Browsing by Subject "In-vitro"
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Item Open Access Epigenetic Mechanisms Underlying the Dynamic Expression of Cancer-Testis Genes, PAGE2,-2B and SPANX-B, during Mesenchymal-to-Epithelial Transition(pone, 2014) Yilmaz Ozcan, S.; Sade, A.; Kucukkaraduman, B.; Kaygusuz, Y.; Senses, K. M.; Banerjee, S.; Gure, A. O.Cancer-testis (CT) genes are expressed in various cancers but not in normal tissues other than in cells of the germline. Although DNA demethylation of promoter-proximal CpGs of CT genes is linked to their expression in cancer, the mechanisms leading to demethylation are unknown. To elucidate such mechanisms we chose to study the Caco-2 colorectal cancer cell line during the course of its spontaneous differentiation in vitro, as we found CT genes, in particular PAGE2,-2B and SPANX-B, to be up-regulated during this process. Differentiation of these cells resulted in a mesenchymal-toepithelial transition (MET) as evidenced by the gain of epithelial markers CDX2, Claudin-4 and E-cadherin, and a concomitant loss of mesenchymal markers Vimentin, Fibronectin-1 and Transgelin. PAGE2 and SPAN-X up-regulation was accompanied by an increase in Ten-eleven translocation-2 (TET2) expression and cytosine 5-hydroxymethylation as well as the disassociation of heterochromatin protein 1 and the polycomb repressive complex 2 protein EZH2 from promoter-proximal regions of these genes. Reversal of differentiation resulted in down-regulation of PAGE2,-2B and SPANX-B, and induction of epithelial-to-mesenchymal transition (EMT) markers, demonstrating the dynamic nature of CT gene regulation in this model. © 2014 Yilmaz-Ozcan et al.Item Open Access Estimating the chance of success in IVF treatment using a ranking algorithm(Springer, 2015) Güvenir, H. A.; Misirli, G.; Dilbaz, S.; Ozdegirmenci, O.; Demir, B.; Dilbaz, B.In medicine, estimating the chance of success for treatment is important in deciding whether to begin the treatment or not. This paper focuses on the domain of in vitro fertilization (IVF), where estimating the outcome of a treatment is very crucial in the decision to proceed with treatment for both the clinicians and the infertile couples. IVF treatment is a stressful and costly process. It is very stressful for couples who want to have a baby. If an initial evaluation indicates a low pregnancy rate, decision of the couple may change not to start the IVF treatment. The aim of this study is twofold, firstly, to develop a technique that can be used to estimate the chance of success for a couple who wants to have a baby and secondly, to determine the attributes and their particular values affecting the outcome in IVF treatment. We propose a new technique, called success estimation using a ranking algorithm (SERA), for estimating the success of a treatment using a ranking-based algorithm. The particular ranking algorithm used here is RIMARC. The performance of the new algorithm is compared with two well-known algorithms that assign class probabilities to query instances. The algorithms used in the comparison are Naïve Bayes Classifier and Random Forest. The comparison is done in terms of area under the ROC curve, accuracy and execution time, using tenfold stratified cross-validation. The results indicate that the proposed SERA algorithm has a potential to be used successfully to estimate the probability of success in medical treatment.Item Open Access Gauss tabanlı modelleme kullanarak canlı hücre görüntülerinin öğreticisiz bölütlenmesi(2011-04) Arslan, Salim; Durmaz, İrem; Çetin-Atalay, Rengül; Gündüz-Demir, ÇiğdemThe first step of targeted cancer drug development is to screen and determine drug candidates by in vitro measuring the effectiveness of the drugs. The tests developed for this purpose can be time consuming due to their procedures and cannot be conducted in every laboratory due to the required hardwares. On the other hand, an image-based screening test has a potential to be less time consuming since it can directly be carried out on the live cell images and to be more extensively used because of the availability of its required equipments and their relatively less expensive cost. With such an image-based test, it is possible to quantify the cell death by finding cellular regions and comparing it against the control group. In this work, we propose a new method that automatically locates the cellular regions by the unsupervised segmentation of live cell images. This method relies on approximately locating cellular regions and the background with gradient-based thresholding and morphological operators and then finding the final boundaries by modeling the gradient of these regions with Gaussians. Working on the images of different cell lines captured with different magnifications, our experiments show that the proposed method leads to promising results. © 2011 IEEE.Item Open Access Heating of magnetic fluid systems driven by circularly polarized magnetic field(Elsevier BV * North-Holland, 2010) Ahsen, O. O.; Yilmaz, U.; Aksoy, M. Deniz; Ertas, G.; Atalar, ErginA theory is presented to calculate the heat dissipation of a magnetic suspension, a ferrofluid, driven by circularly polarized magnetic field. Theory is tested by in vitro experiments and it is shown that, regardless of the character of the relaxation process, linearly and circularly polarized magnetic field