A framework for modeling the growth and development of neurons and networks

Frontiers in Computational Neuroscience

Volumn 3, Issue NOV, 2009, Pages

  Zubler, Frederic ^a   Douglas, Rodney ^a  

^a Institute of Neuroinformatics Zurich   (Switzerland)

Author keywords

Axon guidance; Computational neuroanatomy; Cortex; Modeling; Neural development

Indexed keywords

AXON GUIDANCES; COMPUTATIONAL NEUROANATOMY; CORTEX; GROWTH AND DEVELOPMENT; LOCALIZED INTERACTION; NEURAL DEVELOPMENT; PHYSICAL INTERACTIONS; SIGNALING MOLECULES;

BIOMECHANICS; COMPLEX NETWORKS; COMPUTER SIMULATION; MECHANICAL PROPERTIES; MODELS; NEURONS; TISSUE;

NEURAL NETWORKS;

EID: 77955480071     PISSN: 16625188     EISSN: None     Source Type: Journal    
DOI: 10.3389/neuro.10.025.2009     Document Type: Article

References (67)

1. Aeschlimann, M. (2000). Biophysical Models of Axonal Path Finding. Ph.D. Thesis, University of Lausanne.
2. Alves, R., Antunes, F., and Salvador, A. (2006). Tools for kinetic modeling of biochemical networks. Nat. Biotechnol. 24, 667-672.
3. Ascoli, G. A., Krichmar, J. L., Scorcioni, R., Nasuto, S. J., and Senft, S. L. (2001). Computer generation and quantitative morphometric analysis of virtual neurons. Anat. Embryol. 204, 283-301.
4. Assadi, A. H., Zhang, G., Beffert, U., McNeil, R. S., Renfro, A. L., Niu, S., Quattrocchi, C. C., Antalffy, B. A., Sheldon, M., Armstrong, D. D., Wynshaw-Boris, A., Herz, J., D'Arcangelo, G., and Clark, G. D. (2003). Interaction of reelin signaling and lis1 in brain development. Nat. Genet. 35, 270-276.
5. Barth, T., and Ohlberger, M. (2004). Encyclopedia of Computational Mechanics, Volume 1, Fundamentals. John Wiley & Sons, Ch. Finite Volume Methods: Foundation and Analysis, pp. 439-474.
6. Bower, J. M., and Beeman, D. (1995). The Book of Genesis: Exploring Realistic Neural Models with the General Neural Simulation System, Electronic Library of Science. New York, Springer-Verlag.
7. Butz, M., Worgotter, F., and van Ooyen, A. (2009). Activity-dependent structural plasticity. Brain Res. Rev. 60, 287-305.
8. Cai, A. Q., Landman, K. A., and Hughes, B. D. (2006). Modelling directional guidance and motility regulation in cell migration. Bull. Math. Biol. 68, 25-52.
9. Castellani, V., and Bolz, J. (1997). Membrane-associated molecules regulate the formation of layer-specific cortical circuits. Proc. Natl. Acad. Sci. U.S.A. 94, 7030-7035.
10. Chilton, J. K. (2006). Molecular mechanisms of axon guidance. Dev. Biol. 292, 13-24.
11. Collier, J. R., Monk, N. A., Maini, P. K., and Lewis, J. H. (1996). Pattern formation by lateral inhibition with feedback: a mathematical model of delta-notch intercellular signalling. J. Theor. Biol. 183, 429-446.
12. Cooper, J. A. (2008). A mechanism for inside-out lamination in the neocortex. Trends Neurosci. 31, 113-119.
13. da Fontoura Costa, L., and Coelho, R. C. (2005). Growth-driven percolations: the dynamics of connectivity in neuronal systems. Eur. Phys. J. B Condens Matter Complex Syst. 47, 571-581.
14. Dantzker, J. L., and Callaway, E. M. (1998). The development of local, layer-specific visual cortical axons in the absence of extrinsic influences and intrinsic activity. J. Neurosci. 18, 4145-4154.
15. de Gennes, P.-G. (2007). Collective neuronal growth and self organization of axons. Proc. Natl. Acad. Sci. U.S.A. 104, 4904-4906.
16. de Lima, A. D., Gieseler, A., and Voigt, T. (2009). Relationship between gabaergic interneurons migration and early neocortical network activity. Dev. Neurobiol. 69, 105-123.
17. Dennerll, T. J., Joshi, H. C., Steel, V. L., Buxbaum, R. E., and Heidemann, S. R. (1988). Tension and compression in the cytoskeleton of pc-12 neurites. ii: Quantitative measurements. J. Cell Biol. 107, 665-674.
18. Dennerll, T. J., Lamoureux, P., Buxbaum, R. E., and Heidemann, S. R. (1989). The cytomechanics of axonal elongation and retraction. J. Cell Biol. 109(Pt 1), 3073-3083.
