Methods in Systems Biology

Methods in Systems Biology

1st Edition - September 19, 2011

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  • Editors: Hans Westerhoff, Malkhey Verma
  • eBook ISBN: 9780123851192
  • Hardcover ISBN: 9780123851185

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Systems biology is a term used to describe a number of trends in bioscience research and a movement that draws on those trends. This volume in the Methods in Enzymology series comprehensively covers the methods in systems biology. With an international board of authors, this volume is split into sections that cover subjects such as machines for systems biology, protein production and quantification for systems biology, and enzymatic assays in systems biology research.

Key Features

  • This volume in the Methods in Enzymology series comprehensively covers the methods in systems biology
  • With an international board of authors, this volume is split into sections that cover subjects such as machines for systems biology, protein production and quantification for systems biology, and enzymatic assays in systems biology research


Biochemists, biophysicists, molecular biologists, analytical chemists, and physiologists

Table of Contents

  • Contributors


    Volume in series

    Chapter one: Systems Biology Left and Right

    1 A Fundamental Definition of Systems Biology

    2 The Importance of the Integration of In Vivo and In Vitro Analyses

    3 Alternative Definitions of Systems Biology

    4 Different Types of Systems Biology

    Chapter two: Mass Spectrometry in Systems Biology

    1 Introduction

    2 What is Mass Spectrometry?

    3 Mass Spectrometer Configurations

    4 The Benefits of Mass Spectrometry

    5 Applications of Mass Spectrometry in Systems Biology

    Chapter three: High-Throughput Quantification of Posttranslational Modifications In Situ by CA-FLIM

    1 Introduction

    2 Methods

    3 Results and Discussion

    4 Conclusion: Why Use CA-FLIM?

    Appendix 1 Frequency Domain Fluorescence Lifetime Imaging Microscopy

    Appendix 2 Global Analysis of FRET–FLIM Data

    Appendix 3 Materials

    Chapter four: Absorption Spectroscopy

    1 Introduction

    2 Theory of Absorption Spectroscopy

    3 Hardware

    4 Applications of UV–Visible Spectrometry

    5 Perspective

    Chapter five: A Strand-Specific Library Preparation Protocol for RNA Sequencing

    1 Introduction

    2 ssRNA-Seq Protocol

    Chapter Six: Quantitative Real-Time PCR-Based Analysis of Gene Expression

    1 Introduction

    2 Primer Design

    3 Primer Validation Experiments

    4 Cell Culture-Based Isolation and Quantification of RNA

    5 Reverse Transcription

    Chapter seven: Quantification of Proteins and Their Modifications Using QconCAT Technology

    1 Introduction

    2 Expression and Purification of QconCAT Proteins

    3 Preparation of Samples for Analysis

    4 Mass Spectrometric Analysis

    5 Quantification of Posttranslational Modifications

    6 Replicate Analysis—Biological Versus Technical Replicates

    7 Summary and General Considerations

    Chapter eight: Mass Spectrometric-Based Quantitative Proteomics Using SILAC

    1 Introduction

    2 SILAC: The Method

    3 General SILAC Protocol

    4 Applications

    5 Conclusion

    Chapter nine: Nucleic Acid Programmable Protein Array

    1 Introduction

    2 Overview of NAPPA Chemistry

    3 Array Production

    4 Detection of Protein Expression

    Chapter ten: Systems Biology of Recombinant Protein Production Using Bacillus megaterium

    1 Introduction

    2 Handling B. megaterium

    3 Systems Biology of B. megaterium

    Chapter eleven: Protein Production in Saccharomyces cerevisiae for Systems Biology Studies

    1 Introduction

    2 Comparison of Commonly Used Expression Systems

    3 Comprehensive Libraries for Protein Production in S. cerevisiae

    4 Protocols for Protein Expression and Purification from Tagged Collections of S. cerevisiae

    5 Protein Analysis and Quantification

    6 Protein Use in Proteomics and Enzyme Kinetics Measurements

    7 Concluding Remarks

    Chapter twelve: Towards a Full Quantitative Description of Yeast Metabolism

    1 Introduction

    2 Enzyme Kinetics for Systems Biology

    3 Production and Purification of Isoenzymes

    4 General Protocol for Enzymatic Assays

    5 Assays for Measuring the Activities of the Glycolytic Isoenzymes of S. cerevisiae

    6 Concluding Remarks

    Chapter thirteen: Enzyme Kinetics for Systems Biology

    1 Enzyme Kinetics for Systems Biology: Five Variations on the Theme

    2 Three System Biology Approaches that Use Different Enzyme Kinetics

    3 Biological Material

    4 Protocols

    5 Perspectives

    Chapter fourteen: The Use of Continuous Culture in Systems Biology Investigations

    1 Introduction

    2 Experimental Considerations

    3 Operation of the Permittistat

    4 Sampling of Biomass for Proteome and Metabolome Analyses

    Chapter fifteen: Sample Preparation Related to the Intracellular Metabolome of Yeast

    1 Introduction

    2 Sample Collection from Batch Cultures with Quenching of Intracellular Metabolism

    3 Extraction of Polar and Nonpolar Metabolites from the Intracellular Metabolome

    4 Targeted Quantification of Organic Acids Applying Gas Chromatography–Mass Spectrometry

    Chapter sixteen: Plant Metabolomics and Its Potential for Systems Biology Research

