Modelling and analysis of growth and form of sponges and scleractinian corals

Simulated growth form and external nutrient gradients

Volume rendered image of a CT scan of the scleractinian coral in Madracis

Animation FIG1E Morphogenesis of a simulated coral

Animation FIG1B surface rendering of the scleractinian coral Madracis mirabilis

Animation FIG1D Morphogenesis of a simulated coral

http://staff.science.uva.nl/~robbel/javascript3d/obj_389.html Interactive visualization of a surface rendering of the scleractinian coral Madracis mirabilis (by Robert Belleman)

This project is a collaboration between the section Computational Science
of the Universiteit van Amsterdam (UvA), coral and sponge biologists,
biologists working on biomechanics and researchers from molecular developmental biology
(see below: ``The research team'').

Abstract

A fundamental question in biology is how the interplay between the
genome and the physical environment drives pattern formation and
morphogenesis. With the availability of new computational
techniques (particle-based techniques as for example lattice gases and the
lattice Boltzmann method) in combination with large scale computing
facilities, in silico experiments are becoming more and more an important
option to study this question and investigate self-organisation and
emergent behaviour in biological systems. Furthermore an enormous
amount of progress has been made this last decade within the
developmental biology. Also, the genomes of some important experimental
organisms have now been or are now being elucidated. Potentially this
combination of new discoveries in developmental biological and
new computational techniques may advance this field enormously. Work on
morphogenesis and pattern formation, using modelling and simulation in
addition to in vitro an in vivo experiments, has many implications for research
in medicine and biology. Examples are studies on carcinogenesis, studies on
regeneration capabilities and ecological studies on growth and form and the
impact of the physical environment.


Within the metazoans, sponges and cnidarians represent the phyla with the
simplest body plan and a relatively simple regulatory network controlling
the development. This makes these organisms an excellent case study
for understanding morphogenesis and the physical translation
of the genetic information into a growth form, using a combination
of a biomechanical models of growth and form and a model of the spatial and
temporal expression of developmental genes.
Understanding external deciding factors in growth and morphology of reef
corals and sponges is essential to elucidate the role of these organisms
in marine ecosystems, and to explain their susceptibility to pollution and global
climate change. An important issue in growth and form of sponges and corals is the
the thickness of boundary layers and mass transfer of metabolites and nutrients
from the external environment to the organism through the boundary layer, it is
hypothesized that this mass transfer is strongly influenced by the physical environment.


We are investigating the morphogenesis in sponges and corals by combining
simulation studies with experimental studies, we are using the
following approaches:


1. We are developing simulation models of regulatory networks, These
models will be based on temporal and spatial gene expression pattern during
development in sponges and scleractinian corals

2. Development of biomechanical models of growth and form (accretive
growth models, models of cell aggregates) and the impact of the
physical environment. The simulated morphologies are compared in
a morphological analysis to three-dimensional images of the actual
organisms, obtained with CT-scanning techniques.

3. Development of advection-diffusion models to study the boundary layer
formation in three-dimensional images of the actual organisms. The
simulation results are compared with data stemming from flume tank experiments,
NMR experiments and Acoustic Doppler velocitymetry

The Research Team