Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection

Permanent URI for this collectionhttps://hdl.handle.net/11147/7148

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Now showing 1 - 10 of 28
  • Article
    Citation - WoS: 1
    Citation - Scopus: 1
    Correlation of Low Field Nuclear Magnetic Resonance Relaxation With Composition and Glass Transition of Hard Candies
    (Frontiers Media S.A., 2024) Ozel, Baris; Berk, Berkay; Uguz, Sirvan Sultan; Grunin, Leonid; Oztop, Mecit Halil
    Hard candies produced from sucrose and doctoring agents such as glucose syrup (GS) and high fructose corn syrup (FS) have been investigated in terms of their final composition, glass transition temperature (Tg), degree of crystallinity, total soluble solids (TSS) content and water activity (aw). Time domain (TD) 1H NMR longitudinal relaxation time (T1) and second moment (M2) measurements have been used to understand the glassy state and crystallization characteristics for different hard candy formulations. The investigated candies include sucrose as the main sugar component. Different levels of doctoring agents have been mixed with sucrose to obtain products with different characteristics. It has been shown that addition of any doctoring agent to sucrose formulations decreases the Tg of the system significantly (p <= 0.05). Furthermore, GS or FS addition also induce significant changes in TSS and aw. T1 and M2 results are almost parallel to each other, both reaching the highest values for the highest sucrose concentration (p <= 0.05). The results demonstrate that the glass transition and crystallization characteristics of hard candy formulations can be monitored and analyzed by TD NMR relaxometry, alternative to other frequently used conventional methods including differential scanning calorimetry (DSC) and X-ray diffraction.
  • Article
    Citation - WoS: 3
    Citation - Scopus: 3
    Shelf-Life Extension of Traditional Licorice Root “sherbet” With a Novel Pulsed Electric Field Processing
    (Frontiers Media S.A., 2023) Akdemir Evrendilek, Gulsun; Demir, Irem; Uzuner, Sibel
    Pulsed electric field (PEF) processing of licorice root "sherbet" (LRS) by various electric field strengths (7.00, 15.50, and 24.10 kV/cm), treatment times (108, 432, and 756 mu sec), and processing temperatures (6, 18, and 30 degrees C) according to the Box-Behnken design were performed. The samples were analyzed for pH, titratable acidity, conductivity, turbidity, total reducing sugar, color (L*, a*, and b*), hue, chroma, total color difference, color intensity, color tone (yellow, red, and blue color tones), total antioxidant capacity, total phenolic substance content, and sensory properties. Results revealed that PEF processing did not adversely affect most of the physical, chemical, and sensory properties of LRS, with a maximum of 2.48, 4.04, 1.78, and 1.20 log reductions on the initial total mesophilic aerobic bacteria, total mold and yeast, Bacillus circulans, and Candida tropicalis. The response variable modeled for the PEF was found to be conductivity, with the optimum processing conditions of 6.90 kV/cm, 756.00 mu s, and 7.48 degrees C. After that, the samples were stored at 4 degrees C and 22 degrees C for shelf-life studies. Control samples at 4 degrees C and 22 degrees C were spoiled on the fifth and second days, whereas PEF-treated samples stored at 4 degrees C began to deteriorate after the 40th day and the samples stored at 22 degrees C after the 30th day, respectively. It was revealed that PEF is a suitable process to extend the shelf-life of licorice "sherbet" with preservation of physicochemical and sensory properties.
