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Metabolomics: a powerful tool in systems biology ; with 14 tables

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Bibliographische Detailangaben
Format:	Buch
Sprache:	English
Veröffentlicht:	Berlin [u.a.] Springer 2007
Schriftenreihe:	Topics in current genetics 18
Schlagworte:	Metabolom - Biochemische Analyse - Systembiologie - Aufsatzsammlung Biological systems Metabolism Systems Biology Systems biology Systembiologie Biochemische Analyse Metabolom Aufsatzsammlung
Online-Zugang:	Inhaltsverzeichnis
Beschreibung:	XV, 284 S. graph. Darst.
ISBN:	3540747184 9783540747185

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Datensatz im Suchindex

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adam_text	Table of contents The role of metabolomics in systems biology ......................................................1 Jens Nielsen and Michael С. Jewett ...................................................................1 Abstract .........................................................................................................1 1 Metabolomics ............................................................................................. I 2 Applications of metabolomics ....................................................................3 3 The role of metabolomics in systems biology ............................................4 4 Outline of this book ....................................................................................6 References .....................................................................................................8 Analytical methods from the perspective of method standardization ............11 Silas G. Villas-Bôas, Albert Koulman, and Geoffrey A. Lane ........................11 Abstract .......................................................................................................11 1 Introduction ..............................................................................................11 2 Pre-analytical variability ..........................................................................13 2.1 Biological variability ........................................................................13 2.2 Variability introduced during sampling ............................................14 2.3 Variability introduced during sample processing .............................19 3 Intra-analytical variability ........................................................................28 З.ЮС-МЗ ..............................................................................................29 3.2ESI-MS .............................................................................................37 3.3 Conclusions .......................................................................................43 4 Post-analytical issues ................................................................................43 5 Final remarks ............................................................................................44 Acknowledgments .......................................................................................45 References ...................................................................................................45 Abbreviations ..............................................................................................51 Reporting standards ............................................................................................53 Nigel Hardy and Helen Jenkins .......................................................................53 Abstract. .......................................................................................................53 1 Introduction ..............................................................................................53 1.1 Data handling in metabolomics ........................................................54 2 Standards, models, and formats ................................................................56 3 Initiatives in metabolomics data standards ...............................................60 3.1MIAMET ..........................................................................................60 3.2ArMet ................................................................................................61 3.3SMRS ................................................................................................61 3.4 MSI ...................................................................................................62 4 Reporting standards in other fields. ..........................................................62 4.1 Transcriptomics ................................................................................62 4.2 Proteomics ........................................................................................64 VIII Table of contents 5 Cross-domain standards ...........................................................................64 6 Issues in metabolomics standards .............................................................66 6.1 The detailed nature of standards .......................................................66 6.2 Controlled vocabularies and ontologies ............................................68 6.3 Chemical identity ..............................................................................69 7 Conclusions ..............................................................................................70 References ...................................................................................................70 The Golm Metabolome Database: a database for GC-MS based metabolite profiling .............................................................................................75 Jan Hummel, Joachim Selbig, Dirk Walther, and Joachim Корка ..................75 Abstract .......................................................................................................75 1 Introduction ..............................................................................................75 1.1 Pathway databases ............................................................................77 1.2 Cheminformatics databases ..............................................................78 1.3 Databases dedicated to metabolite profiling .....................................79 1.4 The Golm Metabolome Database (GMD) ........................................80 2 Database objects .......................................................................................80 3 Information exchange between databases ................................................81 4 The main work flows of metabolite profiling ...........................................82 4.1 The metabolite profiling work flow: from sample to metabolite fingerprint and profile .............................................................................83 4.2 The metabolite mapping work flow: from metabolite to specific and selective GC-MS mass fragment ......................................................85 5 The main database objects ........................................................................87 5.1 Modelling the MST database object ..............................................87 5.2 Modelling the chemical substance database object .......................88 6 Outlook .....................................................................................................90 References ...................................................................................................91 List of abbreviations ....................................................................................95 Reconstruction of dynamic network models from metabolite measurements ......................................................................................................97 Matthias Reuss, Luciano Aguilera-Vázquez, Klaus Mauch ............................97 Abstract .......................................................................................................97 1 Introduction ..............................................................................................97 2 Quantitative measurements of intracellular metabolites ..........................99 3 Use of metabolite measurements for identification of dynamic models .......................................................................................................103 3.1 Modular decomposition of the network ..........................................103 3.2 In sil ico identification of whole cell metabolite dynamics through evolutionary algorithms and parallel computing .....................118 3.3 Identification of kinetic rate expression from series of steady state observations ..................................................................................122 4. Summary and outlook ...........................................................................123 References .................................................................................................124 Table of contents IX Toward metabolome-based 13C flux analysis: a universal tool for measuring in vivo metabolic activity ................................................................129 Nicola Zamboni .............................................................................................129 Abstract .....................................................................................................129 1 Introduction ............................................................................................129 2 Fundamentals of metabolic flux analysis ...............................................132 3 Principles of labeling experiments .........................................................133 4 Current practice of stationary 13C flux analysis ......................................135 4.1 Experimental design .......................................................................135 4.2 From analytes to 13C labeling patterns ............................................136 4.3 From 13C labeling patterns to fluxes ...............................................138 5 Toward metabolome-based bC flux analysis .........................................144 5.1 Experimental proof-of-concept .......................................................144 5.2 Analytics: lessons from metabolomics ...........................................145 5.3 Current developments .....................................................................147 6 Conclusions ............................................................................................151 Acknowledgements ...................................................................................151 References .................................................................................................151 List of abbreviations ..................................................................................157 Data acquisition, analysis, and mining: Integrative tools for discerning metabolic function in Saccharomyces cerevisiae .............................................159 Michael C. Jewett, Michael A.E. Hansen, and Jens Nielsen ..........................159 Abstract .....................................................................................................159 1 Yeast as a model system for metabolomics ............................................159 2 Metabolite analysis workflow ................................................................161 3 Chemical analysis ...................................................................................162 3.1 Quenching .......................................................................................162 3.2 Extraction ........................................................................................162 3.3 Analytical methods .........................................................................163 3.4 Standardization ...............................................................................165 4 Data analysis ..........................................................................................165 4.1 Pre-processing .................................................................................166 4.2 Statistical analysis ...........................................................................169 4.3 Classification ..................................................................................175 4.4 Genetic programming .....................................................................175 4.5 SpectConnect ..................................................................................176 5 Data integration ......................................................................................177 6 Future outlook ........................................................................................180 Acknowledgements ...................................................................................180 References .................................................................................................180 X Table of contents E. coli metabolomics: capturing the complexity of a simple model ..........189 Martin Robert, Tomoyoshi Soga and Masaru Tornita ...................................189 Abstract..... ................................................................................................189 1 Introduction ............................................................................................189 2 Experimental methods ............................................................................190 2.1 Quenching of metabolism and metabolite extraction ......................191 2.2 Main analytical methods tested