Food Engineering / Gıda Mühendisliği
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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.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 Citation - WoS: 30Citation - Scopus: 33Targeting the Panoptosome With 3,4-Methylenedioxy Reduces Panoptosis and Protects the Kidney Against Renal Ischemia-Reperfusion Injury(Taylor & Francis, 2022) Uysal, Erdal; Dokur, Mehmet; Küçükdurmaz, Faruk; Altınay, Serdar; Polat, Sait; Batçıoğlu, Kadir; Sezgin, EfeObjectıves: The objectives of this study were a) to investigate the effect of targeting the PANoptosome with 3,4-methylenedioxy-β-nitrostyrene (MNS) on PANoptosis in the Renal ischemia-reperfussion (RIR) model b) to investigate the kidney protective effect of MNS toward RIR injury. Methods: Thirty-two rats were divided into four groups randomly. The groups were assigned as Control, Sham, DMSO (dimethyl sulfoxide) and MNS groups. The rats in the MNS group were intraperitoneally given 20 mg/kg of MNS 30 minutes before reperfusion. 2% DMSO solvent that dissolves MNS were given to the rats in DMSO group. Left nephrectomy was performed on the rats under anesthesia at the 6th hour after reperfusion. Glutathione peroxidase (GPx), malondialdehyde (MDA), catalase (CAT), superoxide dismutase (SOD) and 8-Okso-2′-deoksiguanozin (8-OHdG) levels were measured. Immunohistochemical analysis, electron microscopic and histological examinations were carried out in the tissues. Results: Total tubular injury score was lower in the MNS group (p < 0.001). Caspase-3, Gasdermin D and MLK (Mixed Lineage Kinase Domain Like Pseudokinase) expressions were considerably decreased in the MNS group (p < 0.001). Apoptotic index (AI) was found to be low in the MNS group (p < 0.001). CAT and SOD levels were higher in the MNS Group (p = 0.006, p = 0.0004, respectively). GPx, MDA, and 8-OH-dG levels were similar (p > 0.05) in all groups. MNS considerably improved the tissue structure, based on the electron microscopic analysis. Conclusıons: Our results suggested that MNS administrated before the reperfusion reduces pyroptosis, apoptosis and necroptosis. These findings suggest that MNS significantly protects the kidney against RIR injury by reducing PANoptosis as a result of specific inhibition of Nod-like receptor pyrin domain-containing 3 (NLRP 3), one of the PANoptosome proteins.Article Citation - WoS: 6Citation - Scopus: 5Excessive Replacement Changes Drive Evolution of Global Sheep Prion Protein (prnp) Sequences(Springer, 2022) Sezgin, Efe; Teferedegn, Eden Yitna; Ün, Cemal; Yaman, YalçınSheep prion protein (PRNP) is the major host genetic factor responsible for susceptibility to scrapie. We aimed to understand the evolutionary history of sheep PRNP, and primarily focused on breeds from Turkey and Ethiopia, representing genome-wise ancient sheep populations. Population molecular genetic analyses are extended to European, South Asian, and East Asian populations, and for the first time to scrapie associated haplotypes. 1178 PRNP coding region nucleotide sequences were analyzed. High levels of nucleotide diversity driven by extensive low-frequency replacement changes are observed in all populations. Interspecific analyses were conducted using mouflon and domestic goat as outgroup species. Despite an abundance of silent and replacement changes, lack of silent or replacement fixations was observed. All scrapie-associated haplotype analyses from all populations also showed extensive low-frequency replacement changes. Neutrality tests did not indicate positive (directional), balancing or strong negative selection or population contraction for any of the haplotypes in any population. A simple negative selection history driven by prion disease susceptibility is not supported by the population and haplotype based analyses. Molecular function, biological process enrichment, and protein-protein interaction analyses suggested functioning of PRNP protein in multiple pathways, and possible other functional constraint selections. In conclusion, a complex selection history favoring excessive replacement changes together with weak purifying selection possibly driven by frequency-dependent selection is driving PRNP sequence evolution. Our results is not unique only to the Turkish and Ethiopian samples, but can be generalized to global sheep populations.Conference Object Does Locoregional Treatment in De Novo Stage Iv Bone-Only Metastatic Breast Cancer Prolong Survival? an Ongoing Multicenter Registry Study(Elsevier, 2019) Soran, Atilla; Işık, Arda; Doğan, Lütfi; Sezgin, Efe; Özbaş, SerdarSurgical treatment of primary tumor is a controversial treatment of stage IV de novo metastatic breast cancer (BC). This study aims to present early results of the ongoing reg istry in a cohort of patients.Article Citation - WoS: 5Citation - Scopus: 3Apol1 Variant Alleles Associate With Reduced Risk for Opportunistic Infections in Hiv Infection(Nature Research, 2021) An, Ping; Sezgin, Efe; Kirk, Gregory D.; Duggal, Priya; Binns-Roemer, Elizabeth; Nelson, George; Limou, SophieApolipoprotein L1 (APOL1), an innate immune factor against African trypanosoma brucei, inhibits HIV-1 in vitro. The impact of APOL1 G1-G2 variants on HIV-1-associated opportunistic infections (OIs) is unknown. Here, we report findings from a metaanalysis of four HIV/AIDS prospective cohorts (ALIVE, LSOCA, MACS, and WIHS) including 2066 African American participants. Using a global test combining all four cohorts, carriage of two APOL1 variant alleles is associated with a 50% reduction in odds of OI (combined OR 0.50, 95% CI 0.33-0.76). Subgroup analysis of OI etiological categories (viral, parasitic, fungal and Mycobacterial) suggests the possibility of specific protection from fungal infections (OR 0.54. 