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    Development of targeted whole genome sequencing approaches for Crimean-Congo haemorrhagic fever virus (CCHFV)
    (Elsevier, 2024) D'Addiego, Jake; Shah, Sonal; Pektas, Ayse Nur; Bagci, Binnur Koksal; Oz, Murtaza; Sebastianelli, Sasha; Elaldi, Nazif
    Crimean-Congo haemorrhagic fever (CCHF) is the most prevalent human tick-borne viral disease, with a reported case fatality rate of 30 % or higher. The virus contains a tri-segmented, negative-sense RNA genome consisting of the small (S), medium (M) and large (L) segments encoding respectively the nucleoprotein (NP), the glycoproteins precursor (GPC) and the viral RNA-dependent RNA polymerase (RDRP). CCHFV is one of the most genetically diverse arboviruses, with seven distinct lineages named after the region they were first reported in and based on S segment phylogenetic analysis. Due to the high genetic divergence of the virus, a single targeted tiling PCR strategy to enrich for viral nucleic acids prior to sequencing is difficult to develop, and previously we have developed and validated a tiling PCR enrichment method for the Europe 1 genetic lineage. We have developed a targeted, probe hybridisation capture method and validated its performance on clinical as well as cell-cultured material of CCHFV from different genetic lineages, including Europe 1, Europe 2, Africa 2 and Africa 3. The method produced over 95 % reference coverages with at least 10x sequencing depth. While we were only able to recover a single complete genome sequence from the tested Europe 1 clinical samples with the capture hybridisation protocol, the data provides evidence of its applicability to different CCHFV genetic lineages. CCHFV is an important tick-borne human pathogen with wide geographical distribution. Environmental as well as anthropogenic factors are causing increased CCHFV transmission. Development of strategies to recover CCHFV sequences from genetically diverse lineages of the virus is of paramount importance to monitor the presence of the virus in new areas, and in public health responses for CCHFV molecular surveillance to rapidly detect, diagnose and characterise currently circulating strains.
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    Evaluation and normalization of a set of reliable reference genes for quantitative sgk-1 gene expression analysis in Caenorhabditis elegans-focused cancer research
    (Taylor & Francis Inc, 2024) Ozdemir, Ozguer Ulkue; Yurt, Kubra; Pektas, Ayse Nur; Berk, Seyda
    Multiple signaling pathways have been discovered to play a role in aging and longevity, including the insulin/IGF-1 signaling system, AMPK pathway, TOR signaling, JNK pathway, and germline signaling. Mammalian serum and glucocorticoid-inducible kinase 1 (sgk-1), which has been associated with various disorders including hypertension, obesity, and tumor growth, limits survival in C. elegans by reducing DAF-16/FoxO activity while suppressing FoxO3 activity in human cell culture. C. elegans provides significant protection for a number of genes associated with human cancer. The best known of these are the lin-35/pRb (mammalian ortholog pRb) and CEP-1 (mammalian ortholog p53) genes. Therefore, in this study, we aimed to investigate the expression analyzes of sgk-1, which is overexpressed in many types of mammalian cancer, in mutant lin-35 and to demonstrate the validation of reference genes in wild-type N2 and mutant lin-35 for C. elegans-focused cancer research. To develop functional genomic studies in C. elegans, we evaluated the expression stability of five candidate reference genes (act-1, ama-1, cdc-42, pmp-3, iscu-1) by quantitative real-time PCR using five algorithms (geNorm, NormFinder, Delta Ct method, BestKeeper, RefFinder) in N2 and lin-35 worms. According to our findings, act-1 and cdc-42 were effective in accurately normalizing the levels of gene expression in N2 and lin-35. act-1 and cdc-42 also displayed the most consistent expression patterns, therefore they were utilized to standardize expression level of sgk-1. Furthermore, our results clearly showed that sgk-1 was upregulated in lin-35 worms compared to N2 worms. Our results highlight the importance of definitive validation using mostly expressed reference genes.
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    Investigating the effect of ribavirin treatment on genetic mutations in Crimean-Congo haemorrhagic fever virus (CCHFV) through next-generation sequencing
    (Wiley, 2023) D'Addiego, Jake; Elaldi, Nazif; Wand, Nadina; Osman, Karen; Bagci, Binnur Koksal; Kennedy, Emma; Pektas, Ayse Nur
    Crimean-Congo haemorrhagic fever (CCHF) is the most widespread tick-borne viral haemorrhagic fever affecting humans, and yet a licensed drug against the virus (CCHFV) is still not available. While several studies have suggested the efficacy of ribavirin against CCHFV, current literature remains inconclusive. In this study, we have utilised next-generation sequencing to investigate the mutagenic effect of ribavirin on the CCHFV genome during clinical disease. Samples collected from CCHF patients receiving ribavirin treatment or supportive care only at Sivas Cumhuriyet University Hospital, Turkey, were analysed. By comparing the frequency of mutations in each group, we found little evidence of an overall mutagenic effect. This suggests that ribavirin, administered at the acute stages of CCHFV infection (at the World Health Organization-recommended dose) is unable to induce lethal mutagenesis that would cause an extinction event in the CCHFV population and reduce viremia.
