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Modeling Morphogenesis in silico and in vitro: Towards Quantitative, Predictive, Cell-based Modeling
R. M. H. Merks1, 2 ; P. Koolwijk3
1CWI, Science Park 123, 1098 XG Amsterdam
2NCSB-NISB, Science Park 904, 1098 XH Amsterdam
3Laboratory for Physiology, Institute for Cardiovascular Research VU University Medical Center, 1081 BT Amsterdam
Mathematical modelling of natural phenomena, Tome 4 (2009) no. 4, pp. 149-171
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Cell-based, mathematical models help make sense of morphogenesis—i.e. cells organizing into shape and pattern—by capturing cell behavior in simple, purely descriptive models. Cell-based models then predict the tissue-level patterns the cells produce collectively. The first step in a cell-based modeling approach is to isolate sub-processes, e.g. the patterning capabilities of one or a few cell types in cell cultures. Cell-based models can then identify the mechanisms responsible for patterning in vitro. This review discusses two cell culture models of morphogenesis that have been studied using this combined experimental-mathematical approach: chondrogenesis (cartilage patterning) and vasculogenesis (de novo blood vessel growth). In both these systems, radically different models can equally plausibly explain the in vitro patterns. Quantitative descriptions of cell behavior would help choose between alternative models. We will briefly review the experimental methodology (microfluidics technology and traction force microscopy) used to measure responses of individual cells to their micro-environment, including chemical gradients, physical forces and neighboring cells. We conclude by discussing how to include quantitative cell descriptions into a cell-based model: the Cellular Potts model.
DOI : 10.1051/mmnp/20094406

R. M. H. Merks  1 , 2   ; P. Koolwijk  3

1 CWI, Science Park 123, 1098 XG Amsterdam
2 NCSB-NISB, Science Park 904, 1098 XH Amsterdam
3 Laboratory for Physiology, Institute for Cardiovascular Research VU University Medical Center, 1081 BT Amsterdam 
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R. M. H. Merks; P. Koolwijk. Modeling Morphogenesis in silico and in vitro: Towards Quantitative, Predictive, Cell-based Modeling. Mathematical modelling of natural phenomena, Tome 4 (2009) no. 4, pp. 149-171. doi: 10.1051/mmnp/20094406

[1] D. Amarie, J. A. Glazier, S. C. Jacobson Anal. Chem. 2007 9471 9477

[2] D. Ambrosi, A. Gamba, G. Serini B. Math. Biol. 2004 1851 1873

[3] A. R. A. Anderson, M. A. J. Chaplain, K. A. Rejniak, editors. Single-Cell-Based Models in Biology and Medicine. Mathematics and Biosciences in Interaction. Birkhaüser, Basel, Switzerland, 2007.

[4] C. Bakal, J. Aach, G. Church, N. Perrimon Science 2007 1753 1756

[5] A. Balter, R. M. H. Merks, N. J. Popławski, M. Swat, J. A. Glazier. The Glazier–Graner–Hogeweg model: Extensions, future directions, and opportunities for further study. In A. R. A. Anderson, M. A. J. Chaplain, K. A. Rejniak, editors, Single-Cell-Based Models in Biology and Medicine, Mathematics and Biosciences in Interaction, pages 151–167. Birkhaüser, Basel, Switzerland, 2007.

[6] J. B. Beltman, A. F. M. Maree, J. N. Lynch, M. J. Miller, R. J. De Boer J. Exp. Med. 2007 771 780

[7] G. W. Brodlan, D. A. Clausi J. Biomech. Eng.-T. ASME 1994 146 155

[8] N. Caille, O. Thoumine, Y. Tardy, J.-J. Meister J. Biomech. 2002 177 187

[9] R. R. Chen, E. A. Silva, W. W. Yuen, A. A. Brock, C. Fischbach, A. S. Lin, R. E. Guldberg, D. J. Mooney FASEB J. 2007 3896 903

[10] S. Christley, M. S. Alber, S. A. Newman. Patterns of mesenchymal condensation in a multiscale, discrete stochastic model. PLoS Comput. Biol., 3 (2007), No. 4, e76.

