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  • Küçük Resim
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    The effects of ellagic acid on experimental corrosive esophageal burn injury
    (Multidisciplinary Digital Publishing Institute (MDPI), 2024) Keşim, Dilek Aygün; Aşır, Fırat; Ayaz, Hayat; Korak, Tuğcan
    This study aimed to investigate the antioxidant effect of Ellagic acid (EA) on wound healing in sodium hydroxide (NaOH)-induced corrosive esophageal burn injury. The interaction networks and functional annotations were conducted using Cytoscape software. A total of 24 Wistar albino rats were divided into control, corrosive esophageal burn (CEB) and CEB + EA groups. Burn injury was created by 20% NaOH and 30 mg/kg EA was per oral administered to rats. At the end of the 28-day experimental period, Malondialdehyde (MDA) content was measured. Esophageal tissue samples were processed for histological staining. The EA–target interaction network was revealed to be involved in regulating crucial cellular mechanisms for burn wound healing, with epidermal growth factor (EGF) identified as a central mediator. An increase in animal weight in the CEB + EA group was observed in the EA-treated group after CEB injury. Burn injury increased MDA content, but EA treatment decreased its level after CEB injury. Stenosis index, collagen degeneration, inflammation, fibrosis and necrosis levels were increased after CEB injury. EA treatment improved histopathology in the CEB + EA group compared to the CEB group. The expression of EGF was decreased in the CEB group but upregulated in the EA-treated group, suggesting a potential involvement of EA in cellular processes and tissue regeneration. EA, through its antioxidative and tissue regenerative properties, significantly contributes to alleviating the adverse effects of CEB injury, promoting wound healing.
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    HOXA1 expression in placentas of woman with fetal growth restriction
    (Perinatal Medicine Foundation, 2024) Aydeniz Acar, Gül Ebru; Sevinç Akdeniz, Ayşenur; Türe, Zeynep; Aşır, Ayşegül; Acar, Mesut; Aşır, Fırat; Korak, Tuğcan
    Objective: In this study, we examined the HOXA1 expression in the placentas of women diagnosed with fetal growth restriction (IUGR) by immunoexpression and in silico analysis. Methods: Placenta samples from 40 control (healthy) and 40 pregnant women diagnosed with IUGR were included in the study. The samples were fixed in zinc-formal and embedded in paraffin. Demographic information of the patients was recorded. Sections taken from paraffin blo-cks were analyzed by Hematoxylin-Eosin and HOXA1 immunostaining. The protein-protein interaction network of HOXA1 was constructed using the STRING database and analyzed with Cytoscape. The route description was made with the DAVID web tool. Results: In histopathological examination, intense fibrin accumulation, structural degeneration of placental components, congestion, dilatation and increased syncytial nodes were observed in the IUGR group compared to the control group. HOXA1 gene expression was significantly increased in the IUGR group. The HOXA1 PPI network contained 201 nodes and 3876 edges. MCODE analysis identified 8 modules, the highest scoring module was related to the “Systemic lupus erythematosus”, “Alcoholism” and “Neutrophil extracellular trap formation” pathways. Conclusion: With immunoexpression and in silico analysis, we showed HOXA1 is a player of immune pathways, tissue development, and placental regulation, suggesting potential research avenues in understanding IUGR mechanisms. © 2024 Perinatal Medicine Foundation.
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    Öğe
    Investigation of Aquaporin Molecules in the Placentas of Pregnant Women with Premature Rupture of Membranes
    (Tıbbi Kayıtlar Derneği, 2024) Kaplan, Özge; Başaran, Süreyya Özdemir; Pala, Ayşegül; Korak, Tuğcan; Aşır, Fırat; Kaplan, Serdar; Ege, Serhat
    Aim: This study aimed to investigate the immunohistochemical expression of Aquaporin 3 (AQP3) in placentas of pregnant women with premature rupture of membrane (PROM) and to explore AQP3-related interactors and signaling pathways using in silico approaches. Material and Method: Placental samples from 21 healthy (control) pregnant women and 21 pregnant women diagnosed with PROM were processed for routine histological tissue preparation. Sections were immunostained with AQP3 and analyzed under light microscope via ImageJ software. Protein-protein interaction (PPI) network of AQP3 was constructed with Cytoscape (version 3.10.2). Nodal centrality indexes (degree, closeness and betweenness) were computed through CentiScaPe plugin. The Enrichr tool was utilized to perform pathway enrichment analysis for 15 central genes. Results: AQP3 immune activity was significantly decreased in the plasma membrane of the trophoblastic cell layer of the PROM group compared to control group. According to network centrality analysis, AQP subfamily proteins predominantly play central roles in the AQP3 network; Major Intrinsic Protein of Lens Fiber (MIP), Glycerol-3-Phosphate Dehydrogenase 2 (GPD2), Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH), Glycerol Kinase 2 (GK2), GK, and Actin Beta (ACTB) with additional central interactors including proteins. Peroxisome proliferator-activated receptors (PPAR) signaling pathway was obtained as the most significantly enriched pathway. Conclusion: Alterations in AQP3 expression level in the PROM group compared with the control group may contribute to disturbances in water transport and cellular homeostasis in placental tissues and in silico potential interaction between AQP3 expression and PPAR signaling suggest the role of AQP3 in cell metabolism in PROM.