    1 An Introduction to Plant Metabolomics

    2 Considerations in Plant Growth and Preparation of Plant Material

    3 GC-TOF/MS Metabolite Profiling, Recommended Experimental Reference Protocols, and Data Preprocessing Approaches

    4 HPLC–PDA–QTOFMS Metabolite Profiling, Recommended Experimental Reference Protocols, and Data Preprocessing Approaches

    5 1H NMR: Experimental Reference Protocols and Data Preprocessing for Plant Metabolite Profiling

    6 Concluding Remarks

    Chapter seventeen: The Study of Mammalian Metabolism through NMR-based Metabolomics

    1 Introduction

    2 Tissue Extraction

    3 Analysis of Biofluids by NMR Spectroscopy

    4 A Brief Overview of Directly Measuring Metabolites in Mammalian Tissues by High-Resolution Magic Angle Spinning 1H NMR Spectroscopy

    5 Data Processing

    6 Conclusions

    Chapter eighteen: Building a Kinetic Model of Trehalose Biosynthesis in Saccharomyces cerevisiae

    1 Introduction

    2 Biological Background

    3 Model Development

    4 Results

    5 Discussion

    Chapter nineteen: Sustainable Model Building

    1 Sustainable Model Building

    2 How to Create Reusable Models

    3 How to Implement Models in Standard Formats

    4 How to Document and Annotate Models

    5 Tools for Model Building and Annotation

    6 How to Create and Draw a Simple Model

    7 Annotations in Genome-Scale Network Reconstructions

    Chapter twenty: From Reaction Networks to Information Flow—Using Modular Response Analysis to Track Information in Signaling Networks

    1 Introduction

    2 Modular Response Analysis

    3 Conservation Analysis

    4 From Reaction Schemes to Influence Networks Using a Monte Carlo Approach

    5 Conclusion

    Chapter twenty-one: Whole-Genome Metabolic Network Reconstruction and Constraint-Based Modeling

    1 Introduction

    2 Metabolic Network Reconstruction

    3 Constraint-Based Modeling Methods

    4 Summary

    Chapter twenty-two: Hands-on Metabolism

    1 Introduction

    2 Elementary Flux Modes

    3 Application

    4 Conclusion

    Appendix Reaction scheme of the photosynthate metabolism in metatool format (discussed in Section 3.2).

    Chapter twenty-three: How to Obtain True and Accurate Rate-Values

    1 Introduction

    2 Quantification of Broth Amount in the Cultivation Vessel

    3 Forgotten Processes

    4 Detecting Forgotten Processes and Systematic Errors

    5 Propagation of Statistical Errors: Accuracy of Calculated Rates

    6 Experimental Design to Obtain True and Accurate R-Values

    7 Mathematics of Reconciliation

    8 Conclusion

    Chapter twenty-four: A Practical Guide to Genome-Scale Metabolic Models and Their Analysis

    1 Introduction

    2 Genome-Scale Metabolic Models: Their Place in the Spectrum of Modeling Options

    3 The Art of Making Genome-Scale Metabolic Models

    4 Applications of Genome-Scale Metabolic Models

    Chapter twenty-five: Supply–Demand Analysis

    1 Introduction

    2 The Functional Organization of Metabolism

    3 Quantitative Analysis of Supply–Demand Systems

    4 Generalized Supply–Demand Analysis

    5 Experimental Applications of Supply–Demand Analysis

    Chapter twenty-six: Modular Kinetic Analysis

    1 Introduction

    2 Description of the Method

    3 Applications

    Chapter twenty-seven: Quantitative Analysis of Flux Regulation Through Hierarchical Regulation Analysis

    1 Introduction

    2 Theory of Regulation Analysis

    3 Experimental Tools for Regulation Analysis

    4 Strategies of Flux Regulation

    5 Concluding Remarks

    Chapter twenty-eight: Origins of Stochastic Intracellular Processes and Consequences for Cell-to-Cell Variability and Cellular Survival Strategies

    1 Cell-to-Cell Heterogeneity and Measurement Techniques

    2 Theoretical Insights and Experimental Evidence

    3 Beneficial and Detrimental Effects of Molecular Noise

    4 Conclusion

    Chapter twenty-nine: The SEEK

    1 Introduction

    2 The SEEK Platform

    3 The Challenges of Data Management

    4 The JERM Infrastructure

    5 The SEEK Functionalities: Annotating and Linking Assets

    6 Incentives for Sharing Data

    7 The SEEK: Experiences

    Chapter Thirty: Crossing the Boundaries

    1 Introduction

    2 Theoretical Management Strategies

    3 Consideration of Real-World Examples

    4 Conclusions

    Author Index

    Subject Index

Product details

  • No. of pages: 668
  • Language: English
  • Copyright: © Academic Press 2011
  • Published: September 19, 2011
  • Imprint: Academic Press
  • eBook ISBN: 9780123851192
  • Hardcover ISBN: 9780123851185

About the Serial Volume Editors

Hans Westerhoff

Malkhey Verma

About the Series Volume Editor

Daniel Jameson

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