Yazar "Abacı, Neslihan" seçeneğine göre listele

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    A brief reconnoitre about effects of MMP9 on aortic dissection
    (DergiPark, 2021) Salman Yaylaz, Burcu; Sarıman, Melda; Ekmekçi, Ahmet; Ergül, Emel; Uluganyan, Mahmut; Çosan, Fulya; Totuk Gedar, Özgün Melike; Abacı, Neslihan
    Objective: Matrix metalloproteinases (MMPs) are the extracellular ma-trix regulators that frequently investigate cardiovascular diseases and cancer metastasis. Our study aimed to examine specific polymorphisms in the MMP9 gene in our patients with aortic dissection and compare the effect of MMP9 on aortic dissection with expression datasets. Materials and Methods: Q279R and P574R polymorphisms were analyzed in 44 aortic dissection patients and 40 healthy donors via polymerase chain reaction-restriction fragment length polymorphism. (PCR-RFLP) methods. Q279R and P574R prevalence was statistically compared with the medical data of the patients. Additionally, we col-lected datasets of aortic dissection from NCBI GEO to reanalyze GEO2R and RStudio to see metalloproteinase activity on samples. Later, enrich-ment analysis was processed on widely used databases. Results: Genotypic distribution of alleles was similar in the two study groups. In addition to this, female CG carriers had a higher risk of de-veloping aortic dissection than those of males. As the results of the protein-protein interaction analysis of MMP9 and patients’ clinical data, hypertension was found to be the significant outcome of P574R varia-tion in the patients. In array analysis, MMP9 expression did not change critically, but TIMPs had been downregulated in many samples. Also, MMP9 targeted miRNA expression levels were detected as low in aortic tissue and blood. Conclusion: Q279R and P574R are two polymorphisms that do not di-rectly affect MMP9 protein structure. Consequently, studied polymor-phisms and performed meta-analysis show that MMP9 does not spark off the phenotype but sets the stage for aortic dissection development as seen in the statistical results. Furthermore, enrichment analysis on datasets shows MMP9 was not a primary reason for vascular remodeling.
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    Dysregulation of MS4A3 and PRDX5 gene expression in multiple myeloma patients
    (AKAD DOKTORLAR YAYINEVI, 2021) Suer, İlknur; Aday, Aynur; Sarıman, Melda; Ayer, Mesut; Hindilerden, İpek Yonal; Ekmekçi, Sema Sırma; Abacı, Neslihan; Palanduz, Şükrü
    Multiple myeloma (MM) is a disease in which plasma cells increase clonally. We aimed to investigate the comparison of our transcriptome data in MM, MGUS (Monoclonal gammopathy of undetermined significance) and control groups in our research. Analysis of transcriptome data revealed that CD74, FUS, MS4A3, PTPN6, PRDX5 and UNC45B genes were significantly different in the MM group compared to control group. Pathway analyzes of these genes have shown that they are associated with certain pathways such as the cellular response and immunological system. In this study, we aimed to examine the expression levels of these genes among the MM (n=50), MGUS (n=15) and control (n=14) groups using the Quantitative Real-Time Polymerase Chain Reaction. According to the consequence of the study, it was determined that MS4A3 gene expression decreased significantly in the MM patient group compared to MGUS and control group, while PRDX5 gene expression was significantly increased. Also ROC (Receiver Operating Characteristic) analysis showed that MS4A3 gene has a significant diagnostic power between MM and MGUS group (area=0.727; p=0.008). Since multiple myeloma is more common in men than in women, it was statistically evaluated whether there is no difference in gene expression between women and men. However, it was determined that there was no statistically significant difference between the groups. As a result, the MS4A3 and PRDX5 genes, which are important in various diseases such as cancer, may shed light on new treatment options for MM disease.
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    Metagenomic analysis of black-stained plaques in permanent dentition
    (Elsevier Ltd, 2021) Çelik, Zeynep Ceren; Çakiris, Aris; Yanıkoğlu, Funda Çalışkan; Abacı, Neslihan; Ekmekçi, Sema Sırma; Ilgın, Can; Çelik, Halil; Ta?tekin, Dilek Arslantunalı
    Objectives: We aimed to determine the aetiologic agent responsible for black staining of permanent dentition using next-generation sequencing and determine the relationship between caries and black stains. Materials and methods: A total of 52 systemically healthy patients with black-stained and caries-free (n = 13), black-stained and carious (n = 13), black stain-free and caries-free (n = 13), and black stain-free and carious (n = 13) teeth were enrolled in the study. The International Caries Detection and Assessment System (ICDAS II) was used for caries classification. Between 08:00 and 10:00, supragingival plaque samples were collected after a minimum of 8–12 h of accumulation and DNA samples were isolated. The samples were processed using the ZymoBIOMICS™ Service. Bioinformatics analysis was performed using mothur at usegalaxy.org. Data were analysed statistically using the Pearson chi-square and Fisher tests. Results: The number of caries-free teeth (ICDAS 0, 1, and 2) was significantly higher in patients with black stains (p = 0.007).Capnocytophaga (4.8 %), Corynebacterium (3.9 %), and Neisseria (5.4 %) species were the most abundant among all black-stained plaques (carious and caries-free) (p < 0.05). Capnocytophaga (10.8 %), Cardiobacterium (3.6 %), and Rothia (1.72 %) species were detected in the black-stained plaques of caries-free patients (p < 0.05). Conclusion: This study is one of the first studies examining the microbial composition of dental plaques with black staining in carious and caries-free adult patients using next generation sequencing technology. In the presence of black staining, plaques have an ultimate complex microbial structure. A lower caries burden was noted in the presence of black staining.