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    Humoral immune response of Galleria mellonella after mono- and co-injection with Hypericum perforatum extract and Candida albicans
    (Wiley, 2024) Genc, Tulay Turgut; Kaya, Serhat; Gunay, Melih; Cakaloglu, Cagla
    Galleria mellonella is used as a model organism to study the innate immune response of insects. In this study, the humoral immune response was assessed by examining phenoloxidase activity, fungal burden, and the expression of phenoloxidase and antimicrobial peptide genes at different time point following separate and combined injections of Hypericum perforatum extract and a nonlethal dose of Candida albicans. The administration of a plant extract at low doses increased phenoloxidase activity, while higher doses had no effect. Similarly, co-injection of a low dose of the extract with the pathogen allowed half of the yeast cells to survive after 24 h. Co-injection of plant extract with the pathogen decreased the phenoloxidase activity at the end of 4 h compared to C. albicans mono-injection. The phenoloxidase gene expressions was reduced in all experimental conditions with respect to the control. When plant extracts and the pathogen were administered together, gallerimycin and hemolin gene expressions were considerably higher compared to mono-injections of plant extracts and the pathogen. The results of this study reveal that gene activation and regulatory mechanisms may change for each immune gene, and that recognition and signaling pathways may differ depending on the involved immunoregulator.
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    In silico molecular docking and in vitro analysis of atomoxetine
    (Taylor & Francis Ltd, 2025) Bolat, Nurullah; Hiz-celikliyurt, Merve Meliha; Akinci, Erhan; Akkus, Gulsum; Gunay, Melih; Korkmaz, Sukru Alperen
    Although atomoxetine, a selective norepinephrine reuptake inhibitor, is widely used in the treatment of attention-deficit/hyperactivity disorder (ADHD), there is limited data on its cytogenetic effects. This study aimed to investigate the cytotoxicity and genotoxicity of atomoxetine in vivo and silico. Chromosome aberration and micronucleus assays were used to analyze the genotoxic effect of atomoxetine in human peripheral blood lymphocytes under culture conditions. The mitotic index was assessed for cytotoxic potential. For the docking analysis, DNA receptor (1BNA) was prepared with ChimeraX, and the Atomoxetine molecule was optimized by Avogadro2.0 software. In silico molecular docking analysis was carried out utilizing SwissDock online platform. The results obtained were visualized using ChimeraX and Pymol software. Atomoxetine doses of 9.6 mu g/mL (equal to about 1.2 mg/kg as a maintenance dose), 14.4 mu g/mL (equal about to 1.8 mg/kg as the highest dose systematically tested), 48.0 mu g/mL (equal about to 6 mg/kg as five times the maintenance dose) and 96.0 mu g/mL (equal about to 12 mg/kg as ten times the maintenance dose) were analyzed. The findings clearly indicate that atomoxetine has no genotoxic effect at the therapeutic dose. However, we observed genotoxic effects at 48.0 and 96.0 mu g/mL doses. No strong binding affinity occurs in silico analyses. As one of the initial inquiries into the in silico and in vivo appraisal of atomoxetine's genotoxic impacts, the research has established that atomoxetine does not significantly affect the frequency of chromosomal damage or micronucleus formation. Genotoxic effects should be kept in mind at doses above clinical practice.
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    Internal transcribed spacer (ITS) sequence-based identification of yeast biota on pomegranate surface and determination of extracellular enzyme profile
    (Univ Sebelas Maret, 2020) Genc, Tulay Turgut; Gunay, Melih
    Yeasts are the most significant organisms to produce fermented products from different types of fruits such as grape, strawberry and pomegranate. The native yeasts on these fruits contribute to beverages' quality and aroma during fermentation. Pomegranate is used in fruit juice and wine production because of high antioxidant characteristic. In order to determine yeast microbiota on the pomegranate fruits collected from Gallipoli (Gelibolu), Canakkale-Turkey, ITS-5.8S rDNA gene region have been utilized. Also, phylogenetic relationships among identified yeast species were assigned by using sequences of ITS-5.8S rDNA gene region. In addition, extracellular enzyme activity of identified yeast strains was detected by using API-ZYM. Kluyveromyces lactis, Aureobasidium pullulans, Hanseniaspora uvarum, Candida zeylanoides, Kwoniella sp., and Metschnikowia pulcherrima and Metschnikowia ziziphicola yeast species were identified on pomegranate surface. Phylogenetic analysis, carried out in ITS-5.8S rDNA gene region of identified yeast strains, revealed the presence of five clades. Kwoniella sp., H. uvarum, M. pulcherrima, and Kl. lactis yeast strains revealed high leucine arylamidase activity. Also valine arylamidase activity was determined in M. pulcherrima and Kl. lactis yeast species. Acid phosphatase activity was determined in H. uvarum and K. lactis yeast species. Uncultured Kwoniella sp. and H. uvarum yeast species displayed high beta-galactosidase and beta-glucosidase activities, respectively.
