Food Engineering / Gıda Mühendisliği
Permanent URI for this collectionhttps://hdl.handle.net/11147/12
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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 Citation - WoS: 8Citation - Scopus: 9Unrevealing the Impact of Pulsed Electric Fields (pef) on Cucumber Seed Vigour and Surface Disinfection(Sciendo, 2021) Atmaca, Bahar; Akdemir Evrendilek, Gülsün; Bulut, Nurullah; Uzuner, SibelChemicals used for seed treatments help to increase the agricultural production by preventing pests and pathogens but also cause environmental and health problems. Thus, environmentally-friendly technologies need to be developed for a seed treatment that inactivates surface microflora and improves seed vigor. One such pulsed electric field (PEF) treatment applied to cucumber seeds in the range of 1.07-17.28 Joule (J) significantly enhanced a mean germination rate (MGR) by up to 9%, a normal seedling rate by 25.73%, and a resistance to 100 and 200 mM salt stresses by 96% and 91.67%, respectively, with a stronger and faster growth of roots and seedlings. PEF treatment provided 3.34 and 3.22 log-reductions in the surface microflora of total mold and yeast and total aerobic mesophilic bacteria, respectively. The electrical conductivity (EC) values of the control samples increased over time, from 4 to 24 h. Those of the PEF-treated samples after 4, 12, and 24th hours were also more affected by the measurement time not by the PEF treatment. The joint optimization of 18 responses based on the best-fit Gaussian process model pointed to 19.78 s and 17.28 J as the optimal settings. The PEF treatment appeared to improve seed germination ability and stress resistance with the adequate inactivation of surface microflora.Conference Object Potential Application of Natural Phenolic Antimicrobials and Edible Film Technology Against Bacterial Plant Pathogens(International Society for Horticultural Science, 2020) Alkan, Derya; Yemenicioğlu, AhmetIn this study, antimicrobial edible film technology used frequently for inhibition of human pathogens in processed food was employed as a postharvest bio-based preservation method to prevent bacterial spoilage of fresh fruits and vegetables. Antimicrobial edible zein films were developed by incorporation of pure phenolic acids (PAs) such as gallic acid (GA), cinnamic acid (CA), vanillic acid (VA); essential oils (EOs) such as carvacrol (CAR), thymol (THY), eugenol (EUG) and citral (CIT) and phenolic extract (PE) from clove. In order to test synergetic effect of PAs, different amounts of PAs were added into film solution to obtain films containing mixture of GA and CA, GA and VA, CA and VA at different concentrations. The antimicrobial performances of edible films were tested on selected plant pathogenic bacteria including Pseudomonas syringae, Erwinia amylovora, Xanthomonas vesicatoria and Erwinia carotovora. The overall results of antimicrobial tests showed that films containing PAs between 1 and 4 mg cm-2 inhibited all pathogens while EOs at concentrations between 2 and 4 mg cm-2 and clove extract between 4 and 8 mg cm-2 were found effective against pathogens except P. syringae. Morover, the incorporation of combination of different PA showed greater inhibitory activity on plant pathogens than incorporation of a single PA into films. The edible zein coatings have already been applied for coating of fresh fruits and vegetables at the postharvest stage to suppress their respiration rate and prolong their refrigerated storage. This work clearly showed the benefit of incorporating a single or mixture of antimicrobial phenolic compounds, EOs and PEs in edible zein films against bacterial plant pathogens. The developed films might be employed against plant pathogens by coating fresh fruits and vegetables, seeds, seedlings, tree stems, soil as well as agricultural tools and constructions without using toxic chemicals. © 2020 International Society for Horticultural Science. All rights reserved.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.Conference Object Citation - Scopus: 2Preparation and Characterization of Hydroxyapatite/Calcium Phosphate Powders(Trans Tech Publications, 2004) Şimşek, Deniz; Çiftçioğlu, Rukiye; Harsa, ŞebnemThe preparation of calcium phosphate based powders through chemical precipitation in order to determine the optimum conditions for the preparation of stoichiometric, thermally stable hydroxyapatite (HA) powders was investigated in this work. The effects of parameters like pH, aging time, and heat treatment temperature on the phase structure and morphology of the powders were investigated by SEM and XRD.HA was prepared at a Ca/P ratio of 1.67. The precipitation pH had a profound influence on the morphology and crystallite size of the powders in the 4-11 pH range. Relatively large 5 mum prismatic particles were obtained at low pH whereas the powders were formed from agglomerates of nano sized particles at high pH. Powders had a HA dominant phase structure above a pH of 8. Phase pure HA powders were obtained with close to theoretical yields at pH = 10 and 11. The crystallite sizes of the powders varied from about 30 nm at 90degreesC to 50-90 mn at 1250degreesC with the smallest crystallite sizes obtained for pH 10 and 11 powders at 1250degreesC. The crystallite size increased significantly with aging temperature.Article Citation - WoS: 4Prevalence and Diversity of Arcobacter Spp. in