminden sorumlu genler (sea, seb, sec, sed, see), toksik şok sendromu toksini geni [tst), eksfoliatif toksin A ve B genleri (eta ve etb), alfa ve beta-hemolizin genleri (hla ve hlb), stafilokokal ekzotoksin benzeri protein-1 geni (sef1), proteaz genleri (sspA, sspB, aur, serine proteaz geni), lipaz geni (geh) ve regülatör genler (sarA ve agrCA) araştırılmıştır. Ayrıca suşların fenotipik olarak biyofilm oluşturma, antibiyotik duyarlılık, proteaz ve lipaz üretimi gibi özellikleri de değerlendirilmiştir. Biyofilm testlerinde, biyofilm yapan ve "slime" üreten suşlara rastlanmamış, ancak tüm suşların biyofilm yapımında rol oynayan icaA genine sahip olduğu bulunmuştur. Bununla birlikte biyofilm yapımında rol oynayan icaC ve bap genleri tespit edilememiştir. Tüm suşlarda mecA geninin varlığı saptanmış ve suşların hepsinin oksasilin, penisilin G ve gentamisine; 10'unun eritromisine ve dokuzunun da ofloksasine dirençli olduğu bulunmuştur. İzolatların tümü vankomisin, teikoplanin ve ko-trimoksazole duyarlı olarak saptanmıştır. Ekzotoksin ve regülatör genlerinin taranması sonucunda, suşların sea, seti, hla, hlb ve sarA genlerini taşıdığı belirlenmiştir. PCR ile tüm suşların, çalışılan bütün proteaz genlerine (sspA, sspB, aur ve serin proteaz geni) sahip olduğu görülmüş, ancak sütlü (skim milk ve milk agar) ve kazein ağarlarda yapılan proteaz üretimi testlerinde negatif sonuç alınmıştır. Lipaz üretiminin belirlenmesi için Tween 20, Tween 80 ve tributyrin içeren besiyerleri kullanılmış ve tüm suşlarda geç dönemde (inkübasyonun üçüncü günü) pozitif sonuç alınmasına karşın, izolatların hiçbirisinde lipaz üretiminden sorumlu geh geni bulunmamıştır. Sonuç olarak, biyomalzeme yüzeylerinden izole edilen S.aureus suşlarında, araştırılan virülans genlerinden bazılarının varlığı saptanmış, ancak bunların tam olarak fenotipe yansımadığı izlenmiştir. İzolat sayısının azlığına ve tüm genlerin ekspresyonlarının fenotipik olarak çalışılamamış olmasına rağmen, bu genlerin varlığının yoğun bakım hastalan için potansiyel bir risk teşkil edebileceği düşünülmüştür.Article Citation - WoS: 150Citation - Scopus: 7Correlation of Tunneling Spectra in Bi2sr2cacu2o8+? With the Resonance Spin Excitation(American Physical Society, 2001) Zasadzinski, John F.; Özyüzer, Lütfi; Miyakawa, Nobuaki; Gray, Kenneth E.; Hinks, David G.; Kendziora, Christopher A.New break-junction tunneling data are reported in Bi2Sr2CaCu2O8+δ over a wide range of hole concentration from underdoped (Tc=74k) to optimal doped (Tc=95k) to overdoped (Tc=48k). The conductances exhibit sharp dips at a voltage, Ω/e, measured with respect to the superconducting gap. Clear trends are found such that the dip strength is maximum at optimal doping and that Ω scales as 4.9kTc over the entire doping range. These features link the dip to the resonance spin excitation and suggest quasiparticle interactions with this mode are important for superconductivity.Article Citation - WoS: 16Citation - Scopus: 19Nmr Studies on Natural and Synthetic Amavadin(Elsevier Ltd., 2000) Armstrong, Elaine M.; Collison, David; Ertok, Nigar; Garner, Catherine D.The stereochemistry of isolated natural product Amavadin, which contains a 1:2 complex of V(IV) with N-hydroxyimino-2,2′-dipropionic acid (HIDPAH3), and some synthetic complexes have been investigated. Amavadin was isolated from Amanita muscaria and oxidized with [NH4]2[Ce(NO3)6]. H2[Δ-V(S,S-HIDPA)2].3H2O, H2[Δ,Λ-V(S,S-HIDPA)2].3H2O and their equivalent oxidized species have been synthesized and characterized spectroscopically. A combination of COSY, NOE, 1H, 13C-NMR and CD spectroscopy have been used to prove that the isolated natural product Amavadin consists of an almost equal mixture of the Δ- and Λ-isomers of [V(S,S-HIDPA)2]2-. The stereochemistry of isolated natural product