PubMed İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/397
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Article Citation - WoS: 1Citation - Scopus: 2Tomatidine, a Steroidal Alkaloid, Synergizes With Cisplatin to Inhibit Cell Viability and Induce Cell Death Selectively on FLT3-ITD+ Acute Myeloid Leukemia Cells(Humana Press inc, 2024-07-11) Ayvaz, Havva Berre; Yenigul, Munevver; Akcok, Emel Basak Gencer; Gencer Akçok, Emel BaşakBackgroundAcute Myeloid Leukemia (AML) is a hematological cancer that frequently presents with a range of side effects and drug resistance during anticancer drug treatment. The current study aims to achieve increased efficacy by combining lower doses of cisplatin with increasing concentrations of tomatidine in AML cells to increase efficacy.MethodsAnti-proliferative effects of single and combination of cisplatin and tomatidine were assessed via MTT cell viability assay. The Annexin V/Propidium Iodide Double Staining method was used to measure the apoptotic effects of combined tomatidine and cisplatin treatment. Then, Western Blot analysis was performed to measure Poly (ADP-ribose) polymerase (PARP) and Caspase-3 protein expression levels.ResultsCisplatin treatment with lower concentrations displayed high cytotoxic effects on AML cells, compared with tomatidine. The combination of the Inhibitory Concentration (IC) 20 value of cisplatin and increasing doses of tomatidine exhibited a significant decrease in cell viability relative to single treatments. The combination index analysis revealed a mild synergistic effect of cisplatin IC20 and varying tomatidine doses. The apoptosis induced when cisplatin was combined with 500 mu M tomatidine by almost 20%, while the percentage of apoptosis in combination with 1 mM tomatidine was measured by 50% for both cell lines. The upregulation of proapoptotic cleaved-PARP (3.2 and 1.08-fold for THP-1 and MOLM-13, respectively) and downregulation in Caspase-3 (0.23 and 0.13-fold for THP-1 and MOLM-13, respectively) was detected.ConclusionsTogether, the study indicated that when tomatidine combined with cisplatin on AML cell lines, a combinatorial anti-proliferative and apoptotic effect is observed. The combination of cisplatin with tomatidine may be a promising approach.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.Book Part Citation - Scopus: 1Measurement of Autophagic Activity in Cancer Cells With Flow Cytometric Analysis Using Cyto-Id Staining(Humana Press Inc., 2024) Şansaçar, Merve; Gencer Akçok, Emel BaşakAutophagy is an evolutionarily conserved process providing the energy that cells need to survive, especially in stress situations, through catabolic processes. Considering the dual role of autophagy in cancer cells depending on the cellular context, it is crucial to comprehend the effect of drug candidates put forward to prevent cancer through the autophagy pathway. The CYTO-ID® Autophagy Detection Kit allows a rapid, specific and quantitative measurement of autophagic activity at the cellular level using a 488 nm-excitable green fluorescent detection reagent via flow cytometer. In this chapter, we present the CYTO-ID® Autophagy Detection method with a stepwise protocol to monitor the autophagy flux after the application of any compound to suspension cancer cell lines with flow cytometric analysis. © 2025 Elsevier B.V., All rights reserved.Article Evaluation of HOTAIR, HOXD8, HOXD9, HOXD11 Gene Expression Levels in Turkish Patients With Acute and Chronic Myeloid Leukemia: A Single Center Experience(Cellular and Molecular Biology Association, 2024-11-27) Saraymen, Esma; Erdem, Yakut; Akalin, Hilal Ünlü; Taşçıoğlu, Nazife; Saraymen, Berkay; Celik, Serhat; Özkul, Yusuf T.Homeobox (HOX) transcript antisense RNA (HOTAIR) and HOX genes are reported to be more expressed in various cancers in humans in recent studies. The role of HOTAIR and HOXD genes in acute myeloid leukemia (AML) and chronic myeloid leukemia (CML) is not well known. In this study, expression levels of HOXD8, HOXD9 and HOXD11 from HOXD gene family and HOTAIR were determined from peripheral blood samples of 30 AML and 30 CML patients and 20 healthy volunteers by quantitative Real Time PCR. We determined that the expression levels of HOXD9 and HOXD11 in the AML patients were significantly lower than the control group (p<0.001 and p=0.002, respectively). There was no significant difference in the expression levels of HOTAIR and HOXD8 when compared to the control group. In the CML patients there was a significant increase in the expression level of HOTAIR when compared to the control group (p=0.002). The expression levels of HOXD9 and HOXD11 were found to be significantly lower than the control group (p<0.001). Our study showed that HOTAIR may not be a biomarker in the diagnosis and is not significantly correlated with the clinicopathological prognostic characteristics of AML. Additionally; it can be said that HOTAIR is oncogenic by suppressing the expression of HOXD9 and HOXD11 but not HOXD8 in CML patients. The expression profiles of HOTAIR may be a potential biomarker in the diagnosis of CML patients in predicting and monitoring drug resistance. © 2025 Elsevier B.V., All rights reserved.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.Book Part Citation - WoS: 20Citation - Scopus: 27Computational Prediction of Functional MicroRNA-mRNA Interactions(Humana Press Inc, 2019) Demirci, Muserref Duygu Sacar; Yousef, Malik; Allmer, Jens; Saçar Demirci, Müşerref DuyguProteins have a strong influence on the phenotype and their aberrant expression leads to diseases. MicroRNAs (miRNAs) are short RNA sequences which posttranscriptionally regulate protein expression. This regulation is driven by miRNAs acting as recognition sequences for their target mRNAs within a larger regulatory machinery. A miRNA can have many target mRNAs and an mRNA can be targeted by many miRNAs which makes it difficult to experimentally discover all miRNA-mRNA interactions. Therefore, computational methods have been developed for miRNA detection and miRNA target prediction. An abundance of available computational tools makes selection difficult. Additionally, interactions are not currently the focus of investigation although they more accurately define the regulation than pre-miRNA detection or target prediction could perform alone. We define an interaction including the miRNA source and the mRNA target. We present computational methods allowing the investigation of these interactions as well as how they can be used to extend regulatory pathways. Finally, we present a list of points that should be taken into account when investigating miRNA-mRNA interactions. In the future, this may lead to better understanding of functional interactions which may pave the way for disease marker discovery and design of miRNA-based drugs.Book Part Citation - Scopus: 4Computational Detection of Pre-MicroRNAs(Humana Press Inc., 2021-08-26) Saçar Demirci, Müşerref DuyguMicroRNA (miRNA) studies have been one of the most popular research areas in recent years. Although thousands of miRNAs have been detected in several species, the majority remains unidentified. Thus, finding novel miRNAs is a vital element for investigating miRNA mediated posttranscriptional gene regulation machineries. Furthermore, experimental methods have challenging inadequacies in their capability to detect rare miRNAs, and are also limited to the state of the organism under examination (e.g., tissue type, developmental stage, stress-disease conditions). These issues have initiated the creation of high-level computational methodologies endeavoring to distinguish potential miRNAs in silico. On the other hand, most of these tools suffer from high numbers of false positives and/or false negatives and as a result they do not provide enough confidence for validating all their predictions experimentally. In this chapter, computational difficulties in detection of pre-miRNAs are discussed and a machine learning based approach that has been designed to address these issues is reviewed. © 2021 Elsevier B.V., All rights reserved.