IZTECH Research Centers Collection / İYTE Araştırma Merkezleri Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/11147/2636
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Article Citation - WoS: 10Citation - Scopus: 9Bi̇yomalzemelerden İ̇zole Edi̇len Staphylococcus Epidermidis Suşlarinin Yüzey Özelli̇kleri̇ni̇n Beli̇rlenmesi̇(Ankara Mikrobiyoloji Derneği, 2010) Sudağıdan, Mert; Erdem, İlker; Çavuşoğlu, Cengiz; Çiftçioğlu, MuhsinThe surface properties of bacteria play an important role on adhesion to the biomaterial surface. In this study, the surface properties of Staphylococcus epidermidis strains isolated from clinically used polymeric biomaterial surfaces were investigated on the basis of zeta potential, hydrophobicity and surface topography. A total of 10 S.epidermidis strains isolated from intravenous catheters (n= 5), endotracheal tubes (n= 3) and central venous catheters (n= 2) which were used in the patients of pulmonary Intensive Care Unit, Ege University Medical Faculty Hospital, were included to the study. Seven of those isolates were biofilm producers, inhabiting biofilm genes, 2 were non-biofilm producers, however, inhabiting biofilm genes, and 1 was non-biofilm producer, inhabiting no biofilm genes. Zeta potential analysis have been performed in 3 different buffers (phosphate-buffered saline, 1 mM potassium chloride and 1 mM potassium phosphate buffer) and at different pH values (pH 4.1-8.2), in order to simulate in vivo environment of the biomaterials. Hydrophobicities of the strains were examined by bacterial adhesion to hydrocarbon (BATH) test and the surface topography of biofilms and slime layers were visualized by atomic force microscopy (AFM) and scanning electron microscopy (SEM) methods. It was found that all strains have negative zeta potential values (surface charge) in all buffers and pH values. In hydrophobicity analysis, the highest value (86%) was determined for non-biofilm forming S.epidermidis strain YT-169b (endotracheal tube isolate) and the lowest hydrophobicity (2.5%) was determined for biofilm forming S.epidermidis strain YT-212 (central venous catheter isolate). Biofilm and slime layers of the strains were imaginated by AFM and SEM analysis in ?m scale. SEM analysis showed that bacteria highly adhered to rough surfaces on biomaterial surfaces and the produced slime layers covered the surface of bacteria. In conclusion, elucidating the surface properties of opportunistic pathogens in different physiologic buffers will give important clues for the production of non-adhesive materials and antibacterial surfaces for those bacteria. It was also estimated that designing the surface of the biomaterial to have negative surface charge in the body and to be as smooth as possible will hamper biofilm formation.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: 3Citation - Scopus: 4Evaluation of Multifunctional Hybrid Analogs for Stilbenes, Chalcones and Flavanones(Bentham Science Publishers, 2017) Çağır, Ali; Odacı, Burcu; Varol, Mehmet; Akçok, İsmail; Okur, Özgür; Koparal, Ayşe T.Aims: In this study, discovery of novel anticancer agents acting by more than one mechanism was aimed. Method: For this purpose, eleven previously synthesized simple-stilbene, chalcone, flavanone derivatives and 31 novel stilbene-fused chalcones and stilbene-fused flavanones were tested for their aromatase inhibition, anti-angiogenic and anti-proliferative properties in cancer (PC3, MCF-7) and healthy (HUVEC) cell lines. MTT cell viability assay was used to evaluate the anti-proliferative activities of the compounds. CYP19/MFC high-throughput screening kit (BD Biosciences, Oxford, UK) was used to search the aromatase inhibition properties and matrigel tube formation assay was applied to determine the anti-angiogenic activities. Results: Results indicate that the simple-chalcone and flavanone derivatives were more cytotoxic than the simple-stilbenes in the both cancer cell lines. In contrast, the simple-stilbene structures were much more effective at aromatase inhibition. The cytotoxicity profiles of stilbene-fused chalcones in cancer cells imply that these molecules mostly mimic the simple chalcone structures. On the other hand, flavanones lose their cytotoxic activities after becoming fused with stilbenes. Additionally, aromatase inhibition assays showed that stilbene-fused chalcones again do mimic the simple-chalcones but not simple-stilbenes and anti-angiogenic profiles of the tested molecules seem to be not related with stilbene fragments. Furthermore, stilbene-fused flavanones may mimic both simple-flavanones and simple-stilbenes depending upon the type and position of the substituent in their respective terminal aromatic rings.