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Stage VII: Computational modelling of plant hormone transport.

▶️ Try the Virtual Root — our open, interactive rebuild of SimuPlant

The original SimuPlant desktop tool went offline, so we rebuilt its core as a free, browser-based simulator. Move the sliders to watch auxin self-organise into a maximum at the root tip, and toggle gravitropism to see auxin redistribute to the lower side — the first step of root bending.

🌱 Open the Virtual Root simulator →  ·  source code & model spec

The Virtual Root simulator

This is a two-compartment (cell + cell-wall) model of polar auxin transport with PIN efflux and AUX1 influx carriers, after Grieneisen et al. 2007 and Band et al. 2014. It reproduces the auxin maximum at the quiescent centre. See the repository for the equations, parameters, and an honest list of its current limitations.

Root Tissue and Gravity Perception

Introduction

Root tissues are vital components of a plant, responsible for numerous functions including anchorage, absorption of water and nutrients, and storage of food. Understanding the structure and function of root tissues is fundamental to grasping how plants interact with their environment, particularly in response to gravity, a phenomenon known as gravitropism.

Anatomy of Root Tissue

It is important to understand the anatomy of Root tissues and how they are organized into several layers, each with distinct roles:

  1. Epidermis
  2. The outermost layer providing protection.
  3. Absorbs water and nutrients from the soil.
  4. Cortex
  5. Located just beneath the epidermis.
  6. Facilitates storage and transport of nutrients and water.
  7. Endodermis
  8. Acts as a selective barrier controlling the flow of substances into the vascular system.
  9. Pericycle
  10. Initiates the growth of lateral roots.
  11. Vascular Tissue (Xylem and Phloem)
  12. Xylem transports water and dissolved minerals from roots to shoots.
  13. Phloem distributes sugars and organic nutrients from shoots to roots.

Gravity Perception in Roots

Gravitropism: Gravitropism, the growth response of plants to gravity, is critical for proper root development. Roots grow downward (positive gravitropism) to anchor the plant and access deeper water sources.

Mechanism of Gravity Perception

  • Amyloplasts: Specialized plastids in root cap cells that act as gravity sensors.
  • Contain dense starch grains that settle within the cell under the influence of gravity.
  • Their movement triggers a signaling pathway modifying the distribution of growth hormones like auxins.
  • Auxins: Hormones regulating cell elongation.
  • Redistribution of auxins to the lower side of the root inhibits cell elongation on that side.
  • This causes the root to bend downward, orienting its growth in the direction of gravity.

Platform Compatibility

The SimuPlant hormone modeling tool is available for both MaxOS and Windows OS users. This ensures that a wide range of users can benefit from its powerful features and tools, regardless of their operating system preference.

Download Instructions

To get started with SimuPlant, follow these steps:

  1. Visit the Official Website: SimuPlant Download Page (offline — site no longer available)
  2. Select Your Operating System: Choose either the MacOS or Windows OS option to ensure compatibility with your device.
  3. Download the Installer: Click on the download button to get the installer file for SimuPlant.

Installation Instructions

After downloading the installer, follow these steps to install SimuPlant on your computer:

  1. Locate the Downloaded File: Find the downloaded installer file on your computer. It is usually located in the "Downloads" folder unless you specified a different location.
  2. Run the Installer:
  3. MacOS Users: Open the .dmg file and drag the SimuPlant application to your Applications folder.
  4. Windows Users: Run the .exe file and follow the on-screen instructions to complete the installation.
  5. Launch SimuPlant: Once installation is complete, you can start using SimuPlant by opening the application from your Applications folder (MacOS) or Start Menu (Windows).

Additional Resources

For more information on how to use SimuPlant and take full advantage of its features, refer to the user manual and tutorials available on the official website.

SimuPlant User Manual (offline)\ SimuPlant Tutorials (offline)

By following these instructions, you will be able to download, install, and begin using the SimuPlant hormone modelling tool on your MacOS or Windows OS computer. If you encounter any issues during the process, consult the troubleshooting section in the user manual or reach out to the support team via the contact information provided on the SimuPlant website. Happy modeling! (Note: the SimuPlant website is no longer online.)

Observational and Data Collection Protocol

Observation

  • Record notes on the Auxin distribution in the different modeles you create
  • Change the model specification
  • Save the time lapse videos of the simulated visualizations
  • Save the simulated output data
  • Save the simulation parameters
  • Make a slideshow and report discussing your models predictions.
  • More information about the model can be found here

Summary and Application Discussion

Follow Up Inquiry:

  • Based on the observations made during this study, what conclusions can be made about the movement of auxin in root tips of plants?
  • Do you think this will influence roots growth?
  • Justify your previous answer?
  • How would this change in the environment such as the absence of gravity effect auxin distribution in the root?

Expansion:

  • Based on these observations, what directions do plants grow towards? (stems, leaves)
  • How can this idea be tested?

STAGE VI: Preparations to be Conducted Prior to Starting Plant Hormone Modeling

  • Literature Review
  • Conduct an extensive literature review to understand existing models and methodologies.
  • Compile recent research papers, review articles, and case studies relevant to plant hormone modeling.
  • Identify Objectives
  • Clearly define the objectives of the modeling study.
  • Determine specific questions you aim to answer through the model.
  • Select Hormones
  • Identify the specific plant hormones to be included in the model (e.g., auxins, gibberellins, cytokinins, abscisic acid, ethylene).
  • Understand the roles and interactions of selected hormones.
  • Gather Data
  • Collect quantitative and qualitative data on hormone levels, environmental factors, and plant responses.
  • Ensure data accuracy and relevance for effective modeling.
  • Choose Modeling Approach
  • Decide on the type of model (e.g., mathematical, computational, statistical).
  • Evaluate the pros and cons of different modeling approaches.
  • Software and Tools
  • Select appropriate software and tools required for the modeling process.
  • Ensure familiarity with the chosen software (e.g., MATLAB, R, Python).
  • Parameter Estimation
  • Identify key parameters that will influence the model.
  • Develop methods for estimating these parameters accurately.
  • Initial Conditions and Assumptions
  • Define initial conditions of the model and the biological system.
  • List and justify any assumptions made during the modeling process.
  • Develop Hypotheses
  • Formulate hypotheses regarding plant hormone dynamics and interactions.
  • Align these hypotheses with the overall objectives of the study.
  • Collaboration and Consultation
  • Consult with experts in plant physiology, biochemistry, and computational biology.
  • Collaborate with interdisciplinary teams to gain diverse insights and expertise.
  • Plan Validation
  • Develop a plan for validating the model.
  • Identify experimental data and real-world scenarios to test model predictions.
  • Risk Assessment
  • Assess potential risks and limitations associated with the modeling project.
  • Develop contingency plans to address these risks.
  • Documentation
  • Document all preparatory steps, assumptions, and methodologies.
  • Maintain a clear and comprehensive record to facilitate future reference and reproducibility.
  • Timeline and Milestones
  • Establish a clear timeline with specific milestones for each phase of the project.
  • Track progress systematically to ensure timely completion of the model.