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Recent studies show that plant organ positioning may be mediated by localized concentrations of the plant hormone auxin. Auxin patterning in the shoot apical meristem is in turn brought about by the subcellular polar distribution of the putative auxin efflux mediator, PIN1. However, the question of what signals determine PIN1 polarization and how this gives rise to regular patterns of auxin concentration remains unknown. Here we address these questions by using mathematical modeling combined with confocal imaging. We propose a model that is based on the assumption that auxin influences the polarization of its own efflux within the meristem epidermis. We show that such a model is sufficient to create regular spatial patterns of auxin concentration on systems with static and dynamic cellular connectivities, the latter governed by a mechanical model. We also optimize parameter values for the PIN1 dynamics by using a detailed auxin transport model, for which parameter values are taken from experimental estimates, together with a template consisting of cell and wall compartments as well as PIN1 concentrations quantitatively extracted from confocal data. The model shows how polarized transport can drive the formation of regular patterns.Arabidopsis thaliana ͉ computable plant ͉ dynamical model ͉ pattern formation ͉ meristem I n the growing plant shoot, new leaf and flower primordia emerge at well defined positions, resulting in strikingly regular patterns (1). These phyllotactic patterns can be whorled (more than one new primordium develops simultaneously) or spiral (single primordia are created sequentially). Spiral phyllotaxis is often connected to the Fibonacci series because the numbers of parastichies (visible spirals) in each direction around the axis are commonly consecutive Fibonacci numbers. Also, consecutive primordia in the spiral often appear at a divergence angle close to the golden angle. The beautiful symmetries apparent in phyllotaxis and its connection to mathematics have inspired scientists to create theories and models to explain these patterns. One important finding from mathematical analysis and physical simulation (2, 3) is that many of the seemingly complex phyllotactic patterns and transitions found in plants can probably be explained to a large degree by any regular spacing mechanism superimposed on a gradually enlarging generative region. This finding is important because it suggests that the problem can be reduced to two potentially independent and smaller questions. The first question regards how meristem size is determined during plant development. The second question involves how a regularly spaced pattern of primordial position is specified. Traditionally, models have concentrated on the second question, and they can be divided into molecular and mechanical ideas (4-6). Because we investigate a model based on molecular experiments, here we discuss some molecular-based ideas in more detail. Schoute (7) first proposed the idea of lateral inhibition based on a diffusible chemical produced b...

BioModels Database (), part of the international initiative BioModels.net, provides access to published, peer-reviewed, quantitative models of biochemical and cellular systems. Each model is carefully curated to verify that it corresponds to the reference publication and gives the proper numerical results. Curators also annotate the components of the models with terms from controlled vocabularies and links to other relevant data resources. This allows the users to search accurately for the models they need. The models can currently be retrieved in the SBML format, and import/export facilities are being developed to extend the spectrum of formats supported by the resource.