How computational models can help unlock biological systems

Seminars in Cell and Developmental Biology

Volumn 47-48, Issue , 2015, Pages 62-73

  Brodland, G Wayne ^a  

^a UNIVERSITY OF WATERLOO   (Canada)

Author keywords

Biological systems; Cell mechanics; Computational modelling; Developmental mechanisms; Embryo mechanics; Embryogenesis; Models; Morphogenetic movements; Review; Tissue mechanics

Indexed keywords

ALGORITHM; BIOLOGY; CELL MIGRATION; CELL MOTION; COMPUTER PROGRAM; COMPUTER SIMULATION; CYTOSKELETON; EMBRYO DEVELOPMENT; EPITHELIUM; GENE EXPRESSION; MATHEMATICAL MODEL; REVIEW; ANIMAL; BIOLOGICAL MODEL; GENE EXPRESSION REGULATION; GENETICS; HUMAN; PHYSIOLOGY; PROCEDURES; REPRODUCIBILITY; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY;

ANIMALS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; EMBRYONIC DEVELOPMENT; GENE EXPRESSION REGULATION, DEVELOPMENTAL; HUMANS; MODELS, BIOLOGICAL; REPRODUCIBILITY OF RESULTS; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY;

EID: 84952638889     PISSN: 10849521     EISSN: 10963634     Source Type: Journal    
DOI: 10.1016/j.semcdb.2015.07.001     Document Type: Review

References (79)

