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Том 15   Выпуск 2   Год 2020
Наймарк О.Б.1, Баяндин Ю.В.1, Белоглазова Ю.А.2, Гагарских О.Н.2, Гришко В.В.2, Никитюк А.С.1, Воронина А.О.2

Трансформация ДНК, эпигенетический ландшафт клеток и динамика открытых комплексов в развитии рака

Математическая биология и биоинформатика. 2020;15(2):251-267.

doi: 10.17537/2020.15.251.

Список литературы

  1. Hoffman B.D., Crocker J.C. Cell mechanics: dissecting the physical responses of cells to force. Annual Review of Biomedical Engineering. 2009;11:259–288. doi: 10.1146/annurev.bioeng.10.061807.160511
  2. Gardel M.L., Kasza K.E., Brangwynne C.P., Liu J., Weitz D.A. Mechanical response of cytoskeletal networks. Methods in Cell Biology. 2008;89:487–519. doi: 10.1016/S0091-679X(08)00619-5
  3. Huber F., Schnauß J., Rönicke S., Rauch P., Müller K., Fütterer C., Käs J. Emergent complexity of the cytoskeleton: from single filaments to tissue. Advances in Physics. 2013;62(1):1–112. doi: 10.1080/00018732.2013.771509
  4. Fletcher D.A., Mullins R.D. Cell mechanics and the cytoskeleton. Nature. 2010;463(7280):485–492. doi: 10.1038/nature08908
  5. Kauffman S.A. Metabolic stability and epigenesis in randomly constructed genetic nets. Journal of Theoretical Biology. 1969;22(3):437–467. doi: 10.1016/0022-5193(69)90015-0
  6. Huang S., Kauffman S.A. In: Complex gene regulatory networks-from structure to biological observables: cell fate determination. 2009:1180–1213. doi: 10.1007/978-0-387-30440-3_79
  7. Huang S. Non-genetic heterogeneity of cells in development: more than just noise. Development. 2009;136(23):3853–3862. doi: 10.1242/dev.035139
  8. Wang J., Xu L., Wang E., Huang S. The potential landscape of genetic circuits imposes the arrow of time in stem cell differentiation. Biophysical Journal. 2010;99(1):29–39. doi: 10.1016/j.bpj.2010.03.058
  9. Huang S., Eichler G., Bar-Yam Y., Ingber D.E. Cell fates as high-dimensional attractor states of a complex gene regulatory network. Physical Review Letters. 2005;94(12):128701. doi: 10.1103/PhysRevLett.94.128701
  10. Huang S. The molecular and mathematical basis of Waddington's epigenetic landscape: A framework for post‐Darwinian biology? Bioessays. 2012;34(2):149–157. doi: 10.1002/bies.201100031
  11. Fumarola L., Urani C., Crosta G.F. Quantitative kinetics of damage and recovery of cytoskeletal structure by means of image analysis. Toxicology in vitro. 2005;19(7):935–941. doi: 10.1016/j.tiv.2005.06.012
  12. Ingber D.E. Mechanical control of tissue growth: function follows form. Proceedings of the National Academy of Sciences. 2005;102(33):11571–11572. doi: 10.1073/pnas.0505939102
  13. Ingber D.E. Tensegrity-based mechanosensing from macro to micro. Progress in Biophysics and Molecular Biology. 2008;97(2–3):163–179. doi: 10.1016/j.pbiomolbio.2008.02.005
  14. Bonakdar N., Gerum R., Kuhn M., Spörrer M., Lippert A., Schneider W., Fabry B. Mechanical plasticity of cells. Nature Materials. 2016;15(10):1090–1094. doi: 10.1038/nmat4689
  15. Naimark O.B. Defect-induced transitions as mechanisms of plasticity and failure in multifield continua. In: Advances in Multifield Theories for Continua with Substructure. Birkhäuser, Boston, MA, 2004. P. 75–114. doi: 10.1007/978-0-8176-8158-6_4
  16. Naimark O.B. Structural-scaling transitions and localized distortion modes in the DNA double helix. Physical Mesomechanics. 2007;1(10):33–45.
