Synthetic Biology

Synthetic Biology

Tools and Applications

1st Edition - March 21, 2013

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  • Editor: Huimin Zhao
  • eBook ISBN: 9780123978202
  • Hardcover ISBN: 9780123944306

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Description

Synthetic Biology provides a framework to examine key enabling components in the emerging area of synthetic biology. Chapters contributed by leaders in the field address tools and methodologies developed for engineering biological systems at many levels, including molecular, pathway, network, whole cell, and multi-cell levels. The book highlights exciting practical applications of synthetic biology such as microbial production of biofuels and drugs, artificial cells, synthetic viruses, and artificial photosynthesis. The roles of computers and computational design are discussed, as well as future prospects in the field, including cell-free synthetic biology and engineering synthetic ecosystems.Synthetic biology is the design and construction of new biological entities, such as enzymes, genetic circuits, and cells, or the redesign of existing biological systems. It builds on the advances in molecular, cell, and systems biology and seeks to transform biology in the same way that synthesis transformed chemistry and integrated circuit design transformed computing. The element that distinguishes synthetic biology from traditional molecular and cellular biology is the focus on the design and construction of core components that can be modeled, understood, and tuned to meet specific performance criteria and the assembly of these smaller parts and devices into larger integrated systems that solve specific biotechnology problems.

Key Features

  • Includes contributions from leaders in the field presents examples of ambitious synthetic biology efforts including creation of artificial cells from scratch, cell-free synthesis of chemicals, fuels, and proteins, engineering of artificial photosynthesis for biofuels production, and creation of unnatural living organisms
  • Describes the latest state-of-the-art tools developed for low-cost synthesis of ever-increasing sizes of DNA and efficient modification of proteins, pathways, and genomes
  • Highlights key technologies for analyzing biological systems at the genomic, proteomic, and metabolomic levels which are especially valuable in pathway, whole cell, and multi-cell applications
  • Details mathematical modeling tools and computational tools which can dramatically increase the speed of the design process as well as reduce the cost of development

Readership

Geneticists, molecular biologists, physicists, chemists, and bioengineers

Table of Contents

  • Contributors

    Introduction

    Synthetic Biology: What is in a Name?

    Synthetic Biology: What’s New?

    Synthetic Biology: What’s Next?

    Section I: Synthesis and Engineering Tools in Synthetic Biology

    Chapter 1. New Tools for Cost-Effective DNA Synthesis

    Introduction

    Oligonucleotide Synthesis

    Gene Assembly

    Quality Control

    Applications of DNA Synthesis

    Conclusion

    Acknowledgments

    References

    Chapter 2. Protein Engineering as an Enabling Tool for Synthetic Biology

    Introduction

    Protein Engineering Methods

    Applications of Protein Engineering in Synthetic Biology

    Conclusions

    References

    Chapter 3. Pathway Engineering as an Enabling Synthetic Biology Tool

    Introduction

    Design and Construction of Pathways

    Pathway Optimization

    Applications of Pathway Engineering Tools

    Conclusions and Future Prospects

    Acknowledgments

    References

    Chapter 4. From Biological Parts to Circuit Design

    Introduction

    The Parts

    Assembling Parts

    Circuit Design

    Conclusion

    Acknowledgments

    References

    Section II: Computational and Theoretical Tools in Synthetic Biology

    Chapter 5. Theoretical Considerations for Reprogramming Multicellular Systems

    Introduction

    Conceptual Framework: Gene Regulatory Networks, Network States, and Cell Types

    The Quasi-Potential Landscape

    How to Obtain a Trajectory on the Quasi-Potential Landscape for Transition Between Two Attractors

    Example: State Transition in Blood Cell and Pancreas Cell Differentiation and Reprogramming

    Conclusion and Outlook

    References

    Chapter 6. Computational Protein Design for Synthetic Biology

    Introduction

    Methods Overview

    Computational Design of Protein–protein Interactions

    Computational Design of Catalytic Activity

    Protein Thermostabilization by Computational Design

    Computational Design of (Novel) Protein Folds

    Complementarity with Directed Evolution

    Conclusion and Outlook

    References

    Chapter 7. Computer-Aided Design of Synthetic Biological Constructs with the Synthetic Biology Software Suite

    Introduction

    Synthetic Logical-AND Gates and Protein Devices

    The Synthetic Biology Software Suite

    Conclusion

    Acknowledgments

    References

    Chapter 8. Computational Methods for Strain Design

    Introduction

    Fundamental Components of Synthetic Biology

    Computational Prediction Tools for Synthetic Biology Components

    Computational Tools for Pathway Prediction

    Computational Tools for Strain Optimization

    Synthetic Biology for Systems-Level Metabolic Engineering

    Concluding Remarks

    Acknowledgments

    References

    Section III: Applications in Synthetic Biology

    Chapter 9. Design and Application of Synthetic Biology Devices for Therapy

    Introduction

    Target Organisms and Cell Types for Therapeutic Applications of Synthetic Biology

    Molecular Toolkit for Synthetic Biology

    Therapeutic Applications of Synthetic Biology

    Conclusion: Challenges and Safety Issues

    References

    Chapter 10. Drug Discovery and Development via Synthetic Biology

    Introduction

    Tools for Pathway Discovery and Engineering

    Applications

    Conclusions and Future Perspectives

    Acknowledgments

    References

    Chapter 11. Synthetic Biology of Microbial Biofuel Production: From Enzymes to Pathways to Organisms

