Topology-based abstraction of complex biological systems: application to the Golgi apparatus.
Many complex cellular processes involve major changes in topology and geometry. We have developed a method using topology-based geometric modelling in which the edge labels of an n-dimensional generalized map (a subclass of graphs) represent the relations between neighbouring biological compartments. We illustrate our method using two topological models of the Golgi apparatus. These models can be animated using transformation rules, which depend on geometric and/or biochemical data and which modify both these data and the topology. Both models constitute plausible topological representations of the Golgi apparatus, but only the model based on a recent hypothesis about the Golgi apparatus is fully compatible with data from electron microscopy. Finally, we outline how our method may help biologists to choose between different hypotheses.
Poudret
Mathieu
M
XLIM-SIC UMR 6172 CNRS, Université de Poitiers, 86962, Futuroscope, France. poudret@sic.univ-poitiers.fr
Arnould
Agnès
A
Comet
Jean-Paul
JP
Le Gall
Pascale
P
Meseure
Philippe
P
Képès
François
F
D000818:Animals; D006056:Golgi Apparatus / Q000502:physiology* / Q000648:ultrastructure*; D006801:Humans; D008953:Models, Anatomic; D008954:Models, Biological; D021381:Protein Transport / Q000502:physiology*; D015398:Signal Transduction / Q000502:physiology*; D049490:Systems Biology / Q000379:methods*