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: 105Citation - Scopus: 125Prevalence of Staphylococcal Enterotoxins, Toxin Genes and Genetic-Relatedness of Foodborne Staphylococcus Aureus Strains Isolated in the Marmara Region of Turkey(Elsevier Ltd., 2011) Aydın, Ali; Sudağıdan, Mert; Muratoğlu, KarloStaphylococcus aureus is a major foodborne pathogen and it has the ability to produce a number of extracellular toxins. We analyzed 1070 food samples obtained from retail markets and dairy farms in the Marmara Region of Turkey for the presence of S. aureus. Out of 147 isolates, 92 (62.6%) were enterotoxigenic. PCR was used to investigate the presence of staphylococcal enterotoxin genes (sea, seb, sec, sed, see, seg, seh, sei, sej, sek, sel, sem, sen, seo, sep, seq and seu), exfoliative toxin genes (eta and etb) and the toxic - shock syndrome toxin gene (tst). The PCR results showed that 53.3% of the isolates contained staphylococcal enterotoxin-like (SEl) toxin genes (seg, seh, sei, sej, sek, sel, sem, sen, seo, sep, seq and seu) which were more frequent than classical enterotoxin genes (sea to see). Furthermore, seo, sei, sem, seg, seu and sec were found in 37.0, 32.7, 30.4, 29.3, 29.3 and 27.2% of the isolates, respectively. The tst gene was detected and confirmed by DNA sequencing in 9 isolates. The presence of eta and etb were not found in the isolates. Enterotoxigenic capabilities of isolates with SEA-SEE were investigated by ELISA. Enterotoxigenic S. aureus isolates produced one to three enterotoxins, with the most frequently produced types being enterotoxin A and C. There was a correlation of 72.1% between production of a specific toxin and the presence of the respective genes. PFGE analysis was used to identify genetic-relatedness of enterotoxigenic S. aureus isolates and the results revealed that 13 groups of isolates from different or the same origin that contained the same genes showed 100% homology with indistinguishable band patterns. The other enterotoxigenic isolates showed related band patterns with 72-86% homology in sea-, 61-90% homology in sec-, 80-96% homology in seh-, and 69-96% homology in sep-positive isolates. To our knowledge, this is the first study to examine enterotoxins and related gene contents of S. aureus food isolates in the Marmara Region of Turkey.Article Citation - WoS: 8Citation - Scopus: 8Nkx3.1 Contributes To S Phase Entry and Regulates Dna Damage Response (ddr) in Prostate Cancer Cell Lines(Academic Press Inc., 2011) Erbaykent Tepedelen, Burcu; Özmen, Besra; Varışlı, Lokman; Gönen Korkmaz, Ceren; Debeleç Bütüner, Bilge; Hamid, Syed Muhammad; Çakmak, Özgür Yılmazer; Korkmaz, Kemal SamiNKX3.1 is an androgen-regulated homeobox gene that encodes a tissue-restricted transcription factor, which plays an important role in the differentiation of the prostate epithelium. Thus, the role of NKX3.1 as a functional topoisomerase I activity enhancer in cell cycle regulation and the DNA damage response (DDR) was explored in prostate cancer cell lines. As an early response to DNA damage following CPT-11 treatment, we found that there was an increase in the γH2AX (S139) foci number and that total phosphorylation levels were reduced in PC-3 cells following ectopic NKX3.1 expression as well as in LNCaP cells following androgen administration. Furthermore, upon drug treatment, the increase in ATM (S1981) phosphorylation was reduced in the presence of NKX3.1 expression, whereas DNA-PKcs expression was increased. Additionally, phosphorylation of CHK2 (T68) and NBS1 (S343) was abrogated by ectopic NKX3.1 expression, compared with the increasing levels in control PC-3 cells in a time-course experiment. Finally, NKX3.1 expression maintained a high cyclin D1 expression level regardless of drug treatment, while total γH2AX (S139) phosphorylation remained depleted in PC-3, as well as in LNCaP, cells. Thus, we suggest that androgen regulated NKX3.1 maintains an active DDR at the intra S progression and contributes to the chemotherapeutic resistance of prostate cancer cells to DNA damaging compounds.Article Citation - WoS: 3Citation - Scopus: 3Effects of Different Lipopolysaccharide Preparations on Neutrophil Function in the Fathead Minnow, Pimephales Promelas Rafinesque(John Wiley and Sons Inc., 2011) Jovanovic, B.; Baran, Ezgi; Goetz, F. W.; Palic, D.The fish innate immune response to pathogensrelies on the adequate function of neu trophilicgranulocytes (Palic´, Andreasen, Herolt, Menzel &Roth 2006). The ability of neutrophils to phago-cytose microor ganisms and cellular