Browsing by Subject "Gene therapy"
Now showing 1 - 8 of 8
Results Per Page
Sort Options
Item Open Access Electrostatics of polymer translocation through membrane nanopores in electrolyte solutions(Bilkent University, 2021-02) Mohamed, Ghada Mahmoud AbdullahThe transport of polymers across membranes in electrolyte solutions happens in most biological systems and is necessary for cells to function. Moreover, the poly-mer translocation process has proven to be very important in experiments and applications as well, providing a rich source of information about the polymer’s size and composition [1], [2], making the polymer translocation procedure a po-tential sequencing method that is efficient, cheap, and quick [3], [4]. However, no consensus on the theoretical understanding of the translocation mechanism has been reached yet [3], leaving it a major challenge for theoretical modelling due to its steric, hydrodynamic, and electrostatic interactions [2], [5]. Here, we calculate the electrostatic energy cost of the translocating polymer in both the approach and translocation phases and investigate the dependence of the poly-mer’s grand potential on different model tunable parameters. In the case of neu-tral membranes, low permittivity carbon-based membranes repel the approaching polymer with energy magnitude between ∼ 11 kBT and ∼ 27 kBT , while high permittivity engineered membranes attract the approaching polymer with almost the same energy magnitude. This behavior can be attributed to polymer image-charge interactions, which become amplified with low permittivity membranes. In strong salt solutions, the membrane exhibits a repulsive barrier that turns to a metastable well in dilute solutions. In pure solvents, the metastable well becomes a deep, stable well that traps the polymer in the pore for some time, where the translocation phase is mainly governed by the attractive trans-cis side interac-tion. For weakly charged membranes, the membrane charge attraction wins over the image-charge repulsion, leading to an attractive minimum at zt ≈ −1 nm followed by a repulsive barrier at lt = L/2 while for stronger membrane charges, the attractive well turns to a metastable point followed by an attractive, stable well. These results suggest that, in translocation experiments, DNA motion can be controlled by tuning the system parameters, such as the solution concentration or the membrane charge.Item Open Access Expression profiles of the individual genes corresponding to the genes generated by cytotoxicity experiments with bortezomib in multiple myeloma(Turkish Society of Hematology, 2016) Ghasemi M.; Alpsoy, S.; Türk, S.; Malkan, Ü. Y.; Atakan, Ş.; Haznedaroğlu, İ. C.; Güneş, G.; Gündüz, M.; Yılmaz, B.; Etgül, S.; Aydın, S.; Aslan, T.; Sayınalp, N.; Aksu S.; Demiroğlu, H.; Özcebe, O, İ.; Büyükaşık, Y.; Göker, H.Objective: Multiple myeloma (MM) is currently incurable due to refractory disease relapse even under novel anti-myeloma treatment. In silico studies are effective for key decision making during clinicopathological battles against the chronic course of MM. The aim of this present in silico study was to identify individual genes whose expression profiles match that of the one generated by cytotoxicity experiments for bortezomib. Materials and Methods: We used an in silico literature mining approach to identify potential biomarkers by creating a summarized set of metadata derived from relevant information. The E-MTAB-783 dataset containing expression data from 789 cancer cell lines including 8 myeloma cell lines with drug screening data from the Wellcome Trust Sanger Institute database obtained from ArrayExpress was “Robust Multi-array analysis” normalized using GeneSpring v.12.5. Drug toxicity data were obtained from the Genomics of Drug Sensitivity in Cancer project. In order to identify individual genes whose expression profiles matched that of the one generated by cytotoxicity experiments for bortezomib, we used a linear regression-based approach, where we searched for statistically significant correlations between gene expression values and IC50 data. The intersections of the genes were identified in 8 cell lines and used for further analysis. Results: Our linear regression model identified 73 genes and some genes expression levels were found to very closely correlated with bortezomib IC50 values. When all 73 genes were used in a hierarchical cluster analysis, two major clusters of cells representing relatively sensitive