with E. coli ...................................193 3.1 Groundwork ....................................................................................198 3.2 Combining concentration data with enzyme activity and flux measurements .......................................................................................201 3.3 Emergingmetabolomic studies ini?, coli....................................... 202 4 Evaluating the size of the E. coli metabolome .......................................203 4.1 Hints from genome-based models ..................................................203 4.2 Experimental clues ..........................................................................203 4.3 Improving metabolite identification ...............................................204 5 Architecture/anatomy of theii. coli metabolome ...................................206 5.1 Metabolite architecture ...................................................................206 5.2 Pathway architecture .......................................................................206 6 E. coli metabolomics as a powerful tool for functional genomics .........207 6.1 Metabolic footprinting ....................................................................208 6.2 Enzyme discovery using non-targeted metabolomics .....................208 6.3 Deorphanizing enzymatic activities and filling-in metabolic pathway holes .......................................................................................212 6.4 Phenotype microarrays as reporters of metabolic phenotype ..........212 7 Metabolomics to facilitate metabolic engineering of E. coli ..................213 8 Metabolomics in flux analysis ................................................................215 9 Adaptive evolution in E. coli, metabolomics, and metabolic phenotype ..................................................................................................215 10 Metabolic models ofE. coli: the role of metabolomics ........................216 11 Databases and resources .......................................................................218 12 Data integration and visualization ........................................................221 13 Future prospects and developments .....................................................222 14 Concluding remarks .............................................................................223 Acknowledgement .....................................................................................223 References .................................................................................................224 Abbreviations ............................................................................................234 The exo-metabolome in filamentous fungi ......................................................235 Ulf Thrane, Birgitte Andersen, Jens C. Frisvad, torn Smedsgaard ................235 Abstract .....................................................................................................235 1 Introduction ............................................................................................235 2 Exo-metabolome and taxonomy.. ...........................................................236 3 Exo-metabolome and fungal growth ......................................................237 4 Visualisation of the exo-metabolome .....................................................239 5 Extraction of the exo-metabolome .........................................................240 Table of contents XI 6 Analysis of the exo-metabolome by high performance liquid chromatography .........................................................................................242 7 Direct infusion electrospray mass spectrometry for profiling ................247 8 Outlook - a polyphasic approach ...........................................................248 Acknowledgements ...................................................................................249 References .................................................................................................249 The importance of anatomy and physiology in plant metabolomics .............253 Ute Roessner and Filomena Pettolino ............................................................253 Abstract .....................................................................................................253 1 Introduction ............................................................................................253 1.1 Importance of plants .......................................................................253 1.2 Plant metabolomics .........................................................................254 2 Plant anatomy .........................................................................................255 2.1 Whole plant anatomy ......................................................................255 2.2 Cell anatomy ...................................................................................256 3 Plant physiology - Challenges for plant metabolomics ..........................260 3.1 Photosynthesis ................................................................................260 3.2 Photorespiration ..............................................................................260 3.3 Transpiration ...................................................................................262 3.4 Starch and other storage products ...................................................262 3.5 Cell wall synthesis ..........................................................................263 3.6 Secondary metabolites ....................................................................266 4 Unique aspects of plant research ............................................................267 4.1 Functional genomics .......................................................................267 4.2 Breeding and QTL analysis ............................................................268 4.3 Genetic engineering ........................................................................270 5 Recent, current and future of plant metabolomics ..................................272 5.1 Successful applications ...................................................................272 6 Future .....................................................................................................274 References .................................................................................................274 Index ...................................................................................................................279
