Food Engineering / Gıda Mühendisliği
Permanent URI for this collectionhttps://hdl.handle.net/11147/12
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Article Identification of Staphylococcus Aureus Cheese Isolates With Respect To Virulence Properties, Genetic Relatedness and Antibiotic Resistance Profiles(Özkan Özden, 2019) Kadiroğlu, Pınar; Korel, Figen; Ceylan, ÇağatayThe problems on identification of Staphylococcus aureus isolates from cheese samples wereinvestigated by phenotypic and genotypic tests in this study. Among 207 Staphylococcus spp.isolated from 31 cheese samples, 23 isolates that were Gram positive, catalase and slide coagulasepositive, with 1 isolate that was latex agglutination test negative showed different phenotypicproperties. Polymerase chain reaction (PCR) and quantitative PCR (qPCR) analyses showed thatDNase test and target genes (nuc, coa) regarded as gold standard regions for S. aureus were notfound to be unique for identification of S. aureus. The toxin genes (SEA-SEE) were not detected byPCR. Antibiotic resistance profiles of S. aureus isolates demonstrated that two isolates were resistantto penicillin G. This study showed that the unique phenotypic and genotypic test was not adequatefor identification of S. aureus isolates. There was no correlation between the presence of the nucgene and toxin genes. The presence of nuc gene which was used for detection of S. aureus was alsofound to be present in other Staphylococcus isolates. As a conclusion, the results revealed thatbiochemical tests could lead to false positive results for identification of S. aureus. The presence ofnuc gene is not correlated with the presence of toxin genes.Article Extraction and Characterization of Pectin From Fresh Globe Artichoke and Canned Artichoke Waste(Gıda Teknolojisi Derneği, 2017) Ceylan, Çağatay; Bayraktar, Oğuz; Atçı, Erhan; Sarrafi, ŞahinThe pectin contents of fresh globe artichoke (stem, receptacle, and bract) and waste of artichokecanning industry were investigated. The highest pectin amount was found in the stem part of freshglobe artichoke (6.42%) with the highest amount of anhydrogalacturonic acid (AGA) and anhydrouronicacid (AUA) content. The pectin yields of receptacle and bract parts were found to be 5.31 and 4.55%,respectively. The pectin yield from the industrial waste was the lowest, 4.43%. The highest ash content(5.65 %) along with the lowest anhydrouronic acid amount (73.28%) indicated the lowest purity for theindustrial waste. The degrees of esterification for the pectin obtained from the stem, receptacle andbract parts were 55.26%, 52.26%, and 56.17%, respectively indicating the presence of high methyl-esterified(HM) pectin. The pectin from the industrial waste had the lowest degree of esterification (46.02%). TheFTIR results indicated that acid processing affected the structural properties of pectin from the industrialwaste with higher methoxyl content and esterification degree.Book Part Citation - Scopus: 4Bacteria: Arcobacter(Elsevier, 2014) Atabay, Halil İbrahim; Corry, Janet E.L.; Ceylan, ÇağatayThe genus Arcobacter currently comprises many phenotypically different species isolated from diverse niches. Although some Arcobacter spp. (particularly, Arcobacter butzleri, Arcobacter skirrowii, and Arcobacter cryaerophilus) are associated with various diseases in humans and animals, their exact epidemiological and pathological role is not completely understood, and few cases of human infection are reported. The primary mode of Arcobacter transmission is thought to occur via contaminated water and food and contact with pets. As some species are difficult to cultivate and all are difficult to identify using conventional biochemical tests, nucleic acid-based techniques such as polymerase chain reaction (PCR) and real-time PCR are increasingly used for their simultaneous detection, identification, and quantification. Their tendency to be resistant to antibiotics, and their ability to colonize food processing environments indicate that they could cause serious disease in the human population, particularly in susceptible individuals with impaired immune response. © 2014 Elsevier Inc. All rights reserved.Conference Object Antiproliferative and Apoptotic Effects of Ponatinib and Its Effects on Macromolecular Changes in Imatinib-Sensitive and Resistant Chronic Myeloid Leukemia (cml) Cell Lines: a Mechanistic Approach(Ferrata Storti Foundation, 2015) Kartal Yandım, Melis; Ceylan, Çağatay; Elmas, Efe; Baran, Yusuf[No abstract available]Article Citation - WoS: 6Citation - Scopus: 6A Molecular and Biophysical Comparison of Macromolecular Changes in Imatinib-Sensitive and Imatinib-Resistant K562 Cells Exposed To Ponatinib(SAGE Publications Inc., 2016) Kartal Yandım, Melis; Ceylan, Çağatay; Elmas, Efe; Baran, YusufChronic myeloid leukemia (CML) is a type of hematological malignancy that is