Molecular Biology and Genetics / Moleküler Biyoloji ve Genetik
Permanent URI for this collectionhttps://hdl.handle.net/11147/9
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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 Determination of the Effects of Biomaterials on Human Peripheral Blood Mononuclear Cells (pbmc)(IOS Press, 2002) Sudağıdan, Mert; Güneş, Hatice; Harsa, ŞebnemArticle 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 Citation - WoS: 49Citation - Scopus: 66Bioactive, Functional and Edible Film-Forming Properties of Isolated Hazelnut (corylus Avellana L.) Meal Proteins(Elsevier Ltd., 2014) Aydemir, Levent Yurdaer; Adan Gökbulut, Aysun; Baran, Yusuf; Yemenicioğlu, AhmetThis study aimed characterization of bioactive, functional and edible film making properties of isolated proteins from untreated (HPI), hot extracted (HPI-H), acetone washed (HPI-AW), and acetone washed and hot extracted (HPC-AW-H) hazelnut meals. The most bioactive protein extract was HPC-AW-H, followed by HPI-AW, HPI-H and HPI, based on antioxidant activity (TEAC and ORAC: 158-461mmolTrolox/kg), iron chelation (60.7-126.7mmolEDTA/kg), angiotensin-converting enzyme inhibition (IC50: 0.57-1.0mg/mL) and antiproliferative activity on colon cancer cells (IC50: 3.0-4.6mg/ml). Protein contents of HPI, HPI-H and HPI-AW (93.3-94.5%) were higher than that of HPC-AW-H (86.0%), but HPC-AW-H showed the best pH-solubility profile. The extracts showed good oil absorption (7.4-9.4g/g) and foaming, but limited water holding and gelling capacities, and emulsion stability. The protein extracts gave transparent, yellowish to brownish and reddish colored and water soluble edible films. The HPI gave the lightest colored films with acceptable mechanical properties (elongation up to 144% and tensile strength up to 4.9MPa). 1-D and 2-D electrophoresis clearly showed the molecular and isoelectric profiles of hazelnut proteins. The overall results of this study showed that the bioactive, solubility and gelation properties of hazelnut proteins could be improved by simple processes like acetone washing and/or heat treatment. The hazelnut proteins are valuable as multipurpose food ingredients.Article Citation - WoS: 23Citation - Scopus: 29Physical Properties of Biopolymers Containing Natamycin and Rosemary Extract(John Wiley and Sons Inc., 2009) Türe, Hasan; Özen, Fatma Banu; Eroğlu, Erdal; Soyer, Ferda; Özen, Banu; Soyer, FerdaAntifungal biopolymers were prepared by incorporating natamycin (NA) and NA + rosemary extract (RE) into wheat gluten (WG) and methyl cellulose (MC) films. Interaction between antimicrobial agents and biopolymers was determined with mid-infrared spectroscopy and scanning electron microscopy (SEM). Water vapour permeability and mechanical properties of these films were also measured. Mid-infrared spectroscopy did not indicate any interaction. SEM observations showed that NA crystallises at high concentrations in biopolymers. There were no significant changes in water vapour permeabilities of biopolymers containing active agents at P < 0.05. While NA incorporation did not result in any changes in mechanical properties of WG films a reduction in tensile strength was observed for MC films containing high concentration of NA. In general, active agent incorporation into WG and MC films did not result in any considerable changes in their physical properties that could affect their application.Article Citation - WoS: 66Citation - Scopus: 81Effect of Biopolymers Containing Natamycin Against Aspergillus Niger and Penicillium Roquefortii on Fresh Kashar Cheese(John Wiley and Sons Inc., 2011) Türe, Hasan; Eroğlu, Erdal; Özen, Banu; Soyer, FerdaFungal spoilage during refrigerated storage is one of the main safety and quality-related problems for dairy products. The effect of wheat gluten (WG) and methyl cellulose (MC) biopolymers containing natamycin (NA) on the growth of Aspergillus niger and Penicillium roquefortii on the surface of fresh kashar cheese during storage at 10 C for 30 days was investigated. Wrapping of A. niger-inoculated cheese with MC films containing 5–20 mg NA per 10 g resulted in approximately 2-log reductions in spore count. Two mg NA per 10 g included into WG films was sufficient to eliminate A. niger on the surface of cheese. However, MC and WG films containing NA did not cause any significant decrease in P. roquefortii count on the cheese surface. Therefore, especially use WG films in dairy applications could be an effective way of controlling A. niger growth on these products.Article Citation - WoS: 86Citation - Scopus: 102Total Antioxidant Activity and Total Phenolic Contents in Different Turkish Eggplant (solanum Melongena L.) Cultivars(Taylor and Francis Ltd., 2009) Ökmen, Bilal; Şığva, Hasan Özgür; Mutlu, Sevgi; Doğanlar, Sami; Yemenicioğlu, Ahmet; Frary, AnneIn this study, total water soluble antioxidant activity and phenolic content of 26 eggplant (Solanum melongena L.) cultivars were investigated. Total water soluble antioxidant activity of the cultivars varied from 2664 to 8247 molTrolox/kg, which is a 3.1-fold difference. Cultivars also showed