  17. Bizzarri M., Palombo A., Cucina A. Theoretical aspects of systems biology. Progress in Biophysics and Molecular Biology. 2013;112(1–2):33–43. doi: 10.1016/j.pbiomolbio.2013.03.019
  18. Naimark O. Nonlinear dynamics and damage induced properties of soft matter with application in oncology. AIP Conference Proceedings. 2017;1882(1):020052. doi: 10.1063/1.5001631
  19. Peyrard M. Nonlinear dynamics and statistical physics of DNA. Nonlinearity. 2004;17(2):R1. doi: 10.1088/0951-7715/17/2/R01
  20. Peyrard M., Bishop A.R. Statistical mechanics of a nonlinear model for DNA denaturation. Physical Review Letters. 1989;62(23):2755. doi: 10.1103/PhysRevLett.62.2755
  21. Shigaev A.S., Ponomarev O.A., Lakhno V.D. Theoretical and Experimental Investigations of DNA Open States. Math. Biol. Bioinf. 2013;8(2):553–664. doi: 10.17537/2013.8.553
  22. Wartell R.M., Benight A.S. Thermal denaturation of DNA molecules: a comparison of theory with experiment. Physics Reports. 1985;126(2):67–107. doi: 10.1016/0370-1573(85)90060-2
  23. Likhachev I.V., Lakhno V.D. The direct investigation of DNA denaturation in Peyrard-Bishop-Dauxois model by molecular dynamics method. Chemical Physics Letters. 2019;727:55–58. doi: 10.1016/j.cplett.2019.04.027
  24. Likhachev I.V., Lakhno V.D. Investigation of DNA denaturation in Peyrard-Bishop-Dauxois model by molecular dynamics method. The European Physical Journal B. 2019;92(11):253. doi: 10.1140/epjb/e2019-90741-6
  25. Nikitiuk A.S., Korznikova E.A., Dmitriev S.V., Naimark O.B. DNA breathers and cell dynamics. Mathematical Biology and Bioinformatics. 2019;14(1):137–149. doi: 10.17537/2019.14.
  26. Nikitiuk A.S., Korznikova E.A., Dmitriev S.V., Naimark O.B. Nonlinear dynamics of DNA with topological constraints. Letters on Materials. 2018;8(4):489–493. doi: 10.22226/2410-3535-2018-4-489-493
  27. Tsuchiya M., Giuliani A., Yoshikawa K. Single-Cell Reprogramming in Mouse Embryo Development through a Critical Transition State. Entropy. 2017;19(11):584. doi: 10.3390/e19110584
  28. Woese C.R. A new biology for a new century. Microbiology and Molecular Biology Reviews. 2004;68(2):173–186. doi: 10.1128/MMBR.68.2.173-186.2004
  29. Leontovich M. Introduction to Thermodynamics. Statistical Physics. Moscow: High School, 1983. 416 p.
  30. Goldenfeld N., Woese C. Biology's next revolution. Nature. 2007;445(7126):369–369. doi: 10.1038/445369a
  31. Goldenfeld N., Woese C. Life is physics: evolution as a collective phenomenon far from equilibrium. Annu. Rev. Condens. Matter Phys. 2011;2(1):375–399.
  32. Waddington C.H. Canalization of development and the inheritance of acquired characters. Nature. 1942;150(3811):563–565. doi: 10.1038/150563a0
  33. Waddington C.H. The strategy of the genes. Routledge, 2014. doi: 10.4324/9781315765471
  34. Goldberg A.D., Allis C.D., Bernstein E. Epigenetics: a landscape takes shape. Cell. 2007;128(4):635–638. doi: 10.1016/j.cell.2007.02.006
  35. Tsuchiya M., Selvarajoo K., Piras V., Tomita M., Giuliani A. Local and global responses in complex gene regulation networks. Physica A: Statistical Mechanics and its Applications. 2009;388(8):1738–1746. doi: 10.1016/j.physa.2008.12.030
  36. Tsuchiya M., Hashimoto M., Takenaka Y., Motoike I.N., Yoshikawa K. Global genetic response in a cancer cell: Self-organized coherent expression dynamics. PLoS One. 2014;9(5). Article No. e97411. doi: 10.1371/journal.pone.0097411
  37. Aldana M., Balleza E., Kauffman S., Resendiz O. Robustness and evolvability in genetic regulatory networks. Journal of Theoretical Biology. 2007;245(3):433–448. doi: 10.1016/j.jtbi.2006.10.027
