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Metabolomics: A Powerful Tool in Systems Biology 2007 ed. [Hardback]

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  • Formāts: Hardback, 284 pages, height x width: 235x155 mm, weight: 623 g, 13 Illustrations, color; 40 Illustrations, black and white; XVI, 284 p. 53 illus., 13 illus. in color., 1 Hardback
  • Sērija : Topics in Current Genetics 18
  • Izdošanas datums: 26-Oct-2007
  • Izdevniecība: Springer-Verlag Berlin and Heidelberg GmbH & Co. K
  • ISBN-10: 3540747184
  • ISBN-13: 9783540747185
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  • Formāts: Hardback, 284 pages, height x width: 235x155 mm, weight: 623 g, 13 Illustrations, color; 40 Illustrations, black and white; XVI, 284 p. 53 illus., 13 illus. in color., 1 Hardback
  • Sērija : Topics in Current Genetics 18
  • Izdošanas datums: 26-Oct-2007
  • Izdevniecība: Springer-Verlag Berlin and Heidelberg GmbH & Co. K
  • ISBN-10: 3540747184
  • ISBN-13: 9783540747185
Citas grāmatas par šo tēmu:
Giving a fresh, substantial and in-depth overview of the topic, this book brings together the latest results in the field of metabolomics. It comprehensively presents the current state of the metabolomics field by underscoring experimental methods, analysis techniques, standardization practices, and advances in specific model systems. As a result, it helps to significantly broaden our perspective on the principles and strategies underpinning this emerging field.

The metabolome comprises the complete set of metabolites, the non-genetically encoded substrates, intermediates, and products of metabolic pathways, associated with a cell. Given the increasing demand to quantitatively identify the metabolome and understand how trafficking of metabolites through the metabolic network impact cellular behavior, metabolomics has emerged as an important complementary technology to the cell-wide measurements of mRNA, proteins, fluxes, and interactions (e.g., protein-DNA). Metabolomics is already a powerful tool in drug discovery and development and in metabolic engineering. While maintaining these strengths, the field promises to play a heightened role in systems biology research, which is transforming the practice of medicine and our ability to engineer living organisms. This book brings together the latest results in the field of metabolomics. It comprehensively presents the current state of the metabolomics field by underscoring experimental methods, analysis techniques, standardization practices, and advances in specific model systems. As a result, it significantly broadens our perspective on the principles and strategies underpinning this emerging field.
The role of metabolomics in systems biology
1(10)
Jens Nielsen
Michael C. Jewett
Abstract
1(1)
Metabolomics
1(2)
Applications of metabolomics
3(1)
The role of metabolomics in systems biology
4(2)
Outline of this book
6(5)
References
8(3)
Analytical methods from the perspective of method standardization
11(42)
Silas G. Villas-Boas
Albert Koulman
Geoffrey A. Lane
Abstract
11(1)
Introduction
11(2)
Pre-analytical variability
13(15)
Biological variability
13(1)
Variability introduced during sampling
14(5)
Variability introduced during sample processing
19(9)
Intra-analytical variability
28(15)
GC-MS
29(8)
ESI-MS
37(6)
Conclusions
43(1)
Post-analytical issues
43(1)
Final remarks
44(9)
Acknowledgments
45(1)
References
45(6)
Abbreviations
51(2)
Reporting standards
53(22)
Nigel Hardy
Helen Jenkins
Abstract
53(1)
Introduction
53(3)
Data handling in metabolomics
54(2)
Standards, models, and formats
56(4)
Initiatives in metabolomics data standards
60(2)
MIAMET
60(1)
ArMet
61(1)
SMRS
61(1)
MSI
62(1)
Reporting standards in other fields
62(2)
Transcriptomics
62(2)
Proteomics
64(1)
Cross-domain standards
64(2)
Issues in metabolomics standards
66(4)
The detailed nature of standards
66(2)
Controlled vocabularies and ontologies
68(1)
Chemical identity
69(1)
Conclusions
70(5)
References
70(5)
The Golm Metabolome Database: a database for GC-MS based metabolite profiling
75(22)
Jan Hummel
Joachim Selbig
Dirk Walther
Joachim Kopka
Abstract
75(1)
Introduction
75(5)
Pathway databases
77(1)
Cheminformatics databases
78(1)
Databases dedicated to metabolite profiling
79(1)
The Golm Metabolome Database (GMD)
80(1)
Database objects
80(1)
Information exchange between databases
81(1)
The main work flows of metabolite profiling
82(5)
The metabolite profiling work flow: from sample to metabolite fingerprint and profile
83(2)
The metabolite mapping work flow: from metabolite to specific and selective GC-MS mass fragment
85(2)
The main database objects
87(3)
Modelling the ``MST'' database object
87(1)