Retail Chicken Meat in Turkey(PagePress Publications, 2016) Molva, Çelenk; Atabay, Halil İbrahimArcobacters are food and waterborne pathogens associated with human and animal infections. The objective of the present study was to investigate the prevalence and diversity of Arcobacter spp. in commercially sold chicken meat in Izmir region of Turkey. For this purpose, 100 samples including legs (n= 40), 17 chicken quarters (n= 17), drumstickers (n= 16), breasts (n= 11), wings (n= 10), and carcasses (n= 6) were collected from different retail markets. A total of 65 isolates were confirmed as Arcobacter spp. from 55 samples by genus-specific polymerase chain reaction (PCR). The prevalence of Arcobacter spp. was 32.5, 81.3, 64.7, 72.7, 83.3, and 50% for legs, drumstickers, chicken quarters, breasts, carcasses and wings, respectively. Based on the multiplex-PCR, most of the isolates were identified as A. butzleri (n= 45, 80%), followed by A. cryaerophilus (n= 2, 3.6%), A. skirrowii (n= 1, 1.8%) and 17 isolates (30.9%) could not be identified at the species level.Article Citation - WoS: 12Citation - Scopus: 12Mid-Infrared Spectroscopic Detection of Sunflower Oil Adulteration With Safflower Oil(CSIC Consejo Superior de Investigaciones Cientificas, 2019) Uncu, Oğuz; Özen, Banu; Tokatlı, FigenThe oil industry is in need of rapid analysis techniques to differentiate mixtures of safflower-sunflower oils from pure oils. The current adulteration detection methods are generally cumbersome and detection limits are questionable. The aim of this study was to test the capability of a mid-infrared spectroscopic method to detect the adulteration of sunflower oil with safflower oil compared to fatty acid analysis. Mid-infrared spectra of pure oils and their mixtures at the 10-60% range were obtained at 4000-650 cm(-1) wavenumber and fatty acid profiles were determined. Data were analyzed by multivariate statistical analysis techniques. The lowest level of detection was obtained with mid-infrared spectroscopy at 30% while the fatty acid profile could determine adulteration at around 60%. Adulteration levels were predicted successfully using PLS regression analysis of infrared data with R-2 (calibration) = 0.96 and R-2 (validation) = 0.93. As a rapid and minimum waste generating technique, mid-infrared spectroscopy could be a useful tool for the screening of raw material to detect safflower-sunflower oil mixtures.Article Citation - WoS: 5Citation - Scopus: 5Chemometric Analysis of Chemo-Optical Data for the Assessment of Olive Oil Blended With Hazelnut Oil(Stazione Sperimentale per le Industrie, 2019) Kadiroğlu, Pınar; Korel, Figen; Pardo, MatteoThe main objective of this study was to determine different hazelnut oil concentrations in extra virgin olive oil (EV00) belonging to different geographical regions inside Turkey using the combination of a SAW sensor based electronic nose (e-nose) and a machine vision system (MVS). We leveraged the oil characterisation given by the two easy-to-use and complementary experimental techniques through the adoption of conventional PCA for data exploration and random forests (RF) for supervised learning. The e-nose/MVS combination allows significantly better results both in adulteration detection independently of EVOO's geographical provenance and in EVO0 geographical provenance determination, independently of the adulteration level, with respect to the single characterisation method. RF analysis also produces feature ranking, permitting to shed light on which oils' characteristics influence the learning result. We found that EV00 geographical provenance discrimination is mainly due to yellowness and guaiacol content, while (E)-2-hexenal chiefly determines the prediction of the hazelnut level.Article Citation - WoS: 8Citation - Scopus: 8Usage of Rice Milk in Probiotic Yoghurt Production(North University of Baia Mare, 2016) Uzuner, Aydın Erdem; Kınık, Özer; Korel, Figen; Yıldız, Gamze; Yerlikaya, OktayThere are previous studies focusing on the production of probiotic and fermented dairy products made using vegetable based raw materials like oats and soy, however there is a limited number of studies on the usage of rice milk in fermented dairy products. Four different types of yoghurt samples were produced and stored for 21 days at 4°C. Physical, chemical, microbiological and sensory characteristics of the samples were performed at the 1st, 7th, 14th and 21st days of the storage. It was determined that rice milk increased the viscosity values but decreased the values of the texture, whey separation and the chemical and microbiological properties of yoghurts. Acetaldehyde, acetoin, acetone and diacetyl of carbonyl compounds were detected as main flavor components of yoghurt samples. In the sensory analysis, scores decreased as the rice milk proportions in yoghurt was increased and the panelists reported that P1 sample (25% rice milk + 75% cow's milk) was the closest sample to the control sample (100% cow's milk). Generally speaking, samples containing rice milk did not give good results. However, P1 samples were the most favored products among the samples containing rice milk as they were the closest product to the control group. The consumption of such products is continuously increasing as the customers' tendency to consider them as functional products rather than traditional food products increase.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.