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: 6Citation - Scopus: 6Sex Effect on the Correlation of Immunoglobulin G Glycosylation With Rheumatoid Arthritis Disease Activity(Tubitak Scientific & Technological Research Council Turkey, 2020-12-14) Ercan, AltanRheumatoid arthritis (RA) is a chronic autoimmune disease which affects females more than males with a presence of autoantibodies. Immunoglobulin G (IgG) produced by adaptive arm has 2 functional domains, Fc and Fab. The Fc domain binds Fc gamma receptors and C1q proteins of the innate arm. Therefore, the IgG Fc domain serves as a bridge between the innate and adaptive arms and is regulated by an evolutionarily conserved N-glycosylation with variable structures. These glycans are classified as agalactosylated G0, monogalactosylated G1, and digalactosylated G2, which are further modified by core-fucosylation (F) and bisecting N-acetylglucosamine (B) moieties such as G0F and G0FB. Interestingly, proinflammatory G0F is shown to be regulated by estrogen in vivo. Here, it is hypothesized that the regulation of G0F by estrogen contributes to sex dichotomy in RA by setting up the level of IgG-dependent inflammation and therefore, RA disease activity (Das28-CRP3). To investigate this hypothesis, IgG glycosylation was characterized in serum samples from active RA patients (n = 232) and healthy controls (n = 232) by serum N-glycan analysis using the high performance liquid chromatography. According to the results, the IgG Fc glycan phenotype originates predominantly from the structure of G0F, and both G0F and G0FB correlate with Das28-CRP3 in females, but not in males. In conclusion, IgG G0F-dependent inflammation differs in males and females, and these differences point to the differential regulation of inflammation by sex hormone estrogen via IgG glycosylation.Article Citation - WoS: 1Citation - Scopus: 1RPI-1 (Human DCDC2) Displays Functional Redundancy With Nephronophthisis 4 in Regulating Cilia Biogenesis in C. Elegans(Tubitak Scientific & Technological Research Council Turkey, 2023-01-01) Kaplan, Oktay I.Projecting from most cell surfaces, cilia serve as important hubs for sensory and signaling processes and have been linked to a variety of human disorders, including Bardet-Biedl Syndrome (BBS), Meckel-Gruber Syndrome (MKS), Nephronophthisis (NPHP), and Joubert Syndrome, and these diseases are collectively known as a ciliopathy. DCDC2 is a ciliopathy protein that localizes to cilia; nevertheless, our understanding of the role of DCDC2 in cilia is still limited. We employed C. elegans to investigate the function of C. elegans RPI-1, a Caenorhabditis elegans ortholog of human DCDC2, in cilia and found that C. elegans RPI-1 localizes to the entire ciliary axoneme, but is not present in the transition zone and basal body. We generated a null mutant of C. elegans rpi-1, and our analysis with a range of fluorescence-based ciliary markers revealed that DCDC2 and nephronophthisis 4 (NPHP-4/NPHP4) display functional redundant roles in regulating cilia length and cilia positions. Taken together, our analysis discovered a novel genetic interaction between two ciliopathy disease genes (RPI-1/DCDC2 and NPHP-4/NPHP4) in C. elegans.Article Citation - WoS: 1Citation - Scopus: 2Protocol for Determining the Average Speed and Frequency of Kinesin and Dynein-Driven Intraflagellar Transport (IFT) in C. Elegans(Elsevier, 2022-09) Turan, Merve G.; Kantarci, Hanife; Temtek, Sadiye D.; Cakici, Onur; Cevik, Sebiha; Kaplan, Oktay, IHere, we present a protocol to image a fluorescent-labeled intraflagellar trans-port (IFT) component in Caenorhabditis elegans with fluorescence microscopy, including steps of sample preparations, in vivo live-cell imaging, and post -micro-scopy analysis with kymographs. This protocol breaks down all processes into three categories: (1) pre-imaging preparations, (2) preparations for the time of image acquisition, and (3) post-imaging analyses. The protocol can be applied to determine the speed and frequency