Molecular Biology and Genetics / Moleküler Biyoloji ve Genetik
Permanent URI for this collectionhttps://hdl.handle.net/11147/9
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Article Citation - WoS: 13Citation - Scopus: 13Her2-Targeted, Degradable Core Cross-Linked Micelles for Specific and Dual Ph-Sensitive Dox Release(John Wiley and Sons Inc., 2021) Bayram, Nazende Nur; Ulu, Gizem Tuğçe; Topuzoğulları, Murat; Baran, Yusuf; Dinçer İşoğlu, SevilHere, a targeted, dual-pH responsive, and stable micelle nanocarrier is designed, which specifically selects an HER2 receptor on breast cancer cells. Intracellularly degradable and stabilized micelles are prepared by core cross-linking via reversible addition-fragmentation chain-transfer (RAFT) polymerization with an acid-sensitive cross-linker followed by the conjugation of maleimide-doxorubicin to the pyridyl disulfide-modified micelles. Multifunctional nanocarriers are obtained by coupling HER2-specific peptide. Formation of micelles, addition of peptide and doxorubicin (DOX) are confirmed structurally by spectroscopical techniques. Size and morphological characterization are performed by Zetasizer and transmission electron microscope (TEM). For the physicochemical verification of the synergistic acid-triggered degradation induced by acetal and hydrazone bond degradation, Infrared spectroscopy and particle size measurements are used. Drug release studies show that DOX release is accelerated at acidic pH. DOX-conjugated HER2-specific peptide-carrying nanocarriers significantly enhance cytotoxicity toward SKBR-3 cells. More importantly, no selectivity toward MCF-10A cells is observed compared to HER2(+) SKBR-3 cells. Formulations cause apoptosis depending on Bax and Caspase-3 and cell cycle arrest in G2 phase. This study shows a novel system for HER2-targeted therapy of breast cancer with a multifunctional nanocarrier, which has higher stability, dual pH-sensitivity, selectivity, and it can be an efficient way of targeted anticancer drug delivery.Article Citation - WoS: 22Citation - Scopus: 24Scaffold-Free Biofabrication of Adipocyte Structures With Magnetic Levitation(John Wiley and Sons Inc., 2021) Sarıgil, Öykü; Yalçın Özuysal, Özden; Anıl İnevi, Müge; Meşe Özçivici, Gülistan; Fıratlıgil Yıldırır, Burcu; Fıratlıgil Yıldırır, Burcu; Ünal, Yağmur Ceren; Ünal, Yağmur Ceren; Yalçın Özuysal, Özden; Özçivici, Engin; Meşe, Gülistan; Sarıgil, Öykü; Özçivici, Engin; Anıl İnevi, Müge; Meşe Özçivici, GülistanTissue engineering research aims to repair the form and/or function of impaired tissues. Tissue engineering studies mostly rely on scaffold-based techniques. However, these techniques have certain challenges, such as the selection of proper scaffold material, including mechanical properties, sterilization, and fabrication processes. As an alternative, we propose a novel scaffold-free adipose tissue biofabrication technique based on magnetic levitation. In this study, a label-free magnetic levitation technique was used to form three-dimensional (3D) scaffold-free adipocyte structures with various fabrication strategies in a microcapillary-based setup. Adipogenic-differentiated 7F2 cells and growth D1 ORL UVA stem cells were used as model cells. The morphological properties of the 3D structures of single and cocultured cells were analyzed. The developed procedure leads to the formation of different patterns of single and cocultured adipocytes without a scaffold. Our results indicated that adipocytes formed loose structures while growth cells were tightly packed during 3D culture in the magnetic levitation platform. This system has potential for ex vivo modeling of adipose tissue for drug testing and transplantation applications for cell therapy in soft tissue damage. Also, it will be possible to extend this technique to other cell and tissue types.Article Citation - WoS: 38Citation - Scopus: 47Docetaxel/Zoledronic Acid Combination Triggers Apoptosis Synergistically Through Downregulating Antiapoptotic Bcl-2 Protein Level in Hormone-Refractory Prostate Cancer Cells(John Wiley and Sons Inc., 2009) Karabulut, B.; Erten, C.; Gül, M. K.; Cengiz, E.; Karaca, B.; Küçükzeybek, Y.; Görümlü, G.; Atmaca, H.; Uzunoğlu, S.; Şanlı, U. A.; Baran, Yusuf; Uslu, R.Docetaxel, a semi-synthetic taxane analogue, is used effectively in the treatment