Amavadin, which contains a 1:2 complex of V(IV) with N-hydroxyimino-2,2'-dipropionic acid (HIDPAH3), and some synthetic complexes have been investigated. Amavadin was isolated from Amanita muscaria and oxidized with [NH4]2[Ce(NO3)6]. H2[Δ-V(S,S-HIDPA)2].3H2O, H2[Δ,Λ-V(S,S-HIDPA)2].3H2O and their equivalent oxidized species have been synthesized and characterized spectroscopically. A combination of COSY, NOE, 1H, 13C-NMR and CD spectroscopy have been used to prove that the isolated natural product Amavadin consists of an almost equal mixture of the Δ- and Λ-isomers of [V(S,S-HIDPA)2]2-.Article Mrna Decay Analysis in Drosophila Melanogaster: Drug-Induced Changes in Glutathione S-Transferase D21 Mrna Stability(Academic Press Inc., 2008) Akgül, Bünyamin; Tu, Chen-Pei D.We have established an in vivo system to investigate mechanisms by which pentobarbital (PB), a psychoactive drug with a sedative effect, changes the rate of decay of gstD21 mRNA (encoding a Drosophila glutathione S-transferase). Here we describe methods for the use of hsp70 promoter-based transgenes and transgenic lines to determine mRNA half-lives by RNase protection assays in Drosophila. We are able to identify and map putative decay intermediates by cRT-PCR and DNA sequencing of the resulting clones. Our results indicate that the 3′-UTR of gstD21 mRNA is responsive to PB by regulating mRNA decay and that the cis-acting element(s) responsible for the PB-mediated stabilization resides in a 59 nucleotide sequence in the 3′-UTR of the gstD21 mRNA (Akgül and Tu, 2007).Article Citation - WoS: 2Citation - Scopus: 2Scanning Probe Oxidation Lithography on Ta Thin Films(American Scientific Publishers, 2008) Okur, Salih; Büyükköse, Serkan; Tarı, SüleymanA Semi-Contact Scanning Probe Lithography Technique (SC-SPL) has been applied to create nano-oxide patterns on Ta thin films grown by DC magnetron sputtering method on SiO 2/Si substrates. The height and linewidth profiles of nano-oxide lines created by a conductive AFM tip on Ta film surfaces were measured as a function of applied voltage, oxidation time, humidity, and tip apex curvature. The AFM surface measurements show that the height of the oxides increases linearly with increasing voltage; but there was no oxide growth, when less than 4 V was applied even at 85% relative humidity. Electrical measurements were performed and the resistivities of the TaO x layer and Ta film were obtained as 5.76 × 10 8 and 1.4 × 10 5 Ohm-cm, respectively.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 - Scopus: 18Organogenesis From Transformed Tomato Explants(Humana Press, 2005) Frary, Anne; Van Eck, JoyceTomato was one of the first crops for which a genetic transformation system was reported involving regeneration by organogenesis from Agrobacterium-transformed explants. Since the initial reports, various factors have been studied that affect the efficiency of tomato transformation and the technique has been useful for the isolation and identification of many genes involved in plant disease resistance, morphology and development. In this method, cotyledon explants from in vitro-grown seedlings are precultured overnight on a tobacco suspension feeder layer. The explants are then inoculated with Agrobacterium and returned to the feeder layer for a 2-d period of cocultivation. After cocultivation, the explants are transferred to an MS-based selective regeneration medium containing zeatin. Regenerated shoots are then rooted on a separate selective medium. This protocol has been used with several tomato cultivars and routinely yields transformation efficiencies of 10-15%.Article Citation - WoS: 31Citation - Scopus: 346-Bicycloaryl Substituted (s)- and (r)-5,6 Asymmetric Synthesis, and Anti-Proliferative Properties(Elsevier Ltd., 