PubMed İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/397
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Article Citation - WoS: 2Citation - Scopus: 2Structural Profile Matrices for Predicting Structural Properties of Proteins(World Scientific Publ Co Pte Ltd, 2020-07-10) Azginoglu, Nuh; Aydin, Zafer; Celik, MetePredicting structural properties of proteins plays a key role in predicting the 3D structure of proteins. In this study, new structural profile matrices (SPM) are developed for protein secondary structure, solvent accessibility and torsion angle class predictions, which could be used as input to 3D prediction algorithms. The structural templates employed in computing SPMs are detected by eight alignment methods in LOMETS server, gap affine alignment method, ScanProsite, PfamScan, and HHblits. The contribution of each template is weighted by its similarity to target, which is assessed by several sequence alignment scores. For comparison, the SPMs are also computed using Homolpro, which uses BLAST for target template alignments and does not assign weights to templates. Incorporating the SPMs into DSPRED classifier, the prediction accuracy improves significantly as demonstrated by cross-validation experiments on two difficult benchmarks. The most accurate predictions are obtained using the SPMs derived by threading methods in LOMETS server. On the other hand, the computational cost of computing these SPMs was the highest.Article Citation - WoS: 3Citation - Scopus: 3Pericardial Fluid and Vascular Tissue Engineering: A Preliminary Study(Ios Press, 2021-03-23) Sonmezer, Dilek; Latifoglu, Fatma; Toprak, Guler; Duzler, Ayhan; Isoglu, Ismail AlperBACKGROUND: The heart is surrounded by a membrane called pericardium or pericardial cavity. OBJECTIVE: In this study, we investigated the pericardial fluid (PF) for coating polycaprolactone (PCL) scaffolds. PFS, which is a PF component, was used for the coating material. In addition to using PFS for surface coating, MED and fetal bovine serum (FBS) were also used for comparison. METHODS: Pericardial fluid cells (PFSc) isolated from PF were cultured on coated PCL scaffolds for 1, 3, and 5 days. Cell viability was determined using 3-(4, 5-di-methylthiazol- 2-yl)-2, 5-diphenyltetrazolium bromide (MTT) assay. RESULTS: The MTT assay results showed that the viability of cells on PCL scaffold coated with PFS increased over time (P < 0.005), and cell viability was significantly different between PCL scaffolds coated with PFS and non-coated PCL scaffolds. However, cell viability was significantly higher in the PCL scaffolds coated with PFS than non-coated and coated with FBS, MED, and PCL scaffolds. Scanning electron microscopy (SEM) microscopy images and MTT assay indicated that PFSc are attached, proliferated, and spread on PCL scaffolds, especially on PCL scaffolds coated with PFS. CONCLUSIONS: These results suggest that PFS is a biocompatible material for surface modification of PCL scaffolds, which can be used as a suitable material for tissue engineering applications.Article Citation - WoS: 5Genetic Variants in Genes Correlated to the PI3K/AKT Pathway: The Role of ARAP3, CDH5, KIF22 and RELN in Primary Lymphedema(Lymphology, 2023) Dundar, M. S.; Belanova, I.; Bonetti, G.; Gelanova, V.; Kozacikova, R.; Veselenyiova, D.; Michelini, S.Genetic anomalies affecting lymphatic development and function can lead to lym- phatic dysfunction, which could manifest as lymphedema. Understanding the signaling pathways governing lymphatics function is crucial for developing targeted diagnostic and therapeutic interventions. This study aims to characterize genetic variants in genes involved in the PI3K/AKT signaling pathway, which plays a critical role in lymphangiogenesis. 408 patients diagnosed with primary lymphedema were sequenced using a next-generation se- quencing (NGS) gene panel composed of 28 diagnostic genes and 71 candidate genes. The analysis revealed six variants in genes RELN, ARAP3, CDH5, and KIF11. Five of these vari- ants have never been reported in the literature. All these genes have been correlated to lym- phatic activity and are involved in the PI3K/ AKT pathway. As the PI3K/AKT signaling pathway plays an essential role in lymphangio- genesis and lymphatic function, genetic vari- ants in genes correlated to this pathway could lead to lymphedema. Our findings underscore. the potential of the PI3K/AKT pathway in lymphedema pathogenesis, supporting the role of RELN, ARAP3, CDH5, and KIF11 as diag- nostic and therapeutic targets.Article Citation - WoS: 6Citation - Scopus: 8Dimensionality Reduction for Protein Secondary Structure and Solvent Accesibility Prediction(World Scientific Publ Co Pte Ltd, 2018-10) Aydin, Zafer; Kaynar, Oguz; Gormez, YasinSecondary structure and solvent accessibility prediction provide valuable information for estimating the three dimensional structure of a protein. As new feature extraction methods are developed the dimensionality of the input feature space increases steadily. Reducing the number of dimensions provides several advantages such as faster model training, faster prediction and noise elimination. In this work, several dimensionality reduction techniques have been employed including various feature selection methods, autoencoders and PCA for protein secondary structure and solvent accessibility prediction. The reduced feature set is used to train a support vector machine at the second stage of a hybrid classifier. Cross-validation experiments on two difficult benchmarks demonstrate that the dimension of the input space can be reduced substantially while maintaining the prediction accuracy. This will enable the incorporation of additional informative features derived for predicting the structural properties of proteins without reducing the accuracy due to overfitting.