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Tytuł artykułu

Properties of Topological Networks of Flexible Polygonal Chains

Treść / Zawartość
Warianty tytułu
Języki publikacji
EN
Abstrakty
EN
Trypanosomatida parasites, such as Trypanosoma and Leishmania, are the cause of deadly diseases in many third world countries. The three dimensional structure of their mitochondrial DNA, known as kinetoplast DNA (kDNA), is unique since it is organized into several thousands of minicircles that are topologically linked. How and why the minicircles form such a network have remained unanswered questions. In our previous work we have presented a model of network formation that hypothesizes that the network is solely driven by the confinement of minicircles. Our model shows that upon confinement a percolation network forms. This network grows into a space filling network, called saturation network, upon further confinement of minicircles. Our model also shows, in agreement with experimental data, that the mean valence of the network (that is, the average number of minicircles topologically linked to any minicircle in the network) grows linearly with minicircle density. In our previous studies however we disregarded DNA flexibility and used rigid minicircles to model DNA, here we address this limitation by allowing minicircles to be flexible. Our numerical results show that the topological characteristics that describe the growth and topology of the minicircle networks have similar values to those observed in the case of rigid minicircles suggesting that these properties are robust and therefore a potentially adequate description of the networks observed in Trypanosomatid parasites.
Wydawca
Rocznik
Tom
2
Numer
1
Opis fizyczny
Daty
otrzymano
2014-08-14
zaakceptowano
2014-09-29
online
2014-10-12
Twórcy
autor
  • Department of Mathematics, Department of Molecular and Cellular Biology, University of
    California at Davis, Davis CA 95616, USA, jarsuaga@ucdavis.edu
autor
  • Department of Mathematics and Statistics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA, ydiao@uncc.edu
autor
autor
  • Department of Physics and Astronomy, San Francisco State University, San Francisco, CA 94116, USA, torrodri@mail.sfsu.edu
Bibliografia
  • [1] J. Arsuaga, Y. Diao, and K. Hinson. The effect of angle restriction on the topological characteristics of minicircle networks. J.Statist. Phys., 146(2):434–445, 2012.
  • [2] J. Chen, P. T. Englund, and N. R. Cozzarelli. Changes in network topology during the replication of kinetoplast DNA. EMBOJ., 14(24):6339–6347, 1995.[PubMed]
  • [3] J. Chen, C. A. Rauch, J. H. White, P. T. Englund, and N. R. Cozzarelli. The topology of the kinetoplast DNA network. Cell,80(1):61–69, 1995.
  • [4] Y. Diao, K. Hinson, and J. Arsuaga. The growth of minicircle networks on regular lattices. J. Phys. A: Math. Theor,45:doi:10.1088/1751–8113/45/3/035004, 2012.[Crossref][WoS]
  • [5] Y. Diao, K. Hinson, R. Kaplan, M. Vazquez, and J. Arsuaga. The effects of minicircle density on the topological structure ofthe mitochondrial DNA from trypanosomes. J. Math. Biol., 64(6):1087–1108, 2012.[WoS][Crossref]
  • [6] M. Ferguson, A. F. Torri, D. C. Ward, and P. T. Englund. In situ hybridization to the crithidia fasciculata kinetoplast revealstwo antipodal sites involved in kinetoplast DNA replication. Cell, 70:621–629, 1992.[Crossref][PubMed]
  • [7] Rafael Lozano et al. Global and regional mortality from 235 causes of death for 20 age groups in 1990 and 2010: a systematicanalysis for the global burden of disease study 2010. The Lancet, 380(9859):2095–2128, 2013.
  • [8] C. A. Rauch, D. Perez-Morga, N. R. Cozzarelli, and P. T. Englund. The absence of supercoiling in kinetoplast DNA minicircles.EMBO J., 12(2):403–411, 1993.[PubMed]
  • [9] V Rodriguez, Y Diao, and J Arsuaga. Percolation phenomena in disordered topological networks. Journal of Physics: ConferenceSeries, 454(1):012070, 2013.
  • [10] Robert G. Scharein. KnotPlot. http://www.knotplot.com. Program for drawing, visualizing, manipulating, and energy minimizingknots.
  • [11] T. A. Shapiro and P. T. Englund. The structure and replication of kinetoplast DNA. Annu. Rev. Microbiol., 49:117–143, 1995.[PubMed][Crossref]
  • [12] Pere P Simarro, Giuliano Cecchi, José R Franco, Massimo Paone, Abdoulaye Diarra, José Antonio Ruiz-Postigo, Eric M Fèvre,Raffaele C Mattioli, and Jean G Jannin. Estimating and mapping the population at risk of sleeping sickness. PLoS neglectedtropical diseases, 6(10):e1859, 2012.
  • [13] M. Spera. A survey on the differential and symplectic geometry of linking numbers. Milan J. Math., 74:139–197, 2006.[Crossref]
  • [14] R. Varela, K. Hinson, J. Arsuaga, and Y. Diao. A fast ergodic algorithm for generating ensembles of equilateral randompolygons. J. Phys. A, 42(9):1–13, 2009.
  • [15] A. V. Vologodskii. DNA supercoiling helps to unlink sister duplexes after replication. BioEssays, 32:9–12, 2010.[WoS][Crossref][PubMed]
  • [16] A. V. Vologodskii and N. R. Cozzarelli. Monte carlo analysis of the conformation of DNA catenanes. J. Mol. Biol., 232:1130–1140, 1993.
  • [17] A. V. Vologodskii and V. Rybenkov. Simulation of DNA catenanes. Phys. Chem. Chem. Phys., 11:10543–10552, 2009.[Crossref][PubMed]
Typ dokumentu
Bibliografia
Identyfikatory
Identyfikator YADDA
bwmeta1.element.doi-10_2478_mlbmb-2014-0007
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