[11] T. Cickovski, K. Aras, M. S. Alber, J. A. Izaguirre, M. Swat, J. A. Glazier, R. M. H. Merks, T. Glimm, H. G. E. Hentschel, S. A. Newman Comput. Sci. Eng. 2007 50 60

[12] E. H. Davidson Science 2002 1669 1678

[13] E. Flenner, F. Marga, A. Neagu, L. Kosztin, G. Forgacs Curr. Top. Dev. Biol. 2008 461 483

[14] G. Forgacs, S. A. Newman. Biological physics of the developing embryo. Cambridge University Press, 2005.

[15] A. Gamba, D. Ambrosi, A. Coniglio, A. De Candia, S. D. Talia, E. Giraudo, G. Serini, L. Preziosi, F. Bussolino Phys. Rev. Lett. 2003 118101

[16] J. A. Glazier, A. Balter, N. J. Popławski. Magnetization to morphogenesis: a brief history of the Glazier-Graner-Hogeweg model. In A. R. A. Anderson, M. A. J. Chaplain, and K. A. Rejniak, editors, Single Cell-Based Models in Biology and Medicine, Mathematics and Biosciences in Interaction, pages 79–106. Birkhaüser, Basel, Switzerland, 2007.

[17] J. A. Glazier, F. Graner Phys. Rev. E 1993 2128 2154

[18] V. A. Grieneisen, J. Xu, A. F. M. Marée, P. Hogeweg, B. Scheres Nature 2007 1008 13

[19] D. Guidolin, B. Nico, A. S. Belloni, G. G. Nussdorfer, A. Vacca, D. Ribatti Leukemia 2007 2201 3

[20] M. S. Hutson, G. W. Brodland, J. Yang, D. Viens Phys. Rev. Lett. 2008 4

[21] J. Käfer, T. Hayashi, A. F. M. Marée, R. W. Carthew, F. Graner Proc. Natl. Acad. Sci. U.S.A. 2007 18549 54

[22] K. Keren, Z. Pincus, G. M. Allen, E. L. Barnhart, G. Marriott, A. Mogilner, J. A. Theriot. Mechanism of shape determination in motile cells. Nature, 453 (2008), No. 7194.

[23] M. A. Kiskowski, M. S. Alber, G. L. Thomas, J. A. Glazier, N. B. Bronstein, J. Pu, S. A. Newman Dev. Biol. 2004 372 87

[24] D. Manoussaki ESAIM-Math. Model. Num. 2003 581 599

[25] D. Manoussaki, S. R. Lubkin, R. B. Vernon, J. D. Murray Acta Biotheor. 1996 271 282

[26] A. F. M. Marée, V. A. Grieneisen, P. Hogeweg. The Cellular Potts Model and biophysical properties of cells, tissues and morphogenesis. In A. R. A. Anderson, M. J. Chaplain, K. A. Rejniak, editors, Single-Cell-Based Models in Biology and Medicine, Mathematics and Biosciences in Interaction, pages 107–136. Birkhaüser, Basel, Switzerland, 2007.

[27] A. F. M. Marée, P. Hogeweg B. Math. Biol. 2002 327 353

[28] A. F. M. Marée, A. Jilkine, A. Dawes, V. A. Grieneisen, L. Edelstein-Keshet B. Math. Biol. 2006 1169 1211

[29] R. M. H. Merks, J. A. Glazier Phys. A 2005 113 130

[30] R. M. H. Merks, S. A. Newman, J. A. Glazier Lect. Notes Comput. Sc. 2004 425 434

[31] R. M. H. Merks, S. V. Brodsky, M. S. Goligorksy, S. A. Newman, J. A. Glazier Dev. Biol. 2006 44 54

[32] R. M. H. Merks, J. A. Glazier Nonlinearity 2006 C1 C10

[33] R. M. H. Merks, E. D. Perryn, A. Shirinifard, J. A. Glazier. Contact-inhibited chemotaxis in de novo and sprouting blood-vessel growth. PLoS Comput. Biol., 4 (2008), No. 9, e1000163.