of moving particles. For complete details on the use and execution of this protocol, please refer to Cevik et al. (2021).Article Citation - WoS: 4Citation - Scopus: 4Protocol for Cell Surface Biotinylation of Magnetic Labeled and Captured Human Peripheral Blood Mononuclear Cells(Elsevier, 2022-12) Ayaz-Guner, Serife; Acar, Mustafa Burak; Boyvat, Dudu; Guner, Huseyin; Bozalan, Habibe; Guzel, Melis; Ozcan, ServetAnalysis of the surfaceome of a blood cell subset requires cell sorting, followed by surface protein enrichment. Here, we present a protocol combining magnet-ically activated cell sorting (MACS) and surface biotinylation of the target cell subset from human peripheral blood mononuclear cells (PBMCs). We describe the steps for isolating target cells and their in-column surface biotinylation, fol-lowed by isolation and mass spectrometry analysis of biotinylated proteins. The protocol enables in-column surface biotinylation of specific cell subsets with minimal membrane disruption.Editorial Citation - WoS: 3Citation - Scopus: 4Precision Medicine in Oncology: Challenges, Stakes and New Paradigms(John Libbey Eurotext Ltd, 2019-02) Cox, Stephanie; Rousseau-Tsangaris, Marina; Abou-Zeid, Nancy; Dalle, Stephane; Leurent, Pierre; Cutivet, Arnaud; Denefle, PatriceArticle 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: 4Citation - Scopus: 6One-Pot Conjugated Linoleic Acid Production From Castor Oil by Rhizopus Oryzae Lipase and Resting Cells of Lactobacillus Plantarum(Taylor & Francis Ltd, 2017-10-03) Khaskheli, Abid Ali; Talpur, Farah Naz; Aydin, Aysun Cebeci; Jawaid, Sana; Surhio, Muhammad Ali; Afridi, Hassan ImranConjugated linoleic acid (CLA) has attracted as novel type of fatty acids having unusual health-promoting properties such as anticarcinogenic and antiobesitic effects. The present work employed castor oil as substrate for one-pot production of CLA using washed cells of Lactobacillus plantarum (L. plantarum) and lipases as catalysts. Among the screened lipases, the lipase Rhizopus oryzae (ROL) greatly assisted resting cells to produce CLA. Mass spectral analysis of the product showed that two major isomers of CLA were produced in the reaction mixture i.e. cis-9, trans-11 56.55% and trans-10, cis-12 43.45%. Optimum factors for CLA synthesis were found as substrate concentration (8mg/mL), pH (6.5), washed cell concentration (12% w/v), and incubation time of 20h. Hence, the combination of ROL with L. plantarum offers one pot production of CLA selectively using castor oil as a cost-effective substrate.Article Citation - WoS: 3Citation - Scopus: 3MicroRNA Prediction Based on 3D Graphical Representation of RNA Secondary Structures(Tubitak Scientific & Technological Research Council Turkey, 2019-08-05) Sacar Demirci, Muserref Duygu; Demirci, Müşerref Duygu SaçarMicroRNAs (miRNAs) are posttranscriptional regulators of gene expression. While a miRNA can target hundreds of messenger RNA (mRNAs), an mRNA can be targeted by different miRNAs, not to mention that a single miRNA might have various binding sites in an mRNA sequence. Therefore, it is quite involved to investigate miRNAs experimentally. Thus, machine learning (ML) is frequently used to overcome such challenges. The key parts of a ML analysis largely depend on the quality of input data and the capacity of the features describing the data. Previously, more than 1000 features were suggested for miRNAs. Here, it is shown that using 36 features representing the RNA secondary structure and its dynamic 3D graphical representation provides up to 98% accuracy values. In this study, a new approach for ML-based miRNA prediction is proposed. Thousands of models are generated through classification of known human miRNAs and pseudohairpins with 3 classifiers: decision tree, naive Bayes, and random forest. Although the method is based on human data, the best model was able to correctly assign 96% of nonhuman hairpins from MirGeneDB, suggesting that this approach might be useful for the analysis of miRNAs from other species.