Synthetic Biology

1st Edition

Tools and Applications

Editors: Huimin Zhao
Hardcover ISBN: 9780123944306
eBook ISBN: 9780123978202
Imprint: Academic Press
Published Date: 21st May 2013
Page Count: 352
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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. 


Geneticists, molecular biologists, physicists, chemists, and bioengineers

Table of Contents



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


Oligonucleotide Synthesis

Gene Assembly

Quality Control

Applications of DNA Synthesis




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


Protein Engineering Methods

Applications of Protein Engineering in Synthetic Biology



Chapter 3. Pathway Engineering as an Enabling Synthetic Biology Tool


Design and Construction of Pathways

Pathway Optimization

Applications of Pathway Engineering Tools

Conclusions and Future Prospects



Chapter 4. From Biological Parts to Circuit Design


The Parts

Assembling Parts

Circuit Design




Section II: Computational and Theoretical Tools in Synthetic Biology

Chapter 5. Theoretical Considerations for Reprogramming Multicellular Systems


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


Chapter 6. Computational Protein Design for Synthetic Biology


Methods Overview

Computational Design of Protein–protein I


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© Academic Press 2013
Academic Press
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About the Editor

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

Affiliations and Expertise

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


"Synthetic Biology: Tools and Applications. Edited by Huimin Zhao. Academic Press. Amsterdam (The Netherlands) and Boston (Massachusetts): Elsevier. $149.95. xviii 333 p.; ill.; index. ISBN: 978-0-12-394430-6. 2013." - The Quarterly Review of Biology,September 2014

"Chemical, biological, and biochemical engineers describe tools and methodologies developed for engineering biological systems at a wide range of levels, including molecular, pathway, network, whole cell, and multi-cell. They also explore practical applications of synthetic biology, a branch of genetic engineering that incorporates systems biology."--Reference and Research Book News, August 2013

“The proposed book is exclusively focused on synthetic biology. It brings together the thought leaders in this emerging field, giving expert accounts and their opinions of special topics in synthetic biology…. This might be the first dedicated, edited book for synthetic biology.”--Dr. Qing Lin, State University of New York at Buffalo, Buffalo, NY, USA