Metabolic flux analysis
Subtitle: methods and protocols
By: edited by Jens O. Krömer, Center for Microbial Electrosynthesis (CEMES), Advanced Water Management Centre, The University of Queensland, Brisbane, QLD, Australia, Lars K. Nielsen, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, Australia, Lars M. Blank, Institute of Applied Microbiology, RWTH Aachen University, Aachen, Germany
Series: Methods in molecular biology -- 1191; Springer protocols; Methods in molecular biology (Clifton, N.J.) -- v. 1191.; Springer protocols (Series)
Publisher: Humana Press; Humana
Published: 2014
Place of publication: New York
Language: eng
Number of pages: 316
ISBN-13: 9781493911691; 9781493911707
Copyright date: 2014
Subjects: X.; Methods; Laboratory manuals; Metabolic Engineering; Tissus; Metabolome; Research; Cellules souches; Metabolites; Metabolic Flux Analysis; Régénération; Laboratory Manuals; Systems biology
Description: "This book is dedicated to Metabolic Flux Analysis in systems that can be studied under metabolic steady-state or pseudo-steady-state conditions, also called stationary approaches. Under these conditions the change of intracellular metabolite concentrations ( CMET ) as a function of the stoichiometric matrix S and the flux vector v can be approximated to zero. This approximation converts the equations system from a differential to a linear one and greatly simplifies its solution. We hope that this book will open the field of metabolic flux analysis to a wider scientific community by providing helpful tricks to those who want to start a new flux analysis project but are overwhelmed by the complexity of the approach. We tried to break it up into manageable bits of information that can be implemented step by step following the methods chapters provided. The overview chapters are there to explain the necessary basics to get started and also to review what has been achieved within a few model organisms."--
Notes: Includes bibliographical references and index.
Table of contents: title: PART I.; title: MODELS: STOICHIOMETRY, NETWORK GENERATION -- -- 1.; title: Stoichiometric Modelling of Microbial Metabolism  -- Lars Kuepfer -- 2.; title: Tapping the Wealth of Microbial Data in High-Throughput Metabolic Model Reconstruction  -- Ric Colasanti, Janaka N. Edirisinghe, Tahmineh Khazaei, José P. Faria, Sam Seaver, Fangfang Xia, and Christopher Henry -- PART II.; title: THERMODYNAMICS: A STEP BEYOND MFA -- -- 3.; title: Constraining the Flux Space Using Thermodynamics and Integration of Metabolomics Data  -- Keng Cher Soh and Vassily Hatzimanikatis -- 4.; title: NExT: Integration of Thermodynamic Constraints and Metabolomics Data into a Metabolic Network  -- Verónica Sofía Martínez and Lars K. Nielsen -- PART III.; title: EXPERIMENTS: DESIGN CONSIDERATIONS, FERMENTATION, ANALYTICS -- -- 5.; title: Customization of ¹³C-MFA Strategy According to Cell Culture System  -- Lake-Ee Quek and Lars K. Nielsen -- 6.; title: Quantitative Metabolomics Using ID-MS  -- S. Aljoscha Wahl, Reza Maleki Seifar, Angela ten Pierick, Cor Ras, Jan C. van Dam, Joseph J. Heijnen, and Walter M. van Gulik -- 7.; title: Determining the Biomass Composition of a Sponge Holobiont for Flux Analysis  -- Jabin Watson, Bernard Degnan, Sandie Degnan, and Jens O. Krömer -- 8.; title: Successful Downsizing for High-Throughput ¹³C-MFA Applications  -- Birgitta E. Ebert and Lars M. Blank -- 9.; title: Labelling Analysis for ¹³C MFA Using NMR Spectroscopy  -- Paula Jouhten and Hannu Maaheimo -- 10.; title: GC-MS-Based ¹³C Metabolic Flux Analysis  -- Judith Becker and Christoph Wittmann -- 11.; title: Dynamic Analysis of CO₂ Labeling and Cell Respiration Using Membrane-Inlet Mass Spectrometry  -- Tae Hoon Yang -- PART IV.; title: ¹³C FLUXOMICS DATA PROCESSING -- -- 12.; title: Correction of MS Data for Naturally Occurring Isotopes in Isotope Labelling Experiments  -- Pierre Millard, Fabien Letisse, Serguei Sokol, and Jean-Charles Portais -- 13.; title: Steady-State ¹³C Fluxomics Using OpenFLUX  -- Lake-Ee Quek and Lars K. Nielsen -- 14.; title: Flux Visualization Using VANTED/FluxMap  -- Christian Krach, Astrid Junker, Hendrik Rohn, Falk Schreiber, and Björn H. Junker -- PART V.; title: EXAMPLES -- -- 15.; title: Metabolic Flux Analysis for Escherichia coli by Flux Balance Analysis  -- Yu Matsuoka and Kazuyuki Shimizu -- 16.; title: ¹³C-Metabolic Flux Analysis for Escherichia coli  -- Yu Matsuoka and Kazuyuki Shimizu -- 17.; title: ¹³C-Based Metabolic Flux Analysis of Recombinant Pichia pastoris -- Pau Ferrer and Joan Albiol.