Plant Metabolic Flux Analysis

1. Application of Metabolic Flux Analysis to Plants

Martine Dieuaide-Noubhani and Ana Paula Alonso

2. Metabolic Network Reconstruction and Their Topological Analysis

Marie Beurton-Aimar, Tung Vu-Ngoc Nguyen, and Sophie Colombié

Part I: Experimental Design and Acquistion of Labeling Data (Experimental design and data acquisition for isotopic labeling based Metabolic Flux Analysis)

3. ¹⁴C pulse Labeling to Estimate External Fluxes and Turnovers in Primary Metabolism

Pianelli Katia, Monier Antoine, Andrieu Marie-Hélène, Beauvoit Bertrand, Dieuaide-Noubhani Martine

4. Optimization of Steady-state ¹³C-labeling Experiments for Metabolic Flux

Analysis

N.J. Kruger, S.K.Masakapalli and R.G. Ratcliffe

5. Quantification of ¹³C Enrichments and Isotopomer Abundances for Metabolic Flux analysis using 1D NMR Spectroscopy

Shyam K. Masakapalli, R. George Ratcliffe, and Thomas C.R. Williams

6. Analysis of Proteinogenic Amino Acid and Starch Labeling by 2D NMR

Quyen Truong and Jacqueline V. Shanks

7. Analysis of Kinetic Labeling of Amino Acids and Organic Acids by GC-MS

Wagner L. Araújo, Takayuki Tohge, Adriano Nunes-Nesi , Toshihiro Obata, and Alisdair R. Fernie

8. Quantifying ¹³C-labeling in Free Sugars and Starch by GC-MS

Mohamed Koubaa, Brigitte Thomasset, and Albrecht Roscher

9. Liquid Chromatography Tandem Mass Spectrometry for Measuring ¹³C-labeling in Intermediates of the Glycolysis and Pentose-phosphate Pathway

Jean-Christophe Cocuron and Ana Paula Alonso²

10. In Vivo NMR for ¹³C metabolic Flux Analysis

Albrecht Roscher, Stéphanie Troufflard, and Abdelghani Idrissi Taghki

Part II: From Labeling Data to Flux Maps(from the labeling data to a metabolic map)

11. Steady State and Instationary Modeling of Proteinogenic and Free Amino Acid Isotopomers for Flux Quantification

Yuting Zheng and Ganesh Sriram

12. Isotopically Nonstationary MFA (INST-MFA) of Autotrophic Metabolism

Lara J. Jazmin, John O'Grady, Fangfang Ma, Doug K. Allen, John A. Morgan, and Jamey D. Young

13. Simulating Labeling to Estimate Kinetic Parameters for Flux Control Analysis

Amy Marshall-Colon, Neelanjan Sengupta, David Rhodes, and John A. Morgan

C. Hart Poskar, Jan Huege, Christian Krach, Yair Shachar-Hill, and Björn H. Junker

Part III: Predicting Fluxes in Plants

15. Analysis of Enzyme Activities

Guillaume Ménard, Benoit Biais, Duyên Prodhomme, Patricia Ballias and Yves Gibon

16. Analytical Kinetic Modeling: A Practical Procedure

Gilles Curien, María L. Cárdenas, and Athel Cornish-Bowden

17. Flux Balance Analysis as an Alternative Method to Estimate Fluxes Without Labeling

Eva Grafahrend-Belau, Astrid Junker, Falk Schreiber, and Björn H. Junker

18. Flux Variability Analysis: Application to Developing Oilseed Rape Embryos using Toolboxes for Constraint-Based Modeling

Jordan O. Hay and Jörg Schwender

19. Plant Genome-Scale Modeling and Implementation

Cristiana G.O. Dal'Molin, Lake-Ee Quek, Robin W. Palfreyman, and Lars K. Nielsen

Part IV: Flux Analysis at the Whole Plant Level

20. ³⁴S and ¹⁵N Labelling to Model S and N Flux in Plants and Determine the Different Components of N and S use Efficiency

Christophe Salon, Marie-Paule Bataillé, Karine Gallardo, Christian Jeudy, Anne-Lise Santoni, Jacques Trouverie, Anne-Sophie Voisin, and Jean-Christophe Avice

21. Ecoph