Moleküler Biyoloji ve Genetik Bölümü Koleksiyonu
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Yayın Therapeutic effects of mesenchymal stem cell conditioned medium in rat varicocele model(Korean Society for Sexual Medicine and Andrology, 2024) Şerefoğlu, Ege Can; Kolbaşı, Bircan; Bülbül, Muhammet Volkan; Karabulut, Seda; Çakıcı, Çağrı; Gündoğdu Özdemir, Reyhan Zeynep; Keskin, İlknurPurpose: This study aimed to examine the therapeutic effects of injection of conditioned medium of adipose-derived mesen chymal stem cells (ADMSC-CM) in a surgically created varicocele model in comparison with varicocelectomy. Materials and Methods: Twenty-eight male Wistar Albino rats were randomly divided into four groups: sham group, varico cele group, varicocelectomy group, and ADMSC-CM injection group. Sperm parameters were analyzed in samples taken from the epididymis after treatment. Malondialdehyde and superoxide dismutase (SOD) levels in blood samples were exam ined by biochemical analysis. The testicular tissues were stained with hematoxylin-eosin for histological examination (John sen’s Score). Additionally, Western Blot analyzes were performed to detect Claudin-11 levels, the functional protein of the blood-testis barrier, in testicular tissues. Results: Varicocelectomy and ADMSC-CM treatments significantly improved mean sperm parameters (concentration, pro gressive motility, motility, normal sperm morphology) (p≤0.05 for all). Both treatment groups had increased SOD levels along with a decrease in malondialdehyde levels (p≤0.05 for all). No significant difference was observed between the ADMSC CM group and the varicocelectomy group in preserving normal testicular histology according to Johnsen’s Score (p=0.114). Levels of Claudin-11 were significantly higher in the varicocelectomy and ADMSC-CM groups compared to the varicocele group (p≤0.05 for all). Conclusions: The therapeutic effects of ADMSC-CM in varicocele model may involve secretion of anti-inflammatory and re generative factors from ADMSC. ADMSC-CM injection appears to be a promising new strategy in the treatment of varicocelYayın Overexpression of CDC25A, AURKB, and TOP2A genes could be an important clue for luminal a breast cancer(Galenos Publishing House, 2024) Kaya, Murat; Abuaisha, Asmaa; Süer, İlknur; Alptekin, Melike Sultan; Abanoz, Fahrünnisa; Emiroğlu, Selman; Palanduz, Şükrü; Cefle, Kıvanç; Öztürk, ŞükrüObjective: Breast cancer (BC) is highly heterogeneous and one of the most common cancers. Luminal A (LUM A) is a subtype of BC with a better prognosis than other BC subtypes. The molecular mechanisms underlying the initiation and progression of the LUM A subtype are still unclear. Big data generated from microarray and sequencing systems can be re-analyzed, especially with the help of various in silico tools developed in recent years, and made applicable for in vitro and in vivo research. This work aimed to identify genes that may play a role in the progression of LUM A subtype of BC using both computational and laboratory-based methods. Materials and Methods: Overlapping genes associated with BC were identified from the The Cancer Genome Atlas database, GSE233242, GSE100925 geodata sets, and the geneshot tool. The network functional analysis between overlapping genes was determined with STRING 12.0. Expression levels of overlapping genes in BC were investigated with the TNMplot (https://tnmplot.com/analysis/) in silico tool. The effect of overlapping genes on the overall survival of LUM A cancer patients was defined using the Kaplan-Meier plotter tool. Expressions of genes identified using bioinformatics data were investigated via quantitative real-time -polymerase chain reaction (qRT-PCR) in LUM A tumor and adjacent tissue samples. The data were evaluated using the t-test. Both the sensitivity and specificity of selected genes have been determined using the receiver operating characteristic curve. Results: In silico investigation showed that eleven genes were possibly associated with BC. Among them CDC25A, AURKB, and TOP2A were considerably increased in LUM A samples according to qRT-PCR results. An