characterized by the generation of Philadelphia chromosome encoding BCR/ABL oncoprotein. Tyrosine kinase inhibitors (TKIs), imatinib, nilotinib, and dasatinib, are used for the frontline therapy of CML. Development of resistance against these TKIs in the patients bearing T315I mutation is a major obstacle in CML therapy. Ponatinib, the third-generation TKI, is novel drug that is effective even in CML patients with T315I mutation. The exact mechanism of ponatinib in CML has been still unknown. In this study, we aimed to determine the potential mechanisms and structural metabolic changes activated by ponatinib treatment in imatinib-sensitive K562 human CML cell lines and 3 μM-imatinib-resistant K562/IMA3 CML cell lines generated at our lab. Apoptotic and antiproliferative effects of ponatinib on imatinib-sensitive and 3 μM-imatinib-resistant K562/IMA3 CML cells were determined by proliferation and apoptosis assays. Additionally, the effects of ponatinib on macromolecules and lipid profiles were also analyzed using Fourier transform infrared spectroscopy (FTIR). Our results revealed that ponatinib inhibited cell proliferation and induced apoptosis as determined by loss of mitochondrial membrane potential, increased caspase-3 enzyme activity, and transfer of phosphatidylserine to the plasma membrane in both K562 and K562/IMA-3 cells. Furthermore, cell cycle analyses revealed that ponatinib arrested K562 and K562/IMA-3 cells at G1 phase. Moreover, ponatinib treatment created a more ordered nucleic acid structure in the resistant cells. Although the lipid to protein ratio increased in imatinib-sensitive K562 cells with a little decrease in the K562/IMA-3 cells, ponatinib treatment indicated significant changes in the lipid composition such as a significant increase in the cellular cholesterol amounts much more in the K562/IMA-3 cells than the sensitive counterparts. Unsaturation in lipids was higher in the resistant cells; however, increases in lipids without phosphate and the number of acyl chains were much higher in the K562 cells. Taken together, all these results showed powerful antiproliferative and apoptotic effects of ponatinib in both imatinib-sensitive and imatinib-resistant CML cells in a dose-dependent manner, and hence, the use of ponatinib for the treatment of TKI-resistant CML patients may be an effective treatment approach in the clinic. More importantly, these results showed that FTIR spectroscopy can detect drug-induced physiological changes in cancer drug resistance.Article Citation - WoS: 11Citation - Scopus: 9Biophysical Evaluation of Physiological Effects of Gilthead Sea Bream (sparus Aurata) Farming Using Ftir Spectroscopy(Elsevier Ltd., 2014) Ceylan, Çağatay; Tanrıkul, Tansel; Özgener, HüseyinSparus aurata is one of the two most important cultured fish species in the Mediterranean region. The present work investigates the effects of culturing in S. aurata liver tissue at the molecular level using Fourier Transform Infrared (FTIR) spectroscopy. FTIR spectroscopy revealed dramatic differences between the wild and aquacultured fish liver cells, which mainly indicated that the level of glycogen increased in the aquacultured samples and the protein/lipid ratio decreased by 42.29% indicating that triglycerides and cholesterol esters increased and the protein content decreased in the aquacultured samples. The 15.99% increase in the level of unsaturation indicated elevated lipid peroxidation. Structural/organisational changes in the nucleic acids along with increased transcriptional status of the liver tissue cells were observed in the cultured fish tissue. All these results indicated that culturing induces significant changes in fish physiology. In addition FTIR spectroscopy is a promising method to monitor the physiological changes in fish physiology.Article Citation - WoS: 11Citation - Scopus: 9Quantification of Staphylococcus Aureus in White Cheese by the Improved Dna Extraction Strategy Combined With Taqman and Lna Probe-Based Qpcr(Elsevier Ltd., 2014) Kadiroğlu, Pınar; Korel, Figen; Ceylan, ÇağatayFour different bacterial DNA extraction strategies and two different qPCR probe chemistries were studied for detection of Stapylococcus aureus from white cheeses. Method employing trypsin treatment followed by a commercial kit application and TaqMan probe-based qPCR was the most sensitive one detecting higher counts than standards in naturally contaminated samples.Article Citation - WoS: 13Citation - Scopus: 13Macromolecular Changes in Nilotinib Resistant K562 Cells; an in Vitro Study by Fourier Transform Infrared Spectroscopy(SAGE Publications Inc., 2012) Ceylan, Çağatay; Camgöz, Aylin; Baran, YusufNilotinib is a second generation tyrosine kinase inhibitor which is used in both first and second line treatment of chronic myeloid leukemia (CML). In the present work, the effects of nilotinib resistance on