Plant Metabolic Networks (eBook)

Jörg Schwender (Herausgeber)

eBook Download: PDF

2009 | 2009
XII, 339 Seiten
Springer New York (Verlag)
978-0-387-78745-9 (ISBN)

Infos

Plants are the basis for human nutrition and of increasing interest for the chemical industry as a source of chemical feed stocks. Fuels derived from plant biomass will increasingly replace fossil fuels in the future. In order to increase crop productivity, design new plant products, and create new energy crops, there is need for methods of qualitative and quantitative analysis of metabolism which are able to guide the rational re-design of metabolic networks.

In this book, recent advances in qualitative and quantitative analysis of metabolism are summarized to give an overview of the current state of knowledge. Principles of the analysis of network structure, flux analysis, and kinetic modeling are described. Analytical methods necessary to produce the data needed for metabolic flux analysis and for kinetic modeling are described. The analysis of larger metabolic networks is only possible by using computer assistance. Therefore each chapter of the book shall also describe software available for this purpose.

Jörg Schwender received his Ph.D. in Biology in 1999 from the University of Karlsruhe / Germany. He is currently associate scientist in the biology department of Brookhaven National Laboratory, New York, USA. His main research interests are metabolic flux analysis and related approaches of modeling and analysis of metabolic networks in plants.

 

Inhalt

Foreword 5
Preface 7
Contents 8
Contributors 10
Introduction 12
1.1 Why a Book on Plant Metabolic Networks? 12
1.2 Contents of the Book 14
References 17
Definition of Plant Metabolic Networks 19
2.1 Plant Metabolic Networks - More Complex than Anything Else? 19
2.2 Keeping It Simple - Why Unicells Are Cool 20
2.3 Connections Are Everything - Solute Transport and Metabolic Networks 22
2.4 Sticking Together - Metabolons and Metabolic Channeling 29
2.5 Plastids - Plant-Specific Organelles with a Multitude of Functions 32
2.6 Bridging the Divide - Why Genomics, Phylogenetics, Evolution, and Metabolic Networks Belong Together 38
References 39
Metabolite Measurements 49
3.1 Introduction 49
3.2 Technologies for Metabolite Analyses 50
3.3 Data Analysis 63
3.4 Metabolomics Approaches 68
3.5 Application Examples in Plant Sciences 70
3.6 Summary and Future Outlook 74
References 74
Enzyme Kinetics: Theory and Practice 80
4.1 Introduction 80
4.2 Enzyme Kinetics 80
4.3 Measurement of Enzyme Activity 96
4.4 Conclusion 109
References 110
Quantification of Isotope Label 113
5.1 Introduction 113
5.2 Sample Preparation 115
5.3 Nuclear Magnetic Resonance (NMR) 116
5.4 Mass Spectrometry 128
5.5 Concluding Remarks 149
References 150
Data Integration 158
6.1 Introduction 158
6.2 Overcoming the Noise 159
6.3 The Analysis of the Dataset 162
6.4 Bridging Platforms: Correlation-Based Integration of Large Datasets of Different Origin 169
6.5 Entering the Systems Biology Era: The Challenges 173
6.6 Conclusion 174
References 174
Topology of Plant Metabolic Networks 179
7.1 Introduction 179
7.2 Special Properties of Metabolic Networks 183
7.3 Centralities in Metabolic Networks 186
7.4 Motifs in Metabolic Networks 190
7.5 Clustering of Metabolic Networks 196
7.6 Visualization of Metabolic Networks and Experimental Data 201
References 210
Network Stoichiometry 216
8.1 Overview 216
8.2 Stoichiometric Modeling 217
8.3 Flux Balance Analysis 221
8.4 Metabolic Pathway Analysis 235
8.5 Genome-Scale Networks 240
8.6 Future Directions for Stoichiometric Modeling in Plants 244
References 245
Isotopic Steady-State Flux Analysis 249
9.1 Introduction 249
9.2 Overview of 13C-Metabolic Flux Analysis 256
9.3 13C-Labeling Experiments and Steady-State Assumption 259
9.4 Definition of the Biochemical Network 260
9.5 Estimation of Fluxes from Labeling Data 269
9.6 Concluding Remarks 280
References 280
Application of Dynamic Flux Analysis in Plant Metabolic Networks 289
10.1 Introduction 289
10.2 Dynamic Flux Analysis for the Determination of Precursor- Product Relationships in Plants 291
10.3 Examples of Dynamic Flux Analysis of Whole Plant Organs 298
10.4 Advantages and Disadvantages of Dynamic Flux Analysis 304
10.5 Summary and Conclusions 307
References 307
Kinetic Properties of Metabolic Networks 310
11.1 Introduction 310
11.2 Example Model 310
11.3 Metabolic Control Analysis 319
11.4 Software for Dynamic Simulation 322
References 323
Index 326

Produkt-Details

• Erscheint lt. Verlag: 12.6.2009
• Vorwort: Jacqueline V. Shanks
• Zusatzinfo: XII, 339 p.
• Verlagsort: New York
• Sprache: englisch
• Themenwelt: Naturwissenschaften ► Biologie ► Biochemie
• Themenwelt: Naturwissenschaften ► Biologie ► Botanik
• Themenwelt: Technik
• Schlagworte: currentjks • Enzyme • enzymes • Metabolism • Nutrition • Plant • Plant metabolism • plants • plant science
• ISBN-10: 0-387-78745-3 / 0387787453
• ISBN-13: 978-0-387-78745-9 / 9780387787459