Advertisement

Simulating Tissue Morphogenesis and Signaling

  • Dagmar Iber
  • Simon Tanaka
  • Patrick Fried
  • Philipp Germann
  • Denis Menshykau
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1189)

Abstract

During embryonic development tissue morphogenesis and signaling are tightly coupled. It is therefore important to simulate both tissue morphogenesis and signaling simultaneously in in silico models of developmental processes. The resolution of the processes depends on the questions of interest. As part of this chapter we introduce different descriptions of tissue morphogenesi s. In the simplest approximation tissue is a continuous domain and tissue expansion is described according to a predefined function of time (and possibly space). In a slightly more advanced version the expansion speed and direction of the tissue may depend on a signaling variable that evolves on the domain. Both versions will be referred to as “prescribed growth.” Alternatively tissue can be regarded as incompressible fluid and can be described with Navier-Stokes equations. Local cell expansion, proliferation, and death are then incorporated by a source term. In other applications the cell boundaries may be important and cell-based models must be introduced. Finally, cells may move within the tissue, a process best described by agent-based models.

Key words

Tissue dynamics Signaling networks In silico organogenesis 

Notes

Acknowledgment

The authors thank Erkan Ünal, Javier Lopez-Rios, and Dario Speziale from the Zeller lab for the embryo picture in Fig. 1. The authors acknowledge funding from the SNF Sinergia grant “Developmental engineering of endochondral ossification from mesenchymal stem cells,” a SystemsX RTD on Forebrain Development, a SystemsX iPhD grant, and an ETH Zurich postdoctoral fellowship to D.M.