overall survival analysis also showed that overexpression of these three genes could reduce the overall survival of LUM A patients. Conclusion: The genes CDC25A, AURKB, and TOP2A may play crucial functions in LUM A pathogenesis. Therapeutic strategies that diminish the expression of these connected genes may enhance the prognosis of LUM A patients.Yayın Electrochemical aptamer-based biosensors for disease biomarkers(Taylor & Francis, 2024) İnce, Bahar; Kavacık, Mehmet; Sezgintürk, Mustafa KemalThe increasing prevalence of diseases such as neurodegenerative conditions, cardiovascular dis orders, and cancer represents a significant public health challenge. Timely diagnosis plays a crucial role in improving patient outcomes and alleviating the overall societal burden posed by these disorders. Recently, there has been increasing interest in using electrochemical aptasensors in diagnosing and prognosis neurodegenerative diseases, cardiovascular disorders and cancer. This comprehensive review categorizes and examines the latest advances in electrochemical aptasen sors for evaluating these diseases. The aptasensors under investigation target specific analytes appropriate for each disease group. For cardiovascular diseases, analytes such as Cardiac troponins (cTns), myoglobin (Mb), C-reactive protein (CRP), creatine kinase-MB (CK-MB) and B-type natriuretic peptide (BNP) have been in focus. AβO, Tau, Prion protein and Alpha-synuclein (α-synuclein) were examined in neurodegenerative diseases. Carcinoembryonic antigen (CEA) and Prostate-specific antigen (PSA) biomarkers are of particular interest in the context of cancer. The review includes a comprehensive analysis of the development of these aptasensors over the last 5 years under three main headings, taking into account the advantages and disadvantages of these diagnostic tools and issues such as linear ranges, detection limits and preferred nanomaterials. In addition, this review focuses on an overview of the current problems and achievable solutions of aptasensors in detecting common diseases, and future trends are also predicted.Yayın Genomic analysis to screen potential genes and mutations in children with non-syndromic early onset severe obesity: a multicentre study in Turkey(Springer, 2022) Akıncı, Ayşehan; Kara, Altan; Özgür, Aykut; Türkkahraman, Doğa; Aksu, SonerBackground Obesity is a complex genetic-based pediatric disorder which triggers life-threatening conditions. Therefore, the understanding the molecular mechanisms of obesity has been a significant approach in medicine. Computational methods allow rapid and comprehensive pathway analysis, which is important for generation of diagnosis and treatment of obesity. Methods and results Aims of our study are to comprehensively investigate genetic characteristics of obesity in children with non-syndromic, early-onset (< 7 years), and severe obesity (BMI-SDS > 3) through computational approaches. First, the mutational analyses of 41 of obesity-related genes in 126 children with non-syndromic early-onset severe obesity and 76 healthy non-obese controls were performed using the next generation sequencing (NGS) technique, and the NGS data analyzed by using bioinformatics methods. Then, the relationship between pathogenic variants and anthropometric/biochemical parameters was further evaluated. Obtained results demonstrated that the 15 genes (ADIPOQ, ADRB2, ADRB3, IRS1, LEPR, NPY, POMC, PPARG, PPARGC1A, PPARGC1B, PTPN1, SLC22A1, SLC2A4, SREBF1 and UCP1) which directly related to obesity found linked together via biological pathways and/or functions. Among these genes, IRS1, PPARGC1A, and SLC2A4 stand out as the most central ones. Furthermore, 12 of non-synonymous pathogenic variants, including six novels, were detected on ADIPOQ (G90S and D242G), ADRB2 (V87M), PPARGC1A (E680G, A477T, and R656H), UCP1 (Q44R), and IRS1 (R302Q, R301H, R301C, H250P, and H250N) genes. Conclusion We propose that 12 of non-synonymous pathogenic variations detected on ADIPOQ, ADRB2, PPARGC1A, UCP1, and IRS1 genes might have a cumulative effect on the development and progression of obesity.
