Food Engineering / Gıda Mühendisliği
Permanent URI for this collectionhttps://hdl.handle.net/11147/12
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Article Citation - WoS: 2Citation - Scopus: 2Golden Thistle (scolymus Hispanicus L.) Hydromethanolic Extracts Ameliorated Glucose Absorption and Inflammatory Markers in Vitro(Wiley, 2023) Özel Taşcı, Cansu; Güleç, ŞükrüGolden thistle (GT, Scolymus hispanicus L.) is an edible plant native to the Mediterranean. Several activities have been reported for the GT, as it is used for traditional medicinal purposes in some cultures. In this study, we aimed to investigate the effects of GT crude extract on phenolic bioavailability, antidiabetic, and anti-inflammatory activities by using colonic epithelium (CaCo-2) and murine macrophage (RAW 264.7) cell lines. The CaCo-2 cells were grown on the bicameral membrane system for intestinal bioavailability and glucose efflux. Lipopolysaccharide (LPS, 0.5 mu g/mL) was used to induce systemic inflammation on RAW 264.7. The inflammatory medium of RAW 264.7 cells was given to Caco-2 cells to mimic colonic inflammation. Our results showed that 5-o-caffeoylquinic acid had an apparent permeability of (1.82 +/- 0.07) x 10-6 cm/s after 6 h. The extract lowered the glucose efflux by 39.4%-42.6%, in addition to the reductions in relative GLUT2 mRNA expressions by 49%-66% in pre- and co-treatments (p < .05). Decreases in systemic inflammation markers of nitric oxide, tumor necrosis factor-alpha, and interleukin-6 (IL-6) were also detected in 30%-45% range after pre-treatments with the GT extract (p < .05). Lastly, colonic inflammation markers of IL-6 and IL-8 were reduced by 8.7%-19.5% as a result of GT pre-treatments (p < .05). Thus, an in vitro investigation of GT extract revealed promising results on antidiabetic and anti-inflammatory activities.Editorial Citation - WoS: 2Citation - Scopus: 2Editorial: Population Genomics and Adaptation To Novel Environments: Challenges and Opportunities(Frontiers Media S.A., 2023) Matur, Ferhat; Keskin, Emre; Sezgin, EfeUnderstanding how organisms adapt to novel environments is an active Research Topic in ecological and evolutionary studies. Most ecological and evolutionary studies focus on how organisms find food (utilization of ecological resources), how they avoid being the food (avoidance of predators), or form the next generation (reproductive strategies) in changing environmental conditions. Yet, some novel environments may present with extreme challenges that organisms may need to evolve novel metabolic pathways even just to exist. Population genomics methods can offer reliable estimates of basic population characteristics such as effective population size, inbreeding, demographic history, and population structure, all of which are also important for conservation efforts. Furthermore, population genomics studies can pinpoint specific genetic loci and variants that are under selection for a populations’ ability to evolve and adapt in response to environmental change and manage adaptive variation. The last 10 years have seen a rise in the study of population genetics of non-model organisms, and the findings of this research are increasingly being applied to the conservation and management of wildlife. To understand population genetics and adaptations, it is equally crucial to share and disseminate the research done using these techniques.Article Citation - WoS: 11Citation - Scopus: 10Molecular Evolution and Population Genetics of Glutamate Decarboxylase Acid Resistance Pathway in Lactic Acid Bacteria(Frontiers Media S.A., 2023) Sezgin, Efe; Tekin, BurcuGlutamate decarboxylase (GAD) pathway (GDP) is a major acid resistance mechanism enabling microorganisms’ survival in low pH environments. We aimed to study the molecular evolution and population genetics of GDP in Lactic Acid Bacteria (LAB) to understand evolutionary processes shaping adaptation to acidic environments comparing species where the GDP genes are organized in an operon structure (Levilactobacillus brevis) versus lack of an operon structure (Lactiplantibacillus plantarum). Within species molecular population genetic analyses of GDP genes in L. brevis and L. plantarum sampled from diverse fermented food and other environments showed abundant synonymous and non-synonymous nucleotide diversity, mostly driven by low frequency changes, distributed throughout the coding regions for all genes in both species. GAD genes showed higher level of replacement polymorphism compared to transporter genes (gadC and YjeM) for both species, and GAD genes that are outside of an operon structure