of metastatic prostate cancer. Zoledronic acid, the most potent member of bisphosphonates, has shown pleiotropic anti-tumoral effects on prostate cancer cells. We have explored the possible additive/synergistic effects and the apoptotic pathways induced by combination treatment of docetaxel and zoledronic acid in hormone and drug refractory, PC-3 and DU-145 prostate cancer cells. Combination of docetaxel and zoledronic acid synergistically inhibits cell growth in PC-3 and DU-145 cells. Moreover, this effect was due to downregulation of antiapoptotic protein Bcl-2 in PC-3 and DU-145 cells. In conclusion, docetaxel/zoledronic acid combination is potentially a novel and effective approach for the treatment of prostate cancer.Article Citation - WoS: 23Citation - Scopus: 29Physical 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, FerdaAntifungal 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: 66Citation - Scopus: 81Effect of Biopolymers Containing Natamycin Against Aspergillus Niger and Penicillium Roquefortii on Fresh Kashar Cheese(John Wiley and Sons Inc., 2011) Türe, Hasan; Eroğlu, Erdal; Özen, Banu; Soyer, FerdaFungal spoilage during refrigerated storage is one of the main safety and quality-related problems for dairy products. The effect of wheat gluten (WG) and methyl cellulose (MC) biopolymers containing natamycin (NA) on the growth of Aspergillus niger and Penicillium roquefortii on the surface of fresh kashar cheese during storage at 10 C for 30 days was investigated. Wrapping of A. niger-inoculated cheese with MC films containing 5–20 mg NA per 10 g resulted in approximately 2-log reductions in spore count. Two mg NA per 10 g included into WG films was sufficient to eliminate A. niger on the surface of cheese. However, MC and WG films containing NA did not cause any significant decrease in P. roquefortii count on the cheese surface. Therefore, especially use WG films in dairy applications could be an effective way of controlling A. niger growth on these products.Article Citation - WoS: 46Citation - Scopus: 52Antifungal Activity of Biopolymers Containing Natamycin and Rosemary Extract Against Aspergillus Niger and Penicillium Roquefortii(John Wiley and Sons Inc., 2008) Türe, Hasan; Eroğlu, Erdal; Soyer, Ferda; Özen, Fatma BanuAntimicrobial agent-releasing films have been proposed as an effective way of inhibiting chiefly surface spoilage of food products. Antifungal activities of natamycin (NA), rosemary extract (RE) and NA + RE were tested against Aspergillus niger and Penicillium roquefortii with agar disc diffusion assay. NA, RE and NA + RE were also included into biopolymers made from gluten and methyl cellulose. Minimum inhibitory concentrations (MIC) of NA in both films were 2 and 1 mg NA per 10 g film solution against A. niger and P. roquefortii, respectively. RE did not show any inhibitory antifungal activity alone. Although NA incorporated into both films at a concentration of 1.5 mg NA per 10 g film solution was not effective against A. niger, combination of NA at the same concentration with RE in the films inhibited the growth of this mould. NA in solution or in biopolymers is very effective in inhibiting the growth of selected organisms, and RE acted synergistically with NA to prevent the growth of A. niger when incorporated into both films. © 2008 Institute of Food Science and TechnologyArticle Citation - WoS: 19Citation - Scopus: 19Biofilm Formation by Staphylococcus Epidermidis on Nitrogen Ion Implanted Cocrmo Alloy Material(John Wiley and Sons Inc., 2007) Öztürk, Orhan; Sudağıdan, Mert; Türkan, UğurStaphylococcus epidermidis is the primary cause of medical device-related infections due to its adhesion and biofilm forming abilities on biomaterial surfaces. For this reason development of new materials and surfaces to prevent bacterial adhesion is inevitable. In this study, the adhesion of biofilm forming S. epidermidis strain YT-169a on nitrogen (N) ion implanted as well as on as-polished CoCrMo alloy materials were investigated. A medical grade CoCrMo alloy was ion implanted with 60 keV N ions to a high dose of 1.9 × 10 18 ions/cm2 at substrate temperatures of 200 and 400°C. The near-surface implanted layer crystal structures, implanted layer thicknesses, and roughnesses were characterized by XRD, SEM and AFM. The number of adherent