  • Article
    Production of Microalgae-Derived Exo-Polygalacturonase for Fruit Juice Clarification
    (Frontiers Media S.A., 2022) Uzuner, Sibel; Evrendilek, Gulsun Akdemir; Kurhan, Sebnem
    Due to the growing demand for commercial enzymes derived from renewable and sustainable resources with higher efficacy, algal biomass has gained more attention. Thus, the production of exo-polygalacturonase (PGase) from Bacillus subtilis under submerged fermentation (SmF) using algal feedstocks as a carbon source in fermentation medium and its potential use for the clarification of apple and carrot juices with the optimization of the enzyme loading, pH, and time using Box-Behnken response surface methodology (RSM) were prompted. The maximum PGase activity of 510.61 +/- 7.86 U/L was achieved at pH 5.0 after 48 h at 40 degrees C using 0.5% (w/v) pectin, 0.1% (w/v) yeast extract, 0.02% (w/v) MgSO47H2O, 0.02% (w/v) K2HPO4, 0.3% (w/v) glucose, and 0.583% (w/v) microalgae hydrolysate as a fermentation medium. PGase production without glucose was favored by SmF with a shake flask working volume of 100 ml (248.90 +/- 4.58 U/L) as compared to a bioreactor with a working volume of 1 L (192.99 +/- 0.84) for 48 h. Both carrot and apple juices were treated with the crude PGase (248.9 U/L) at different concentrations (0.1-0.5%), temperature (30-50 degrees C), and time (30-120 min), and the maximal clarification conditions were obtained as 0.3% (w/v) enzyme concentration at 50 degrees C for 30 min exposure time. This study revealed that microalgae-derived PGase in crude form could be effectively used for clarification of the juices.
  • Article
    Citation - WoS: 8
    Citation - Scopus: 8
    Canonical Wnt and Tgf-β/Bmp Signaling Enhance Melanocyte Regeneration but Suppress Invasiveness, Migration, and Proliferation of Melanoma Cells
    (Frontiers Media S.A., 2023) Katkat, Esra; Demirci, Yeliz; Heger, Guillaume; Karagülle, Doğa; Papatheodorou, Irene; Brazma, Alvis; Özhan, Güneş
    Melanoma is the deadliest form of skin cancer and develops from the melanocytes that are responsible for the pigmentation of the skin. The skin is also a highly regenerative organ, harboring a pool of undifferentiated melanocyte stem cells that proliferate and differentiate into mature melanocytes during regenerative processes in the adult. Melanoma and melanocyte regeneration share remarkable cellular features, including activation of cell proliferation and migration. Yet, melanoma considerably differs from the regenerating melanocytes with respect to abnormal proliferation, invasive growth, and metastasis. Thus, it is likely that at the cellular level, melanoma resembles early stages of melanocyte regeneration with increased proliferation but separates from the later melanocyte regeneration stages due to reduced proliferation and enhanced differentiation. Here, by exploiting the zebrafish melanocytes that can efficiently regenerate and be induced to undergo malignant melanoma, we unravel the transcriptome profiles of the regenerating melanocytes during early and late regeneration and the melanocytic nevi and malignant melanoma. Our global comparison of the gene expression profiles of melanocyte regeneration and nevi/melanoma uncovers the opposite regulation of a substantial number of genes related to Wnt signaling and transforming growth factor beta (TGF-beta)/(bone morphogenetic protein) BMP signaling pathways between regeneration and cancer. Functional activation of canonical Wnt or TGF-beta/BMP pathways during melanocyte regeneration promoted melanocyte regeneration but potently suppressed the invasiveness, migration, and proliferation of human melanoma cells in vitro and in vivo. Therefore, the opposite regulation of signaling mechanisms between melanocyte regeneration and melanoma can be exploited to stop tumor growth and develop new anti-cancer therapies.