95% CI 0.32-0.93; P-Bonferroni corrected=0.08). We observe an association of APOL1 variant alleles with host protection against OI in HIV-positive individuals. The study suggests a broader role of APOL1 variant alleles in innate immunity in vivo. An et al. determine the presence of variants of the innate immune factor APOL1 in four cohorts of HIV-positive patients. The study suggests that APOL1 might confer carriers of two variant alleles protection from HIV related opportunistic infections, especially fungal infections.Conference Object Citation - WoS: 2The Effect of Primary Surgery in Patients With Stage Iv Breast Cancer With Bone Metastasis Only (protocol Bomet Mf14-01); a Multi-Center, Registry Study(Churchill Livingstone, 2021) Soran, Atilla; Doğan, Lütfi; Özbaş, Serdar; Işık, Arda; Trablus, D.; Demirci, U.; Sezgin, EfeGoals: More evidence shows that primary surgery for de novo metastatic breast cancer (BC) prolongs overall survival (OS) in selected cases. The aim of this study was to evaluate the role of locoregional treatment (LRT) in BC patients with de novo stage IV bone only metastasis (BOM).Conference Object Citation - WoS: 83Citation - Scopus: 87Primary Surgery With Systemic Therapy in Patients With De Novo Stage Iv Breast Cancer: 10-Year Follow-Up; Protocol Mf07-01 Randomized Clinical Trial(Elsevier, 2021) Soran, Atilla; Özmen, Vahit; Özbaş, Serdar; Karanlık, Hasan; Müslümanoğlu, Mahmut; İğci, Abdullah; Cantürk, Nuh Zafer; Utkan, Zafer; Evrensel, Türkkan; Sezgin, EfeBackground: The aim of this randomized clinical trial was to evaluate the overall survival (OS) data of patients diagnosed with de novo stage IV breast cancer (BC) who received locoregional treatment (LRT) over a 10-year follow-up. Study Design: The MF07-01 is a 1:1 multicenter, randomized clinical trial comparing the LRT with systemic therapy (ST), where ST was given to all patients either immediately after randomization or after surgical resection of the intact primary tumor. Results: A total of 278 patients were randomized and 265 patients were in the final analysis. At 10-year follow-up, survivals were 19% (95% CI 13%–28%) and 5% (95% CI 2%–12%) in the LRT group and ST group, respectively. Median survival was 46 months for the LRT group and 35 months for the ST group, and hazard of death was 29% lower in the LRT group compared with the ST group (hazard ratio [HR] 0.71; 95% CI 0.59–0.86; p = 0.0003). Conclusions: Patients with a diagnosis of de novo stage IV BC who underwent LRT followed by ST had a 14% higher chance of OS by the end of the 10-year follow-up compared with the patients who received only ST. The longer study follow-up revealed that LRT should be presented to patients when discussing treatment options. © 2021 American College of SurgeonsConference Object The Importance of Loco-Regional Tumor Burden and Surgery on Survival in Patients With De Novo Stage Iv Breast Cancer; Post-Hoc Analyses of Protocol Mf07-01(American Association for Cancer Research, 2017) Özmen, Vahit; Özbaş, Serdar; Karanlık, Hasan; Müslümanoğlu, Mahmut; İğci, Abdullah; Cantürk, Z.; Sezgin, EfeBackground: The MF07-01 trial is a multicenter phase III randomized controlled trial of treatment naive stage IV BC patients comparing loco-regional surgery (LRS) followed by appropriate systemic therapy (ST) versus ST alone. Aims: To evaluate the importance of loco-regional tumor burden and surgery on overall survival rate in patients with de novo stage IV breast cancer.Article Citation - WoS: 25Citation - Scopus: 35Evolutionary Determinants of Polycystic Ovary Syndrome: Part 1(Elsevier Ltd., 2016) Ünlütürk, Uğur; Sezgin, Efe; Yıldız, Bülent OkanPolycystic ovary syndrome (PCOS) is a common and complex genetic disorder that develops under varying degrees of hyperandrogenemic and hyperinsulinemic conditions that cause phenotypic variability ranging from mild hirsutism to anovulation and infertility. In addition to increased risk of reproductive disability, PCOS is associated with metabolic diseases including type 2 diabetes, dyslipidemia, and cardiovascular disease. Similar prevalence rates and shared genetic susceptibility of PCOS among different populations suggest that genetic risk factors were already present in the ancestors of humans. Contemporary human genetic studies inform us that the origin of human ancestors is from Africa. Sharing common susceptibility loci between Chinese and European ancestry suggests that PCOS may have persisted for more than 50,000 years, before the migration of humans out of Africa. Although PCOS is the most common cause of anovulatory infertility, its high prevalence is still a paradox. From an evolutionary perspective, the pathogenic mechanisms underlying PCOS might be candidate factors for survival advantage of the human being. Former compensatory advantageous factors may become pathogenic mechanisms underlying complex metabolic disease with prolonged life expectancy and transition to sedentary lifestyle.