[34] P. Namy, J. Ohayon, P. Tracqui J. Theor. Biol. 2004 103 120

[35] T. Newman Math. Biosci. Eng. 2005 613 624

[36] E. Palsson J. Theor. Biol. 2008 1 13

[37] S. Petronis, C. Gretzer, B. Kasemo, J. Gold J. Biomed. Mater. Res. A 2003 707 21

[38] N. J. Popławski, A. Shirinifard, M. Swat, J. A. Glazier Math. Biosci. Eng. 2008 355 388

[39] C. A. Reinhart-King, M. Dembo, D. A. Hammer Biophys. J. 2005 676 89

[40] C. A. Reinhart-King, M. Dembo, D. A. Hammer Biophys. J. 2008 6044 51

[41] K. A. Rejniak J. Theor. Biol. 2007 186 204

[42] K. A. Rejniak, A. R. A. Anderson B. Math. Biol. 2008 677 712

[43] J. P. Rieu, A. Upadhyaya, J. A. Glazier, N. B. Ouchi, Y. Sawada Biophys. J. 2000 1903 1914

[44] S. A. Sandersius, T. J. Newman Phys. Biol. 2008 015002

[45] N. J. Savill, P. Hogeweg J. Theor. Biol. 1997 229 235

[46] B. G. Sengers, C. C. V. Donkelaar, C. W. J. Oomens, F. P. T. Baaijens Ann. Biomed. Eng. 2004 1718 1727

[47] B. G. Sengers, M. Taylor, C. P. Please, R. O. C. Oreffo Biomaterials 2007 1926 1940

[48] G. Serini, D. Ambrosi, E. Giraudo, A. Gamba, L. Preziosi, F. Bussolino EMBO J. 2003 1771 9

[49] A. Shamloo, N. Ma, M.-M. Poo, L. L. Sohn, S. C. Heilshorn Lab Chip 2008 1292 9

[50] T. Sun, P. Mcminn, S. Coakley, M. Holcombe, R. Smallwood, S. Macneil J. Roy. Soc. Interface 2007 1077 1092

[51] A. Szabo, E. Mehes, E. Kosa, A. Czirok Biophys. J. 2008 2702 10

[52] A. Szabo, E. D. Perryn, A. Czirok Phys. Rev. Lett. 2007 038102

[53] Y. Tsukada, K. Aoki, T. Nakamura, Y. Sakumura, M. Matsuda, S. Ishii. Quantification of local morphodynamics and local GTPase activity by edge evolution tracking. PLoS Comput. Biol., 4 (2008), No. 11, e1000223.

[54] N. Tymchenko, J. Wallentin, S. Petronis, L. M. Bjursten, B. Kasemo, J. Gold Biophys. J. 2007 335 45

[55] A. Vaziri, A. Gopinath Nat. Mater. 2008 15 23

[56] D. Walker, J. Southgate, G. Hill, A. Holcombe, D. Hose, S. Wood, S. M. Neil, R. Smallwood Biosystems 2004 89 100

[57] G. M. Walker, J. Sai, A. Richmond, M. Stremler, C. Y. Chung, J. P. Wikswo Lab Chip 2005 611 618

[58] Z. Xu, N. Chen, S. C. Shadden, J. E. Marsden, M. M. Kamocka, E. D. Rosen, M. S. Alber Soft Matter 2009 769 779

[59] Z. Yin, D. Noren, C. J. Wang, R. Hang, A. Levchenko Mol. Syst. Biol. 2008 232

[60] W. Zeng, G. L. Thomas, J. A. Glazier Phys. A 2004 482 494

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