References

  1. 1.
    Iber D, Zeller R (2012) Making sense-data-based simulations of vertebrate limb development. Curr Opin Genet Dev 22:570–577PubMedCrossRefGoogle Scholar
  2. 2.
    Donea J, Huerta A, Ponthot J, Rodriguez-Ferran A (2004) Arbitrary Lagrangian-Eulerian methods. In: Encyclopedia of computational mechanics. Wiley, New York, pp 1–38Google Scholar
  3. 3.
    Probst S, Kraemer C, Demougin P, Sheth R, Martin GR, Shiratori H, Hamada H, Iber D, Zeller R, Zuniga A (2011) SHH propagates distal limb bud development by enhancing CYP26B1-mediated retinoic acid clearance via AER-FGF signalling. Development 138:1913–1923PubMedCrossRefPubMedCentralGoogle Scholar
  4. 4.
    Menshykau D, Kraemer C, Iber D (2012) Branch mode selection during early lung development. PLoS Comput Biol 8:e1002377PubMedCrossRefPubMedCentralGoogle Scholar
  5. 5.
    Cellière G, Menshykau D, Iber D (2012) Simulations demonstrate a simple network to be sufficient to control branch point selection, smooth muscle and vasculature formation during lung branching morphogenesis. Biol Open 1:775–788PubMedCrossRefPubMedCentralGoogle Scholar
  6. 6.
    Badugu A, Kraemer C, Germann P, Menshykau D, Iber D (2012) Digit patterning during limb development as a result of the BMP-receptor interaction. Sci Rep 2:991PubMedCrossRefPubMedCentralGoogle Scholar
  7. 7.
    Germann P, Menshykau D, Tanaka S, Iber D (2011) Simulating organogenesis in COMSOL. Proceedings of COMSOL conference, pp 1–5Google Scholar
  8. 8.
    Menshykau D, Iber D (2012) Simulation organogenesis in COMSOL: deforming and interacting domains. Proceedings of COMSOL conference, MilanGoogle Scholar
  9. 9.
    Gregg CL, Butcher JT (2012) Quantitative in vivo imaging of embryonic development: opportunities and challenges. Differentiation 84:149–162PubMedCrossRefPubMedCentralGoogle Scholar
  10. 10.
    Bookstein FL (1989) Principal warps: thin-plate splines and the decomposition of deformations. IEEE Trans Pattern Anal Mach Intell 11:567–585CrossRefGoogle Scholar
  11. 11.
    Forgacs G, Foty RA, Shafrir Y, Steinberg MS (1998) Viscoelastic properties of living embryonic tissues: a quantitative study. Biophys J 74:2227–2234PubMedCrossRefPubMedCentralGoogle Scholar
  12. 12.
    Chen S, Doolen GD (1998) Lattice Boltzmann methods for fluid flows. Annu Rev Fluid Mech 30:329–364CrossRefGoogle Scholar
  13. 13.
    Dillon R, Gadgil C, Othmer HG (2003) Short- and long-range effects of Sonic hedgehog in limb development. Proc Natl Acad Sci U S A 100:10152–10157PubMedCrossRefPubMedCentralGoogle Scholar
  14. 14.
    Bittig T, Wartlick O, Kicheva A, González-Gaitán M, Jülicher F (2008) Dynamics of anisotropic tissue growth. New J Phys 10:063001CrossRefGoogle Scholar
  15. 15.
    Boehm B, Westerberg H, Lesnicar-Pucko G, Raja S, Rautschka M, Cotterell J, Swoger J, Sharpe J (2010) The role of spatially controlled cell proliferation in limb bud morphogenesis. PLoS Biol 8:e1000420PubMedCrossRefPubMedCentralGoogle Scholar
  16. 16.
    Dillon R, Owen M, Painter K (2000) A single-cell-based model of multicellular growth using the immersed boundary method. Contemporary Mathematics 466:1–15CrossRefGoogle Scholar
  17. 17.
    Rejniak KA, Kliman HJ, Fauci LJ (2004) A computational model of the mechanics of growth of the villous trophoblast bilayer. Bull Math Biol 66:199–232PubMedCrossRefGoogle Scholar
  18. 18.
    Rejniak KA (2007) An immersed boundary framework for modelling the growth of individual cells: an application to the early tumour development. J Theor Biol 247:186–204PubMedCrossRefGoogle Scholar
  19. 19.
    Peskin CS (2002) The immersed boundary method. Acta Numerica. 11:479–517Google Scholar
  20. 20.
    Rejniak KA, Anderson AR (2008) A computational study of the development of epithelial acini: I. Sufficient conditions for the formation of a hollow structure. Bull Math Biol 70:677–712PubMedCrossRefGoogle Scholar
  21. 21.
    Rejniak KA, Anderson AR (2008) A computational study of the development of epithelial acini: II. Necessary conditions for structure and lumen stability. Bull Math Biol 70:1450–1479PubMedCrossRefGoogle Scholar
  22. 22.
    Graner F, Glazier J (1992) Simulation of biological cell sorting using a two-dimensional extended Potts model. Phys Rev Lett 69:2013–2016PubMedCrossRefGoogle Scholar
  23. 23.
    Izaguirre JA, Chaturvedi R, Huang C et al (2004) CompuCell, a multi-model framework for simulation of morphogenesis. Bioinformatics (Oxford, England) 20:1129–1137CrossRefGoogle Scholar
  24. 24.
    Bauer AL, Beauchemin CAA, Perelson AS (2008) Agent-based modeling of host-pathogen systems: the successes and challenges. Inf Sci 179:1379–1389CrossRefGoogle Scholar
  25. 25.
    Meyer-Hermann ME, Maini PK, Iber D (2006) An analysis of B cell selection mechanisms in germinal centers. Math Med Biol 23:255–277PubMedCrossRefGoogle Scholar
  26. 26.
    Thorne BC, Bailey AM, DeSimone DW, Peirce SM (2007) Agent-based modeling of multicell morphogenic processes during development. Birth Defects Res C Embryo Today 81:344–353PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • Dagmar Iber
    • 1
  • Simon Tanaka
    • 1
  • Patrick Fried
    • 1
  • Philipp Germann
    • 1
  • Denis Menshykau
    • 1
  1. 1.Department for Biosystems Science and Engineering (D-BSSE)ETH ZurichBaselSwitzerland

Personalised recommendations