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.Data Paper Knockdown of Death Receptor 5 Antisense Long Noncoding Rna and Cisplatin Treatment Modulate Similar Macromolecular and Metabolic Changes in Hela Cells(TÜBİTAK - Türkiye Bilimsel ve Teknolojik Araştırma Kurumu, 2022) Gürer, Dilek Cansu; Erdoğan Vatansever, İpek; Ceylan, Çağatay; Akgül, BünyaminBackground/aim: Despite great progress in complex gene regulatory mechanisms in the dynamic tumor microenvironment, the potential contribution of long noncoding RNAs (lncRNAs) to cancer cell metabolism is poorly understood. Death receptor 5 antisense (DR5-AS) is a cisplatin inducible lncRNA whose knockdown modulates cell morphology. However, its effect on cell metabolism is unknown. The aim of this study is to examine metabolic changes modulated by cisplatin and DR5-AS lncRNA in HeLa cells. Materials and methods: We used cisplatin as a universal cancer therapeutic drug to modulate metabolic changes in HeLa cervix cancer cells. We then examined the extent of metabolic changes by Fourier transform infrared spectroscopy (FTIR). We also performed transcriptomics analyses by generating new RNA-seq data with total RNAs isolated from cisplatin-treated HeLa cells. Then, we compared cisplatin-mediated transcriptomics and macromolecular changes with those mediated by DR5-AS knockdown. Results: Cisplatin treatment caused changes in the unsaturated fatty acid and lipid-to-protein ratios and the glycogen content. These observations in altered cellular metabolism were supported by transcriptomics analyses. FTIR spectroscopy analyses have revealed that DR5-AS knockdown causes a 20.9% elevation in the lipid/protein ratio and a 76.6% decrease in lipid peroxidation. Furthermore, we detected a 3.42% increase in the chain length of the aliphatic lipids, a higher content of RNA, and a lower amount of glycogen indicating relatively lower metabolic activity in the DR5-AS knockdown HeLa cells. Interestingly, we observed a similar gene expression pattern under cisplatin treatment and DR5-AS knockdown HeLa cells. Conclusion: These results suggest that DR5-AS lncRNA appears to account for a fraction of cisplatin-mediated macromolecular ametabolic changes in HeLa cervix cancer cells.Article Citation - WoS: 3Citation - Scopus: 4Comparison of the Effects of Statins on A549 Nonsmall-Cell Lung Cancer Cell Line Lipids Using Fourier Transform Infrared Spectroscopy: Rosuvastatin Stands Out(Wiley, 2021) Aksoy, Hatice Nurdan; Ceylan, ÇağatayStatins are commonly prescribed antilipidemic and anticholesterol class of drugs. In addition to their major role, they have been found to have anticancer effects on in vitro, animal and clinical studies. The aim of this study was to investigate the effects of six different statins (rosuvastatin, pravastatin, simvastatin, lovastatin, fluvastatin, and atorvastatin) on A549 cancer cells lipids by Fourier transform infrared (FTIR) spectroscopy. Proliferation tests were carried out to detect the half-maximal inhibitory concentrations (IC50) of each statin on A549 cells. The IC50 values were 50 mu M for simvastatin, 150 mu M for atorvastatin and pravastatin, and 170 mu M for fluvastatin, 200 mu M for rosuvastatin and lovastatin on A549 cells. No correlation was found between the antiproliferative effects of the statins and lipid-lowering effect. The cells were treated with IC5, IC10, and IC50 values of each statins concentration and lipid extracts were compared using FTIR spectroscopy. The results indicated that different statins had different effects on the lipid content of A549 cells. The FTIR spectra of the lipid exctracts of statin-treated A549 cells indicated that the value of hydrocarbon chain length, unsaturation index, oxidative stress level, and phospholipid containing lipids increased except for rosuvastatin-treated A549 cells. In addition, rosuvastatin significantly lowered cholesterol ester levels. In conclusion, the contrasting effects of rosuvastatin should be further investigated.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.Article 2’-Methylklavuzon Causes Lipid-Lowering Effects on A549 Non-Small Cell Lung Cancer Cells and Significant Changes on Dna Structure Evidenced by Fourier Transform Infrared Spectroscopy(Elsevier, 2020) Ceylan, Çağatay; Aksoy, Hatice Nurdan; Çağır, Ali; Çetinkaya, HakkıVarious chemical agents are used in the treatment of Non-Small Cell Lung Cancer (NSCLC). 2?-methylklavuzon was proposed as a potential chemotherapeutic agent in cancer treatment based on its topoisomerase inhibition activity. In this study the cellular effects of 2?-methylklavuzon was evaluated on A549 cancer cells using FTIR spectroscopy. 2?-methylklavuzon induced significant changes on both the whole cell lyophilizates and the lipid extracts of the A549 lung cancer cells. 2?-methylklavuzon caused significant structural changes in A549 cell DNA structure: T, A and G DNA breathing modes are lost after the drug application indicating the loss of topoisomerase activity. The level of transcription and RNA synthesis was enhanced. 2?-methylklavuzon induced single stranded DNA formation evidenced by the increase in the ratio of asymmetric/symmetric phosphate stretching modes. 2?-methylklavuzon induced band shifts only in the asymmetric mode of phosphate bonds not in the symmetrical phosphate bond stretching. 2?-methylklavuzon induced A form of DNA topography. In addition to the changes in the DNA structure and transcription 2?-methylklavuzon also caused lipid-lowering effect in A549 cancer cells. 2?-methylklavuzon suppressed lipid unsaturation, however, it induced formation of lipids with ring structures. 2?-methylklavuzon suppressed phosphate-containing lipids significantly and decreased carbonyl containing lipids and cholesterol slightly. 2?-methylklavuzon caused increases in the hydrocarbon chain length. Overall, 2?-methylklavuzon can be used as a lipid-lowering compound in the treatment of NSCLC and other cancer therapies. © 2020 Elsevier B.V.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.