adam_txt	Table of contents The role of metabolomics in systems biology .1 Jens Nielsen and Michael С. Jewett .1 Abstract .1 1 Metabolomics . I 2 Applications of metabolomics .3 3 The role of metabolomics in systems biology .4 4 Outline of this book .6 References .8 Analytical methods from the perspective of method standardization .11 Silas G. Villas-Bôas, Albert Koulman, and Geoffrey A. Lane .11 Abstract .11 1 Introduction .11 2 Pre-analytical variability .13 2.1 Biological variability .13 2.2 Variability introduced during sampling .14 2.3 Variability introduced during sample processing .19 3 Intra-analytical variability .28 З.ЮС-МЗ .29 3.2ESI-MS .37 3.3 Conclusions .43 4 Post-analytical issues .43 5 Final remarks .44 Acknowledgments .45 References .45 Abbreviations .51 Reporting standards .53 Nigel Hardy and Helen Jenkins .53 Abstract. .53 1 Introduction .53 1.1 Data handling in metabolomics .54 2 Standards, models, and formats .56 3 Initiatives in metabolomics data standards .60 3.1MIAMET .60 3.2ArMet .61 3.3SMRS .61 3.4 MSI .62 4 Reporting standards in other fields. .62 4.1 Transcriptomics .62 4.2 Proteomics .64 VIII Table of contents 5 Cross-domain standards .64 6 Issues in metabolomics standards .66 6.1 The detailed nature of standards .66 6.2 Controlled vocabularies and ontologies .68 6.3 Chemical identity .69 7 Conclusions .70 References .70 The Golm Metabolome Database: a database for GC-MS based metabolite profiling .75 Jan Hummel, Joachim Selbig, Dirk Walther, and Joachim Корка .75 Abstract .75 1 Introduction .75 1.1 Pathway databases .77 1.2 Cheminformatics databases .78 1.3 Databases dedicated to metabolite profiling .79 1.4 The Golm Metabolome Database (GMD) .80 2 Database objects .80 3 Information exchange between databases .81 4 The main work flows of metabolite profiling .82 4.1 The metabolite profiling work flow: from sample to metabolite fingerprint and profile .83 4.2 The metabolite mapping work flow: from metabolite to specific and selective GC-MS mass fragment .85 5 The main database objects .87 5.1 Modelling the "MST" database object .87 5.2 Modelling the "chemical substance" database object .88 6 Outlook .90 References .91 List of abbreviations .95 Reconstruction of dynamic network models from metabolite measurements .97 Matthias Reuss, Luciano Aguilera-Vázquez, Klaus Mauch .97 Abstract .97 1 Introduction .97 2 Quantitative measurements of intracellular metabolites .99 3 Use of metabolite measurements for identification of dynamic models .103 3.1 Modular decomposition of the network .103 3.2 In sil ico identification of whole cell metabolite dynamics through evolutionary algorithms and parallel computing .118 3.3 Identification of kinetic rate expression from series of steady state observations .122 4. Summary and outlook .123 References .124 Table of contents IX Toward metabolome-based 13C flux analysis: a universal tool for measuring in vivo metabolic activity .129 Nicola Zamboni .129 Abstract .129 1 Introduction .129 2 Fundamentals of metabolic flux analysis .132 3 Principles of labeling experiments .133 4 Current practice of stationary 13C flux analysis .135 4.1 Experimental design .135 4.2 From analytes to 13C labeling patterns .136 4.3 From 13C labeling patterns to fluxes .138 5 Toward metabolome-based bC flux analysis .144 5.1 Experimental proof-of-concept .144 5.2 Analytics: lessons from metabolomics .145 5.3 Current developments .147 6 Conclusions .151 Acknowledgements .151 References .151 List of abbreviations .157 Data acquisition, analysis, and mining: Integrative tools for discerning metabolic function in Saccharomyces cerevisiae .159 Michael C. Jewett, Michael A.E. Hansen, and Jens Nielsen .159 Abstract .159 1 Yeast as a model system for metabolomics .159 2 Metabolite analysis workflow .161 3 Chemical analysis .162 3.1 Quenching .162 3.2 Extraction .162 3.3 Analytical methods .163 3.4 Standardization .165 4 Data analysis .165 4.1 Pre-processing .166 4.2 Statistical analysis .169 4.3 Classification .175 4.4 Genetic programming .175 4.5 SpectConnect .176 5 Data integration .177 6 Future outlook .180 Acknowledgements .180 References .180 X Table of contents E. coli metabolomics: capturing the complexity of a "simple" model .189 Martin Robert, Tomoyoshi Soga and Masaru Tornita .189 Abstract. .189 1 Introduction .189 2 Experimental methods .190 2.1 Quenching of metabolism and metabolite extraction .191 2.2 Main analytical methods tested with E. coli .193 3.1 Groundwork .198 3.2 Combining concentration data with enzyme activity and flux measurements .201 3.3 Emergingmetabolomic studies ini?, coli. 202 4 Evaluating the size of the E. coli metabolome .203 4.1 Hints from genome-based models .203 4.2 Experimental clues .203 4.3 Improving metabolite identification .204 5 Architecture/anatomy of theii. coli metabolome .206 5.1 Metabolite architecture .206 5.2 Pathway architecture .206 6 E. coli metabolomics as a powerful tool for functional genomics .207 6.1 Metabolic footprinting .208 6.2 Enzyme discovery using non-targeted metabolomics .208 6.3 Deorphanizing enzymatic activities and filling-in metabolic pathway holes .212 6.4 Phenotype microarrays as reporters of metabolic phenotype .212 7 Metabolomics to facilitate metabolic engineering of E. coli .213 8 Metabolomics in flux analysis .215 9 Adaptive evolution in E. coli, metabolomics, and metabolic phenotype .215 10 Metabolic models ofE. coli: the role of metabolomics .216 11 Databases and resources .218 12 Data integration and visualization .221 13 Future prospects and developments .222 14 Concluding remarks .223 Acknowledgement .223 References .224 Abbreviations .234 The exo-metabolome in filamentous fungi .235 Ulf Thrane, Birgitte Andersen, Jens C. Frisvad, torn Smedsgaard .235 Abstract .235 1 Introduction .235 2 Exo-metabolome and taxonomy. .236 3 Exo-metabolome and fungal growth .237 4 Visualisation of the exo-metabolome .239 5 Extraction of the exo-metabolome .240 Table of contents XI 6 Analysis of the exo-metabolome by high performance liquid chromatography .242 7 Direct infusion electrospray mass spectrometry for profiling .247 8 Outlook - a polyphasic approach .248 Acknowledgements .249 References .249 The importance of anatomy and physiology in plant metabolomics .253 Ute Roessner and Filomena Pettolino .253 Abstract .253 1 Introduction .253 1.1 Importance of plants .253 1.2 Plant metabolomics .254 2 Plant anatomy .255 2.1 Whole plant anatomy .255 2.2 Cell anatomy .256 3 Plant physiology - Challenges for plant metabolomics .260 3.1 Photosynthesis .260 3.2 Photorespiration .260 3.3 Transpiration .262 3.4 Starch and other storage products .262 3.5 Cell wall synthesis .263 3.6 Secondary metabolites .266 4 Unique aspects of plant research .267 4.1 Functional genomics .267 4.2 Breeding and QTL analysis .268 4.3 Genetic engineering .270 5 Recent, current and future of plant metabolomics .272 5.1 Successful applications .272 6 Future .274 References .274 Index .279
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physical	XV, 284 S. graph. Darst.