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    Öğe
    Investigation of Aquaporin Molecules in the Placentas of Pregnant Women with Premature Rupture of Membranes
    (2024) Kaplan, Özge; Başaran, Süreyya Özdemir; Aşır, Ayşegül; Korak, Tuğcan; Aşır, Fırat; Kaplan, Serdar; Ege, Serhat
    Aim: This study aimed to investigate the immunohistochemical expression of Aquaporin 3 (AQP3) in placentas of pregnant women with premature rupture of membrane (PROM) and to explore AQP3-related interactors and signaling pathways using in silico approaches. Material and Method: Placental samples from 21 healthy (control) pregnant women and 21 pregnant women diagnosed with PROM were processed for routine histological tissue preparation. Sections were immunostained with AQP3 and analyzed under light microscope via ImageJ software. Protein-protein interaction (PPI) network of AQP3 was constructed with Cytoscape (version 3.10.2). Nodal centrality indexes (degree, closeness and betweenness) were computed through CentiScaPe plugin. The Enrichr tool was utilized to perform pathway enrichment analysis for 15 central genes. Results: AQP3 immune activity was significantly decreased in the plasma membrane of the trophoblastic cell layer of the PROM group compared to control group. According to network centrality analysis, AQP subfamily proteins predominantly play central roles in the AQP3 network; Major Intrinsic Protein of Lens Fiber (MIP), Glycerol-3-Phosphate Dehydrogenase 2 (GPD2), Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH), Glycerol Kinase 2 (GK2), GK, and Actin Beta (ACTB) with additional central interactors including proteins. Peroxisome proliferator-activated receptors (PPAR) signaling pathway was obtained as the most significantly enriched pathway. Conclusion: Alterations in AQP3 expression level in the PROM group compared with the control group may contribute to disturbances in water transport and cellular homeostasis in placental tissues and in silico potential interaction between AQP3 expression and PPAR signaling suggest the role of AQP3 in cell metabolism in PROM.
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    Öğe
    Multiple sequence alignment quality comparison in T-Coffee, MUSCLE and M-Coffee based on different benchmarks
    (2021) Korak, Tuğcan; Işık, Esin; Aşır, Fırat; Cengiz, Nur
    Multiple sequence alignment (MSA) is a fundamental process in the studies for determination of evolutionary, structural and functional relationships of biological sequences or organisms. There are various heuristic approaches comparing more than two sequences to generate MSA. However, each tool used for MSA is not suitable for every dataset. Considering the importance of MSA in wide range of relationship studies, we were interested in comparing the performance of different MSA tools for various datasets. In this study, we applied three different MSA tools, T-Coffee, MUSCLE and M -Coffee, on several datasets, BAliBase, SABmark, DIRMBASE, ProteinBali and DNABali. It was aimed to evaluate the differences in the performance of these tools based on the stated benchmarks regarding the % consistency, sum of pairs (SP) and column scores (CS) by using Suite MSA. We also calculated the average values of these scores for each tool to examine the results in comparative perspective. Eventually, we conclude that all three tools performed their best with the datasets from ProteinBali (average % consistency: 29.6, 32.3, 29.7; SP: 0.74, 0.73, 0.74; CS with gaps: 0.27, 0.27, 0.26 for T-Coffee, MUSCLE, M-Coffee, respectively), whereas the lowest performance was obtained in datasets from DIRMBASE (average % consistency: 1.8, 1.1, 4.3; SP: 0.05, 0.04, 0.04 CS with gaps: 0.01, 0, 0.008 for T-Coffee, MUSCLE, M-Coffee, respectively)
  • Küçük Resim
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    Three MSA tools analysis in DNA and protein datasets
    (INESEG Yayıncılık, 2021) Aşır, Fırat; Korak, Tuğcan; Öztürk, Özgür
    Multiple sequence alignment (MSA) is the alignment of three or more sequences of DNA,RNA, and protein. MSA is used to construct phylogenetic trees and to compare evolutionaryrelationships between sequences analyzing similarities and dissimilarities. A variety of multiplesequence alignment tools are available, each using different methods and parameters to alignsequences. In this article three MSA tools; CLUSTALW, SAGA, and MAFFT were used to analyze fivedatasets BALiBASE_R9, DIRMBASE, SABmark, DNABali, and ProteinBali. The results showed that MAFFT may be more useful to align DNA and protein sequences than the other two tools.