1. Brodland G.W. Computational modeling of cell sorting, tissue engulfment, and related phenomena: a review. Appl. Mech. Rev. 2004, 57:47-76.
2. Mofrad M.R.K., Kamm R.D. Cytoskeletal Mechanics: Models and Measurements 2006, Cambridge University Press, Cambridge/New York.
3. Chauvière A., Preziosi L., Verdier C. Cell Mechanics: From Single Scale-based Models to Multiscale Modeling 2010, Chapman & Hall/CRC, Boca Raton, FL.
4. Kam Y., Rejniak K.A., Anderson A.R. Cellular modeling of cancer invasion: integration of in silico and in vitro approaches. J. Cell. Physiol. 2012, 227:431-438.
5. Anderson A.R.A., Chaplain M.A.J., Rejniak K.A. Single-cell-based Models in Biology and Medicine 2007, Birkhäuser, Basel/Boston.
6. Steinberg M.S. Does differential adhesion govern self-assembly process in histogenesis? Equilibrium configurations and the emergence of a hierarchy among populations of embryonic cells. J. Exp. Zool. 1970, 173:395-434.
7. Harris A.K. Is cell sorting caused by differences in the work of intercellular adhesion? A critique of the Steinberg hypothesis. J. Theor. Biol. 1976, 61(September).
8. Zienkiewicz O.C., Taylor R.L. The Finite Element Method for Solid and Structural Mechanics 2005, Elsevier, Oxford.
9. Sandersius S.A., Newman T.J. Modeling cell rheology with the Subcellular Element Model. Phys. Biol. 2008, 5:015002.
10. Kim T., Gardel M.L., Munro E. Determinants of fluidlike behavior and effective viscosity in cross-linked actin networks. Biophys. J. 2014, 106:526-534.
11. Gemp I.M., Carthew R.W., Hilgenfeldt S. Cadherin-dependent cell morphology in an epithelium: constructing a quantitative dynamical model. PLoS Comput. Biol. 2011, 7:e1002115.
12. Honda H., Nagai T. Cell models lead to understanding of multi-cellular morphogenesis consisting of successive self-construction of cells. J. Biochem. 2015, 157:129-136.
13. Magno R., Grieneisen V.A., Maree A.F. The biophysical nature of cells: potential cell behaviours revealed by analytical and computational studies of cell surface mechanics. BMC Biophys. 2015, 8. 8-015-0022-x (eCollection 2015).
14. Swat M., Thomas G.L., Belmonte J.M., Shirinifard A., Hmeljak D., Glazier J.A. Multi-scale modeling of tissues using CompuCell3D. Methods Cell Biol 2012, 110:325-366.
15. Resasco D.C., Gao F., Morgan F., Novak I.L., Schaff J.C., Slepchenko B.M. Virtual cell: computational tools for modeling in cell biology. Wiley Interdiscip. Rev. Syst. Biol. Med. 2012, 4:129-140.
16. Robinson M., Andrews S.S., Erban R. Multiscale Reaction-Diffusion Simulations with Smoldyn 2015, Bioinformatics.
17. Bootsma G.J., Brodland G.W. Automated 3-D reconstruction of the surface of live early-stage amphibian embryos. IEEE Trans. Biomed. Eng. 2005, 52:1407-1414.
18. Mammoto T., Mammoto A., Ingber D.E. Mechanobiology and developmental control. Annu. Rev. Cell Dev. Biol. 2013, 29:27-61.
19. Kim S., Coulombe P.A. Emerging role for the cytoskeleton as an organizer and regulator of translation. Nat. Rev. Mol. Cell Biol. 2010, 11:75-81.
20. Alberts B., Bray D., Hopkin K., Johnson A., Lewis J., Roberts K., et al. Essential Cell Biology 2014, Garland Publishing Inc., New York. 4th ed.
21. Chen X., Brodland G.W. Multi-scale finite element modeling allows the mechanics of amphibian neurulation to be elucidated. Phys. Biol. 2008, 5:015003.
22. Staple D.B., Farhadifar R., Roper J.C., Aigouy B., Eaton S., Julicher F. Mechanics and remodelling of cell packings in epithelia. Eur. Phys. J. E. Soft Matter 2010, 33:117-127.
23. Chen H.H., Brodland G.W. Cell-level finite element studies of viscous cells in planar aggregates. J. Biomech. Eng. 2000, 122:394-401.
24. Brodland G.W., Chen X., Lee P., Marsden M. From genes to neural tube defects (NTDs): insights from multiscale computational modeling. HFSP J. 2010, 4:142-152.
25. Ma X., Lynch H.E., Scully P.C., Hutson M.S. Probing embryonic tissue mechanics with laser hole drilling. Phys. Biol. 2009, 6:036004.
26. Lippincott-Schwartz J., Patterson G.H. Development and use of fluorescent protein markers in living cells. Science 2003, 300:87-91.