debris is essen-tial for normal development an d survival of animalpopulations (Segal 2005). The evaluation of neu-trophil function is valuable for assessing the healthstatus of individuals and fish populations (Smith &Lumsden 1983). Resistance of fishes to septic shockand tolerance to high concentrations of lipopoly-saccharide (LPS) was observed as a major differencebetween mammalian and fish innate immuneresponses (Berczi, Bertok & Bereznai 1966). Thisfunctional difference could be attri buted to severalcostimulatory molecules and intracellular mediatorsbeing absent in fish, but active in mammals duringresponse to LPS stimulation (Iliev, Roach, Mac-kenzie, Planas & Goetz 2005). Most fish do notpossess a Toll-like receptor (TLR) with sequencesimilarity to mammalian TLR4 (Leulier & Lemai-tre 2008) and the ones that do have no ability forTLR4 downstream signalling (Sepulcre, Alcaraz-Perez, Lopez-Munoz, Roca, Meseguer, Cayuela &Mulero 2009). Regardless of the absence andfunctionality of TLR4 and costimulatory molecules,bacterial LPS can induce a robus t inflammatorygene response in innate immune fish cells, but atconcentrations 1000-fold higher than is commonlyobserved in mammalian species ( lgmL)1vs.ng mL)1) (Palic´, Ostojic, Andreasen & Roth2007; Mackenzie, Roher, Boltan˜a & Goetz 2010).In contrast, ultrapure LPS preparations are rela-tively inactive in fish (Iliev et al. 2005).Article Citation - WoS: 20Citation - Scopus: 19Virulence Properties of Methicillin-Susceptible Staphylococcus Aureus Food Isolates Encoding Panton-Valentine Leukocidin Gene(Elsevier Ltd., 2010) Sudağıdan, Mert; Aydın, AliIn this study, three Panton-Valentine Leukocidin gene carrying methicillin-susceptible Staphylococcus aureus (MSSA) strains (M1-AAG42B, PY30C-b and YF1B-b) were isolated from different food samples in Kesan-Edirne, Turkey. These strains were characterized on the basis of MLST type, spa type, virulence factor gene contents, antibiotic susceptibilities against 21 antibiotics and biofilm formation. The genetic relatedness of the strains was determined by PFGE. In addition, the complete gene sequences of lukS-PV and lukF-PV were also investigated. All strains were found to be susceptible to tested antibiotics and they were mecA negative. Three strains showed the same PFGE band pattern, ST152 clonal type and t355 spa type. In the detection of virulence factor genes, sea, seb, sec, sed, see, seg, seh, sei, sej, sek, sel, sem, sen, seo, sep, seq, seu, eta, etb, set1, geh and tst genes were not detected. All strains showed the positive results for α- and β-haemolysin genes (hla and hlb), protease encoding genes (sspA, sspB and aur), lukE and lukD leukocidin genes (lukED). The strains were found to be non-biofilm formers. By this study, the virulence properties of the strains were described and this is one of the first reports regarding PVL-positive MSSA strains from food. © 2010 Elsevier B.V.Article Citation - WoS: 39Citation - Scopus: 49Prevalence and Antibiotic Resistance of Foodborne Staphylococcus Aureus Isolates in Turkey(Mary Ann Liebert Inc., 2011) Aydın, Ali; Muratoğlu, Karlo; Sudağıdan, Mert; Bostan, Kamil; Okuklu, Burcu; Harsa, ŞebnemIn this study, 154 Staphylococcus aureus isolates were detected from 1070 food samples (14.4%) collected from seven cities in Turkey. Antimicrobial susceptibility testing against 21 antibiotics was performed by agar disk diffusion method, and those isolates resistant to any antibiotic were further analyzed to determine minimum inhibitory concentration by E-test and polymerase chain reaction analysis of vanA and mecA genes. According to disk diffusion test results, a total of 139 strains were resistant to at least one tested antibiotic, with 39 (25.3%) strains being multidrug resistant (MDR) and the other 15 strains being susceptible to all antibiotics. Penicillin G, linezolid, erythromycin, and tetracycline took up 71.4%, 23.4%, 18.2%, and 15.6% of the tested strains, respectively. In addition, all of the strains were susceptible to vancomycin, oxacillin, cefoxitin, and imipenem. Only one strain (S158B) was resistant to both teicoplanin and cefazolin. On the other hand, the presence of vanA and mecA genes was not detected in the strains. Pulsed-field gel electrophoresis analysis was used to identify genetic-relatedness of the MDR strains. It is noteworthy that some strains from different sources showed 100% homology; however, some of MDR strains were found unrelated with 60% or less homology. The high diversity observed in pulsed-field gel electrophoresis results indicated the possible contamination of S. aureus from different sources and routes.