PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7645
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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 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: 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.Article Citation - WoS: 8Citation - Scopus: 10Factors Associated With the Occurrence and Healing of Umbilical Pilonidal Sinus: a Rare Clinical Entity(Lippincott Williams and Wilkins Ltd., 2022) Işık, Arda; Wysocki, Arkadiusz Peter; Memiş, Ufuk; Sezgin, Efe; Yezhikova, Assel; Islambekov, YersultanObjective: Pilonidal sinus disease (PSD) is a chronic inflammatory condition of skin that is thought to be related to implanted loose hair. Although PSD is most frequently seen in the sacrococcygeal region, it can also occur at the axilla, perineum, suprapubic regions, hands, and umbilicus. The aim of this project was to find factors influencing the development and treatment of umbilical PSD. Methods: In this retrospective study, the authors evaluated 82 patients (19 women, 63 men) with a history of umbilical PSD between 2012 and 2020 to determine predisposing factors and treatment modalities. Results: There was a 20% concordance with intergluteal PSD. Smoking was the only modifying factor for recurrence. The three different treatment methods studied (conservative treatment, surgical treatment, silver nitrate) did not differ in recurrence rate (P =.57). Conclusions: Because of its rare nature, umbilical PSD can be misdiagnosed or underdiagnosed. Key aspects of treatment include smoking cessation and a conservative approach.Article Citation - WoS: 2Citation - Scopus: 2Importance of Multigene Panel Test in Patients With Consanguineous Marriage and Family History of Breast Cancer(Spandidos Publications, 2022) Özmen, Vahit; Çağlayan, Ahmet Okay; Yararbaş, Kanay; Ordu, Çetin; Aktepe, Fatma; Özmen, Tolga; Sezgin, EfeNext-generation sequencing (NGS) technology is used to evaluate hereditary cancer risks of patients worldwide; however, information concerning the germline multigene mutational spectrum among patients with breast cancer (BC) with consanguineous marriage (CM) is limited. Therefore, this prospective study aimed to determine the molecular characteristics of patients with BC who were tested with multigene hereditary cancer predisposition NGS panel and to show the effect of CM on cancer-related genes. Patients with BC with or without CM and family history (FH) of BC treated in our breast center were selected according to The National Comprehensive Cancer Network (NCCN) criteria for hereditary BC. In these patients, the analysis of a panel of 33 genes involved in hereditary cancer predisposition was performed after genetic counseling by using NGS. The pathogenic variant (PV) and the variant of uncertain significance (VUS) were found to be 15.8 and 47.4%, respectively. PVs were identified in 10/33 genes in 34 patients; 38.2% in BRCA1/2 genes; 6, 24, and 14% in other high, moderate and low-risk genes, respectively. The CM rate was 17.7% among the 215 patients with BC. The PV rate was 13.2% in patients with CM and 16.4% in patients without CM (P=0.80). When PV and VUS were evaluated together, the PV+VUS ratio was significantly higher in patients with CM and FH of BC than patients without CM and FH of BC (88.2 vs. 63.3%, P=0.045). Analysis of multigene panel provided 9.76% additional PVs in moderate/low-risk genes. The PV rate was similar in patients with BC with or without CM. A high PV+VUS ratio in patients with CM and FH of BC suggests that genes whose importance are unknown are likely to be pathogenic genes later.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.Letter Citation - Scopus: 3Reply: the Effect of Primary Surgery in Patients With Stage Iv Breast Cancer With Bone Metastasis Only (protocol Bomet Mf 14-01): a Multi-Center, Registry Study(Springer, 2021) Soran, Atilla; Sezgin, Efe; Özbaş, Serdar; Doğan, LütfiDear Editor, We’d like to thank Drs. Ishizuka and Horimoto for their letter to the editor. We’re glad to see their interest to our prospective study. Regarding their recommendation that univariate Kaplan–Meier analysis does not eliminate confounding factors, such as age, tumor size, number of bone metastasis, etc., we employed propensity score methods for the results, including Fig. 1.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 SurgeonsArticle Citation - WoS: 10Inflammatory Response Markers in Rats Undergoing Abdominal Surgical Procedures(Hellenic Society of Gastroenterology, 2020) Kırdak, Türkay; Uysal, Erdal; Sezgin, Efe; Çeçen, Gülce Sevdar; Cavun, SinanBackground The aim of this study was to determine the effectiveness of cortisol, interleukin (IL)-6, C-reactive protein (CRP), and white blood cell (WBC) count as inflammatory markers to evaluate the postoperative inflammatory response associated with various abdominal surgical procedures in rats. Methods Wistar albino rats (N=152) were randomly assigned to 7 groups: control, hepatectomy, splenectomy, nephrectomy, colectomy, gastrectomy, and sham. Apart from the control group, each group was then divided into 3 subgroups: 6th, 24th and 48th h. Thus, a total of 19 groups were defined, each including 8 rats. At the 6th, 24th and 48th h following the surgical procedures blood samples from each rat were collected. The plasma concentrations of IL- 6, cortisol, CRP, and WBC were measured. Results Both the surgery category and the elapsed time after the surgery had a significant effect on IL-6 levels (P<0.0001). Blood CRP levels were primarily determined by the surgery category (P<0.0001). Neither surgery nor the elapsed time had a significant effect on the cortisol levels. The elapsed time after surgery was the major factor that influenced the differences in WBC count among the surgery groups (P<0.0001). Conclusions Our results cumulatively indicate that the levels of IL-6, CRP, and cortisol and WBC count change at different time points after several abdominal surgical procedures. Cortisol level is not related to the type of surgical procedure or the elapsed time, while WBC count decreases with the elapsed time. None of the changes in the markers investigated in this study is specifically related to the category of abdominal surgical procedure.Article Citation - WoS: 3Citation - Scopus: 4Comparison of Radio-Guided Occult Lesion Localization (roll) and Magnetic Occult Lesion Localization (moll) for Non-Palpable Lesions: a Phantom Model Study(Elsevier, 2020) Aydoğan, Tumay; Sezgin, Efe; İlvan, Şennur; Yılmaz, Osman Cem; Aslan, Nesrin; Golshan, Mehra; Aydoğan, FatihWe sought to compare radio-guided localization and magnetic tracer localization techniques by using a phantom model for excision of nonpalpable breast lesions. There was no difference between the groups in the duration of operative excision, specimen weight, or specimen volume. Magnetic occult lesion localization can be performed in clinics without the need for a nuclear medicine team and radiation safety procedures. Background: Localization of nonpalpable breast cancers can be achieved with several techniques. We sought to compare radio-guided localization (ROLL) and magnetic tracer localization (MOLL) techniques by using a phantom model we previously developed, which can provide an accurate simulation for excision of nonpalpable breast lesions. Materials and Methods: We designed 20 phantom models (10 MOLL, 10 ROLL group) for localization. A handheld gamma probe for the ROLL group and a manual magnetometer (SentiMag) for the MOLL group were used to test the ability of the modality to detect olives in turkey breasts. The excision time for each procedure, specimen size, and weight of the specimens removed from the turkey breasts were recorded. Results: Both techniques resulted in 100% retrieval of the lesions. There was no difference between the groups in the duration of operative excision, specimen weight, or specimen volume. Conclusion: This experimental trial found similar success rates for ROLL and MOLL in localization of occult lesions using the turkey breast phantom model. MOLL can be performed in clinics without the need for a nuclear medicine team and radiation safety procedures. (C) 2019 Elsevier Inc. All rights reserved.