  38. Kurdyumov S.P. Evolution and self-organization laws in complex systems. Advances in Theoretical Physics. 1990:134.
  39. Naimark O.B. Structural-scale transitions in solids with defects and symmetry aspects of field theory. Physical Mesomechanics. 2010;13(5–6):306–317. doi: 10.1016/j.physme.2010.11.011
  40. Damasco A., Giuliani A. A resonance based model of biological evolution. Physica A: Statistical Mechanics and its Applications. 2017;471:750–756. doi: 10.1016/j.physa.2016.12.016
  41. Naimark O. Mesoscopic cell dynamics in different environment and problem of cancer. AIP Conference Proceedings. 2019;2167(1):020237. doi: 10.1063/1.5132104
  42. Longo G., Montévil M. From physics to biology by extending criticality and symmetry breakings. In: Perspectives on Organisms. Berlin, Heidelberg: Springer, 2014. P. 161–185.
  43. Longo G., Montévil M.R., Pocheville A. From bottom-up approaches to levels of organization and extended critical transitions. Frontiers in Physiology. 2012;3:232. doi: 10.3389/fphys.2012.00232
  44. Huang S., Ingber D.E. Shape-dependent control of cell growth, differentiation, and apoptosis: switching between attractors in cell regulatory networks. Experimental Cell Research. 2000;261(1):91–103. doi: 10.1006/excr.2000.5044
  45. Huang S., Ingber D.E. A non-genetic basis for cancer progression and metastasis: self-organizing attractors in cell regulatory networks. Breast Disease. 2007;26(1):27–54. doi: 10.3233/BD-2007-26104
  46. Auffray C., Nottale L. Scale relativity theory and integrative systems biology: 1: founding principles and scale laws. Progress in Biophysics and Molecular Biology. 2008;97(1):79–114. doi: 10.1016/j.pbiomolbio.2007.09.002
  47. Auffray C., Imbeaud S., Roux-Rouquié M., Hood L. Self–organized living systems: conjunction of a stable organization with chaotic fluctuations in biological space–time. Philosophical Transactions of the Royal Society of London. Series A: Mathematical, Physical and Engineering Sciences. 2003;361(1807):1125–1139.
  48. Bailly F., Longo G. Extended critical situations: the physical singularity of life phenomena. Journal of Biological Systems. 2008;16(02):309–336. doi: 10.1142/S0218339008002514
  49. Bailly F., Longo G. Biological organization and anti-entropy. Journal of Biological Systems. 2009;17(01):63–96. doi: 10.1142/S0218339009002715
  50. Landau L.D. On the theory of phase transitions. Zh. Eksp. Teor. Fiz. 1937;11:19.
  51. Ginzburg V.L., Landau L.D. On the theory of superconductors. Zh. Eksp. Ttjr. Fiz. 1950;20:1064–1082.
  52. Weinberg A.M. On the Relation Between Information and Energy Systems. A Family of Maxwell's Demons. Interdisciplinary Science Reviews. 1982;7(1):47–52. doi: 10.1179/030801882789801322
  53. Tsuchiya M., Giuliani A., Hashimoto M., Erenpreisa J., Yoshikawa K. Emergent Self-Organized Criticality in gene expression dynamics: Temporal development of global phase transition revealed in a cancer cell line. PLoS One. 2015;10(6). Article No. e0128565. doi: 10.1371/journal.pone.0128565
  54. Tsuchyia M., Wong S.T., Yeo Z.X., Colosimo A., Palumbo M.C., Farina L., Selvarajoo K. Gene expression waves: cell cycle independent collective dynamics in cultured cells. The FEBS Journal. 2007;274(11):2878–2886. doi: 10.1111/j.1742-4658.2007.05822.x
  55. Naimark O.B. Collective properties of defect ensembles and some nonlinear problems of plasticity and fracture. Physical Mesomechanics. 2003;6(4):39–64.
