Plant Systems Biology: Methods and Protocols

ISBN-13: 9781071618141 / Angielski / Twarda / 2021 / 386 str.

Mikaël Lucas

Spis treści

Dedication…

Preface…

Table of Contents…

Contributing Authors…

1. Plant Systems Biology: Lessons from Teaching

Mikaël Lucas 

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

Julien Lavenus and Mikaël Lucas

3. Gene Regulatory Network Investigation Using Ordinary Differential Equations

Etienne Farcot and Nathan Mellor

4. Gene Regulatory Network Dynamical Logical Models for Plant Development

Jose Davila-Velderrain, Jose Luis Caldu-Primo, Juan Carlos Martinez-Garcia, Elena R. Alvarez-Buylla

5. Post-Embryonic Organogenesis in Plants: Experimental Induction of New Shoot and Root Organs

Soazig Guyomarc’h, Mikaël Lucas, and Laurent Laplaze

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

Vincent Mirabet, Nelly Dubrulle, Léa Rambaud, Léna Beauzamy, Mathilde Dumond, Yuchen Long, Pascale Milani, and Arezki Boudaoud

7. Introduction to Computational Modeling of Multicellular Tissues 

Jean-Louis Dinh, Christophe Godin, and Eugenio Azpeitia

8. The Virtual Root: Mathematical Modelling of Auxin Transport in the Arabidopsis Root Tip using the Open Source Software SimuPlant

Heather Collis, Leah Band, John Fozard, Teodor Ghetiu, Michael Wilson, Nathan Mellor, Malcolm Bennett, and Markus Owen

9. Modeling Plant Tissue Development using VirtualLeaf

Claudiu-Cristi Antonovici, Guacimo Y. Peerdeman, Harold B. Wolff, and Roeland M.H. Merks

10. Identifying Developmental Patterns in Structured Plant Phenotyping Data

Yann Guédon, Yves Caraglio, Christine Granier, Pierre-Éric Lauri, and Bertrand Muller

11. 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

12. 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, and Jean-Louis Chopart

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

Félicien Meunier, Valentin Couvreur, Xavier Draye, Guillaume Lobet, Katrin Huber, Nathalie Schroerder, Helena Jorda, Axelle Koch, Magdalena Landl, Andrea Schnepf, Jan Vanderborght, Harry Vereecken, and Mathieu Javaux

14. 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, and Mathieu Javaux

15. Simulating Crop Root Systems using OpenSimRoot

Ernst D. Schäfer, Markus R. Owen, Johannes Postma, Christian Kuppe, Christopher K. Black, Jonathan P. Lynch

16. Future Challenges in Plant Systems Biology

Mikaël Lucas

17. Plant Systems Biology: Further Reading and Resources

Mikaël Lucas

Subject Index List…

Blurb

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.