Abstract
In this paper we demonstrate a spatio-temporal gene regulatory network for early gastrulation in the sea anemone Nematostella vectensis. We measure gene expression during early gastrulation using a gene expression quantification tool. We measure gene expression during early gastrulation when the embryo is more or less radial symmetrical and where there is only one body axis (the aboral - oral body axis in the case of Nematostella), allowing us, to use a one-dimensional model. The shape changes are induced by mechanical forces that are defined as rules or explicitly coupled to genetic regulation. The morphological evolution of the Nematostella embryo during gastrulation is described by a cell-based model, which can potentially be coupled with the one-dimensional gene regulatory network.
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References
Armstrong, N.J., Painter, K.J., Sheratt, J.A.: A continuum approach to modelling cell-cell adhesion. J. Theor. Biol. 243, 98–113 (2006)
Ashyraliyev, M., Fomekong Nanfack, Y., Kaandorp, J.A., Blom, J.G.: Systems biology: Parameter estimation for biochemical models. FEBS Journal 276, 886–902 (2009)
Dallon, J.C., Othmer, H.G.: How cellular movement determines the collective force generated by the Dictyostelium discoideum slug. J. Theor. Biol. 231, 203–222 (2004)
Davidson, E.H.: The regulatory genome: gene regulatory networks in development and evolution. Academic Press, London (2006)
de Jong, H.: Modeling and simulation of genetic regulatory systems: A literature review. J. Comp. Biol. 9, 67–103 (2002)
de Jong, J.: Quantitative analysis of gene expression in Nematostella vectensis. Master’s thesis, Faculty of Science, University of Amsterdam (2009)
Fauré, A., Naldi, A., Chaouiya, C., Thieffry, D.: Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle. Bioinformatics 22(14), e124–e131 (2006)
Finnerty, J.R., Pang, K., Burton, P., Paulson, D., Martindale, M.Q.: Origins of Bilateral Symmetry: Hox and Dpp expression in a Sea Anemone Science, vol. 304, pp. 1335–1336 (2004)
Fomekong Nanfack, Y., Kaandorp, J.A., Blom, J.G.: Efficient parameter estimation for spatio-temporal models of pattern formation: Case study of Drosophila melanogaster. Bioinformatics 23, 3356–3363 (2007)
Gutenkunst, R.N., Waterfall, J.J., Casey, F.P., Brown, K.S., Myers, C.R., et al.: Universally Sloppy Parameter Sensitivities in Systems Biology Models. PLoS Comput. Biol. 3(10) (2007)
Honda, H., Tanemura, M., Nagai, T.: A three-dimensional vertex dynamics cell model of space-filling polyhedra simulating cell behavior in a cell aggregate. J. Theor. Biol. 226, 439–453 (2004)
Jaeger, J., Surkova, S., Blagov, M., Janssens, H., Kosman, D., Kozlov, K.N., Manu, M.E., Vanario-Alonso, C.E., Samsonova, M., Sharp, D.H., Reinitz, J.: Dynamic control of positional information in the early Drosophila blastoderm. Nature 430, 368–371 (2004)
Kauffman, S.A.: The Origins of Order: Self Organization and Selection in Evolution. Oxford University Press, Oxford (1993)
Magie, C.R., Pang, K., Martindale, M.Q.: Martindale Genomic inventory and expression of Sox and Fox genes in the cnidarian Nematostella vectensis. Dev. Genes Evol. 215, 618–630 (2005)
Maree, A.F., Hogeweg, P.: Modelling Dictyostelium discoideum morphogenesis: the culmination. Bull. Math. Biol. 64(2), 327–353 (2002)
Martindale, M.Q., Pang, K., Finnerty, J.R.: Investigating the origins of triploblasty: mesodermal gene expression in a diploblastic animal, the sea anemone Nematostella vectensis (phylum, Cnidaria; class, Anthozoa). Development 131, 2463–2474 (2004)
Mjolsness, E., Sharp, D.H., Reinitz, J.: A connectionist model of development. J. Theor. Biol. 152, 429–453 (1991)
Odell, G., Oster, G., Burnside, B., Alberch, P.: A mechanical model for epithelial morphogenesis. J. Math. Biol. 9, 291–295 (1980)
Reinitz, J., Sharp, D.H.: Mechanisms of eve stripe formation. Mechanisms of Development 49, 133–158 (1995)
Reinitz, J., Hou, S., Sharp, D.H.: Transcriptional Control in Drosophila. ComPlexUs 1, 54–64 (2003)
Schaller, G., Meyer-Hermann, M.: Multicellular tumor spheroid in an off-lattice Voronoi-Delaunay cell model. Phys. Rev. E. Stat. Nonlin. Soft. Matter Phys. 71(5 pt. 1), 51910 (2005)
Sánchez, L., Thieffry, D.: A logical analysis of the Drosophila gap-gene system. J. Theor. Biol. 211, 115–141 (2001)
Surkova, S., Kosman, D., Kozlov, K., Manu Myasnikova, E., et al.: Characterization of the Drosophila segment determination morphome. Dev. Biol. 313, 844–862 (2008)
Tamulonis, C., Postma, M., Marlow, H., Magie, C., de Jong, J., Kaandorp, J.A.: Morphometrics and Modeling of Nematostella vectensis Gastrulation. Developmental Biology 351, 217–228 (2011)
Wikramanayake, A.H., Hong, M., Lee, P.N., Pang, K., Byrum, C.A., Bince, J.M., Xu, R., Martindale, M.Q.: An ancient role for beta-catenin in the evolution of axial polarity and germ layer segregation. Nature 426, 446–450 (2003)
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Kaandorp, J.A., Botman, D., Tamulonis, C., Dries, R. (2012). Multi-scale Modeling of Gene Regulation of Morphogenesis. In: Cooper, S.B., Dawar, A., Löwe, B. (eds) How the World Computes. CiE 2012. Lecture Notes in Computer Science, vol 7318. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-30870-3_36
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DOI: https://doi.org/10.1007/978-3-642-30870-3_36
Publisher Name: Springer, Berlin, Heidelberg
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