significant variation for total phenolic contents ranging from 615 to 1376 mg/kg, a 2.2-fold difference. The two traits were significantly correlated and results of this study suggested that breeders can use the information to develop eggplant cultivars with high antioxidant activity.Article Citation - WoS: 14Citation - Scopus: 23Water-Soluble Antioxidant Potential of Turkish Pepper Cultivars(American Society for Horticultural Science, 2008) Frary, Anne; Keçeli, Mehmet Ali; Ökmen, Bilal; Şığva, Hasan Özgür; Yemenicioğlu, Ahmet; Doğanlar, SamiIn this work, 29 pepper cultivars that represent the diversity of types and varieties grown in Turkey were analyzed for water-soluble antioxidant capacity and phenolic and vitamin C contents. In addition, 14 non-Turkish cultivars were tested for comparison. Significant diversity was observed in the different cultivars with the most variation (7.4-fold) seen for total antioxidant capacity, which ranged from 2.57 to 18.96 mmol Trolox/kg. Vitamin C content for the peppers ranged from 522 to 1631 mg·kg-1, a 3.1-fold difference, whereas total phenolic content for the pepper cultivars ranged from 607 to 2724 mg·kg-1, a 4.5-fold difference. When cultivars were grouped by morphology/ use, it was found that some types had significantly more variation and higher antioxidant activities than other types. Thus, for water-soluble antioxidant capacity, most variation was seen in long, blunt-ended Çarliston types, whereas long, pointed Sivri peppers had the highest mean capacity. Bell-shaped Dolmalik and Sivri peppers had the most variation for phenolic content, but fancy Süs and Sivri types had the highest means for this trait. Dolmalik types showed the most variation for vitamin C content, whereas Süs and Sivri peppers had the highest means for this character. All three parameters were significantly and positively correlated with the strongest correlation between total antioxidant capacity and phenolic content (r = 0.71). The presence of significant variation for antioxidant content in Turkish germplasm indicates that this material can be used for improvement and genetic mapping of nutritional content in pepper.Article Citation - WoS: 125Citation - Scopus: 156Antimicrobial and Antioxidant Activity of Edible Zein Films Incorporated With Lysozyme, Albumin Proteins and Disodium Edta(Elsevier Ltd., 2007) Mecitoğlu Güçbilmez, Çiğdem; Yemenicioğlu, Ahmet; Arslanoğlu, AlperIn this study, partially purified lysozyme was incorporated into zein films in combination with chickpea albumin extract (CPAE), bovine serum albumin (BSA) and disodium EDTA. The zein films showed an inherent free radical scavenging activity. Incorporation of lysozyme did not contribute to soluble free radical scavenging activity of zein films. However, the incorporation of lysozyme in combination with CPAE increased the soluble and immobilized free radical scavenging activity of zein films 17% to 25% and almost 84%, respectively. The incorporation of CPAE also improved the distribution of partially purified lysozyme preparation in zein films and enabled the controlled release of lysozyme by reducing its release rate from zein films between 1.5- and 3.5-fold, depending on the concentration of incorporated CPAE. In contrast, the BSA incorporation made distribution of lysozyme more heterogeneous and it did not contribute to the free radical scavenging activity of films significantly. The combinational incorporation of partially purified lysozyme with disodium EDTA · 2H2O or CPAE and disodium EDTA · 2H2O gave zein films effective on Escherichia coli and Bacillus subtilis. This study clearly showed the benefits of using functional protein extracts to control lysozyme distribution and release rate and to improve antioxidant activity in zein films.Article Citation - WoS: 46Citation - Scopus: 52Antifungal Activity of Biopolymers Containing Natamycin and Rosemary Extract Against Aspergillus Niger and Penicillium Roquefortii(John Wiley and Sons Inc., 2008) Türe, Hasan; Eroğlu, Erdal; Soyer, Ferda; Özen, Fatma BanuAntimicrobial agent-releasing films have been proposed as an effective way of inhibiting chiefly surface spoilage of food products. Antifungal activities of natamycin (NA), rosemary extract (RE) and NA + RE were tested against Aspergillus niger and Penicillium roquefortii with agar disc diffusion assay. NA, RE and NA + RE were also included into biopolymers made from gluten and methyl cellulose. Minimum inhibitory concentrations (MIC) of NA in both films were 2 and 1 mg NA per 10 g film solution against A. niger and P. roquefortii, respectively. RE did not show any inhibitory antifungal activity alone. Although NA incorporated into both films at a concentration of 1.5 mg NA per 10 g film solution was not effective against A. niger, combination of NA at the same concentration with RE in the films inhibited the growth of this mould. NA in solution or in biopolymers is very effective in inhibiting the growth of selected organisms, and RE acted synergistically with NA to prevent the growth of A. niger when incorporated into both films. © 2008 Institute of Food Science and Technology