Food Engineering / Gıda Mühendisliği

Permanent URI for this collectionhttps://hdl.handle.net/11147/12

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Start date: 2020Publisher: search.filters.publisher.Frontiers Media S.A.

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  • 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.
  • 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: 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.