Description
SPRINGER Plant Systems Biology Methods And Protocols 2Ed (Hb 2022) by LUCAS M.
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. Dedication...Preface...Table of Contents...Contributing Authors...1. Plant Systems Biology: Lessons from TeachingMikael Lucas 2. How to Use the TDCor Algorithm to Infer Gene Regulatory Networks from Time Series Transcriptomic DataJulien Lavenus and Mikael Lucas3. Gene Regulatory Network Investigation Using Ordinary Differential EquationsEtienne Farcot and Nathan Mellor4. Gene Regulatory Network Dynamical Logical Models for Plant DevelopmentJose Davila-Velderrain, Jose Luis Caldu-Primo, Juan Carlos Martinez-Garcia, Elena R. Alvarez-Buylla5. Post-Embryonic Organogenesis in Plants: Experimental Induction of New Shoot and Root OrgansSoazig Guyomarc'h, Mikael Lucas, and Laurent Laplaze6. NanoIndentation, an ImageJ Plugin for the Quantification of Cell MechanicsVincent Mirabet, Nelly Dubrulle, Lea Rambaud, Lena Beauzamy, Mathilde Dumond, Yuchen Long, Pascale Milani, and Arezki Boudaoud7. Introduction to Computational Modeling of Multicellular Tissues Jean-Louis Dinh, Christophe Godin, and Eugenio Azpeitia8. The Virtual Root: Mathematical Modelling of Auxin Transport in the Arabidopsis Root Tip using the Open Source Software SimuPlantHeather Collis, Leah Band, John Fozard, Teodor Ghetiu, Michael Wilson, Nathan Mellor, Malcolm Bennett, and Markus Owen9. Modeling Plant Tissue Development using VirtualLeafClaudiu-Cristi Antonovici, Guacimo Y. Peerdeman, Harold B. Wolff, and Roeland M.H. Merks10. Identifying Developmental Patterns in Structured Plant Phenotyping DataYann Guedon, Yves Caraglio, Christine Granier, Pierre-Eric Lauri, and Bertrand Muller11. 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 ModelsClaude Doussan12. 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 ProfilesAwa Faye, Laurent Laplaze, Bassirou Sine, and Jean-Louis Chopart13. Investigating Soil-Root Interactions with the Numerical Model R-SWMSFelicien 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 Javaux14. How to Define the Appropriate Spatial Resolution of Root Segments When Solving Water Flow in Root System Hydraulic Architectures?Felicien Meunier, Valentin Couvreur, Jan Vanderborght, and Mathieu Javaux15. Simulating Crop Root Systems using OpenSimRootErnst D. Schafer, Markus R. Owen, Johannes Postma, Christian Kuppe, Christopher K. Black, Jonathan P. Lynch16. Future Challenges in Plant Systems BiologyMikael Lucas17. Plant Systems Biology: Further Reading and ResourcesMikael LucasSubject Index List...