Food Engineering / Gıda Mühendisliği
Permanent URI for this collectionhttps://hdl.handle.net/11147/12
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Article Citation - WoS: 6Citation - Scopus: 5Basidiomycota Species in Drosophila Gut Are Associated With Host Fat Metabolism(Nature Research, 2023) Bozkurt, Berkay; Terlemez, Gamze; Sezgin, EfeThe importance of bacterial microbiota on host metabolism and obesity risk is well documented. However, the role of fungal microbiota on host storage metabolite pools is largely unexplored. We aimed to investigate the role of microbiota on D. melanogaster fat metabolism, and examine interrelatedness between fungal and bacterial microbiota, and major metabolic pools. Fungal and bacterial microbiota profiles, fat, glycogen, and trehalose metabolic pools are measured in a context of genetic variation represented by whole genome sequenced inbred Drosophila Genetic Reference Panel (DGRP) samples. Increasing Basidiomycota, Acetobacter persici, Acetobacter pomorum, and Lactobacillus brevis levels correlated with decreasing triglyceride levels. Host genes and biological pathways, identified via genome-wide scans, associated with Basidiomycota and triglyceride levels were different suggesting the effect of Basidiomycota on fat metabolism is independent of host biological pathways that control fungal microbiota or host fat metabolism. Although triglyceride, glycogen and trehalose levels were highly correlated, microorganisms’ effect on triglyceride pool were independent of glycogen and trehalose levels. Multivariate analyses suggested positive interactions between Basidiomycota, A. persici, and L. brevis that collectively correlated negatively with fat and glycogen pools. In conclusion, fungal microbiota can be a major player in host fat metabolism. Interactions between fungal and bacterial microbiota may exert substantial control over host storage metabolite pools and influence obesity risk. © 2023, Springer Nature Limited.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.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.Erratum Correction To: Excessive Replacement Changes Drive Evolution of Global Sheep Prion Protein (prnp) Sequences (heredity, (2022), 128, 5, (377-385), 10.1038/S41437-022-00520-6)(Springer, 2023) Teferedegn, Eden Yitna; Yaman, Yalçın; Sezgin, Efe; Ün, CemalIn this article the affiliation details for Author Cemal Ün were incorrectly given as Armauer Hansen research institute, Biotechnology and Bioinformatic Directorate, Addis Ababa, Ethiopia but should have been Department of Biology, Molecular Biology Division, Ege University, Izmir, Turkey. The original article has been corrected. © 2022, The Author(s), under exclusive licence to The Genetics Society.Article Evrimsel epidemiyoloji: Epidemiyoloji ve evrimsel biyolojinin sentezi(Türk Tabipleri Birliği, 2016) Sezgin, EfeEpidemiology investigates the distribution and causes of health and disease among individuals and populations. Evolutionary medicine, in other words Darwinian medicine, is a new discipline that aims to bring novel approaches to health problems that traditional medicine cannot understand and cannot find cures for, in order to improve the overall health of human populations. Epidemiology, the primary discipline of public health, is one of the medical branches that benefited the most from evolutionary approaches in medicine. Traditional epidemiology focuses on proximate causes and seeks answers to 'what' and 'how' questions on the dynamics between factors, environment, and humans. Evolutionary epidemiology focuses on the ultimate causes of diseases and seeks answers to 'how' and 'why' questions on the origin and function. In order to find answers, it compares the evolutinary process of Homo sapiens (modern humans) with that of its relatives, it examines the fast changes in human ecology, demographic and social dynamics, it looks at the epidemiology of modern diseases from an evolutionary process perspective. Using contemporary molecular and statistical genetic methods, it examines the contemporary human genetic variation and its evolution. It searches why diseases causing genetic variation are still not eliminated from human populations. Adaption of evolutionary ideas into epidemiologic research will enhance population health and provide novel solutions for diseases.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: 1Aso Visual Abstract: Intervention for Hepatic and Pulmonary Metastases in Breast Cancer Patients-Prospective, Multi-Institutional Registry Study: Imet; Protocol Mf 14-02(Springer, 2022) Soran, Atilla; Özbaş, Serdar; Özçınar, Beyza; Işık, Arda; Doğan, L.; Şenol, Kazım; Dağ, Ahmet; Karanlık, Hasan; Aytaç, Özgür; Karadeniz Çakmak, Güldeniz; Dalcı, Kubilay; Doğan, Mutlu; Sezer, Atakan Y.; Gökgöz, Şehsuvar; Özyar, Enis; Sezgin, EfeThe aim of our prospective, multicenter registry study was to investigate the importance of interventions for operable lung and/or liver metastasis for breast cancer (BC) survival (https://doi.org/10.1245/s10434-022-12239-z). The results reveal that surgical resection or ablative interventions may contribute to survival in patients with BC with limited number and operable metachronous hepatic/pulmonary metastases. Ultimately, randomized studies will determine whether intervention on lung and liver metastatic sites should be performed. In the meantime, such interventions can be considered on select patients.Conference Object Intervention To Hepatic and Pulmonary Metastases in Breast Cancer Patients: Prospective, Multi-Institutional Registry Study-Imet; Protocol Mf 14-02(Springer, 2022) Soran, Atilla; Özbaş, Serdar; Özçınar, Beyza; Işık, Arda; Doğan, Lütfi; Şenol, Kazım; Dağ, Ahmet; Karanlık, Hasan; Aytaç, Özgür; Karadeniz Çakmak, Güldeniz; Dalcı, Kubilay; Doğan, Mutlu; Sezer, Atakan Y.; Gökgöz, Şehsuvar; Özyar, Enis; Sezgin, EfeBackground/Objective: One‐fourth of early‐stage breast cancer (BC) becomes metastatic at follow‐up. Limited metastases represents a clinical state of metastatic disease that is limited in the number of metastatic sites and extent of disease, and amenable to metastasis‐directed intervention. The aim of this prospective study is to evaluate intervention to limited metastases in lung and/or liver.