Dynamical modules in metabolism, cell and developmental biology.

Modularity is an essential feature of any adaptive complex system. Phenotypic traits are modules in the sense that they have a distinguishable structure or function, which can vary (quasi-)independently from its context. Since all phenotypic traits are the product of some underlying regulatory dynamics, the generative processes that constitute the genotype-phenotype map must also be functionally modular.

Auxin influx importers modulate serration along the leaf margin.

Leaf shape in Arabidopsis is modulated by patterning events in the margin that utilize a PIN-based auxin exporter/CUC2 transcription factor system to define regions of promotion and retardation of growth, leading to morphogenesis. In addition to auxin exporters, leaves also express auxin importers, notably members of the AUX1/LAX family. In contrast to their established roles in embryogenesis, lateral root and leaf initiation, the function of these transporters in leaf development is poorly understood.

Bioattractors: dynamical systems theory and the evolution of regulatory processes.

In this paper, we illustrate how dynamical systems theory can provide a unifying conceptual framework for evolution of biological regulatory systems. Our argument is that the genotype-phenotype map can be characterized by the phase portrait of the underlying regulatory process. The features of this portrait--such as attractors with associated basins and their bifurcations--define the regulatory and evolutionary potential of a system.

The inheritance of process: a dynamical systems approach.

A central unresolved problem of evolutionary biology concerns the way in which evolution at the genotypic level relates to the evolution of phenotypes. This genotype-phenotype map involves developmental and physiological processes, which are complex and not well understood. These processes co-determine the rate and direction of adaptive change by shaping the distribution of phenotypic variability on which selection can act.

A shift toward smaller cell size via manipulation of cell cycle gene expression acts to smoothen Arabidopsis leaf shape.

Understanding the relationship of the size and shape of an organism to the size, shape, and number of its constituent cells is a basic problem in biology; however, numerous studies indicate that the relationship is complex and often nonintuitive. To investigate this problem, we used a system for the inducible expression of genes involved in the G1/S transition of the plant cell cycle and analyzed the outcome on leaf shape. By combining a careful developmental staging with a quantitative analysis of the temporal and spatial response of cell division pattern and leaf shape to these manipulations, we found that changes in cell division frequency occurred much later than the observed changes in leaf shape.

LEAFPROCESSOR: a new leaf phenotyping tool using contour bending energy and shape cluster analysis.

*Significant progress has been made in the identification of the genetic factors controlling leaf shape. However, no integrated solution for the quantification and categorization of leaf form has been developed. In particular, the analysis of local changes in margin growth, which define many of the differences in shape, remains problematical.

Regulative feedback in pattern formation: towards a general relativistic theory of positional information.

Positional specification by morphogen gradients is traditionally viewed as a two-step process. A gradient is formed and then interpreted, providing a spatial metric independent of the target tissue, similar to the concept of space in classical mechanics. However, the formation and interpretation of gradients are coupled, dynamic processes.

Development: dissecting the dynamics of segment determination.

A novel combination of high-resolution time-course expression data and computational modelling has provided a remarkably detailed picture of a key stage of Drosophila segment determination, highlighting the dynamic nature of this process.