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Plant Systems Biology

Methods and Protocols

  • Book
  • © 2022

Overview

Editors:
  1. Mikaël Lucas

    1. DIADE, Univ Montpellier, IRD,, CIRAD, Montpellier, France

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  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 2395)

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Table of contents (17 protocols)

  1. Front Matter

    Pages i-xiii
    Download chapter PDF

  2. Plant Systems Biology : Lessons from Teaching

    • Mikaël Lucas
    Pages 1-12

  3. How to Use the TDCor Algorithm to Infer Gene Regulatory Networks from Time Series Transcriptomic Data

    • Julien Lavenus, Mikaël Lucas
    Pages 13-31

  4. Gene Regulatory Network Investigation Using Ordinary Differential Equations

    • Etienne Farcot, Nathan Mellor
    Pages 33-58

  5. Gene Regulatory Network Dynamical Logical Models for Plant Development

    • José Dávila-Velderrain, José Luis Caldú-Primo, Juan Carlos Martínez-García, María Elena Álvarez-Buylla Roces
    Pages 59-77

  6. Postembryonic Organogenesis in Plants: Experimental Induction of New Shoot and Root Organs

    • Soazig Guyomarc’h, Mikaël Lucas, Laurent Laplaze
    Pages 79-95

  7. NanoIndentation, an ImageJ Plugin for the Quantification of Cell Mechanics

    • Vincent Mirabet, Nelly Dubrulle, Léa Rambaud, Léna Beauzamy, Mathilde Dumond, Yuchen Long et al.
    Pages 97-106

  8. Introduction to Computational Modeling of Multicellular Tissues

    • Jean-Louis Dinh, Christophe Godin, Eugenio Azpeitia
    Pages 107-145

  9. The Virtual Root : Mathematical Modeling of Auxin Transport in the Arabidopsis Root Tip Using the Open-Source Software SimuPlant

    • Heather Collis, Leah R. Band, John A. Fozard, Teodor Ghetiu, Michael H. Wilson, Nathan L. Mellor et al.
    Pages 147-164

  10. Modeling Plant Tissue Development Using VirtualLeaf

    • Claudiu-Cristi Antonovici, Guacimo Y. Peerdeman, Harold B. Wolff, Roeland M. H. Merks
    Pages 165-198

  11. Identifying Developmental Patterns in Structured Plant Phenotyping Data

    • Yann Guédon, Yves Caraglio, Christine Granier, Pierre-Éric Lauri, Bertrand Muller
    Pages 199-225

  12. Putting Plant Roots at Light: Temporal Imaging of Plant Roots and Soil Water with a Light Transmission Technique for Linking Water and Root Observations to Soil–Plant Models

    • Claude Doussan
    Pages 227-246

  13. RACINE2.2: A Software Application for Processing and Mapping Spatial Distribution of Root Length Density and Potential Root Extraction Ratio from Root Counts on Trench Profiles

    • Awa Faye, Laurent Laplaze, Bassirou Sine, Jean-Louis Chopart
    Pages 247-258

  14. Investigating Soil–Root Interactions with the Numerical Model R-SWMS

    • Félicien Meunier, Valentin Couvreur, Xavier Draye, Guillaume Lobet, Katrin Huber, Nathalie Schroeder et al.
    Pages 259-283

  15. How to Define the Appropriate Spatial Resolution of Root Segments When Solving Water Flow in Root System Hydraulic Architectures

    • Félicien Meunier, Valentin Couvreur, Jan Vanderborght, Mathieu Javaux
    Pages 285-291

  16. Simulating Crop Root Systems Using OpenSimRoot

    • Ernst D. Schäfer, Markus R. Owen, Johannes A. Postma, Christian Kuppe, Christopher K. Black, Jonathan P. Lynch
    Pages 293-323

  17. Future Challenges in Plant Systems Biology

    • Mikaël Lucas
    Pages 325-337

  18. Plant Systems Biology: Further Reading and Resources

    • Mikaël Lucas
    Pages 339-346

  19. Back Matter

    Pages 347-348
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Keywords

About this book

This second edition volume expands on the previous edition with an update on the latest techniques used to study plant systems biology on three specific scales: the molecular level, the tissue level, and the whole plant. Chapters cover topics such as gene regulatory network inference and dynamic modeling using ordinary differential equations or Boolean formalisms; protocols for at-will induction of plant aerial or root organs, or quantification of tissue mechanical properties; mathematical modeling of plant tissue using SimuPlant or VirtualLeaf; and simulating crop root systems using OpenSimRoot or R-SWMS. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, step-by-step, readily reproducible laboratory protocols or software tutorials, and tips on troubleshooting and avoiding known pitfalls. 

Comprehensive and cutting-edge, Plants Systems Biology: Methods and Protocols, Second Edition is a valuable resource for plant biologists looking for different approaches to finding solutions to their questions and generating new ideas, as well as for students who desire to discover the field of plant systems biology. 


Editors and Affiliations

  • DIADE, Univ Montpellier, IRD,, CIRAD, Montpellier, France

    Mikaël Lucas

Bibliographic Information

  • Book Title: Plant Systems Biology

  • Book Subtitle: Methods and Protocols

  • Editors: Mikaël Lucas

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-1816-5

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2022

  • Hardcover ISBN: 978-1-0716-1814-1Published: 26 November 2021

  • eBook ISBN: 978-1-0716-1816-5Published: 25 November 2021

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 2

  • Number of Pages: XIII, 348

  • Number of Illustrations: 6 b/w illustrations, 67 illustrations in colour

  • Topics: Plant Sciences

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