27. Benko R., Brodland G.W. Measurement of in vivo stress resultants in neurulation-stage amphibian embryos. Ann. Biomed. Eng. 2007, 35:672-681.
28. Wiebe C., Brodland G.W. Tensile properties of embryonic epithelia measured using a novel instrument. J. Biomech. 2005, 38:2087-2094.
29. Brodland G.W., Veldhuis J.H., Kim S., Perrone M., Mashburn D., Hutson M.S. CellFIT: a cellular force-inference toolkit using curvilinear cell boundaries. PLoS ONE 2014, 9:e99116.
30. Ishihara S., Sugimura K., Cox S.J., Bonnet I., Bellaiche Y., Graner F. Comparative study of non-invasive force and stress inference methods in tissue. Eur. Phys. J. E. Soft Matter 2013, 36. 9859-13045-8 (epub 2013 Apr 26).
31. Chiou K.K., Hufnagel L., Shraiman B.I. Mechanical stress inference for two dimensional cell arrays. PLoS Comput. Biol. 2012, 8:e1002512.
32. Jacobson A.G., Gordon R. Changes in shape of the developing vertebrate nervous system analyzed experimentally, mathematically and by computer simulation. J. Exp. Zool. 1976, 197:191-246.
33. Elul T., Koehl M.A.R., Keller R. Cellular mechanism underlying neural convergent extension inxenopus laevis embryos. Dev. Biol. 1997, 191:243-258.
34. Brodland G.W. Do lamellipodia have the mechanical capacity to drive convergent extension?. Int. J. Dev. Biol. 2006, 50:151-155.
35. Brodland G.W., Veldhuis J.H. Lamellipodium-driven tissue reshaping: a parametric study. CMBBE 2006, 9:17-23.
36. Brodland G.W., Veldhuis J.H. Computer simulations of mitosis and interdependencies between mitosis orientation, cell shape and epithelia reshaping. J. Biomech. 2002, 35:673-681.
37. Gibson W.T., Veldhuis J.H., Rubinstein B., Cartwright H.N., Perrimon N., Brodland G.W., et al. Control of the mitotic cleavage plane by local epithelial topology. Cell 2011, 144:427-438.
38. Turlier H., Audoly B., Prost J., Joanny J.F. Furrow constriction in animal cell cytokinesis. Biophys. J. 2014, 106:114-123.
39. Brodland G.W., Clausi D.A. Embryonic tissue morphogenesis modeled by FEM. J. Biomech. Eng. 1994, 116:146-155.
40. Ramasubramanian A., Latacha K.S., Benjamin J.M., Voronov D.A., Ravi A., Taber L.A. Computational model for early cardiac looping. Ann. Biomed. Eng. 2006, 34:1355-1369.
41. Savin T., Kurpios N.A., Shyer A.E., Florescu P., Liang H., Mahadevan L., et al. On the growth and form of the gut. Nature 2011, 476:57-62.
42. Hannezo E., Prost J., Joanny J.F. Instabilities of monolayered epithelia: shape and structure of villi and crypts. Phys. Rev. Lett. 2011, 107:078104.
43. Shyer A.E., Tallinen T., Nerurkar N.L., Wei Z., Gil E.S., Kaplan D.L., et al. Villification: how the gut gets its villi. Science 2013, 342:212-218.
44. Davidson L.A., Joshi S.D., Kim H.Y., von Dassow M., Zhang L., Zhou J. Emergent morphogenesis: elastic mechanics of a self-deforming tissue. J. Biomech. 2010, 43:63-70.
45. Kabla A.J. Collective cell migration: leadership, invasion and segregation. J. R. Soc. Interface 2012, 9:3268-3278.
46. Bi D., Lopez J.H., Schwarz J.M., Manning M.L. Energy barriers and cell migration in densely packed tissues. Soft Matter 2014, 10:1885-1890.
47. Yang L., Effler J.C., Kutscher B.L., Sullivan S.E., Robinson D.N., Iglesias P.A. Modeling cellular deformations using the level set formalism. BMC Syst. Biol. 2008, 2. 68-0509-2-68.
48. Shao D., Levine H., Rappel W.J. Coupling actin flow, adhesion, and morphology in a computational cell motility model. Proc. Natl. Acad. Sci. U.S.A. 2012, 109:6851-6856.
49. Brugues A., Ester V., Conte J.H., Veldhuis M., Gupta J., Colombelli, et al. Forces Driving Epithelial Wound Healing 2014, Nature Physics, (advance online publication).
50. Steinberg M.S. Reconstruction of tissues by dissociated cells. Science 1963, 141:401-408.
51. Armstrong P.B. Cell sorting out: the self-assembly of tissues in vitro. Crit. Rev. Biochem. Mol. Biol. 1989, 24:119-149.
52. Brodland G.W., Chen H.H. The mechanics of heterotypic cell aggregates: insights from computer simulations. J. Biomech. Eng. 2000, 122:402-407.