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    Molecular identification of yeasts from Turkish traditional cheeses: Extracellular enzyme activities and physiological properties important for dairy industry
    (Univ Sebelas Maret, 2023) Gunay, Melih; Genc, Tulay Turgut
    Gunay M, Genc TT. 2023. Molecular identification of yeasts from Turkish traditional cheeses: Extracellular enzyme activities and physiological properties important for dairy industry. Nusantara Bioscience 15: 1-11. The determination of yeast microbiota in cheeses and the physiological properties of yeasts are very important for the dairy industry. In addition, the physiological features, proteolytic and lipolytic activities, and stress tolerance of yeasts have a significant role in the selection of starter yeast species for cheese ripening. This study aimed to determine industrially important yeasts isolated from cheese samples. Molecular techniques identified the isolated yeast strains. The yeast strains' extracellular enzyme activities, fermentation capacities, and thermotolerance and osmotolerance properties were also evaluated. A total of 81 yeast strains were isolated and characterized from three types of cheese samples. PCRRFLP determined the isolated yeast strains and sequence analysis of ITS1-5.8S-ITS2 and 26S rDNA regions. A maximum parsimony tree was constructed by MEGA X software to evaluate the phylogenetic relationship of identified yeast strains. Candida intermedia, Candida parapsilosis, Clavispora lusitaniae, Debaryomyces hansenii, Kluyveromyces marxianus, Pichia kudriavzevii, and Wickerhamomyces anomalus yeast species were identified on cheese samples. The distribution of identified yeast species on cheese samples was determined as 48.1% for W. anomalus, 17.3% for K. marxianus, 14.8% for C. parapsilosis, 8.6% for D. hansenii, 4.9% for Cl. lusitaniae, 3.7% for C. intermedia and 2.5% for P. kudriavzevii. The W. anomalus yeast species was common in three cheese types. All strains of W. anomalus and P. kudriavzevii yeast species, three C. parapsilosis, and two Cl. lusitaniae yeast strains have important physiological properties for industrial applications. These yeast strains have the potential to be used in combination as starter cultures to improve cheese maturation in the future. This comprehensive study identifies yeast species by ITS1-5.8S-ITS2 and 26S rDNA regions and determines industrially important yeast species using multiple criteria (extracellular enzyme activity, stress tolerance, and fermentation capacity).
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    Recent insights into depression from transcriptomic analysis
    (Termedia Publishing House Ltd, 2025) Gunay, Melih; Cicekliyurt, Meliha M.
    Purpose: Depression is a widespread mood disorder with a high rate of relapse and chronicity that can be affected by gender, and caused by traumatic or stressful events. Transcriptome analysis measures gene expression heterogeneity in cells, tissues, organs, and the whole body. The purpose of the study was to investigate both gender-specific and tissue-specific variations in gene expression regarding depression based on transcriptomic analysis using RNA-Seq data. Methods: The depression datasets GSE190518 and GSE214921 were downloaded from the Gene Expression Omnibus database provided by the NCBI. The GSE190518 datasets include peripheral blood samples (4 patients, 4 healthy controls), and the GSE214921 datasets contain human postmortem orbitofrontal cortex bulk tissue (20 patients, 19 healthy controls). All datasets were analyzed separately with the DESeq2 package in R. Later, GO and KEGG enrichment analyses of differentially expressed genes were performed using the clusterProfiler package in R. Results: Our results reveal that depression stimulates genes linked to the immune system, which is a common denominator in both brain tissue and blood samples. Overall, tissue-specific factors contribute to the association between depression and the immune system via distinct genes. Furthermore, gene ontology analyses revealed that HSPA6, HSPA7, HSPA1L, HSPA1A, and HSPA1B genes are co-represented in different pathways involved in molecular function, biological processes, and cellular components. Conclusions: Comparative transcriptomic evidence supports the immune hypothesis of depression in different tissue samples. Gender-specific depression may be triggered by protein misfolding.