publishDate	2007
publishDateSearch	2007
publishDateSort	2007
publisher	Springer
record_format	marc
series	Topics in current genetics
series2	Topics in current genetics
spelling	Metabolomics a powerful tool in systems biology ; with 14 tables Jens Nielsen ... (eds.) Berlin [u.a.] Springer 2007 XV, 284 S. graph. Darst. txt rdacontent n rdamedia nc rdacarrier Topics in current genetics 18 Metabolom - Biochemische Analyse - Systembiologie - Aufsatzsammlung Biological systems Metabolism Systems Biology Systems biology Systembiologie (DE-588)4809615-5 gnd rswk-swf Biochemische Analyse (DE-588)4255721-5 gnd rswk-swf Metabolom (DE-588)4807318-0 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content Metabolom (DE-588)4807318-0 s Biochemische Analyse (DE-588)4255721-5 s Systembiologie (DE-588)4809615-5 s DE-604 Nielsen, Jens Sonstige oth Erscheint auch als Online-Ausgabe 978-3-540-74719-2 Topics in current genetics 18 (DE-604)BV035420113 18 Digitalisierung UB Regensburg application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016657290&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis
spellingShingle	Metabolomics a powerful tool in systems biology ; with 14 tables Topics in current genetics Metabolom - Biochemische Analyse - Systembiologie - Aufsatzsammlung Biological systems Metabolism Systems Biology Systems biology Systembiologie (DE-588)4809615-5 gnd Biochemische Analyse (DE-588)4255721-5 gnd Metabolom (DE-588)4807318-0 gnd
subject_GND	(DE-588)4809615-5 (DE-588)4255721-5 (DE-588)4807318-0 (DE-588)4143413-4
title	Metabolomics a powerful tool in systems biology ; with 14 tables
title_auth	Metabolomics a powerful tool in systems biology ; with 14 tables
title_exact_search	Metabolomics a powerful tool in systems biology ; with 14 tables
title_exact_search_txtP	Metabolomics a powerful tool in systems biology ; with 14 tables
title_full	Metabolomics a powerful tool in systems biology ; with 14 tables Jens Nielsen ... (eds.)
title_fullStr	Metabolomics a powerful tool in systems biology ; with 14 tables Jens Nielsen ... (eds.)
title_full_unstemmed	Metabolomics a powerful tool in systems biology ; with 14 tables Jens Nielsen ... (eds.)
title_short	Metabolomics
title_sort	metabolomics a powerful tool in systems biology with 14 tables
title_sub	a powerful tool in systems biology ; with 14 tables
topic	Metabolom - Biochemische Analyse - Systembiologie - Aufsatzsammlung Biological systems Metabolism Systems Biology Systems biology Systembiologie (DE-588)4809615-5 gnd Biochemische Analyse (DE-588)4255721-5 gnd Metabolom (DE-588)4807318-0 gnd
topic_facet	Metabolom - Biochemische Analyse - Systembiologie - Aufsatzsammlung Biological systems Metabolism Systems Biology Systems biology Systembiologie Biochemische Analyse Metabolom Aufsatzsammlung
url	http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016657290&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA
volume_link	(DE-604)BV035420113
work_keys_str_mv	AT nielsenjens metabolomicsapowerfultoolinsystemsbiologywith14tables

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