Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
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Article Citation - WoS: 2Citation - Scopus: 2Exploring Noncentrifugal Sugar as a Partial Replacement for White Sugar in Low Methoxyl Pectin Confectionery Gels: Impacts on Physical and Rheological Properties(American Chemical Society, 2024) Fakhar, Hafiz Imran; Çavdaroğlu, Elif; Hayat, Muhammad Qasim; Janjua, Hussnain A.; Oztop, Mecit HalilNoncentrifugal sugar (NCS) is an unrefined, dark brown sugar containing minerals and plant secondary metabolites, unlike refined white sugar (WS). This study explored using NCS in confectionary jellies as an alternative sugar. We used different concentrations of NCS and WS to prepare low methoxyl pectin (LMP) confectionery gels characterized by their physical and rheological properties along with time-domain nuclear magnetic resonance (TD-NMR) relaxometry. The strongest LMP gel, with a hardness of 0.94 N, was achieved by substituting 25% of WS with NCS at a low CaCl2 concentration (0.075 M). Gels with up to 50% WS replaced by NCS showed comparable hardness to standard LMP gels made solely with WS at a 0.15 M CaCl2 concentration, attributed to NCS's unique constituents. The NCS-WS gel exhibited the shortest T2 values (139.8 ms) and self-diffusion coefficient values (4.99 x 10-10 m2/s), indicating a denser, more cross-linked structure that restricted water mobility. These findings suggest NCS's complex role in affecting LMP gels' chemical and physical properties, highlighting its potential as a partial WS replacement in LMP gelation-based products, with an additional source of minerals and antioxidants.Article Citation - WoS: 2Citation - Scopus: 2Enhanced Reducing Sugar Production and Extraction for Chlorella Vulgaris in Mixotrophic Cultivation Using High Hydrostatic Pressure Processing and Ultrasound(Taylor & Francis, 2023) Uzuner, Sibel; Kurhan, Şebnem; Akdemir Evrendilek, GülsünAlthough extraction of polysaccharides to convert reducing sugars (RS) from microalgae by acid or alkali pretreatments and enzymatic hydrolysis has been extensively studied, few reports exploring the use of high hydrostatic pressure processing (HHP) and ultrasonication (US) as emerging technologies for the extraction of sugars from microalgae biomass exist. Thus, the present study was conducted to determine the effects of mixotrophic growth and stress conditions (NaNO3 and CO2 concentration and light intensity) on RS and protein accumulation in the unicellular green alga Chlorella vulgaris in addition to optimization of the effectiveness of the sequential applications of HHP and US with dilute acid as well as simultaneous enzymatic saccharification on the production of RS from microalga cells. High light intensity, high CO2 concentration and limited nitrogen concentration promoted RS production. The maximum protein content (0.0683 mg g(-1)) was achieved at 0.3 g l(-1) NaNO3 concentration, 7000 mu mol photons m(-2) s(-1) and 6 l min(-1) CO2 concentration. The highest RS content of C. vulgaris after 48 h enzymatic saccharification (583.86 +/- 13.23 mg g(-1)) was obtained at 1% (w/w) acid concentration and 80% amplitude for 30 min with 79.4% RS yield. Combined US-assisted dilute acid pretreatment and enzymatic hydrolysis were also found to be more effective than HHP assisted dilute acid pretreatment and enzymatic saccharification. Therefore, microalgal biomass can be considered a suitable renewable feedstock used in fermentation. Highlights center dot The cultivation period of Chlorella vulgaris was reduced from 25 days to 14 days using mixotrophic growing conditions.center dot Mixotrophic conditions enhanced reducing sugar productivity.center dot Novel extraction techniques enhanced the extraction of reducing sugar from microalgae.Review Citation - WoS: 25Citation - Scopus: 27Bacillus Cereus: a Review of “fried Rice Syndrome” Causative Agents(Academic Press, 2023) Leong, Sui Sien; King, Jie Hung; Korel, Figen“Fried rice syndrome” originated from the first exposure to a fried rice dish contaminated with Bacillus cereus. This review compiles available data on the prevalence of B. cereus outbreak cases that occurred between 1984 and 2019. The outcome of B. cereus illness varies dramatically depending on the pathogenic strain encounter and the host's immune system. B. cereus causes a self-limiting, diarrheal illness caused by heat-resistant enterotoxin proteins, and an emetic illness caused by the deadly toxin named cereulide. The toxins together with their extrinsic factors are discussed. The possibility of more contamination of B. cereus in protein-rich food has also been shown. Therefore, the aim of this review is to summarize the available data, focusing mainly on B. cereus physiology as the causative agent for “fried rice syndrome.” This review emphasizes the prevalence of B. cereus in starchy food contamination and outbreak cases reported, the virulence of both enterotoxins and emetic toxins produced, and the possibility of contaminated in protein-rich food. The impact of emetic or enterotoxin-producing B. cereus on public health cannot be neglected. Thus, it is essential to constantly monitor for B. cereus contamination during food handling and hygiene practices for food product preparation. © 2023 Elsevier LtdReview Citation - WoS: 7Citation - Scopus: 7Ultrasonication Effects on Quality of Tea-Based Beverages(MDPI, 2023) Uzuner, SibelTea is the most popular consumed drink after water. Teas and tea-based beverages have grown in popularity due to bioactive compounds. Tea-based beverages have started to take their place in the market. Extraction is a crucial step for the production of functional tea-based beverages. Compared to conventional methods, ultrasound is attractive due to its lower energy requirements, and shorter extraction time. This review aimed to discuss recent marketing aspects of tea-based beverages as well as the potential and challenges of a novel infusion technique. This review describes the health