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Metabolic Flux Analysis in Eukaryotic Cells

Methods and Protocols

  • Book
  • © 2020

Overview

Editors:
  1. Deepak Nagrath

    1. Department of Biomedical Engineering, University of Michigan, Ann Arbor, USA

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  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 2088)

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Table of contents (17 protocols)

  1. Front Matter

    Pages i-xiii
    Download chapter PDF

  2. Determination of Isotopologue and Tandem Mass Isotopologue Ratios Using Gas Chromatography Chemical Ionization Time of Flight Mass Spectrometry - Methodology and Uncertainty of Measurement

    • Teresa Mairinger, Stephen Hann
    Pages 1-16

  3. Non-Targeted Mass Isotopolome Analysis Using Stable Isotope Patterns to Identify Metabolic Changes

    • Christian-Alexander Dudek, Lisa Schlicker, Karsten Hiller
    Pages 17-32

  4. Liquid Chromatography Methods for Separation of Polar and Charged Intracellular Metabolites for 13C Metabolic Flux Analysis

    • Damini Jaiswal, Anjali Mittal, Deepak Nagrath, Pramod P. Wangikar
    Pages 33-50

  5. Deuterium Tracing to Interrogate Compartment-Specific NAD(P)H Metabolism in Cultured Mammalian Cells

    • Esther W. Lim, Seth J. Parker, Christian M. Metallo
    Pages 51-71

  6. Large-Scale Profiling of Cellular Metabolic Activities Using Deep 13C Labeling Medium

    • Nina Grankvist, Jeramie D. Watrous, Mohit Jain, Roland Nilsson
    Pages 73-92

  7. Analyzing the Metabolism of Metastases in Mice

    • Patricia Altea-Manzano, Dorien Broekaert, João A. G. Duarte, Juan Fernández-García, Mélanie Planque, Sarah-Maria Fendt
    Pages 93-118

  8. Robust Analytical Methods for the Accurate Quantification of the Total Biomass Composition of Mammalian Cells

    • Diana Széliová, Harald Schoeny, Å pela Knez, Christina Troyer, Cristina Coman, Evelyn Rampler et al.
    Pages 119-160

  9. Quantifying Nitric Oxide Flux Distributions

    • Darshan M. Sivaloganathan, Xuanqing Wan, Mark P. Brynildsen
    Pages 161-188

  10. SWATH: A Data-Independent Tandem Mass Spectrometry Method to Quantify 13C Enrichment in Cellular Metabolites and Fragments

    • Damini Jaiswal, Pramod P. Wangikar
    Pages 189-204

  11. Quantifying Metabolic Transfer Mediated by Extracellular Vesicles Using Exo-MFA: An Integrated Empirical and Computational Platform

    • Abhinav Achreja, Noah Meurs, Deepak Nagrath
    Pages 205-221

  12. Comparative Metabolic Network Flux Analysis to Identify Differences in Cellular Metabolism

    • Sarah McGarrity, Sigurður T. Karvelsson, Ólafur E. Sigurjónsson, Óttar Rolfsson
    Pages 223-269

  13. Software Supporting a Workflow of Quantitative Dynamic Flux Maps Estimation in Central Metabolism from SIRM Experimental Data

    • Vitaly A. Selivanov, Silvia Marin, Josep Tarragó-Celada, Andrew N. Lane, Richard M. Higashi, Teresa W.-M. Fan et al.
    Pages 271-298

  14. Inferring Metabolic Flux from Time-Course Metabolomics

    • Scott Campit, Sriram Chandrasekaran
    Pages 299-313

  15. Metabolic Network Reconstructions to Predict Drug Targets and Off-Target Effects

    • Kristopher Rawls, Bonnie V. Dougherty, Jason Papin
    Pages 315-330

  16. Single-cell Digital Twins for Cancer Preclinical Investigation

    • Marzia Di Filippo, Chiara Damiani, Marco Vanoni, Davide Maspero, Giancarlo Mauri, Lilia Alberghina et al.
    Pages 331-343

  17. Supply and Demand Analysis of Autophagy

    • André du Toit, Ben Loos, Jan Hendrik S. Hofmeyr
    Pages 345-357

  18. Thermodynamic Approaches in Flux Analysis

    • Sabine Peres, Vincent Fromion
    Pages 359-367

  19. Back Matter

    Pages 369-370
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Keywords

About this book

This volume explores the latest metabolic flux analysis (MFA) techniques that cover the analysis of cellular, organ level, and whole-body metabolism. The chapters in this book discuss topics such as deutrium tracing; isotopologue fractions using GC-TOF; non-targeted mass isotopolome analysis; large-scale profiling of cellular metabolic activities using deep 13C labeling medium; metastases in mice; SWATH; Exo-MFA; metabolic flux from time-course metabolomics; and thermodynamic approaches in flux analysis. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.
 
Cutting-edge and comprehensive, Metabolic Flux Analysis in Eukaryotic Cells: Methods and Protocols is a valuable resourcefor both experts in MFA techniques and researchers getting involved in the role of quantitative studies to uncover the dysregulated pathways in human diseases.



Editors and Affiliations

  • Department of Biomedical Engineering, University of Michigan, Ann Arbor, USA

    Deepak Nagrath

Bibliographic Information

  • Book Title: Metabolic Flux Analysis in Eukaryotic Cells

  • Book Subtitle: Methods and Protocols

  • Editors: Deepak Nagrath

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-0159-4

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2020

  • Hardcover ISBN: 978-1-0716-0158-7Published: 01 January 2020

  • Softcover ISBN: 978-1-0716-0161-7Published: 26 August 2021

  • eBook ISBN: 978-1-0716-0159-4Published: 31 December 2019

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XIII, 370

  • Number of Illustrations: 23 b/w illustrations, 64 illustrations in colour

  • Topics: Metabolomics, Cell Biology, Biotechnology

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