excitations, having the same root-mean-square magnitude, are equivalent in terms of heating efficiency.Item Open Access In vitro biocompatibility of plasma-aided surface-modified 316L stainless steel for intracoronary stents(Institute of Physics Publishing, 2010) Bayram, C.; Mizrak, A.K.; Aktürk, S.; Kurşaklioǧlu H.; Iyisoy, A.; Ifran, A.; Denkbaş, E.B.316L-type stainless steel is a raw material mostly used for manufacturing metallic coronary stents. The purpose of this study was to examine the chemical, wettability, cytotoxic and haemocompatibility properties of 316L stainless steel stents which were modified by plasma polymerization. Six different polymeric compounds, polyethylene glycol, 2-hydroxyethyl methacrylate, ethylenediamine, acrylic acid, hexamethyldisilane and hexamethyldisiloxane, were used in a radio frequency glow discharge plasma polymerization system. As a model antiproliferative drug, mitomycin-C was chosen for covalent coupling onto the stent surface. Modified SS 316L stents were characterized by water contact angle measurements (goniometer) and x-ray photoelectron spectroscopy. C1s binding energies showed a good correlation with the literature. Haemocompatibility tests of coated SS 316L stents showed significant latency (t-test, p < 0.05) with respect to SS 316L and control groups in each test. © 2010 IOP Publishing Ltd.Item Open Access Induction of ROS, p53, p21 in DEHP-and MEHP-exposed LNCaP cells-protection by selenium compunds(Elsevier, 2011-07) Erkekoglu, P.; Rachidi, W.; Yazgullu, O. G.; Giray, B.; Ozturk, M.; Favier, A.; Hincal, F.This study was designed to investigate the hypothesis that the toxic effects of di(2-ethylhexyl)phthalate (DEHP), the most abundantly used plasticizer and ubiquitous environmental contaminant that cause alterations in endocrine and spermatogenic functions in animals is mediated through the induction of reactive oxygen species (ROS) and activation of nuclear p53 and p21 proteins in LNCaP human prostate adenocarcinoma cell line. Protective effects of two selenocompounds, sodium selenite (SS) and selenomethionine (SM) were also examined. It was demonstrated that 24. h exposure of the cells to 3. mM DEHP or its main metabolite, mono(2-ethylhexyl)phthalate (MEHP, 3 μM) caused strongly amplified production of ROS. Both SS (30. nM) and SM (10 μM) supplementations reduced ROS production, and p53 and p21 activation that induced significantly only by MEHP-exposure. The overall results of this study indicated that the induction of oxidative stress is one of the important mechanisms underlying the toxicity of DEHP and this is mainly through the effects of the metabolite, MEHP. Generated data also emphasized the critical role of Se in modulation of intracellular redox status, implicating the importance of the appropriate Se status in cellular response against testicular toxicity of phthalates. © 2011 Elsevier Ltd.Item Open Access Material Binding Peptides for Nanotechnology(MDPI AG, 2011) Seker, U. O. S.; Demir, Hilmi VolkanRemarkable progress has been made to date in the discovery of material binding peptides and their utilization in nanotechnology, which has brought new challenges and opportunities. Nowadays phage display is a versatile tool, important for the selection of ligands for proteins and peptides. This combinatorial approach has also been adapted over the past decade to select material-specific peptides. Screening and selection of such phage displayed material binding peptides has attracted great interest, in particular because of their use in nanotechnology. Phage display selected peptides are either synthesized independently or expressed on phage coat protein. Selected phage particles are subsequently utilized in the synthesis of nanoparticles, in the assembly of nanostructures on inorganic surfaces, and oriented protein immobilization as fusion partners of proteins. In this paper, we present an overview on the research conducted on this area. In this review we not only focus on the selection process, but also on molecular binding characterization and utilization of peptides as molecular linkers, molecular assemblers and material synthesizers.Item Open Access Peptide functionalized superparamagnetic iron oxide nanoparticles as MRI contrast agents(The Royal Society of Chemistry, 2011) Sulek, S.; Mammadov, B.; Mahcicek, D. I.; Sozeri, H.; Atalar, Ergin; Tekinay, A. B.; Güler, Mustafa O.Magnetic resonance imaging (MRI) attracts great attention in cellular and molecular imaging due to its non-invasive and multidimensional tomographic capabilities. Development of new contrast agents is necessary to enhance the MRI signal in tissues of interest. Superparamagnetic iron oxide nanoparticles (SPIONs) are used as contrast agents for signal enhancement as they have revealed extraordinary magnetic properties at the nanometre size and their toxicity level is very low compared to other commercial contrast agents. In this study, we developed a new method to functionalize the surface of SPIONs. Peptide amphiphile molecules are used to coat SPIONs non-covalently to provide water solubility and to enhance biocompatibility. Superparamagnetic properties of the peptide-SPION complexes and their ability as contrast agents are demonstrated. In vitro cell culture experiments reveal that the peptide-SPION complexes are biocompatible and are localized around the cells due to their peptide coating.