showed even higher level of replacement polymorphism. Population genetic tests suggest negative selection against replacement changes in all genes. Molecular structure and amino acid characteristics analyses showed that in none of the GDP genes replacement changes alter 3D structure or charge distribution supporting negative selection against non-conservative amino acid changes. Phylogenetic and between species divergence analyses suggested adaptive protein evolution on GDP genes comparing phylogenetically distant species, but conservative evolution comparing closely related species. GDP genes within an operon structure showed slower molecular evolution and higher conservation. All GAD and transporter genes showed high codon usage bias in examined LAB species suggesting high expression and utilization of acid resistance genes. Substantial discordances between species, GAD, and transporter gene tree topologies were observed suggesting molecular evolution of GDP genes do not follow speciation events. Distribution of operon structure on the species tree suggested multiple independent gain or loss of operon structure in LABs. In conclusion, GDP genes in LABs exhibit a dynamic molecular evolutionary history shaped by gene loss, gene transfer, negative and positive selection to maintain its active role in acid resistance mechanism, and enable organisms to thrive in acidic environments.Article Citation - WoS: 9Citation - Scopus: 8Development of a New Electrochemical Sensor Based on Molecularly Imprinted Biopolymer for Determination of 4,4'-methylene Diphenyl Diamine(MDPI, 2023) Ghaani, Masoud; Büyüktaş, Duygu; Carullo, Daniele; Farris, StefanoA new molecularly imprinted electrochemical sensor was proposed to determine 4,4' methylene diphenyl diamine (MDA) using molecularly imprinted polymer-multiwalled carbon nanotubes modified glassy carbon electrode (MIP/MWCNTs/GCE). GCE was coated by MWCNTs (MWCNTs/GCE) because of their antifouling qualities and in order to improve the sensor sensitivity. To make the whole sensor, a polymeric film made up of chitosan nanoparticles was electrodeposited by the cyclic voltammetry method on the surface of MWCNTs/GCE in the presence of MDA as a template. Different parameters such as scan cycles, elution time, incubation time, molar ratio of template molecules to functional monomers, and pH were optimized to increase the performance of the MIP sensor. With a detection limit of 15 nM, a linear response to MDA was seen in the concentration range of 0.5-100 mu M. The imprinting factor (IF) of the proposed sensor was also calculated at around 3.66, demonstrating the extremely high recognition performance of a MIP/MWCNT-modified electrode. Moreover, the sensor exhibited good reproducibility and selectivity. Finally, the proposed sensor was efficiently used to determine MDA in real samples with satisfactory recoveries ranging from 94.10% to 106.76%.Article Citation - WoS: 2Citation - Scopus: 2Improvement of Fermentable Sugar Extraction From Hazelnut Shells Through Microwave Assisted Dilute Acid Pretreatment(North Carolina State University, 2023) Uzuner, SibelThe most effective method for producing fermentable sugars (FSs) from biomass is thermochemical pretreatment assisted by enzymatic hydrolysis. However, the enzymatic hydrolysis-assisted thermochemical pretreatment method is limited by the formation of fermentation inhibitors, and it is time-consuming. There is growing interest in using a microwave (MW) pretreatment due to its uniform and rapid heating. This study aimed to determine, perform data-driven modeling, and optimize the effect of MW combined with dilute acid pretreatment (MW-DA) on the production of FSs from hazelnut shells. An artificial neural networks (ANNs) model based on Box-Behnken Design (BBD) was the best model described for fermentable sugar extraction (FSE). Optimization via BBD-based ANNs model was carried out for an acid concentration of 0.5 to 2% (w/w), a pretreatment time of 5 to 25 min, a pressure of 5 to 15 bar, and a temperature of 120 to 160 °C. The optimized FSE was estimated at 374 mg/g (81.4% conversion efficiency), with a severity factor of 3.61 under 1.58% H2SO4 for 13 min at 160 °C and 8.5 bar. Using the MW-DA pretreatment process lowered the costs significantly due to the decreases in acid concentration and pretreatment time.Article Citation - WoS: 12Citation - Scopus: 12Quantitative Real-Time Pcr Analysis of Bacterial Biomarkers Enable Fast and Accurate Monitoring in Inflammatory Bowel Disease(PeerJ Inc., 2022) Sezgin, Efe; Terlemez, Gamze; Bozkurt, Berkay; Bengi, Göksel; Akpınar, Hale; Büyüktorun, İlkerInflammatory