Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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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 The Use of Organic Sun-Dried Fruits for Delivery of Phenolic Compounds(İzzet KARA, 2022) Dervişoğlu, Gökhan; Yemenicioğlu, AhmetThe aim of this study is to characterize and increase the total soluble (water soluble + alcohol soluble) phenolic (SPCT) and flavonoid content (SFCT) and total soluble free radical scavenging based antioxidant capacity (SACT) of major sun-dried fruits such as raisins, figs, prunes and apricots. Due to their high insoluble dietary fiber content, the bound antioxidant capacity formed 61 to 67% of the overall antioxidant capacity (water soluble + alcohol soluble + bound) of sun-dried fruits. The SPCT, SFCT and SACT of sun-dried fruits changed between 1675 and 3860 μg catechin/g (d.w.), 161 and 495 μg catechin/g (d.w.) and 13 and 28.5 μmol Trolox/kg (d.w.), respectively. The incorporation of green tea polyphenols into sun-dried raisins, figs and apricots by controlled rehydration conducted in green tea extracts increased their SPCT, SFCT and SACT 1.5 to 1.8 fold, 1.3 to 1.6 fold, and 1.5 to 2.6 fold, respectively. The method applied caused limited increases in SPCT (1.1 fold) and SFCT (1.2 fold) of prunes, but it increased SACT of these fruits 1.6 fold. This study showed the possibility of using sun-dried fruits not only as source of dietary fiber, but also for delivery of phenolic compounds. The methods used in this study for delivery of green tea phenolic compounds to selected organic sun-dried fruits could be an alternative method to increase intake of these invaluable antioxidant compounds and increase functionality of sun-dried fruits which are already accepted as good source of dietary fiber.Article Citation - WoS: 1Citation - Scopus: 1In Vitro Assessment of Food-Derived Bioaccessibility and Bioavailability in Bicameral Cell Culture System(Türk Biyokimya Derneği, 2020) Özel Taşcı, Cansu; Pilatin, Gözde; Edeer, Özgür; Güleç, ŞükrüBackground: Functional foods can help prevent metabolic diseases, and it is essential to evaluate functional characteristics of foods through in vitro and in vivo experimental approaches. Objective: We aimed to use the bicameral cell culture system combined with the in vitro digestion to evaluate glucose bioavailability. Materials and methods: Cake, almond paste, and pudding were modified by adding fiber and replacing sugar with sweeteners and polyols. Digestion process was modeled in test tubes. Rat enterocyte cells (IEC-6) were grown in a bicameral cell culture system to mimic the physiological characteristics of the human intestine. The glucose bioaccessibility and cellular glucose efflux were measured by glucose oxidase assay. Results and discussion: The glucose bioaccessibilities of modified foods were significantly lower (cake: 2.6 fold, almond paste: 9.2 fold, pudding 2.8 fold) than the controls. Cellular glucose effluxes also decreased in the modified cake, almond paste, and pudding by 2.2, 4, and 2 fold respectively compared to their controls. Conclusion: Our results suggest that combining in vitro enzymatic digestion with cell culture studies can be a practical way to test in vitro glucose bioaccessibility and bioavailability in functional food development.Article Citation - WoS: 4Citation - Scopus: 4The Volatile Compounds, Free Fatty Acid Composition and Microbiological Properties of Sepet Cheese Packaged With Different Modified Atmosphere Conditions(Kafkas Üniversitesi, 2017) Akpınar, Aslı; Yerlikaya, Oktay; Kınık, Özer; Kahraman, Cihan; Korel, Figen; Uysal, Harun RaşitThe objective of this present study was to investigate traditional sepet cheese samples which were packaged with different modified atmosphere conditions (MAP). The volatile compounds, free fatty acid composition and microbiological properties of Sepet cheeses were analyzed on 1., 45., 90. and 180. day of the storage period at +4°C. In packaking of cheese, three different modified atmosphere packaging conditions were tried. These cheeses were packaged into polystyrene packages that include 100% N2 (N), 80% N2 + 20% CO2 (NC), 100% CO2 (C). In accordance with volatile compounds of sepet cheese samples, it was shown that control cheese sample was different from MAP samples in terms of aroma fractions. MAP samples showed variability in preservation of aroma fractions. When fatty acid composition during the storage period was researched, it was found that there was a significant difference in all samples. When microbiological properties were investigated statistically, it was determined that there was not a significant difference in samples during storage. In general, it could be said that sepet cheeses that were packaged in different modified conditions protected their specialities better.Article Citation - WoS: 13Citation - Scopus: 14Evaluation of Orange Peel, an Industrial Waste, for the Production of Aspergillus Sojae Polygalacturonase Considering Both Morphology and Rheology Effects(TUBITAK, 2014) Gögüş, Nihan; Hakgüder Taze, Bengi; Demir, Hande; Tarı, Canan; Ünlütürk, Sevcan; Lahore, Marcelo FernandezOrange peel is an agroindustrial waste rich in pectin and known to be an inducer for pectinase production. The use of this low-cost substrate for the production of an industrially