Modeling the Growing Plant The Arabidopsis Shoot Apical
Modeling the Growing Plant: The Arabidopsis Shoot Apical Meristem Bruce E. Shapiro Biological Network Modeling Center The Beckman Institute at Caltech bshapiro@caltech. edu www. computableplant. org
• • Some Background Information Fluorescent Probe Confocal Microscopy Arabidopsis Connectivity & Cell Walls form Delaunay and Voronoi • Cell Division and Plant Growth • Phyllotaxis • Cell Differentiation
http: //www. computableplant. org • National Science Foundation (US) Frontiers in Integrative Biological Research (FIBR) Program Grants (First grants: Sept. 2003) – must integrate research tools from across multiple disciplines: biology, math, physical sciences, information technology – not limited by organizational boundaries – must answer a fundamental biological question – 5 year duration, renewable, ≈$1, 000/year – 5± new grants annually
• "To analyze the charms of flowers is like dissecting music; it is one of those things which it is far better to enjoy than to attempt to understand. ” [Henry Tuckerman, 1853] • “The project will track cell-by-cell changes in the mustard plant's meristem - the tissue in which cells actively divide and then differentiate into specialized cells. With fluorescent proteins marking specific cell types in specially designed transgenic plants, researchers will be able to trace the development of leaves and flowers. ” [NSF Press Release, 2003]
Elliot Meyerowitz Marcus Heisler Venu Reddy Adrienne Roeder Vikas Agrawal* Bruce Shapiro Victoria Gor Henrik Jönsson Eric Mjolsness (PI) Pierre Baldi Alex Sadovsky Tigran Bacarian Alexi Vorbyov Ashish Bhan Fang Nikolai Kolchanov Nadya Omelianchuk Nikolay Podkolodny Sergei Nikolaev Vitali Likhoshvai US National Science Foundation FIBR Grant 0330786
. . . to bring together Caltech biologists, bioengineers, mathematicians, and computer scientists to develop and apply state-of-the-art computational tools for modeling and analyzing complex biological systems.
Mjolsness E. Stochastic Process Semantics for Dynamical Grammer Syntax: An Overview. 9 th International Symposium on Artificial Intelligence and Mathematics, Jan 2006. Reddy GV, Meyerowitz EM. Stem-Cell Homeostasis Growth Dynamics can be Uncoupled in the Arabidopsis Shoot Apex. Science 310(5748): 663 -667.
Systems Biology Ontology
• Fluorescent Probe Confocal Microscopy • Arabidopsis • Connectivity & Cell Walls form Delaunay and Voronoi • Cell Division and Plant Growth • Phyllotaxis • Cell Differentiation
Luminescent Jellyfish Aequoria victoria lifesci. ucsb. edu/~biolum www. reefs. org
Luminescent Jellyfish Aequoria victoria Marc Zimmer (Photo: Osamu Shimomura) http: //www. conncoll. edu/ccacad/zimmer/GFP-ww/GFP 2. htm
GFP: Green Fluorescent Protein Marc Zimmer
GFP: Green Fluorescent Protein Neurons J. Lichtman, Science (2003) Commercial Markers www. anticancer. com Transgenic Art Eduardo Kac Nikon’s Microscopyu. com
Fluorescence Microscopy Higher Energy State Internal Energy Loss Intermediate State Sample absorbs high energy photon from laser Photon Emitted Ground State
Laser Scanning Confocal Microscope Zeiss LSM-510 Venu Reddy Marcus Heisler
• Fluorescent Probe Confocal Microscopy • Arabidopsis • Connectivity & Cell Walls form Delaunay and Voronoi • Cell Division and Plant Growth • Phyllotaxis • Cell Differentiation
Shoot Apical Meristem