  56. Naimark O.B., Nikitiuk A.S., Baudement M.O., Forné T., Lesne A. The physics of cancer: The role of epigenetics and chromosome conformation in cancer progression. AIP Conference Proceedings. 2016;1760(1):020051. doi: 10.1063/1.4960270
  57. Barenblatt G.I., Zel'dovich Y.B. Intermediate asymptotics in mathematical physics. Russian Math. Surveys. 1971;26(2):45–61.
  58. Barenblatt G.I. Similarity, Self-Similarity, Intermediate Asymtotics. Leningrad: Gidrometeoizdat, 1982.
  59. Naimark O.B. Some regularities of scaling in plasticity, fracture, and turbulence. Physical Mesomechanics. 2016;19(3):307–318. doi: 10.1134/S1029959916030097
  60. Naimark O.B., Uvarov S.V., Davydova M.M., Bannikova I.A. Multiscale statistical laws of dynamic fragmentation. Physical Mesomechanics. 2017;20(1):90–101. doi: 10.1134/S1029959917010088
  61. Ignatyev P.S., Indukaev K.V., Osipov P.A., Sergeev I.K. Laser interference microscopy for nanobiotechnologies. Biomedical Engineering. 2013;47(1):32–35. doi: 10.1007/s10527-013-9328-7
  62. Naimark O. Nonlinear dynamics and damage induced properties of soft matter with application in oncology. AIP Conference Proceedings. 2017;1882(1):020052. doi: 10.1063/1.5001631
  63. Naimark O. Mesoscopic cell dynamics in different environment and problem of cancer. AIP Conference Proceedings. 2019;2167(1):020237. doi: 10.1063/1.5132104
  64. Naimark O.B., Grishko V.V., Bayandin Yu.V., Nikityuk A.S. Mechanobiological study of the dynamics and morphology of cell structures by laser microscopy and applications in oncology. Perm Federal Research Center Journal. 2020;1:70–87.
  65. Gerasimova E., Audit B., Roux S.G., Khalil A., Argoul F., Naimark O., Arneodo A. Multifractal analysis of dynamic infrared imaging of breast cancer. Europhysics Letters. 2014;104(6):68001. doi: 10.1209/0295-5075/104/68001
  66. Gerasimova E., Audit B., Roux S.G., Khalil A., Gileva O., Argoul F., Naimark O., Arneodo A. Wavelet-based multifractal analysis of dynamic infrared thermograms to assist in early breast cancer diagnosis. Frontiers in Physiology. 2014;5:176. doi: 10.3389/fphys.2014.00176
  67. Gerasimova-Chechkina E., Toner B., Marin Z., Audit B., Roux S.G., Argoul F., Khalil A., Gileva O., Naimark O., Arneodo A. Comparative multifractal analysis of dynamic infrared thermograms and X-ray mammograms enlightens changes in the environment of malignant tumors. Frontiers in Physiology. 2016;7:336. doi: 10.3389/fphys.2016.00336
  68. Naimark O.B. Energy release rate and criticality of multiscale defects kinetics. International Journal of Fracture. 2016;202(2):271–279. doi: 10.1007/s10704-016-0161-3
  69. Bizzarri M., Naimark O., Nieto-Villa J., Fedeli V., Giuliani A. Complexity in Biological Organization: Deconstruction (and Subsequent Restating) of Key Concepts. Entropy. 2020;22(8):885. doi: 10.3390/e22080885
Содержание Оригинальная статья
Мат. биол. и биоинф.
2020;15(2):251-267
doi: 10.17537/2020.15.251
опубликована на англ. яз.

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