important enzyme, polygalacturonase (PG), can be an alternative way to turn this waste into a value-added product, contributing to the reduction of environmental waste disposal problems. Enzyme productions by fungal microorganisms are affected by environmental and nutritional factors, demanding the determination of optimum conditions for maximum enzyme production with the desired fungal morphology and broth rheology. Therefore, complex and additional carbon sources were optimized with respect to PG production by Aspergillus sojae using statistical approaches. Effect of pH, another significant parameter affecting the rheology and morphology of the strain, was investigated in the serial bioreactor system using the optimized medium composition. Highest PG enzyme yield and productivity together with the maximum PG enzyme production (93.48 U/mL) were obtained under uncontrolled pH conditions. Under these conditions, morphologically, pellet sizes exhibited a normal distribution ranging between 0.5-1.0 mm and 1.0-1.5 mm, and rheological measurements revealed that fermentation broths showed non-Newtonian flow. The low pH trend observed during the course of the fermentation was another important positive outcome for industrial fermentations, prone to contamination problems.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.Article Citation - WoS: 1Citation - Scopus: 1Prevalence of Salmonella in Edible Offal in Afyonkarahisar Province, Turkey(Kafkas Üniversitesi, 2012) Akkaya, Levent; Atabay, Halil İbrahim; Gök, Veli; Yaman, HilmiIn this study, the prevalence of Salmonella sp. was examined using a total of 205 edible bovine offal samples collected from different abattoirs (n=105) and butcheries (n=100) by immunomagnetic separation (IMS) method. The isolation rate of Salmonella was found to be 8.57%, 5.71% and 5.71% for the liver, kidney and tripe samples collected from the abattoir, respectively. Of the offal samples obtained from the butcheries, the detection rate of Salmonella sp. was 16% in the liver and 4% in the kidney, tripe and brain samples. Overall, it was found that 8.29% of all the offal samples obtained from the abattoirs and butcheries were determined to be contaminated with Salmonella sp. The results of this study shows that edible offal are cross-contaminated by Salmonella sp. at the abattoirs and retail sale points until they reach to the consumer. It is recommended that adequate hygienic and sanitary measures be taken in these kind of places in order to protect public health.Article Citation - WoS: 28Citation - Scopus: 32Optimization of the Process Parameters for the Utilization of Orange Peel To Produce Polygalacturonase by Solid-State Fermentation From an Aspergillus Sojae Mutant Strain(TUBITAK, 2012) Demir, Hande; Göğüş, Nihan; Tarı, Canan; Heerd, Doreen; Lahore, Marcelo FernandezThe effect of orange peel concentration, HCl concentration, incubation time and temperature, and inoculum size on the spore count and activity of polygalacturonase (PG) enzyme produced from Aspergillus sojae M3 by solidstate fermentation was screened using 2k factorial design. Orange peel and HCl concentrations and incubation time were significant factors affecting the responses. Optimum conditions favoring both PG and spore production from Aspergillus sojae M3 were determined as 2% orange peel and 50 mM HCl concentrations at 22 °C and 4.3 days of incubation. An overlay plot was constructed for use as a practical chart for production of high enzyme activity (>35.0 U/g substrate) and spore count (9.0 × 108 to 2.0 × 109 spore/mL) by superimposing the contours of PG activity and spore count responses. The accuracy and reliability of the constructed models on the responses was validated with the maximum calculated error rate between the predicted and actual activities at 14.1% and 22.4%, respectively. © TÜBİTAK.Article Citation - WoS: 8Citation - Scopus: 7Commercially Suitable Pectin Methylesterase From Valencia Orange Peels(Türkiye Klinikleri Journal of Medical Sciences, 2010) Şimşek, Şebnem; Yemenicioğlu, AhmetA simple and effective procedure was developed to extract pectin methylesterase (PME) from Valencia orange peels. Orange peels contain 25-34 μmol of COOH min-1 g-1 of peel PME activity. The enzyme was ionically bound to cell walls and could not be extracted with water. This enables removal of water soluble pectic substances and oils from peels via homogenization and washing with water before enzyme extraction. Enzyme extraction can be conducted simply by addition of suitable amounts of NaCl (optimum: 10 g of NaCl 100 g-1 of extraction mixture) to peel homogenate and stirring (optimum: 30 min at 200 rpm). The PME extracted from orange peels contains almost the same amount of heat-stable and heat-labile fraction, and the enzymes cannot be activated by mild heating. A slight activation of enzyme (almost 20%) was achieved by adding 1 mM CaCl2 to enzyme extracts, but this agent was inhibitory at higher concentrations. The extracts stabilized by Na-benzoate and K-sorbate maintained more than 90% of their PME activity at 4 °C for at least 5 months. The obtained PME was successfully used to prepare low-methoxyl citrus pectin used in edible film formation in the presence of CaCl2. This study shows the potential of using Valencia orange peels as a source of commercial PME. © TÜBİTAK.