Geographical distribution of Arabidopsis thaliana. Koornneff, Ann. Rev. Plant Biol. 2004
Live Imaging Cell 88: 299 -308 (1997)
51 image “z-stack”
PIN 1: GFP (blue), REVOLUTA: YFP (green) and p. FIL: ds. RED (red) Marcus Heisler, Caltech
Tracing Cell Lineages Cell 88: 299 -308 (1997) Development 131: 4225 (2004) Reddy et al
Venu Reddy, Caltech
Cell centers: Gradient Descent
Tracking cell motion Thin Plate Splines Softassign
Stress Tensor
Walls. Extracted by Watershed/Voronoi Model PIN 1
Auxin Derived from PIN 1 p. H=5. 0 p. H=4. 5 p. H=5. 5
• Fluorescent Probe Confocal Microscopy • Arabidopsis • Connectivity & Cell Walls form Delaunay and Voronoi • Cell Division and Plant Growth • Phyllotaxis • Cell Differentiation
Cell Walls: Voronoi Model
Cell Connectivity: Delaunay
Raw Data - (x, y, z) cell “centers”
3 D modified Voronoi Cross-section
Slabs Flattened to 2 D, modified Voronoi
Discrete. Math`Computati onal. Geometry`Delaunay Triangulation qdelaunay regtet
• Fluorescent Probe Confocal Microscopy • Arabidopsis • Connectivity & Cell Walls form Delaunay and Voronoi • Cell Division and Plant Growth • Phyllotaxis • Cell Differentiation
Shoot Apical Meristem - tip of plant Central Zone: Provides new cells Flower bud MERISTEM 50 scale bar Peripheral Zone: Leaves, Flower Formation Rib: Cells divide and “push” Meristem up
Protein regulation model Internal External Receptor, c Ligand, b Mjolsness, Sharp & Reinitz J. Theor. Biol. 152: 429 (1991) Shapiro, Levchenko, Mjolsness, Meyerowitz, Wold, Bioinformatics 19(5): 677 (2003)
Growth Model • Constant growth rate: • Cell division on mass threshold • Viscous spring model:
Meristem Maintenance and Growth Mjolsness, Shapiro, Jönnson & Meyerowitz in BGRS, Kluwer (2002); also EMBS (2002)
• Fluorescent Probe Confocal Microscopy • Arabidopsis • Connectivity & Cell Walls form Delaunay and Voronoi • Cell Division and Plant Growth • Phyllotaxis • Cell Differentiation
Phyllotaxis
Auxin - A Plant Hormone Indole-3 -acetic acid Synthesized from tryptophan?
Jönsson, Heisler, Shapiro, Meyerowitz, Mjolsness, PNAS, USA, 103(5): 1633, 2006
• Fluorescent Probe Confocal Microscopy • Arabidopsis • Connectivity & Cell Walls form Delaunay and Voronoi • Cell Division and Plant Growth • Phyllotaxis • Cell Differentiation
Shoot Apical Meristem - tip of plant Central Zone: Provides new cells Flower bud MERISTEM 50 scale bar Peripheral Zone: Leaves, Flower Formation Rib: Cells divide and “push” Meristem up
Cell Division and Differentiation
Activator Model Simulation in Cellerator 270 cells 6402 reactions 1080 ODEs Jönsson, Heisler, Reddy, Agrawal, Gor, Shapiro, Mjolsness, Meyerowitz. Bioinformatics 21(S 1): i 232 -i 240; ISMB 2005
Activator Model
Natural Template
Ablation Experiments Control WUS domain Side view of ablated area After Ablation. No WUS 24 hrs later Two Wus Domains Reinhardt et al. (2003) Development, 130: 4073
Ablated Center
Ablation, random initial conditions
Coming. . . • • • Multiscale models Weighted & Dynamic Delaunay Physics-based cell dynamic model Root & Leaf Models 3 D Simulations on Template Mesh/Finite element simulations
Elliot Meyerowitz Marcus Heisler Venu Reddy Adrienne Roeder Vikas Agrawal* Bruce Shapiro Victoria Gor Henrik Jönsson http: //www. computableplant. org Eric Mjolsness (PI) Pierre Baldi Alex Sadovsky Tigran Bacarian Alexi Vorbyov Ashish Bhan Fang Nikolai Kolchanov Nadya Omelianchuk Nikolay Podkolodny Sergei Nikolaev Vitali Likhoshvai
- Slides: 64