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.Book Part Citation - Scopus: 1Arcobacter(Elsevier, 2023) Ceylan,Ç.Arcobacter is a gram-negative, microaerophilic, water- and food-borne emerging pathogen with a spiral shape. The bacterium appears to have metabolic and genomic plasticity properties and is found to be ubiquitously distributed and densely populated in environmental waters. Although not studied in detail this genus presents a potential problem as a gastrointestinal and opportunistic pathogen with inherent difficulties in classification. However, the species represents a wide genomic and metabolic plasticity that could be used in the production of industrially important moieties and for environmental protection purposes. © 2023 Elsevier Inc. All rights reserved.Review Citation - WoS: 25Citation - Scopus: 27Bacillus Cereus: a Review of “fried Rice Syndrome” Causative Agents(Academic Press, 2023) Leong, Sui Sien; King, Jie Hung; Korel, Figen“Fried rice syndrome” originated from the first exposure to a fried rice dish contaminated with Bacillus cereus. This review compiles available data on the prevalence of B. cereus outbreak cases that occurred between 1984 and 2019. The outcome of B. cereus illness varies dramatically depending on the pathogenic strain encounter and the host's immune system. B. cereus causes a self-limiting, diarrheal illness caused by heat-resistant enterotoxin proteins, and an emetic illness caused by the deadly toxin named cereulide. The toxins together with their extrinsic factors are discussed. The possibility of more contamination of B. cereus in protein-rich food has also been shown. Therefore, the aim of this review is to summarize the available data, focusing mainly on B. cereus physiology as the causative agent for “fried rice syndrome.” This review emphasizes the prevalence of B. cereus in starchy food contamination and outbreak cases reported, the virulence of both enterotoxins and emetic toxins produced, and the possibility of contaminated in protein-rich food. The impact of emetic or enterotoxin-producing B. cereus on public health cannot be neglected. Thus, it is essential to constantly monitor for B. cereus contamination during food handling and hygiene practices for food product preparation. © 2023 Elsevier LtdArticle 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: 22Citation - Scopus: 33Uv-C Irradiation of Freshly Squeezed Grape Juice and Modeling Inactivation Kinetics(John Wiley and Sons Inc., 2014) Ünlütürk, Sevcan; Atılgan, Mehmet ReşatUV inactivation kinetics of freshly squeezed turbid white grape juice (FSTGJ) treated with an annular flow UV reactor by applying UV dosages ranging from 0 to 116.7J/mL, at three different flow rates (0.90, 1.75 and 3.70mL/s), were modeled by using log-linear, Weibull, Hom and modified Chick-Watson models. FSTGJ was circulated five times in the UV system, i.e., UV exposure time was 20.33min during processing. The populations of Escherichia coli K-12, lactic acid bacteria (LAB) and foodborne yeasts were reduced by 3.759, 4.133 and 1.604log cfu/mL, respectively, after exposure to UV dosage of 116.7J/mL at the lowest flow rate. The inactivation kinetics of foodborne yeasts were best described by the modified Chick-Watson model, with the least root mean squared error (RMSE=0.001, R2=0.999). Besides, the inactivation kinetics of E.coli K-12 and LAB were best fitted by Weibull model (R2=0.999). Additionally, when the UV exposure time was increased up to 32.5min (i.e., eight cycles), UV-C treatment of FSTGJ resulted in 5.341log cfu/mL reduction in E.coli K-12, which meets the Food and Drug Administration requirement of a 5log reduction of microorganisms in fruit juices. Practical Applications Consumer demand for high-quality fruit juice with fresh-like characteristics has markedly expanded in recent years. UV-C irradiation is a nonthermal method and allows the processing of fruit juices with a minimal or no changes in flavor, essential nutrients and vitamins. Although thermal pasteurization is the most convenient way of increasing the shelf life of fruit juices, it causes a "cook taste" in grape juice. So, in this study, the application of UV-C irradiation to process grape juice was investigated. The shape of the microbial inactivation curve is sigmoidal in UV treatment. Therefore, different kinetic models (e.g., log-linear, Weibull, Hom and modified Chick-Watson) are applied to describe the inactivation kinetics of Escherichia coli K-12, lactic acid bacteria and foodborne yeasts. Kinetic parameters (e.g., k and D) and models can be used for the development of UV-C irradiation process to ensure microbial safety in juice products.Article Citation - WoS: 10Citation - Scopus: 11Removal of Bacteria by Clinoptilolite Rich Mineral and Its Surfactant Modified Forms(Springer Verlag, 2013) Cansever Erdoğan, Beyhan; Ülkü, SemraBatch experiments were carried out to understand the potential values of clinoptilolite rich mineral and its surfactant modified forms in the removal of Gram-positive and Gram-negative bacteria. Zeta potential and Fourier Transform IR analysis were performed to explain the possible interactions between the bacteria and the zeolite samples. The results revealed that hydrogen bonding was significant mechanism in the removal of bacteria with clinoptilolite rich mineral and anionic surfactant modified clinoptilolite rich mineral whereas both attractive electrostatic forces and hydrogen bonding were dominant mechanism in the removal of bacteria with cationic surfactant modified clinoptilolite rich mineral. Cationic and anionic surfactant modified clinoptilolite rich mineral are promising materials in removal of bacteria studies.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: 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.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.Article Citation - WoS: 30Citation - Scopus: 42Effect of Various Process Parameters on Morphology, Rheology, and Polygalacturonase Production by Aspergillus Sojae in a Batch Bioreactor(American Institute of Chemical Engineers, 2007) Öncü, Şelale; Tarı, Canan; Ünlütürk, SevcanThe effects of pH, agitation speed, and dissolved oxygen tension (DOT), significant in common fungal fermentations, on the production of polygalacturonase (PG) enzyme and their relation to morphology and broth rheology were investigated using Aspergillus sojae in a batch bioreactor. All three factors were effective on the response parameters under study. An uncontrolled pH increased biomass and PG activity by 27% and 38%, respectively, compared to controlled pH (pH 6) with an average pellet size of 1.69 ± 0.48 mm. pH did not significantly affect the broth rheology but created an impact on the pellet morphology. Similarly, at constant agitation speed the maximum biomass obtained at 500 rpm and at 30 h was 3.27 and 3.67 times more than at 200 and 350 rpm, respectively, with an average pellet size of 1.08 ± 0.42 mm. The maximum enzyme productivity of 0.149 U mL-1 h-1 was obtained at 200 rpm with an average pellet size of 0.71 ± 0.35 mm. Non-Newtonian and pseudoplastic broth rheology was observed at 500 rpm agitation speed, broth rheology exhibited dilatant behavior at the lower agitation rate (200 rpm), and at the medium agitation speed (350 rpm) the broth was close to Newtonian. Furthermore, a DOT range of 30-50% was essential for maximum biomass formation, whereas only 10% DOT was required for maximum PG synthesis. Non-Newtonian shear thickening behavior (n > 1.0) was depicted at DOT levels of 10% and 30%, whereas non-Newtonian shear thinning behavior (n < 1.0) was dominant at 50% DOT. The overall fermentation duration (50-70 h) was considerably shorter compared to common fungal fermentations, revealing the economic feasibility of this particular process. As a result this study not only introduced a new strain with a potential of producing a highly commercially significant enzyme but also provided certain parameters significant in the design and mathematical modeling of fungal bioprocesses.