bowel diseases (IBD) affect millions of people worldwide with increasing incidence. Ulcerative colitis (UC) and Crohn’s disease (CD) are the two most common IBDs. There is no definite cure for IBD, and response to treatment greatly vary among patients. Therefore, there is urgent need for biomarkers to monitor therapy efficacy, and disease prognosis. We aimed to test whether qPCR analysis of common candidate bacteria identified from a patient’s individual fecal microbiome can be used as a fast and reliable personalized microbial biomarker for efficient monitoring of disease course in IBD. Next generation sequencing (NGS) of 16S rRNA gene region identified species level microbiota profiles for a subset of UC, CD, and control samples. Common high abundance bacterial species observed in all three groups, and reported to be associated with IBD are chosen as candidate marker species. These species, and total bacteria amount are quantified in all samples with qPCR. Relative abundance of anti-inflammatory, beneficial Faecalibacterium prausnitzii, Akkermansia muciniphila, and Streptococcus thermophilus was significantly lower in IBD compared to control samples. Moreover, the relative abundance of the examined common species was correlated with the severity of IBD disease. The variance in qPCR data was much lower compared to NGS data, and showed much higher statistical power for clinical utility. The qPCR analysis of target common bacterial species can be a powerful, cost and time efficient approach for monitoring disease status and identify better personalized treatment options for IBD patients.Article Citation - WoS: 2Citation - Scopus: 2Diverse Selection Pressures Shaping the Genetic Architecture of Behçet Disease Susceptibility(Frontiers Media S.A., 2022) Sezgin, Efe; Kaplan, ElifBehçet disease (BD) is a polygenic, multifactorial, multisystem inflammatory condition with unknown etiology. Global distribution of BD is geographically structured, highest prevalence observed among East Asian, Middle Eastern, and Mediterranean populations. Although adaptive selection on a few BD susceptibility loci is speculated, a thorough evolutionary analysis on the genetic architecture of BD is lacking. We aimed to understand whether increased BD risk in the human populations with high prevalence is due to past selection on BD associated genes. We performed population genetics analyses with East Asian (high BD prevalence), European (low/very low BD prevalence), and African (very low/no BD prevalence) populations. Comparison of ancestral and derived alleles’ frequencies versus their reported susceptible or protective effect on BD showed both derived and ancestral alleles are associated with increased BD risk. Variants showing higher risk to and more significant association with BD had smaller allele frequency differences, and showed less population differentiation compared to variants that showed smaller risk and less significant association with BD. Results suggest BD alleles are not unique to East Asians but are also found in other world populations at appreciable frequencies, and argue against selection favoring these variants only in populations with high BD prevalence. BD associated gene analyses showed similar evolutionary histories driven by neutral processes for many genes or balancing selection for HLA (Human Leukocyte Antigen) genes in all three populations studied. However, nucleotide diversity in several HLA region genes was much higher in East Asians suggesting selection for high nucleotide and haplotype diversity in East Asians. Recent selective sweep for genes involved in antigen recognition, peptide processing, immune and cellular differentiation regulation was observed only in East Asians. We conclude that the evolutionary processes shaping the genetic diversity in BD risk genes are diverse, and elucidating the underlying specific selection mechanisms is complex. Several of the genes examined in this study are risk factors (such as ERAP1, IL23R, HLA-G) for other inflammatory diseases. Thus, our conclusions are not only limited to BD but may have broader implications for other inflammatory diseases.Article Citation - WoS: 307Citation - Scopus: 364Iron Absorption: Factors, Limitations, and Improvement Methods(American Chemical Society, 2022) Pişkin, Elif; Cianciosi, Danila; Güleç, Şükrü; Tomas, Merve; Çapanoğlu, EsraIron is an essential element for human life since it participates in many functions in the human body, including oxygen transport, immunity, cell division and differentiation, and energy metabolism. Iron homeostasis is