Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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Article Citation - WoS: 1Citation - Scopus: 1Improved Isolation of Ultra-High Genomic Dna Suitable for Third-Generation Sequencing(Mdpi, 2025) Ova, Ayse Oyku; Joffre, Enrique; Shafagh, Reza Zandi; Assuncao, Mariana F. G.; Sidorov, Roman Y.; Santos, Lilia M. A.; Romling, UteAlthough a variety of protocols to isolate high-molecular-weight genomic DNA exist, the isolation and preservation of ultra-high-molecular-weight genomic DNA of sufficient quality and length for error-free third-generation sequencing remains challenging. Inspired by the isolation of high-molecular-weight DNA in agarose plugs suitable to be separated by pulsed-field gel electrophoresis, we report the construction of an incubation chamber for DNA isolation. The chamber is flanked by semi-permeable polycarbonate membranes of variable pore size for the selective diffusion of compounds and components, which allows efficient cell lysis and the subsequent isolation of ultra-high-molecular-weight genomic DNA without shearing. The designed experimental approach is simple, but effective in isolating high-quality ultra-long genomic DNA that is suitable for third-generation sequencing by Oxford Nanopore Technology from challenging bacterial samples. We envisage that genomic DNA isolation using the incubation chamber, or variations thereof, will facilitate the regular sequencing of megabasepair-long DNA fragments, with a multitude of applications in microbiology, immunology, oncology, paleontology and forensic science.Article Citation - WoS: 62Citation - Scopus: 73Antioxidant and Antimicrobial Activities of Thyme and Clove Essential Oils and Application in Minced Beef(John Wiley and Sons Inc., 2015) Zengin, Hatice; Baysal, Ayşe HandanIn this study, thyme and clove essential oils (EOs) were studied for their chemical composition, antioxidant, antiradical and antibacterial activity and application in ground beef. Carvacrol (75.27%) and eugenol (75.2%) were detected by gas chromatography-mass spectrometry analysis as the main components of thyme and clove EOs, respectively. Broth microdilution method showed all bacteria inhibited by the EOs, while Shewanella putrefaciens and Listeria innocua were the most resistant bacteria to thyme and clove EOs, respectively. EO treatment restricted the growth of artificially inoculated Salmonella typhimurium and native Coliforms in the ground beef. Antioxidant activity determined by ferric-reducing antioxidant power and 1,1 diphenyl-2-picrylhydrazyl methods demonstrated that clove EO had higher in vitro antioxidant activity than thyme EO. Similar results were obtained in ground beef application using 2-thiobarbituric acid value. EOs of clove (2MIC) exerted remarkable higher antioxidant activity in ground beef than EOs of thyme (4MIC), which represent valid alternative antioxidant in meat products. Practical Applications: Plant essential oils (EOs) serve as a "safe" alternative to chemical or synthetic antimicrobials and antioxidants to struggle with the foodborne pathogens or spoilage organisms, inhibiting lipid oxidation and thus extending shelf life. Antioxidant activity determined by ferric-reducing antioxidant power and 1,1 diphenyl-2-picrylhydrazyl methods showed that clove EO had higher in vitro antioxidant activity than thyme EO. Results obtained using 2-thiobarbituric acid value in ground beef application were found similar. EOs of clove (2MIC) exerted higher antioxidant activity in ground beef than EOs of thyme (4MIC). Therefore, EOs could be a valid alternative antioxidant in meat products.Article Citation - WoS: 23Citation - Scopus: 26Cr(vi) Sorption by Using Clinoptilolite and Bacteria Loaded Clinoptilolite Rich Mineral(Elsevier Ltd., 2012) Cansever Erdoğan, Beyhan; Ülkü, SemraBatch sorption experiments were performed in order to understand the potential value of local clinoptilolite rich mineral and its bacteria loaded form in Cr(VI) sorption. The results indicated that Cr(VI) sorption capacities of the sorbents were increased after bacteria loading and the clinoptilolite rich mineral is a promising material in Cr(VI) sorption. Zeta potential and Fourier Transform IR (FTIR) analysis were performed to explain the possible mechanism involved in the Cr(VI) sorption. The results revealed that non-electrostatic forces played a significant role rather than the electrostatic forces. The existence of non-electrostatic forces was confirmed by the FTIR results. © 2011 Elsevier Inc. All rights reserved.Article Citation - WoS: 7Citation - Scopus: 10Quality of Flavored Yogurt Containing Added Coffee and Sugar(Hindawi Publishing Corporation, 2007) Tan, Gürdal; Korel, FigenYogurts flavored with instant coffee (0.5, 0.7 and 0.9%) and sweetened with sugar (4 or 5%) and a control yogurt (no coffee or sugar) were evaluated for chemical, physical, microbiological and sensory properties. The added ingredients generally had no effect on the chemical, physical and microbiological quality of yogurts at day 1 after preparation as compared to the control. During 15 days at 5-7C, pH and lactic acid bacteria counts decreased (P < 0.05) and titratable acidity increased (P < 0.05) in all samples. Yogurts with 0.5% coffee flavoring and 4 and 5% sugar met Turkish Institute Standards for yogurt sensory quality when evaluated by a trained 10-member panel. Yogurt flavored with 0.5% coffee and containing 5% sugar had most attributes rated in the "like" category by 50% or more of 51 consumer panelists.