benefits and technological aspects of tea-based beverages in relation to how to best solve nutritional and microbial concerns. Current and future challenges and opportunities of the novel infusion technique and its scaling-up for the extraction of bioactive compounds are also covered in the present review.Article Citation - WoS: 6Citation - Scopus: 4Early Detection of Breast Cancer-Related Lymphedema: Accuracy of Indocyanine Green Lymphography Compared With Bioimpedance Spectroscopy and Subclinical Lymphedema Symptoms(Mary Ann Liebert, 2023) Soran, Atilla; Bengur, Fuat Barış; Rodriguez, Wendy; Chroneos, Maria Z.; Sezgin, EfeIntroduction: The reported incidences of breast cancer-related lymphedema (LE) affecting the arms vary greatly. Reason for this variability includes different diagnostic techniques used across studies. In the current study, we compared the accuracy of indocyanine green lymphography (ICG_L) and bioimpedance spectroscopy (BIS) in detecting LE before presentation of clinical signs.Methods and Results: Patients with no initial detectable signs of clinical LE of their arms after axillary lymph node dissection or removal of >5 lymph nodes on sentinel lymph node biopsy were included. Subclinical LE was defined as BIS values outside the normal range [(>= 7 units (or >10 units)] or a 7-unit (or 10 unit) change between two measurements. We tracked ICG_L and BIS measurements for 133 potentially affected arms (n = 123). ICG_L detected signs of lymphatic flow disruption in 63 arms (47%). Based on the BIS value of 7 units, 60 arms (45%) had values outside the normal range. When using ICG_L-identified LE cases as true positives, BIS had a 54% accuracy (area under the curve [AUC] = 0.54) in detecting LE. Accuracy was 61% for subclinical LE symptoms when compared with ICG_L (AUC = 0.62). Both BIS and subclinical LE symptoms had <0.70 AUC-receiver characteristic operator curve, suggesting that BIS and development of subclinical LE symptoms are not adequate for identifying patients with subclinical LE.Conclusion: ICG_L is a reliable diagnostic tool for detecting early signs of lymphatic flow disruption in subclinical LE. Utilizing ICG_L to diagnose subclinical LE followed by a personalized treatment plan may provide patients the best chance of preventing disease progression.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.Erratum Correction: Intervention for Hepatic and Pulmonary Metastases in Breast Cancer Patients: Prospective, Multi-Institutional Registry Study–imet, Protocol Mf 14-02(Springer, 2023) Soran, Atilla; Özbaş, Serdar; Özçınar, Beyza; Işık, Arda; Doğan, Lütfi; Şenol, Kazım; Sezgin, EfeThe authors‘ given names are correct as reflected here. © Society of Surgical Oncology 2022.Article Citation - WoS: 6Citation - Scopus: 6Organosolv Pretreatment of Corncob for Enzymatic Hydrolysis of Xylan(Springer, 2023) Büyükkileci, Ali Oğuz; Temelli, NuranXylan is a renewable polysaccharide, readily available in agricultural and forestry residues. It can be hydrolyzed to produce xylooligosaccharides (XOS) with prebiotic activity and xylose, a precursor for several industrial chemicals. Enzymatic hydrolysis of xylan in the lignocellulosic biomass to obtain xylose and XOS requires a pretreatment to facilitate xylanase activity. In this study, organosolv was evaluated for the delignification of corncob while retaining xylan in the pretreated biomass. The treatment at 170 °C for 1 h with 70% ethanol provided 50% lignin removal and 81% xylan recovery. Increasing temperatures and decreasing ethanol fractions decreased the pH and the xylan recovery. Loss of xylan in the organosolv at 190 °C and in the liquid hot water treatment could be prevented by the addition of 100 mM MgO, without compromising lignin removal. Pretreated corncob was suspended in citrate buffer and hydrolyzed by commercial xylanases. Accellerase XY (250 U/ml) at pH 5.5 and 55 °C and Econase XT (0.6 U/ml) at pH 6.0 and 70 °C provided around 65% xylan digestibility and generated xylose (9.8 g/l) and XOS (10.9 g/l), respectively. This approach could decrease xylan loss and degradation in the pretreatment step and yield clear hydrolysates composed of essentially xylose or XOS. Lignocellulosic biorefineries can benefit from the efficient utilization of xylan, increasing sustainability. © 2023, The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.Article Citation - WoS: 3Citation - Scopus: 3Comparison of Apical and Basolateral Cu Treatment for Iron-Related Gene Regulation During Deferoxamine Induced Iron Deficiency(BioMed Central Ltd., 2022) Evcan, Ezgi; Güleç, ŞükrüBackground: Intestinal copper transporter (Atp7a) mutant-brindled mice with systemic Cu deficiency had elevated Cu levels in enterocyte cells without any perturbation of iron-regulating genes, suggesting that blood Cu level might be important for intestinal iron homeostasis during iron deficiency (ID). We hypothesized that the blood Cu level and polarization (apical and basolateral) of enterocyte cells might be important regulators for the compensatory response on the regulation of genes in enterocyte cells during iron deficiency. Methods: We grew Caco-2 cells on a bicameral cell culture plate to mimic the human intestine system and on a regular tissue culture plate. Iron deficiency was induced by deferoxamine (DFO). The cells were treated with Cu and Cu with Fe following mRNA expressions of DMT1, FPN, TFR, and ANKRD37 were analyzed. Results: Our main finding was that basolateral treatment of Cu significantly reduced mRNA expressions of iron-regulated genes, including DMT1, FPN, TFR, and ANKRD37, compared to DFO-treated and DFO with apical Cu-treated groups in both bicameral and regular tissue culture plates. Conclusions: Cu level in the basolateral side of Caco-2 cells significantly influenced the intracellular gene regulation in DFO-induced iron-deficient condition, and polarization of the cells might be important factor gene regulation in enterocyte cells.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.