1. 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

2. Some Background Information Fluorescent Probe Confocal Microscopy Arabidopsis Connectivity & Cell Walls form Delaunay and Voronoi Cell Division and Plant Growth Phyllotaxis Cell Differentiation

3. 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, ≈$1,000,000/year –5± new grants annually

4. "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]

5. 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

6. ... 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.

7. Mjolsness E. Stochastic Process Semantics for Dynamical Grammer Syntax: An Overview. 9th 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.

8. Systems Biology Ontology

9. Fluorescent Probe Confocal Microscopy Arabidopsis Connectivity & Cell Walls form Delaunay and Voronoi Cell Division and Plant Growth Phyllotaxis Cell Differentiation

10. lifesci.ucsb.edu/~biolum www.reefs.org Luminescent Jellyfish Aequoria victoria

11. Marc Zimmer (Photo: Osamu Shimomura) http://www.conncoll.edu/ccacad/zimmer/GFP-ww/GFP2.htm

12. Marc Zimmer GFP: Green Fluorescent Protein

13. Commercial Markers www.anticancer.com Transgenic Art Eduardo Kac Neurons J. Lichtman,Science (2003) Nikon’s Microscopyu.com

14. Fluorescence Microscopy Ground State Higher Energy State Internal Energy Loss Photon Emitted Sample absorbs high energy photon from laser Intermediate State

16. Venu Reddy Marcus Heisler Laser Scanning Confocal Microscope Zeiss LSM-510

17. Fluorescent Probe Confocal Microscopy Arabidopsis Connectivity & Cell Walls form Delaunay and Voronoi Cell Division and Plant Growth Phyllotaxis Cell Differentiation

18. Shoot Apical Meristem

19. Geographical distribution of Arabidopsis thaliana. Koornneff, Ann. Rev. Plant Biol. 2004

20. Cell 88:299-308 (1997) Live Imaging

21. 51 image “z-stack”

22. PIN1:GFP (blue), REVOLUTA:YFP (green) and pFIL:dsRED (red) Marcus Heisler, Caltech

23. Cell 88:299-308 (1997) Tracing Cell Lineages Development 131:4225 (2004) Reddy et al

24. Venu Reddy, Caltech

25. Cell centers: Gradient Descent

26. Tracking cell motion Thin Plate Splines Softassign

27. Stress Tensor

28. WallsExtracted by Watershed/Voronoi Model PIN1

29. Auxin Derived from PIN1 pH=5.0 pH=5.5pH=4.5

30. Fluorescent Probe Confocal Microscopy Arabidopsis Connectivity & Cell Walls form Delaunay and Voronoi Cell Division and Plant Growth Phyllotaxis Cell Differentiation

31. Cell Walls: Voronoi Model

32. Cell Connectivity: Delaunay

33. Raw Data - (x, y, z) cell “centers”

39. 3D modified Voronoi Cross-section

40. Slabs Flattened to 2D, modified Voronoi

42. DiscreteMath`Computati onalGeometry`Delaunay Triangulation qdelaunay regtet

43. Fluorescent Probe Confocal Microscopy Arabidopsis Connectivity & Cell Walls form Delaunay and Voronoi Cell Division and Plant Growth Phyllotaxis Cell Differentiation

44. Shoot Apical Meristem - tip of plant Central Zone: Provides new cells Peripheral Zone: Leaves, Flower Formation Rib:Cells divide and “push” Meristem up STEM Flower bud MERISTEM 50  scale bar

45. 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) Protein regulation model

46. Growth Model Constant growth rate: Cell division on mass threshold Viscous spring model:

47. Meristem Maintenance and Growth Mjolsness, Shapiro, Jönnson & Meyerowitz in BGRS, Kluwer (2002); also EMBS (2002)

48. Fluorescent Probe Confocal Microscopy Arabidopsis Connectivity & Cell Walls form Delaunay and Voronoi Cell Division and Plant Growth Phyllotaxis Cell Differentiation

49. Phyllotaxis

50. Auxin - A Plant Hormone Indole-3-acetic acid Synthesized from tryptophan?

51. Jönsson, Heisler, Shapiro, Meyerowitz, Mjolsness, PNAS, USA, 103(5):1633, 2006

54. Fluorescent Probe Confocal Microscopy Arabidopsis Connectivity & Cell Walls form Delaunay and Voronoi Cell Division and Plant Growth Phyllotaxis Cell Differentiation

55. Shoot Apical Meristem - tip of plant Central Zone: Provides new cells Peripheral Zone: Leaves, Flower Formation Rib:Cells divide and “push” Meristem up STEM Flower bud MERISTEM 50  scale bar

56. Cell Division and Differentiation

57. Activator Model Simulation in Cellerator 270 cells 6402 reactions 1080 ODEs Jönsson, Heisler, Reddy, Agrawal, Gor, Shapiro, Mjolsness, Meyerowitz. Bioinformatics 21(S1): i232-i240; ISMB 2005

58. Activator Model

59. Natural Template

60. Ablation Experiments Control WUS domain After Ablation- No WUS 24 hrs later Two Wus Domains Side view of ablated area Reinhardt et al. (2003) Development, 130:4073

61. Ablated Center

62. Ablation, random initial conditions

63. Coming... Multiscale models Weighted & Dynamic Delaunay Physics-based cell dynamic model Root & Leaf Models 3D Simulations on Template Mesh/Finite element simulations

64. 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 http://www.computableplant.org