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The Computable Plant

The Computable Plant. Claire Schulkey Kiri Hamaker. California Institute of Technology Dr. Bruce E. Shapiro. Overview. What are the shoot apical meristem (SAM) and auxin? What is our project? How does our project involve the SAM and auxin?

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The Computable Plant

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  1. The Computable Plant Claire Schulkey Kiri Hamaker California Institute of Technology Dr. Bruce E. Shapiro

  2. Overview • What are the shoot apical meristem (SAM) and auxin? • What is our project? • How does our project involve the SAM and auxin? • How are we going to make an auxin transport model?

  3. Shoot Apical Meristem (SAM) The SAM is a bunching of plant stem cells at the very tip of a plant stem. The SAM is at a dynamic equilibrium, maintaining a stock of stem cells while allowing other cells to differentiate into specific plant tissues. A SAM and forming leaf primordia http://www.science.siu.edu/landplants/Lycophyta/lycophyta.html

  4. Auxin Auxin is a signaling hormone in plants believed to influence a variety of a plant’s physiological processes though regulation of gene expression. Indole-3-acetic acid (IAA), the most prevalent auxin in plant growth Image released to public domain by author, and modified by C. Schulkey

  5. Project Overview • Create a working model of how auxin is transported throughout a network of cells. • This model represents a 2-D slice of the SAM in the L1 layer with chemical reactions denoted by differential equations with robust initial conditions, formulated by the xCellerator plugin in Mathematica. Image released to public domain by author, and modified by Kiri Hamaker

  6. A long term project whose encompassing goal is to determine: How genetic makeup and environment affect developmental processes involved in forming tissue and organs in undifferentiated cells. This project has implications in forefront biomathematics, systems biology, and microbiological imaging and has played a part in key development of revolutionary tools in the field. The Computable Plant Image released to public domain by author

  7. SBML (Systems Biology Markup Language) Tools • xCellerator • Mathematica

  8. SBML • Low-level computer-readable format • Created for modeling microbiological pathways • Users employ high-level tools to interface with SBML • In Mathematica, we use a specific form of SBML created by Dr. Shapiro: MathSBML Sample code taken from basic model definition handbook: Systems Biology Markup Language (SBML) Level 1: Structures and Facilities for Basic Model Definitions, Michael Hucka, Andrew Finney, Herbert Sauro, Hamid Bolouri, http://sbml.org/specifications/sbml-level-1/version-2/html/sbml-level-1.html

  9. xCellerator • User-friendly Mathematica package • Accepts inputs into chemical reactions selectable through an organized xCellerator palette • xCellerator translates chemical reactions into sets of ordinary differential equations Mathematica can use • xCellerator package functions with multiple plugins for employing sets of ODEs to create models as desired, including: • MathSBML – interprets/edits SBML • Cellzilla – creates/manipulates cell networks • Qhull – supports coordinate modeling in 2D, 3D, and further dimensions

  10. Mathematica • Powerful and flexible mathematical computing software • Main framework for computing lists of differential equations generated by xCellerator

  11. Determine the important processes influencing auxin transport and Aux/IAA regulation Create a model for a single cell Expand the single cell model to a network Project Stepping Stones

  12. Auxin Influx/Efflux Proteins PIN1, AUX1 (EIR1?, AXR4?) These auxin transport proteins, with passive diffusion, move auxin into and out of a cell. Proteins and genes involved in Aux/IAA protein pathway ARF, auxin response factor Active/inactive Aux/IAA gene Proteasomal degredation Charged and uncharged auxin Step 1: Process Selection

  13. Step 2: Model a single cell Simple Overview

  14. Step 2: Model a single cell

  15. Step 3: A network of cells (future work) The model can then be expanded to encompass a number of cells to model the flow of auxin in a network. Visual representations of the auxin flow may be created for more complete understanding of the model’s implications. Image taken from wild-type Wuschel activity simulation: Jönsson, Henrik et. al. Modeling the organization of the WUSCHEL expression domain in the shoot apical meristem. Bioinformatics 21(S1):i232-i240 (July 2005).

  16. Acknowledgements • Dr. Bruce E. Shapiro • Biological Network Modeling Center (BNMC) • The Computable Plant Team • SoCalBSI mentors and students Special Thanks to: NIH NSF Los Angeles – Orange County Biotechnology Center

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