K562 cells were investigated at the molecular level using Fourier transform infrared (FT-IR) spectroscopy. Human K562 CML cells were exposed to step-wise increasing concentrations of nilotinib, and sub-clones of K562 cells resistant to 50 nM nilotinib were generated and referred to as K562/NIL-50 cells. Antiproliferative effects of nilotinib were determined by XTT cell proliferation assay. Changes in macromolecules in parental and resistant cells were studied by FT-IR spectroscopy. Nilotinib resistance caused significant changes which indicated increases in the level of glycogen and membrane/lipid order. The amount of unsaturated lipids increased in the nilotinib resistant cells indicating lipid peroxidation. The total amount of lipids did not change significantly but the relative proportion of cholesterol and triglycerides altered considerably. Moreover, the transcriptional status decreased but metabolic turn-over increased as revealed by the FT-IR spectra. In addition, changes in the proteome and structural changes in both proteins and the nucleus were observed in the K562/NIL-50 cells. Protein secondary structural analyses revealed that alpha helix structure and random coil structure decreased, however, anti-parallel beta sheet structure, beta sheet structure and turns structure increased. These results indicate that the FT-IR technique provides a method for analyzing drug resistance related structural changes in leukemia and other cancer types.Article Kinetic and Structural Characterization of Interaction Between Trypsin and Equisetum Arvense Extract(Türk Biyokimya Derneği, 2014) Uslu, Mehmet Emin; Bayraktar, Oğuz; Ceylan, ÇağatayObjective: In this study the inhibitory effect of E. arvense extract on trypsin activity and the effect of trypsin on E. arvense extract were studied. In addition the nature of the interaction between the extract and trypsin was investigated. Methods: The inhibitory effect ethanol extract of E. arvense on trypsin activity was determined using trypsin enzyme assay. The structural effects of the extract-trypsin interaction for the extract were analyzed by FTIR. Finally, the HPLC analyses were carried out to analyze the individual components of the extract and the supernatant and soluble precipitate phases. Results: E. arvense extract was found to decrease total percent activity of trypsin to 5% in 24 hour at 24 °C. FTIR analyses indicated that the interaction between trypsin and E. arvense extract caused changes in the structure and hydrogen bonding behavior and composition of the extract proteins. These interactions also caused the extract lipids to accumulate in the insoluble precipitate phase. Most of the phenolics remained in the supernatant phase enhancing the inactivation of trypsin. However, the precipitated compounds were shown to be of apolar in nature as shown in the HPLC chromatograms. Conclusion: The methods that were used showed that the high phenolic content of E. arvense was the main reason for the inhibition of trypsin enzyme activity by denaturing the enzyme.Article Citation - WoS: 1Citation - Scopus: 2Structural and Functional Characterization of Solution, Gel, and Aggregated Forms of Trypsin in Organic Solvent-Assisted and Ph-Induced Phase Changes(Türk Biyokimya Derneği, 2015) Ceylan, Çağatay; Karaçiçek, BilgeIn this study the effect of three different physicochemical parameters on pHtriggered gelation and aggregation of bovine pancreatic trypsin changes and structural and functional changes in these changes in alcohol-water mixtures were studied. Methods: Trypsin gelation times were studied using inverted tube method. Trypsin stability was studied using trypsin enzyme assay. Protein secondary structural changes were monitored using FTIR spectroscopy. Gel and aggregate macrostructures and morphologies were viewed using Scanning Electron Microscopy. Results: The solution phase was observed in the absence of both NaOH and CaCl2. The gel phase was observed in the absence of the either. The aggregate phase was observed in the presence of the both agents all depending on trypsin concentrations used. Trypsin stability studies showed that there were a nearly 53 and 32% specific activity losses after the gelation and aggregation processes. According to FTIR studies β–sheet structure in 1637 cm-1 band disappeared in trypsin gel and trypsin aggregates. Increases in α–helix structure in 1651 cm-1 in trypsin gel and aggregates were observed. Iodoacetamide delayed the gelation and prevented the aggregation indicating the importance of intermolecular disulfides in the both processes. Conclusion: Trypsin gelation was caused by the denaturation of the protein three dimensional structures. The gel and aggregate formation indicates a secondary structural change towards α–helix structure formation at the expense of β–sheet structure and formation of intermolecular disulfide bonds.