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    Methylation of the e-cadherin (ECAD) gene in clear cell renal cell carcinoma (CCRCC)
    (Parlar Scientific Publications, 2020) Kitapci, Aytul; Dastan, Taner; Dundar, Gokce; Pektas, Ayse Nur; Dastan, Sevgi Durna; Korgali, Esat; Turkoglu, Sifa
    Clear cell renal carcinoma is one of the most common sub-types of renal cell cancer. Methylation is the leading type of epigenetic changes. Many studies in the field emphasized that hypermethylation of some genes is efficient on the formation of many cancer types. In this study, the aim is to analyze DNA methylation, one of the epigenetic changes in the ECAD gene of renal cell carcinoma (RCC) patients, and to determine the relations by comparing the present epigenetic features with clinic-pathologic parameters. Studies were organized in two groups: a control group with 153 individuals and a patient group with 113 individuals. The methylation of blood samples was determined by displaying in the gel after methylation specific PCR (MSP) steps. Some descriptive statistics and Wilcoxon, Correlation and Logistic Regression analyses were performed using SPSS. As a result of this study, it was found out that the probability of the occurrence of this disease was 5 times higher in people who have methylation in their ECAD genes than those who have not. Furthermore, it was observed that women are 4.253 times more likely to have disease compared to men. This research is a very important and fundamental study on the diagnosis and treatment of CCRCC disease in terms of the effect of epigenetic mechanisms such as methylation analysis. © 2020 Parlar Scientific Publications. All rights reserved.
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    METHYLATION OF THE E-CADHERIN (ECAD) GENE IN CLEAR CELL RENAL CELL CARCINOMA (CCRCC)
    (Parlar Scientific Publications (P S P), 2020) Kitapci, Aytul; Dastan, Taner; Dundar, Gokce; Pektas, Ayse Nur; Dastan, Sevgi Durna; Korgali, Esat; Turkoglu, Sifa
    Clear cell renal carcinoma is one of the most common sub-types of renal cell cancer. Methylation is the leading type of epigenetic changes. Many studies in the field emphasized that hypermethylation of some genes is efficient on the formation of many cancer types. In this study, the aim is to analyze DNA methylation, one of the epigenetic changes in the ECAD gene of renal cell carcinoma (RCC) patients, and to determine the relations by comparing the present epigenetic features with clinic-pathologic parameters. Studies were organized in two groups: a control group with 153 individuals and a patient group with 113 individuals. The methylation of blood samples was determined by displaying in the gel after methylation specific PCR (MSP) steps. Some descriptive statistics and Wilcoxon, Correlation and Logistic Regression analyses were performed using SPSS. As a result of this study, it was found out that the probability of the occurrence of this disease was 5 times higher in people who have methylation in their ECAD genes than those who have not. Furthermore, it was observed that women are 4.253 times more likely to have disease compared to men. This research is a very important and fundamental study on the diagnosis and treatment of CCRCC disease in terms of the effect of epigenetic mechanisms such as methylation analysis.
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    Novel antimicrobial defensin peptides from different coleopteran insects (Coleoptera: Insecta): identification, characterisation and antimicrobial properties
    (Taylor & Francis Ltd, 2025) Pektas, Ayse Nur; Korkmaz, Ertan Mahir
    Antimicrobial peptides are crucial components of the immune systems of both vertebrates and invertebrates. Here, defensins, the most studied class of antimicrobial molecules in arthropods were investigated in four coleopteran insect species: Harpalus rufipes (DeGeer, 1774), Mylabris quadripunctata (Linnaeus, 1767), Sphaeridium marginatum (Linnaeus, 1758), and Ocypus mus (Brull & eacute;, 1832). The peptides synthesized with over 95% purity and their antimicrobial activities were evaluated by MIC test method. As a result, it was determined that Mylabris quadripunctata defensin (MqDef) showed high antimicrobial activity against Staphylococcus aureus and MRSA, whereas Sphaeridium marginatum (SmDef) and Harpalus rufipes (HrDef) defensins against Candida tropicalis.
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    The combination of metformin and high glucose increased longevity of Caenorhabditis elegans a DAF-16/FOXO-independent manner: cancer/diabetic model via C. elegans
    (Frontiers Media Sa, 2024) Berk, Seyda; Cetin, Ali; Ozdemir, Ozgur Ulkue; Pektas, Ayse Nur; Yurtcu, Nazan; Dastan, Sevgi Durna
    Introduction Sedentary lifestyles and diets with high glycemic indexes are considered to be contributing factors to the development of obesity, type 2 diabetes in humans. Metformin, a biguanide medication commonly used to treat type 2 diabetes, has been observed to be associated with longevity; however, the molecular mechanisms underlying this observation are still unknown.Methods The effects of metformin and high glucose, which have important roles in aging-related disease such as diabetes and cancer, were studied in lin-35 worms because they are associated with cancer-associated pRb function in mammals and have a tumour suppressor property.Results and Discussion According to our results, the negative effect of high glucose on egg production of lin-35 worms was greater than that of N2 worms. High glucose shortened lifespan and increased body length and width in individuals of both strains. Metformin treatment alone extended the lifespan of N2 and lin-35 worms by reducing fertilization efficiency. However, when metformin was administered in the presence of high glucose, the lifespan of lin-35 worms was clearly longer compared to N2 worms. Additionally, we conclude that glucose and metformin in lin35 worms can extend life expectancy through a DAF-16/FOXO-independent mechanism. Furthermore, the results of this study will provide a new perspective on extending mammalian lifespan through the model organism C. elegans.