Organogensis

VI.1 COORDINATORS
VI.2 PARTICIPANTS
VI.3 SUMMARY
VI.4 INTRODUCTION
VI.5 SPECIFIC AIMS
VI.6 BACKGROUND AND SIGNIFICANCE
VI.7 THEORETICAL FRAMEWORK
VI.8 PRELIMINARY RESULTS
VI.9 RESEARCH DESIGN AND METHODS
VI.10 RELATIONSHIP TO CYTOSKELETON (PROJECT 2) AND BIOLOGICAL NETWORKS (PROJECT 1)
VI.11 TIMELINE

< Previous | Page 27 of 27 | Organogenesis Home ||

VI.11 TIMELINE

Year I
Year II
Year III
Year IV
Year V

Year I

Experiment

Initial data acquisition on condensation patterns from wing cultures and leg cultures using existing chicken fibronectin amino-terminal domain wild type and human mutant constructs. Test effect of initial cell density on condensation patterns. Determine if RNAi expression can knock down fibronectin and FGF receptor expression in chicken. Quantify cell movement patterns during limb development and gastrulation.

Simulation

Initial simulation of mesenchymal cell condensation and the emergence of a skeletal pattern in simple geometries including TGF-β, fibronectin and cells. Statistical analysis of the experimental patterns. Initial simulations of chondrogenesis and nerve innervation in static domains in the presence of simple nodular structures. Investigate effects of geometry and biochemistry on form and function. Develop stable fast solvers for reaction-diffusion equations.

     

^ To top of page

Year II

Experiment

Construction of mutants in chicken fibronectin cDNA constructs in putative heparan sulfate binding and integrin binding regions of the fibronectin amino-terminal domain. Data acquisition from wing cultures and leg cultures transfected with these constructs. Analyze role of FGF receptors in lateral inhibition. Visualize PIP3 cell-cell signaling. Begin chemoattractant screen in chick. Digital encoding and statistical analysis of Hoffman images. Analyze effects of various TGF-beta and FGF-2 and -8 treatment protocols on condensation patterns in vitro in a quantitative fashion.

Simulation

Integration of experimental results on chicken into 3D cellular automata and Potts models. Basic aggregate analysis using clustering and classification algorithms. Basic viscoelastic property module. Study the influence of evolving limb geometry on chondrogenesis and nerve innervation. Develop models of cytoskeletal growth. Integration of stochastic dynamics, continuum model, and computational geometry for the cytoskeleton tool. Experimental validation of simulations. Extended Potts model with reaction diffusion for complex growing domains of model organisms (chicken, snail, sea urchin). Multilevel integration with tissue and subcellular levels through aggregate analysis and XML descriptors. Study the development of vasculature in the avian limb.

     

^ To top of page

Year III

Experiment

Continue chemoattractant screen in chick. Begin mapping of gene expression/cell movement pathways in chick. Generate site-directed mutants of fibronectin amino-terminal domain and test for enhancing or dominant negative effects on wing and leg condensation patterns in vitro.

Simulation

Integration of genetics results into 2D cellular automata and Potts models. Continue refining comprehensive computational 3D limb model which models cell aggregates, organ formation and tissue viscoelasticity. Combine the software modules. Extended Potts model with reaction diffusion for complex growing domains of model organisms (chicken, snail, sea urchin). Multilevel integration with tissue and subcellular levels through aggregate analysis and XML descriptors. Experimental validation of simulations. Digital encoding and statistical analysis of Hoffman images. Hypothesis testing using Potts model simulations. Start development of cross-scale simulations linking Organogenesis, Cytoskeleton and Network Projects.

     

^ To top of page

Year IV

Experiment

Develop clones encoding other domains of chicken fibronectin (e.g., EIIIA, EIIIB) and test quantitatively for effects of expression on patterns of condensations in wing and leg cell cultures. Perform in vivo transfections of limb buds with fibronectin constructs and compare results of perturbations of limb patterns with predictions of comprehensive limb model. Continue chemoattractant screen in chick. Continue pathway mapping in chick.

Simulation

Investigation of continuum limits of Potts model. Integration and continuation of simulation projects. Experimental validation continued. Tool integration continued.

     

^ To top of page

Year V

Experiment	Integration and continuation of experimental projects. Continue chemoattractant screen in chick. Continue pathway mapping in chick.
Simulation	Experimental validation continued. Tool integration continued. Web services accessible through bioinformatics resources. Tutorials and other publications finalized. Prepare for public release of multiscale modeling software.