and resistant cells could be identified. Pathway and molecular function analysis of all the significant genes was also investigated, as well as the genes involved in pathways. Conclusion: The findings of our present in silico study could be important not only for the understanding of the genomics of MM but also for the better arrangement of the targeted anti-myeloma therapies, such as bortezomib. � 2016, Turkish Society of Hematology. All rights reserved.Item Open Access In vitro transfection of HeLa cells with temperature sensitive polycationic copolymers(Elsevier, 2004-04-28) Turk, M.; Dincer, S.; Yulug, I.; Piskin, E.In this study, we investigated different types of polyethyleneimine (PEI) and their block copolymers with N-isopropylacrylamide (NIPA) as temperature-sensitive polycationic non-viral vectors for transfection of HeLa cells in cell culture media. First carboxyl-terminated poly(NIPA) was synthesized and then copolymerized with PEIs branched or linear and with two different molecular weights (2 and 25 kDa). Addition of PEI units to the poly(NIPA) chains increased the LCST values up to body temperature. Zeta potentials of the copolymers were significantly lower than the corresponding PEI homopolymers. A green fluorescent protein expressing plasmid was used as a model. Complexes of this plasmid both with PEIs and their copolymers were formed. The zeta potentials of these complexes were between -3.1 and +21.3. Higher values were observed for the complexes prepared with branched and higher molecular weight PEIs. Copolymerization caused a profound decrease in the positive charges. Particle sizes of the complexes were in the range of 190-1235 nm. Using high polymer/plasmid ratios caused aggregation. The smallest complexes were obtained with the copolymer prepared with branched PEI with 25-kDa molecular weight. Copolymers were able to squeeze plasmid DNA more at the body temperature. Cytotoxicity was observed with PEIs especially with the branched higher molecular weights. Copolymerization reduced the cytotoxicity. The best in vitro DNA uptake efficiency (70%) was achieved with the complex prepared with poly(NIPA)/PEI25B. However, poly(NIPA)/PEI25L was the most successful vector for an effective gene expression without any significant toxicity.Item Open Access Like-Charge Attraction And Opposite-Charge Decomplexation Between Polymers and DNA Molecules(American Physical Society, 2017) Buyukdagli, S.We scrutinize the effect of polyvalent ions on polymer-DNA interactions. We extend a recently developed test-charge theory [S. Buyukdagli, Phys. Rev. E 94, 042502 (2016)1539-375510.1103/PhysRevE.94.042502] to the case of a stiff polymer interacting with a DNA molecule in an electrolyte mixture. The theory accounts for one-loop level electrostatic correlation effects such as the ionic cloud deformation around the strongly charged DNA molecule as well as image-charge forces induced by the low DNA permittivity. Our model can reproduce and explain various characteristics of the experimental phase diagrams for polymer solutions. First, the addition of polyvalent cations to the electrolyte solution results in the attraction of the negatively charged polymer by the DNA molecule. The glue of the like-charge attraction is the enhanced shielding of the polymer charges by the dense counterion layer at the DNA surface. Second, through the shielding of the DNA-induced electrostatic potential, mono- and polyvalent cations of large concentration both suppress the like-charge attraction. Within the same formalism, we also predict a new opposite-charge repulsion effect between the DNA molecule and a positively charged polymer. In the presence of polyvalent anions such as sulfate or phosphate, their repulsion by the DNA charges leads to the charge screening deficiency of the region around the DNA molecule. This translates into a repulsive force that results in the decomplexation of the polymer from DNA. This opposite-charge repulsion phenomenon can be verified by current experiments and the underlying mechanism can be beneficial to gene therapeutic applications where the control over polymer-DNA interactions is the key factor.Item Open Access MRI-guided gene therapy(John Wiley & Sons Ltd., 2006-05-22) Yang, X.; Atalar, ErginMRI has the ability to generate high-contrast and high-resolution images, to obtain multiple diagnostic evaluations of organ function and morphology, and to provide multiple image planes with no risk of ionizing radiation. Recent efforts have focused on using MR technology to monitor gene delivery, to enhance gene transfection/transduction, and to track gene expression. This review summarizes the current status of MRIguided gene therapy.Item Open Access Simultaneous radiofrequency (RF) heating and magnetic resonance (MR) thermal mapping using an intravascular MR imaging/RF heating system(John Wiley & Sons, 2005-06) Qiu, B.; El-Sharkawy, A.