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.
Section 1 - Strategies in systems biology. top down, middle-out and bottom-up strategies - Hans V. Westerhoff
Section 2 - Machines for systems biology - Roy Goodacre 4 chapters explaining the workings of four of the most important measurement techniques for systems biology: Mass spectrometry Microscopy Spectroscopy
Section 3 - Nucleic acids and systems biology - James Adaye 4 Chapters on DNA sequencing, Arrays studies, PCR, deep sequencing
Section 4 - Protein production and quantification for Systems Biology -Naglis Malys and Kathleen Carroll Chapter 1: Quantification of proteins and their modifications using QconCAT technology Chapter 2: Mass spectrometric based quantitative proteomics using SILAC Chapter 3: Nucleic Acid Programmable Protein Array (NAPPA) - a just-in-time multiplexed protein expression and purification platform Chapter 4: Economical high throughput protein production and purification in prokaryotic and eukaryotic systems Chapter 5: Systems biology of recombinant protein production using Bacillus megaterium Chapter 6: Protein production in S. cerevisiae for systems biology studies
Section 5 - Enzymatic Assays in Systems Biology Research Farid Khan, Hanan Messiha and Malgorzata Adamczyk Chapter 1: Enzymatic Assays in Systems Biology Research: Strategies and challenges. Chapter 2: Real-time kinetic assay technologies for characterising enzymes in metabolic pathways. Chapter 3: A bottom-up approach towards a full quantitative description of yeast energy metabolism: A systematic approach for estimating the kinetic parameters of isoenzymes under in vivo like conditions Chapter 4: A top-down approach for measuring enzyme kinetics in cell lysates: mimicking an in vivo environment.
Section 6 - Sample preparation in Metabolomics Studies -Warwick Dunn & Catherine Winder Chapter 1 - The use of continuous culture in systems biology investigations Chapter 2 - Metabolomic studies of yeast - methods for sample collection in profiling and quantitation studies Chapter 3 - The role of metabolomics in plant studies - views on sampling and data acquisition Chapter 4 - The study of mammaliam metabolism - how, when and why Chapter 5 - The study of the environment from a metabolomic perspective
Section 7 - Mathematical modelling in Systems Biology -Kieran Smallbone & Evangelos Simeonidis Chapter 1: Building a kinetic model of a metabolic pathway Chapter 2: Making systems biology models reusable: the role of standards and biological semantics Chapter 3: From reaction networks to information flow - using modular response analysis to track the routes of information in large signalling networks Chapter 4: The mathematics of Metabolic Control Analysis Chapter 5: Constraint-based analysis of biochemical networks
Section 8 - Understanding systems biology (Hans Westerhoff) 1. Elementary mode analysis 2. Flux analysis 3. Flux balance analysis 4. Metabolic control analysis 5. Supply-demand analysis 6. Modular kinetic analysis 7. Regulation Analysis 8. Noise and heterogeneity
Section 9 - Dealing with Systems Biology Research: - Neil W. Hayes Chapter 1 - Crossing the Boundaries; Delivering Interdisciplinary Science in a Disciplinary World