19. Goddard, N. H., Hucka, M., Howell, F., Cornelis, H., Shankar, K., and Beeman, D. (2001). Towards neuroml: model description methods for collaborative modelling in neuroscience. Philos. Trans. R. Soc. Lond., B, Biol. Sci. 356, 1209-1228.
20. Goodhill, G. J. (2003). A theoretical model of axon guidance by the robo code. Neural. Comput. 15, 549-564.
21. Goodhill, G. J., Gu, M., and Urbach, J. S. (2004). Predicting axonal response to molecular gradients with a computational model of filopodial dynamics. Neural. Comput. 16, 2221-2243.
22. Goodhill, G. J., and Richards, L. J. (1999). Retinotectal maps: molecules, models and misplaced data. Trends Neurosci. 22, 529-534.
23. Hamilton, P. (1993). A language to describe the growth of neurites. Biol. Cybern. 68, 559-565.
24. Hentschel, H. G., and van Ooyen, A. (1999). Models of axon guidance and bundling during development. Proc. Biol. Sci. 266, 2231-2238.
25. Herms, J., Anliker, B., Heber, S., Ring, S., Fuhrmann, M., Kretzschmar, H., Sisodia, S., and Müller, U. (2004). Cortical dysplasia resembling human type 2 lissencephaly in mice lacking all three app family members. EMBO J. 23, 4106-4115.
26. Hilgetag, C. C., and Barbas, H. (2006). Role of mechanical factors in the morphology of the primate cerebral cortex. PLoS Comput. Biol. 2, e22. doi: 10.1371/journal.pcbi.0020022.
27. Hines, M. L., and Carnevale, N. T. (1997). The neuron simulation environment. Neural. Comput. 9, 1179-1209.
28. Huang, H., Kamm, R. D., and Lee, R. T. (2004). Cell mechanics and mechanotransduction: pathways, probes, and physiology. Am. J. Physiol. Cell Physiol. 287, C1-C11.
29. Hutchins, B. I., and Kalil, K. (2008). Differential outgrowth of axons and their branches is regulated by localized calcium transients. J. Neurosci. 28, 143-153.
30. Izhikevich, E. M., and Edelman, G. M. (2008). Large-scale model of mammalian thalamocortical systems. Proc. Natl. Acad. Sci. U.S.A. 105, 3593-3598.
31. Kageyama, R., Ohtsuka, T., Shimojo, H., and Imayoshi, I. (2008). Dynamic notch signaling in neural progenitor cells and a revised view of lateral inhibition. Nat. Neurosci. 11, 1247-1251.
32. Kiddie, G., McLean, D., Ooyen, A. V., and Graham, B. (2005). Development, dynamics and pathology of neuronal networks: from molecules to functional circuits, progress in brain research 147. In Biologically Plausible Models of Neurite Outgrowth, J. Van Pelt, M. Kamermans, C. N. Levelt, A. Van Ooyen, G. J. A. Ramakers, and P. R. Roelfsema, eds (Elsevier Science), pp. 67-80.
33. Kliemann, W. (1987). A stochastic dynamical model for the characterization of the geometrical structure of dendritic processes. Bull. Math. Biol. 49, 135-152.
34. Kriegstein, A., Noctor, S., and Martínez-Cerdeño, V. (2006). Patterns of neural stem and progenitor cell division may underlie evolutionary cortical expansion. Nat. Rev. Neurosci. 7, 883-890.
35. Kriegstein, A. R., and Noctor, S. C. (2004). Patterns of neuronal migration in the embryonic cortex. Trends Neurosci. 27, 392-399.
36. Krottje, J. K., and van Ooyen, A. (2007). A mathematical framework for modeling axon guidance. Bull. Math. Biol. 69, 3-31.
37. Lamoureux, P., Buxbaum, R. E., and Heidemann, S. R. (1989). Direct evidence that growth cones pull. Nature 340, 159-162.
38. Lamoureux, P., Ruthel, G., Buxbaum, R. E., and Heidemann, S. R. (2002). Mechanical tension can specify axonal fate in hippocampal neurons. J. Cell Biol. 159, 499-508.
39. Lindenmayer, A. (1968). Mathematical models for cellular interactions in development. parts 1 and 2. J. Theor. Biol. 18, 280-315.
40. Luczak, A. (2006). Spatial embedding of neuronal trees modeled by diffusive growth. J. Neurosci. Methods 157, 132-141.
41. Markram, H. (2006). The blue brain project. Nat. Rev. Neurosci. 7, 153-160.
42. Maskery, S., and Shinbrot, T. (2005). Deterministic and stochastic elements of axonal guidance. Annu. Rev. Biomed. Eng. 7, 187-221.
