book

Fundamental Bioengineering

by John Villadsen, Sang Yup Lee, Jens Nielsen, Gregory Stephanopoulos

February 2016

Intermediate to advanced

574 pages

19h 10m

English

Wiley-Blackwell

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Summary2.0 Introduction2.1 Mass Balances for a CSTR Operating at Steady State2.2 Operation of the Steady-State CSTRReferences
Summary3.1 Black-Box Stoichiometry Obtained in a CSTR Operated at Steady State3.2 Calculation of Stoichiometric Coefficients by Means of a Redox Balance3.3 Applications of the Redox Balance3.4 Composition of the Biomass X3.5 Combination of Black-Box Models3.6 Application of Carbon and Redox Balances in Bio-Remediation ProcessesReferences

Summary4.0 Introduction4.1 Glycolysis4.2 Fermentative Metabolism: Regenerating the NAD+ Lost in Glycolysis4.3 The TCA Cycle: Conversion of Pyruvate to NADH + FADH2, to Precursors or Metabolic Products4.4 NADPH and Biomass Precursors Produced in the PP Pathway4.5 Oxidative Phosphorylation: Production of ATP from NADH (FADH2) in Aerobic Fermentation4.6 Summary of the Biochemistry of Primary Metabolic Pathways4.7 Metabolic Flux Analysis Discussed in Terms of Substrate to Product Pathways4.8 Metabolic Flux Analysis Discussed in Terms of Individual Pathway Rates in the Network4.9 Propagation of Experimental Errors in MFA4.10 ConclusionsReferences
Summary5.1 Introduction5.2 Input and Output Data of 13C MFA5.3 A Brief History of 13C MFA5.4 An Illustrative Toy Example5.5 The Atom Transition Network5.6 Isotopomers and Isotopomer Fractions5.7 The Isotopomer Transition Network5.8 Isotopomer Labeling Balances5.9 Simulating an Isotope Labeling Experiment5.10 Isotopic Steady State5.11 Flux Identifiability5.12 Measurement Models5.13 Statistical Considerations5.14 Experimental Design5.15 Exchange Fluxes5.16 Multidimensional Flux Identifiability5.17 Multidimensional Flux Estimation5.18 The General Parameter Fitting Procedure5.19 Multidimensional Statistics5.20 Multidimensional Experimental Design5.21 The Isotopically Nonstationary Case5.22 Some Final Remarks on Network Specification5.23 Algorithms and Software Frameworks for 13C MFAGlossaryReferences
Summary6.1 Introduction6.2 Reconstruction Process of Genome-Scale Models6.3 Genome-Scale Model Prediction6.4 Genome-Scale Models of Prokaryotes6.5 Genome-Scale Models of Eukaryotes6.6 Integration of Polyomic Data into Genome-Scale ModelsAcknowledgmentReferences
Summary7.1 Simple Models for Enzymatic Reactions and for Cell Reactions with Unstructured Biomass7.2 Variants of Michaelis–Menten and Monod kinetics7.3 Summary of Enzyme Kinetics and the Kinetics for Cell Reactions7.4 Cell Reactions with Unsteady State Kinetics7.5 Cybernetic Modeling of Cellular Kinetics7.6 Bioreactions with Diffusion Resistance7.7 Sequences of Enzymatic Reactions: Optimal Allocation of Enzyme LevelsReferences
Summary8.1 Introduction8.2 Kinetics of Pathway Reactions: the Need to Measure in a Very Narrow Time Window8.3 Tools for In Vivo Diagnosis of Pathway Reactions8.4 Examples: The Pentose-Phosphate Shunt and Kinetics of Phosphofructokinase8.5 Additional Approaches for Dynamic Modeling Large Metabolic Networks8.6 Dynamic Models Used for Redesigning Cell Factories. Examples: Optimal Ethanol Production in Yeast and Optimal Production of Tryptophan in E. Coli8.7 Target Identification for Drug DevelopmentReferences
Summary9.0 Introduction9.1 Chemical Equilibrium and Thermodynamic State Functions9.2 Thermodynamic Properties Obtained from Galvanic Cells9.3 Conversion of Free Energy Harbored in NADH and FADH2 to ATP in Oxidative Phosphorylation9.4 Calculation of Heat of Reaction Q=(−ΔHc) and of (−ΔGc) Based on Redox BalancesReferences
Summary10.0 Introduction10.1 The Design Basis for a Once-Through Steady-State CSTR10.2 Combination of Several Steady-State CSTRs in Parallel or in Series10.3 Recirculation of Biomass in a Single Steady-State CSTR10.4 A Steady-State CSTR with Uptake of Substrates from a Gas Phase10.5 Fed-Batch Operation of a Stirred Tank Reactor in the Bio-Industry10.6 Loop Reactors: a Modern Version of Airlift ReactorsReferences
Summary11.0 Introduction11.1 Definitions of Mixing Processes11.2 The Power Input P Delivered by Mechanical Stirring11.3 Mixing and Mass Transfer in Industrial Reactors11.4 ConclusionsReferences
Summary12.0 Introduction12.1 Steps in Downstream Processing and Product Recovery12.2 Baker's Yeast12.3 Xanthan Gum12.4 Penicillin12.5 α-A Interferon12.6 Insulin12.7 ConclusionsReferences
Summary13.1 Methods and Types of Separations in Chromatography13.2 Materials Used in Chromatographic Separations13.3 Chromatographic Theory13.4 Practical Considerations in Column Chromatographic Applications13.5 Scale-Up13.6 Industrial Applications13.7 Some Alternatives to Column Chromatographic Techniques13.8 Electrodialysis13.9 Electrophoresis13.10 ConclusionsReferences
Summary14.1 Introduction14.2 Variables that should be Known14.3 Variables Easily Accessible and Standard14.4 Variables Requiring More Monitoring Effort and Not Yet Standard14.5 Data EvaluationReferences
Summary15.1 Introduction15.2 Bioprocess Control15.3 Principles and Basic Algorithms in Process ControlReferences
Summary16.1 Introduction16.2 Description of the Large Scale16.3 Scale-Down16.4 Investigations at Lab Scale16.5 Scale-Up16.6 OutlookReferences
Summary17.1 Introduction17.2 Basic Principles of Developing New Fermentation Processes17.3 Techno-economic Analysis: the Link Between Science, Engineering, and Economy17.4 From Fermentation Process Development to the Market17.5 The Industrial Angle and Opportunities in the Chemical Industry17.6 Evaluation of Business Opportunities17.7 Concluding Remarks and OutlookAcknowledgmentReferences

Overview

A thorough introduction to the basics of bioengineering, with a focus on applications in the emerging "white" biotechnology industry.
As such, this latest volume in the "Advanced Biotechnology" series covers the principles for the design and analysis of industrial bioprocesses as well as the design of bioremediation systems, and several biomedical applications. No fewer than seven chapters introduce stoichiometry, kinetics, thermodynamics and the design of ideal and real bioreactors, illustrated by more than 50 practical examples. Further chapters deal with the tools that enable an understanding of the behavior of cell cultures and enzymatically catalyzed reactions, while others discuss the analysis of cultures at the level of the cell, as well as structural frameworks for the successful scale-up of bioreactions. In addition, a short survey of downstream processing options and the control of bioreactions is given.
With contributions from leading experts in industry and academia, this is a comprehensive source of information peer-reviewed by experts in the field.