-M.; Paliwal, V.; Karmarkar, P.; Gao, F.; Atalar, Ergin; Yang, X.Previous studies have confirmed the possibility of using an intravascular MR imaging guidewire (MRIG) as a heating source to enhance vascular gene transfection/expression. This motivated us to develop a new intravascular system that can perform MR imaging, radiofrequncy (RF) heating, and MR temperature monitoring simultaneously in an MR scanner. To validate this concept, a series of mathematical simulations of RF power loss along a 0.032-inch MRIG and RF energy spatial distribution were performed to determine the optimum RF heating frequency. Then, an RF generator/amplifier and a filter box were built. The possibility for simultaneous RF heating and MR thermal mapping of the system was confirmed in vitro using a phantom, and the obtained thermal mapping profile was compared with the simulated RF power distribution. Subsequently, the feasibility of simultaneous RF heating and temperature monitoring was successfully validated in vivo in the aorta of living rabbits. This MR imaging/RF heating system offers a potential tool for intravascular MR-mediated, RF-enhanced vascular gene therapy.Item Embargo The potential of gene editing for Huntington’s disease(Elsevier, 2023-05) Wenzhen, D.; Urani, Ece; Mattson, M. P.Huntington’s disease (HD) is a dominantly inherited neurodegenerative disorder caused by a trinucleotide repeat expansion in the huntingtin gene resulting in long stretches of polyglutamine repeats in the huntingtin protein. The disease involves progressive degeneration of neurons in the striatum and cerebral cortex resulting in loss of control of motor function, psychiatric problems, and cognitive deficits. There are as yet no treatments that can slow disease progression in HD. Recent advances in gene editing using clustered regularly interspaced short palindromic repeats (CRISPR)–CRISPR-associated protein 9 (Cas9) systems and demonstrations of their ability to correct gene mutations in animal models of a range of diseases suggest that gene editing may prove effective in preventing or ameliorating HD. Here we describe (i) potential CRISPR-Cas designs and cellular delivery methods for the correction of mutant genes that cause inherited diseases, and (ii) recent preclinical findings demonstrating the efficacy of such gene-editing approaches in animal models, with a focus on HD.Item Open Access TIMP-2 gene transfer by positively charged PEG-lated monosized polycationic carrier to smooth muscle cells(Springer Netherlands, 2012) Laçin, N.; Utkan, G.; Kutsal, T.; Dedeoğlu, B. G.; Yuluğ, I. G.; Pişkin, E.Remodeling of the extracellular matrix resulting from increased secretion of metalloproteinase enzymes is implicated in restenosis following balloon angioplasty. Matrix metalloproteinases (MMPs) and the tissue inhibitors of metalloproteinases play an essential role in both normal and pathological extracellular matrix degradation. Tissue inhibitor of matrix metalloproteinase- 2 is the most extensively studied tissue inhibitor of metalloproteinases inmyocardial tissue in animalmodels and clinical examples of cardiac disease; therefore it is selected for this study. Gene transfer of tissue inhibitor of matrix metalloproteinase-2 may have a therapeutic potential by inhibition of matrix metalloproteinase activity. We have used PEG-lated nanoparticles poly(St/PEG-EEM/DMAPM) which were synthesized previously in our laboratory. The nanoparticles, with an average size of 77.6 ± 2.05 nm with a zeta potential of +64. 4 ± 1.14 mVand 201.9 ± 1.83 nmwith +54.2 ± 0.77 mV were used in the transfection studies. Zeta Potential values and size of polyplex were appropriate for an effective transfection. TIMP-2 expression was detected by western blotting. Increased protein level in smoothmuscle cells according to non-transfected smooth muscle cells confirms the successful delivery and expression of the tissue inhibitor of matrix metalloproteinase- 2 gene with the non-viral vector transfection approach. © Springer Science+Business Media B.V. 2012.