    Introduction

    Pathway Design and Optimization

    Host Engineering

    Future Prospects

    References

    Chapter 12. Tools for Genome Synthesis

    Introduction

    DNA Size Limit by E. coli Plasmid

    Genome Cloning Using a Bottom-Up Approach

    The KEIO Method

    Mitochondria and Chloroplast: Organelle Guest Genomes in BGM

    Bottom-Up Approaches for De Novo Genome Production

    Costs to Synthesize Genomes

    Relevant Methods to Support Genome Synthesis

    Future Perspectives of BGM Systems Accrued from the Present Achievements

    Summary

    References

    Chapter 13. Synthetic Microbial Consortia and their Applications

    Introduction

    Communication in Synthetic Multicellular Systems

    Engineering Unidirectional Communication

    Engineered Cooperation in Synthetic Microbial Consortia

    Programming Antagonistic Interactions between Populations

    Spatial Organization in Synthetic Consortia

    Synthetic Biofilms Lead to Stable Consortia Behavior Over a Long Period of Time

    Advances in Technology Allow the Precise Spatial Arrangement of Synthetic Consortia

    The Evolution of Cooperation Can Yield Novel Behaviors in Synthetic Consortia

    Applications of Synthetic Consortia in Industrial Processes and Medicine

    Future Challenges

    References

    Section IV: Future Prospects

    Chapter 14. Semi-Synthetic Minimal Cells: Biochemical, Physical, and Technological Aspects

    Introduction

    The Conceptual Framework of Semisynthetic Minimal Cells

    Reconstruction of Genetic/Metabolic Processes in Semisynthetic Minimal Cells

    Physical Aspects of SSMC Construction: Implications for the Origin of Life

    SSMCs as a Biotechnological Tool

    Some Open Questions and Future Perspectives

    Concluding Remarks

    Acknowledgments

    References

    Chapter 15. Transforming Synthetic Biology with Cell-Free Systems

    Introduction

    Cell-Free Biology

    Advantages of Cell-Free Biology

    Existing Technologies and Applications in Cell-Free Synthetic Biology

    Challenges and Opportunities

    Summary

    Acknowledgments

    References

    Chapter 16. Towards Engineered Light–Energy Conversion in Nonphotosynthetic Microorganisms

    Introduction

    Incorporation of Simple Light-Driven Proton Pumps Into Engineered Microorganisms

    Increasing the Complexity and Efficiency of Light-Energy Capture and Conversion

    Combining Light-Energy Conversion and CO2 Fixation

    From Biological to Artificial Photosynthetic Systems

    Future Directions

    References

    Chapter 17. Applications of Engineered Synthetic Ecosystems

    Introduction

    Targeting Microbial Communities for Forward Engineering

    Towards Synthetic Community Engineering

    Future Prospects for Synthetic Ecosystems

    Acknowledgments

    References

    Index

Product details

  • No. of pages: 352
  • Language: English
  • Copyright: © Academic Press 2013
  • Published: March 21, 2013
  • Imprint: Academic Press
  • eBook ISBN: 9780123978202
  • Hardcover ISBN: 9780123944306

About the Editor

Huimin Zhao

Huimin Zhao

Dr. Huimin Zhao is the Centennial Endowed Chair Professor of chemical and biomolecular engineering, and professor of chemistry, biochemistry, biophysics, and bioengineering at the University of Illinois at Urbana-Champaign (UIUC). He received his B.S. degree in Biology from the University of Science and Technology of China in 1992 and his Ph.D. degree in Chemistry from the California Institute of Technology in 1998 under the guidance of Dr. Frances Arnold. Prior to joining UIUC in 2000, he was a project leader at the Industrial Biotechnology Laboratory of the Dow Chemical Company. He was promoted to full professor in 2008. Dr. Zhao has authored and co-authored 150 research articles and 20 issued and pending patent applications with several being licensed by industry. In addition, he has given plenary, keynote or invited lectures in more than 170 international meetings and institutions. Eight of his former graduate students and postdocs became professors in the US and other countries.

Dr. Zhao received numerous research and teaching awards and honors, including Guggenheim Fellowship (2012), Fellow of the American Association for the Advancement of Science (AAAS) (2010), Fellow of the American Institute of Medical and Biological Engineering (AIMBE) (2009), American Institute of Chemical Engineers (AIChE) Food, Pharmaceutical, and Bioengineering Division Plenary Award Lecturer (2009), the American Chemical Society (ACS) Division of Biochemical Technology Young Investigator Award (2008), Outstanding Overseas Young Chinese Scholars Award (2007), DuPont Young Professor Award (2005), National Science Foundation CAREER Award (2004), Dow Chemical Special Recognition Award (1999), Xerox Award for Faculty Research from UIUC College of Engineering (2005), Petit Scholar from UIUC College of Liberal Arts and Sciences (2006), and University Scholar from UIUC (2007). Dr. Zhao served as a consultant for over 10 companies such as Pfizer, Maxygen, BP, Gevo, and zuChem, and a Scientific Advisory Board member of Gevo and Myriant Technologies. He is also an advisor to the Department of Energy’s Biological and Environmental Research program. Dr. Zhao is an Associate Editor of ACS Catalysis and an editor of ACS Synthetic Biology, Journal of Industrial Microbiology and Biotechnology, and Scientific Reports (Nature). His primary research interests are in the development and applications of synthetic biology tools to address society’s most daunting challenges in human health and energy, and in the fundamental aspects of enzyme catalysis, cell metabolism, and gene regulation.

Affiliations and Expertise

University of Illinois at Urbana-Champaign, Urbana, IL, USA

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