bacteria on the surfaces of N implanted specimens was found to be 191 × 106 CFU/cm2 for the 200°C and 70 × 106 CFU/cm2 for the 400°C specimens compared to the as-polished specimen (3 × 106 CFU/cm2). The adhesion test results showed that S. epidermidis strain YT-169a adhere much more efficiently to the N implanted surfaces than to the as-polished CoCrMo alloy surface. This was attributed mainly to the rougher surfaces associated with the N implanted specimens in comparison with the relatively smooth surface of the as-polished specimen.Article Citation - WoS: 7Citation - Scopus: 8Identification of Extracellular Enzyme Producing Alkalophilic Bacilli From Izmir Province by 16s-Its Rdna Rflp(John Wiley and Sons Inc., 2004) Akbalık, Güney; Güneş, Hatice; Yavuz, Elif; Yaşa, İhsan; Harsa, Hayriye Şebnem; Elmacı, Zehra Seda; Yenidünya, Ali FazılAims: To screen industrially important extracellular enzymes from the newly isolated alkalophilic bacilli and to characterize them by phenotypic and 16S-internal transcribed spacer (ITS) rDNA restriction pattern analysis. Methods and Results: Three different environmental samples, soil, leather and horse faeces, were collected within the province of Izmir. Isolates grown on Horikoshi-I medium for 24 h at 37°C were screened for extracellular enzyme activity by using eight different substrates: birchwood xylan, carboxymethylcellulose, casein, citrus pectin, polygalacturonic acid, soluble starch, and Tween 20 and 80. In total, 115 extracellular enzyme-producing bacilli were obtained. Casein was hydrolysed by 78%, soluble starch by 67%, citrus pectin by 63%, polygalacturonic acid by 62%, Tween 20 by 34%, birchwood xylan by 16%, Tween 80 by 12%, and carboxymethylcellulose by 3% of the isolates. The isolates were differentiated into 19 distinct homology groups by the 16S-ITS rDNA restriction pattern analysis. Conclusions: Eight different extracellular enzyme activities were determined in 115 endospore forming bacilli. The largest 16S-ITS rDNA homology group (HT1) included 36% of the isolates, 98% of which degraded casein, polygalacturonic acid, pectin and starch. Significance and Impact of the Study: This study is the first report on the characterization of the industrial enzyme-producing alkalophilic bacilli by 16S-ITS rDNA restriction fragment length polymorphism (RFLP). Restriction profiles of 64% of the isolates were found to be different from those of five reference strains used.Article Citation - WoS: 24Citation - Scopus: 25Identification of Extracellular Enzyme Producing Thermophilic Bacilli From Balcova (agamemnon) Geothermal Site by Its Rdna Rflp(John Wiley and Sons Inc., 2004) Yavuz, Elif; Güneş, Hatice; Harsa, Hayriye Şebnem; Yenidünya, Ali FazılAims: Molecular characterization of extracellular enzyme producing thermophilic bacilli from Balcova geothermal site. Methods and Results: Three types of geothermal samples were collected: mud, re-injection water, and samples from uncontrolled hydrothermal vents. Isolates grown at 55°C in culture media prepared in sterilized re-injection water, were screened for extracellular enzyme activity by using eight different substrates: casein, carboxymethyl-cellulose, pectin, polygalacturonic acid (PGA), soluble starch, Tween 20 and 80, and xylan. In total, 109 thermoaerophilic isolates were selected. All of the isolates could hydrolyse Tween 20 (100%) but not Tween 80. Soluble starch was hydrolysed by 96%, casein by 55%, xylan and carboxymethylcellulose by 9%, and pectin and PGA by 2% of the isolates. The isolates were grouped into 14 different homology groups by the restriction pattern analysis of 16S-internal transcribed spacer (ITS) rDNA RFLP. Each of the RFLP groups was also studied by 16S rRNA gene partial sequence analysis. Plasmid DNA profiles revealed that 15 of the isolated strains contained small plasmid DNA molecules ranging in size from 12 000 to 35 000 bp. Conclusions: Combined analysis of 16S-ITS rDNA RFLP and 16S rRNA gene partial sequence results indicated the presence of novel or existing species of Anoxybacillus (nine species) and Geobacillus (three species). Significance and Impact of the Study: In this study 16S-ITS rDNA RFLP was applied for the first time to differentiate thermophilic bacilli. It was also the first study on thermophilic bacilli of Balcova geothermal site.