2009) Kasaplar, Pınar; Yılmazer, Özgür; Çağır, Ali(R)-Goniothalamin, is a member of styryl lactones, possesses selective cytotoxicity against cancer cell lines. In this work, replacement of styryl substituent with 2-naphthyl and 3-quinoyl gave new analogues which may have less conformational changes compared to the lead compound. Anti-proliferative tests indicated that 2-naphthyl substituted (R)-5,6-dihydro-2H-pyran-2-one has slightly better cytotoxicity than (R)-goniothalamin. To clarify the effect of 2-naphthyl substituent additional aryl substituted (R)-5,6-dihydro-2H-pyran-2-ones have been synthesized enantioselectively and tested against PC-3 and MCF-7 cell lines.Article Citation - WoS: 20Citation - Scopus: 23Estimation of Suspended Sediment Concentration in Rivers Using Acoustic Methods(Springer Verlag, 2009) Elçi, Şebnem; Aydın, Ramazan; Work, Paul A.Acoustic Doppler current meters (ADV, ADCP, and ADP) are widely used in water systems to measure flow velocities and velocity profiles. Although these meters are designed for flow velocity measurements, they can also provide information defining the quantity of particulate matter in the water, after appropriate calibration. When an acoustic instrument is calibrated for a water system, no additional sensor is needed to measure suspended sediment concentration (SSC). This provides the simultaneous measurements of velocity and concentration required for most sediment transport studies. The performance of acoustic Doppler current meters for measuring SSC was investigated in different studies where signal-to-noise ratio (SNR) and suspended sediment concentration were related using different formulations. However, these studies were each limited to a single study site where neither the effect of particle size nor the effect of temperature was investigated. In this study, different parameters that affect the performance of an ADV for the prediction of SSC are investigated. In order to investigate the reliability of an ADV for SSC measurements in different environments, flow and SSC measurements were made in different streams located in the Aegean region of Turkey having different soil types. Soil samples were collected from all measuring stations and particle size analysis was conducted by mechanical means. Multivariate analysis was utilized to investigate the effect of soil type and water temperature on the measurements. Statistical analysis indicates that SNR readings ob tained from the ADV are affected by water temperature and particle size distribution of the soil, as expected, and a prediction model is presented relating SNR readings to SSC mea surements where both water temperature and sediment characteristics type are incorporated into the model. The coefficients of the suggested model were obtained using the multivariate anal ysis. Effect of high turbidity conditions on ADV performance was also investigated during and after rain events.Article Citation - WoS: 16Citation - Scopus: 16Multidrug Resistance Mediated by Mrp1 Gene Overexpression in Breast Cancer Patients(Taylor and Francis Ltd., 2009) Abaan, Ogan Demir; Mutlu, Pelin Kaya; Baran, Yusuf; Atalay, Can; Gündüz, UfukMultidrug resistance (MDR) is a serious handicap towards the effective treatment of breast cancer patients. One of the most prevalent MDR mechanisms is through the overexpression of genes coding the proteins called Multidrug Resistance-associated Proteins (MRPs). The aim of this study was to investigate the expression of MRP1 in tumor tissues from breast cancer patients. In this study, a semi-quantitative RT-PCR approach was utilized. Our results suggest that MRP1 overexpression can mediate MDR in patients. Pre-evaluation of the level of such MDR mediators before chemotherapy can increase the efficacy of the treatment.