53. Brodland G.W. The Differential Interfacial Tension Hypothesis (DITH): a comprehensive theory for the self-rearrangement of embryonic cells and tissues. J. Biomech. Eng. 2002, 124:188-197.
54. Glazier J.A., Graner F. Simulation of the differential adhesion driven rearrangement of biological cells. Phys. Rev. E 1993, 47:2128-2154.
55. Hutson M.S., Brodland G.W., Yang J., Viens D. Cell sorting in three dimensions: topology, fluctuations, and fluidlike instabilities. Phys. Rev. Lett. 2008, 101:148105.
56. Gordon R. A review of the theories of vertebrate neurulation and their relationship to the mechanicsof neural tube defects. J. Embryol. Exp. Morph. 1985, 89(Suppl.):229-255.
57. Clausi D.A., Brodland G.W. Mechanical evaluation of theories of neurulation using computer simulations. Development 1993, 118:1013-1023.
58. Brodland G.W., Chen D.I., Veldhuis J.H. A cell-based constitutive model for embryonic epithelia and other planar aggregates of biological cells. Int. J. Plast. 2006, 22:965-995.
59. Beloussov L.V., Dorfman J.G., Cherdantzev V.G. Mechanical stresses and morphological patterns in amphibian embryos. J. Embryol. Exp. Morphol. 1975, 34:559-574.
60. Hutson M.S., Veldhuis J.H., Ma X., Lynch H.E., Cranston P.G., Brodland G.W. Combining laser microsurgery and finite element modeling to assess cell-level epithelial mechanics. Biophys. J. 2009, 97:3075-3085.
61. Ambrosi D., Ateshian G.A., Arruda E.M., Cowin S.C., Dumais J., Goriely A., et al. Perspectives on biological growth and remodeling. J. Mech. Phys. Solids 2011, 59:863-883.
62. Brodland G.W. A framework for connecting gene expression to morphogenetic movements in embryos. IEEE Trans. Biomed. Eng. 2011, 58:3033-3036.
63. Taber L.A. Biophysical mechanisms of cardiac looping. Int. J. Dev. Biol. 2006, 50:323-332.
64. Davidson L.A. Integrating morphogenesis with underlying mechanics and cell biology. Curr. Top. Dev. Biol. 2008, 81:113-133.
65. Kondo S., Miura T. Reaction-diffusion model as a framework for understanding biological pattern formation. Science 2010, 329:1616-1620.
66. Malvern L.E. Introduction to the Mechanics of Continuous Medium 1969, Prentice-Hall, New Jersey.
67. Grieneisen V.A., Scheres B. Back to the future: evolution of computational models in plant morphogenesis. Curr. Opin. Plant Biol. 2009, 12:606-614.
68. Engler A.J., Humbert P.O., Wehrle-Haller B., Weaver V.M. Multiscale modeling of form and function. Science 2009, 324:208-212.
69. Meier-Schellersheim M., Fraser I.D., Klauschen F. Multiscale modeling for biologists. Wiley Interdiscip. Rev. Syst. Biol. Med. 2009, 1:4-14.
70. Fontana A., Wrobel B. Embryogenesis, morphogens and cancer stem cells: putting the puzzle together. Med. Hypotheses 2013, 81:643-649.
71. Kelleher F.C., Fennelly D., Rafferty M. Common critical pathways in embryogenesis and cancer. Acta Oncol. 2006, 45:375-388.
72. Jessen J.R. Noncanonical Wnt signaling in tumor progression and metastasis. Zebrafish 2009, 6:21-28.
73. Levin M. Morphogenetic fields in embryogenesis, regeneration, and cancer: non-local control of complex patterning. Biosystems 2012, 109:243-261.
74. Brodland G.W., Veldhuis J.H. The mechanics of metastasis: insights from a computational model. PLoS ONE 2012, 7:e44281.
75. Turner S., Sherratt J.A. Intercellular adhesion and cancer invasion: a discrete simulation using the extended Potts model. J. Theor. Biol. 2002, 216:85-100.
76. Scianna M., Preziosi L., Wolf K. A Cellular Potts Model simulating cell migration on and in matrix environments. Math. Biosci. Eng. 2013, 10:235-261.
77. McGrath D.M., Foltz W.D., Al-Mayah A., Niu C.J., Brock K.K. Quasi-static magnetic resonance elastography at 7 T to measure the effect of pathology before and after fixation on tissue biomechanical properties. Magn. Reson. Med. 2012, 68:152-165.
78. Brodland G.W., Conte V., Cranston P.G., Veldhuis J., Narasimhan S., Hutson M.S., et al. Video force microscopy reveals the mechanics of ventral furrow invagination in Drosophila. Proc. Natl. Acad. Sci. U.S.A. 2010, 107:22111-22116.
79. Box G.E.P., Draper N.R. Empirical Model-building and Response Surfaces 1987, John Wiley & Sons, Oxford, England.