  • Editorial
    Citation - WoS: 1
    Citation - Scopus: 1
    Editorial: Biomaterial Applications in Soft Tissue Engineering and Replacement
    (Frontiers Media S.A., 2023) Hornyak, Istvan; Jedlovszky-Hajdu, Angela; Kehr, Seda
    The research related to the application of biomaterials encompasses a large area within the field of tissue engineering and regenerative medicine (TERM), and this Research Topic was dedicated to the versatile possibilities in the use of biomaterials. The sum of 10 manuscripts were submitted to this Research Topic and six were selected for this Research Topic with the contribution of 35 authors, Four of the accepted manuscripts were original research articles and two were review articles
  • Editorial
    Citation - WoS: 2
    Citation - Scopus: 2
    Editorial: Population Genomics and Adaptation To Novel Environments: Challenges and Opportunities
    (Frontiers Media S.A., 2023) Matur, Ferhat; Keskin, Emre; Sezgin, Efe
    Understanding 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: 11
    Citation - Scopus: 10
    Molecular Evolution and Population Genetics of Glutamate Decarboxylase Acid Resistance Pathway in Lactic Acid Bacteria
    (Frontiers Media S.A., 2023) Sezgin, Efe; Tekin, Burcu
    Glutamate 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: 3
    Citation - Scopus: 3
    A Subtractive Proteomics Approach for the Identification of Immunodominant Acinetobacter Baumannii Vaccine Candidate Proteins
    (Frontiers Media S.A., 2022) Acar, Mustafa Burak; Ayaz Güner, Şerife; Güner, Hüseyin; Dinç, Gökçen; Ulu Kılıç, Ayşegül; Doğanay, Mehmet; Özcan, Servet
    Background: Acinetobacter baumannii is one of the most life-threatening multidrug-resistant pathogens worldwide. Currently, 50%–70% of clinical isolates of A. baumannii are extensively drug-resistant, and available antibiotic options against A. baumannii infections are limited. There is still a need to discover specific de facto bacterial antigenic proteins that could be effective vaccine candidates in human infection. With the growth of research in recent years, several candidate molecules have been identified for vaccine development. So far, no public health authorities have approved vaccines against A. baumannii. Methods: This study aimed to identify immunodominant vaccine candidate proteins that can be immunoprecipitated specifically with patients’ IgGs, relying on the hypothesis that the infected person’s IgGs can capture immunodominant bacterial proteins. Herein, the outer-membrane and secreted proteins of sensitive and drug-resistant A. baumannii were captured using IgGs obtained from patient and healthy control sera and identified by Liquid Chromatography- Tandem Mass Spectrometry (LC-MS/MS) analysis. Results: Using the subtractive proteomic approach, we determined 34 unique proteins captured only in drug-resistant A. baumannii strain via patient sera. After extensively evaluating the predicted epitope regions, solubility, transverse membrane characteristics, and structural properties, we selected several notable vaccine candidates. Conclusion: We identified vaccine candidate proteins that triggered a de facto response of the human immune system against the antibiotic-resistant A. baumannii. Precipitation of bacterial proteins via patient immunoglobulins was a novel approach to identifying the proteins that could trigger a response in the patient immune system.
  • Article
    Citation - WoS: 2
    Citation - Scopus: 2
    Diverse Selection Pressures Shaping the Genetic Architecture of Behçet Disease Susceptibility
    (Frontiers Media S.A., 2022) Sezgin, Efe; Kaplan, Elif
    Behçet 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: 14
    Citation - Scopus: 16
    Plaqview 2.0: a Comprehensive Web Portal for Cardiovascular Single-Cell Genomics
    (Frontiers Media S.A., 2022) Ma, Wei Feng; Turner, Adam W.; Gancayco, Christina; Wong, Doris; Song, Yipei; Mosquera, Jose Verdezoto; Auguste, Gaëlle; Hodonsky, Chani J.; Prabhakar, Ajay; Ekiz, Hüseyin Atakan; van der Laan, Sander W.; Miller, Clint L.
    Single-cell RNA-seq (scRNA-seq) is a powerful genomics technology to interrogate the cellular composition and behaviors of complex systems. While the number of scRNA-seq datasets and available computational analysis tools have grown exponentially, there are limited systematic data sharing strategies to allow rapid exploration and re-analysis of single-cell datasets, particularly in the cardiovascular field. We previously introduced PlaqView, an open-source web portal for the exploration and analysis of published atherosclerosis single-cell datasets. Now, we introduce PlaqView 2.0 (www.plaqview.com), which provides expanded features and functionalities as well as additional cardiovascular single-cell datasets. We showcase improved PlaqView functionality, backend data processing, user-interface, and capacity. PlaqView brings new or improved tools to explore scRNA-seq data, including gene query, metadata browser, cell identity prediction, ad hoc RNA-trajectory analysis, and drug-gene interaction prediction. PlaqView serves as one of the largest central repositories for cardiovascular single-cell datasets, which now includes data from human aortic aneurysm, gene-specific mouse knockouts, and healthy references. PlaqView 2.0 brings advanced tools and high-performance computing directly to users without the need for any programming knowledge. Lastly, we outline steps to generalize and repurpose PlaqView's framework for single-cell datasets from other fields.