Modelling the ``chemical substance'' database object
88(2)
Outlook
90(7)
References
91(4)
List of abbreviations
95(2)
Reconstruction of dynamic network models from metabolite measurements
97(32)
Matthias Reuss
Luciano Aguilera-Vazquez
Klaus Mauch
Abstract
97(1)
Introduction
97(2)
Quantitative measurements of intracellular metabolites
99(4)
Use of metabolite measurements for identification of dynamic models
103(20)
Modular decomposition of the network
103(15)
In silico identification of whole cell metabolite dynamics through evolutionary algorithms and parallel computing
118(4)
Identification of kinetic rate expression from series of steady state observations
122(1)
Summary and outlook
123(6)
References
124(5)
Toward metabolome-based 13C flux analysis: a universal tool for measuring in vivo metabolic activity
129(30)
Nicola Zamboni
Abstract
129(1)
Introduction
129(3)
Fundamentals of metabolic flux analysis
132(1)
Principles of labeling experiments
133(2)
Current practice of stationary 13C flux analysis
135(9)
Experimental design
135(1)
From analytes to 13C labeling patterns
136(2)
From 13C labeling patterns to fluxes
138(6)
Toward metabolome-based 13C flux analysis
144(7)
Experimental proof-of-concept
144(1)
Analytics: lessons from metabolomics
145(2)
Current developments
147(4)
Conclusions
151(8)
Acknowledgements
151(1)
References
151(6)
List of abbreviations
157(2)
Data acquisition, analysis, and mining: Integrative tools for discerning metabolic function in Saccharomyces cerevisiae
159(30)
Michael C. Jewett
Michael A.E. Hansen
Jens Nielsen
Abstract
159(1)
Yeast as a model system for metabolomics
159(2)
Metabolite analysis workflow
161(1)
Chemical analysis
162(3)
Quenching
162(1)
Extraction
162(1)
Analytical methods
163(2)
Standardization
165(1)
Data analysis
165(12)
Pre-processing
166(3)
Statistical analysis
169(6)
Classification
175(1)
Genetic programming
175(1)
SpectConnect
176(1)
Data integration
177(3)
Future outlook
180(9)
Acknowledgements
180(1)
References
180(9)
E. coli metabolomics: capturing the complexity of a ``simple'' model
189(46)
Martin Robert
Tomoyoshi Soga
Masaru Tomita
Abstract
189(1)
Introduction
189(1)
Experimental methods
190(13)
Quenching of metabolism and metabolite extraction
191(2)
Main analytical methods tested with E. coli
193(5)
Groundwork
198(3)
Combining concentration data with enzyme activity and flux measurements
201(1)
Emerging metabolomic studies in E. coli
202(1)
Evaluating the size of the E. coli metabolome
203(3)
Hints from genome-based models
203(1)
Experimental clues
203(1)
Improving metabolite identification
204(2)
Architecture/anatomy of the E. coli metabolome
206(1)
Metabolite architecture
206(1)
Pathway architecture
206(1)
E. coli metabolomics as a powerful tool for functional genomics
207(6)
Metabolic footprinting
208(1)
Enzyme discovery using non-targeted metabolomics
208(4)
Deorphanizing enzymatic activities and filling-in metabolic pathway holes
212(1)
Phenotype microarrays as reporters of metabolic phenotype
212(1)
Metabolomics to facilitate metabolic engineering of E. coli
213(2)
Metabolomics in flux analysis
215(1)
Adaptive evolution in E. coli, metabolomics, and metabolic phenotype
215(1)
Metabolic models of E. coli: the role of metabolomics
216(2)
Databases and resources
218(3)
Data integration and visualization
221(1)
Future prospects and developments
222(1)
Concluding remarks
223(12)
Acknowledgement
223(1)
References
224(10)
Abbreviations
234(1)
The exo-metabolome in filamentous fungi
235(18)
Ulf Thrane
Birgitte Andersen
Jens C. Frisvad
Jørn Smedsgaard
Abstract
235(1)
Introduction
235(1)
Exo-metabolome and taxonomy
236(1)
Exo-metabolome and fungal growth
237(2)
Visualisation of the exo-metabolome
239(1)
Extraction of the exo-metabolome
240(2)
Analysis of the exo-metabolome by high performance liquid chromatography
242(5)
Direct infusion electrospray mass spectrometry for profiling
247(1)
Outlook - a polyphasic approach
248(5)
Acknowledgements
249(1)
References
249(4)
The importance of anatomy and physiology in plant metabolomics
253(26)
Ute Roessner
Filomena Pettolino
Abstract
253(1)
Introduction
253(2)
Importance of plants
253(1)
Plant metabolomics
254(1)
Plant anatomy
255(5)
Whole plant anatomy
255(1)
Cell anatomy
256(4)
Plant physiology - Challenges for plant metabolomics
260(7)
Photosynthesis
260(1)
Photorespiration
260(2)
Transpiration
262(1)
Starch and other storage products
262(1)
Cell wall synthesis
263(3)
Secondary metabolites
266(1)
Unique aspects of plant research
267(5)
Functional genomics
267(1)
Breeding and QTL analysis
268(2)
Genetic engineering
270(2)
Recent, current and future of plant metabolomics
272(2)
Successful applications
272(2)
Future
274(5)
References
274(5)
Index 279