43. Massobrio, P., Massobrio, G., and Martinoia, S. (2007). Multi-program approach for simulating recorded extracellular signals generated by neurons coupled to microelectrode arrays. Neurocomputing 70, 2467-2476.
44. Mulchandani, K. (1995). Morphological modelling of neurons. Ph.D. Thesis, Texas A&M University.
45. Ng, H. N., and Grimsdale, R. L. (1996). Computer graphics techniques for modeling cloth. IEEE Comput. Graph. Appl. 16, 28-41.
46. Pattana, S. (2006). Division d'un milieu cellulaire sous contraintes mecaniques. utilisation de la mecanique des materiaux granulaires. Ph.D. Thesis, Université Montpellier II.
47. Pecevski, D. A., Natschläger, T., and Schuch, K. (2009). PCSIM: a parallel simulation environment for neural circuits fully integrated with Python. Front. Neuroinformatics 3, doi: 10.3389/neuro.11.011.2009.
48. Polleux, F., Dehay, C., Goffinet, A., and Kennedy, H. (2001). Pre-and postmitotic events contribute to the progressive acquisition of area-specific connectional fate in the neocortex. Cereb. Cortex 11, 1027-1039.
49. Rakic, P. (1972). Mode of cell migration to the superficial layers of fetal monkey neocortex. J. Comp. Neurol. 145, 61-83.
50. Reber, M., Burrola, P., and Lemke, G. (2004). A relative signalling model for the formation of a topographic neural map. Nature 431, 847-853.
51. Ryder, E. F., Bullard, L., Hone, J., Olmstead, J., and Ward, M. O. (1999). Graphical simulation of early development of the cerebral cortex. Comput. Methods Programs Biomed. 59, 107-114.
52. Samsonovich, A. V., and Ascoli, G. A. (2005). Statistical determinants of dendritic morphology in hippocampal pyramidal neurons: a hidden markov model. Hippocampus 15, 166-183.
53. Samuels, D. C., Hentschel, H. G., and Fine, A. (1996). The origin of neuronal polarization: a model of axon formation. Philos. Trans. R. Soc. Lond., B, Biol. Sci. 351, 1147-1156.
54. Schaller, G., and Meyer-Hermann, M. (2004). Kinetic and dynamic delaunay tetrahedralizations in three dimensions. Comput. Phys. Commun. 162, 9.
55. Schaller, G., and Meyer-Hermann, M. (2005). Multicellular tumor spheroid in an off-lattice voronoi-delaunay cell model. Phys. Rev. E. Stat. Nonlin. Soft Matter Phys. 71(Pt 1), 051910.
56. Shefi, O., Harel, A., Chklovskii, D. B., Ben-Jacob, E., and Ayali, A. (2004). Biophysical constraints on neuronal branching. Neurocomputing 58-60, 487-495.
57. Shinbrot, T. (2006). Simulated morphogenesis of developmental folds due to proliferative pressure. J. Theor. Biol. 242, 764-773.
58. Stepanyants, A., Hirsch, J. A., Martinez, L. M., Kisvárday, Z. F., Ferecskó, A. S., and Chklovskii, D. B. (2008). Local potential connectivity in cat primary visual cortex. Cereb. Cortex 18, 13-28.
59. Stepanyants, A., Hof, P. R., and Chklovskii, D. B. (2002). Geometry and structural plasticity of synaptic connectivity. Neuron 34, 275-288.
60. Stiefel, K. M., and Sejnowski, T. J. (2007). Mapping function onto neuronal morphology. J. Neurophysiol. 98, 513-526.
61. Turrigiano, G. G. (2008). The self-tuning neuron: synaptic scaling of excitatory synapses. Cell 135, 422-435.
62. VanEssen, D. C. (1997). A tension-based theory of morphogenesis and compact wiring in the central nervous system. Nature 385, 313-318.
63. van Ooyen, A. (2003). Modeling Neural Development. The MIT Press.
64. van Ooyen, A., and Willshaw, D. J. (1999). Competition for neurotrophic factor in the development of nerve connections. Proc. Biol. Sci. 266, 883-892.
65. van Pelt, J., and Verwer, R. W. (1983). The exact probabilities of branching patterns under terminal and segmental growth hypotheses. Bull. Math. Biol. 45, 269-285.
66. Ward, K., Bertails, F., Kim, T.-Y., Marschner, S. R., Cani, M. P., and Lin, M. C. (2007). A survey on hair modeling: styling, simulation, and rendering. IEEE Trans. Vis. Comput. Graph 13, 213-234.
67. Willshaw, D. (2006). Analysis of mouse epha knockins and knockouts suggests that retinal axons programme target cells to form ordered retinotopic maps. Development 133, 2705-2717.