mainly controlled by intestinal absorption because iron does not have active excretory mechanisms for humans. Thus, efficient intestinal iron bioavailability is essential to reduce the risk of iron deficiency anemia. There are two forms of iron, heme and nonheme, found in foods. The average daily dietary iron intake is 10 to 15 mg in humans since only 1 to 2 mg is absorbed through the intestinal system. Nutrient-nutrient interactions may play a role in dietary intestinal iron absorption. Dietary inhibitors such as calcium, phytates, polyphenols and enhancers such as ascorbic acid and proteins mainly influence iron bioavailability. Numerous studies have been carried out for years to enhance iron bioavailability and combat iron deficiency. In addition to traditional methods, innovative techniques are being developed day by day to enhance iron bioavailability. This review will provide information about iron bioavailability, factors affecting absorption, iron deficiency, and recent studies on improving iron bioavailability.Article Citation - WoS: 1Citation - Scopus: 2Fatty Acid Alkyl Ester and Wax Compositions of Olive Oils as Varietal Authentication Indicators(Springer, 2021) Uncu, Oğuz; Özen, BanuMinor components of olive oils can be good markers for their authenticity, which is a significant quality issue for this product. It was aimed to determine individual and total fatty acid alkyl esters and waxes as minor constituents of olive oil and to investigate their novel varietal authentication capability separately and in combination for three main olive cultivars grown in three distinct locations of Aegean Region of Turkey. In addition, basic quality and purity parameters as free fatty acid, K values and fatty acid profiles were also determined for the characterization of the samples. Olive oil samples from different cultivars had different fatty acid profiles and two of these varieties had similar quality parameters. Statistical analyses were conducted with orthogonal partial least squares discriminant analysis (OPLS-DA) to differentiate varieties with respect to their individual and combined parameters of fatty acid alkyl esters and waxes. For calibration sets, use of individual fatty acid alkyl esters profile resulted in 80% correct classification rate while waxes alone was 67% successful in classifying the olive oils according to variety. It was found that alkyl esters in combination with waxes were more effective in discrimination of olive oils with respect to cultivar compared to their individual forms and the correct classification rate for the generated model is 92% for calibration set. Since fatty acid alkyl esters along with waxes have effect on cultivar differentiation, they could have a potential as authentication tools for olive oil besides their known quality characteristics.Article Citation - WoS: 69Citation - Scopus: 89Pectinase Enzyme-Complex Production by Aspergillus Spp. in Solid-State Fermentation: a Comparative Study(Elsevier, 2012) Heerd, Doreen; Yeğin, Sırma; Tarı, Canan; Fernandez Lahore, MarceloA comparative evaluation of three Aspergillus species according to their pectinase production in solid-state fermentation was performed. Solid-state fermentation offers several potential advantages for enzyme production by fungal strains. Utilization of agricultural by-products as low-cost substrates for microbial enzyme production resulted in an economical and promising process. The pectinolytic enzyme activities of two Aspergillus sojae strains were compared to a known producer, Aspergillus niger IMI 91881, and to A. sojae ATCC 20235, which was re-classified as Aspergillus oryzae. Evaluation of polymethylgalacturonase and polygalacturonase activity was performed as well as exo- vs. endo-enzyme activity in the crude pectinase enzyme-complex of the mentioned strains. Furthermore, a plate diffusion assay was applied to determine the presence and action of proteases in the crude extracts. A. sojae ATCC 20235 with highest polymethylgalacturonase activity and highest polygalacturonase activity both exo- and endo-enzyme activity, is a promising candidate for industrial pectinase production, a group of enzymes with high commercial value, in solid-state fermentation processes. Beside the enzymatic assays a protein profile of each strain is given by SDS-PAGE electrophoresis and in addition species-specific zymograms for pectinolytic enzymes were observed, revealing the differences in protein pattern of the A. sojae strains to the re-classified A. oryzae. (C) 2011 The Institution of Chemical Engineers. Published by Elsevier B.V. All rights reserved.