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This volume looks at the latest methodologies used to study cellular metabolism with in silico approaches. The chapters in this book are divided into 3 parts: part I discusses tools and methods used for metabolic reconstructions and basic constraint-based metabolic modeling (CBMM); Part II explores protocols for the generation of experimental data for metabolic reconstruction and modeling, including transcriptomics, proteomics, and mutant generations; and Part III cover advanced techniques for quantitative modeling of cellular metabolism, including dynamic Flux Balance Analysis and multi-objective optimization. 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 thorough, MetabolicNetwork Reconstruction and Modeling: Methods and Protocols is a valuable resource for qualified investigators studying cellular metabolism, and novice researchers who want to start working with CBMM.
List of contents
Reconstructing High-Quality Large-Scale Metabolic Models with merlin.- Analyzing and Designing Cell Factories with OptFlux.- The MONGOOSE Rational Arithmetic Toolbox.- The FASTCORE Family: For the Fast Reconstruction of Compact Context-Specific Metabolic Networks Models.- Reconstruction and Analysis of Central Metabolism in Microbes.- Using PSAMM for the Curation and Analysis of Genome-Scale Metabolic Models.- Integration of Comparative Genomics with Genome-Scale Metabolic Modeling to Investigate Strain-Specific Phenotypical Differences.- Temple-Assisted Metabolic Reconstruction and Assembly of Hybrid Bacterial Models.- Integrated Host-Pathogen Metabolic Reconstruction.- Metabloic Model Reconstruction and Analysis of an Artificial Microbial Ecosystem.- RNA Sequencing and Analysis in Microorganisms for Metabolic Network Reconstruction.- Differential Proteomics Based on 2D-Difference In-Gel Electrophoresis and Tandem Mass Spectrometry for the Elucidation of Biological Processes in Antibiotic-Producer Bacterial Strains.- Techniques for Large-Scale Bacterial Genome Manipulation and Characterization of the Mutants with Respect to In Silico Metabolic Reconstructions.- Computational Prediction of Synthetic Lethals in Genome-Scale Metabolic Models using Fast-SL.- Coupling Fluxes, Enzymes, and Regulation in Genome-Scale Metabolic Models.- Dynamic Flux Balance Analysis using DFBAlab.- Designing Optimized Production Hosts by Metabolic Modeling.- Optimization of Multi-Omic Genome-Scale Models: Methodologies, Hands-On Tutorial and Perspectives.
About the author
Marco Fondi
Department of Biology
University of Florence
Via Madonna del Piano 6, I-50019 Sesto Fiorentino, Italy
Email: marco.fondi@unifi.it
Summary
Includes cutting-edge methods and protocols
Provides step-by-step detail essential for reproducible results
Contains key notes and implementation advice from the experts
