BioBuilder

Table of contents

1. Preface
   1. Who Should Read This Book
   2. Why We Wrote This Book
   3. A Word on Synthetic Biology Today
   4. Navigating This Book
   5. Online Resources
   6. Safari® Books Online
   7. How to Contact Us
   8. Acknowledgments
2. 1. Fundamentals of Synthetic Biology
   1. What Is Synthetic Biology?
      1. Why Synthetic Biology?
      2. Synthetic Biology in Context
   2. Introduction to Engineering and Design
      1. “Traditional” Engineering Solutions
      2. Engineering Toolkits
   3. The Synthetic Biology Toolkit
      1. The Molecular Biology Toolkit
      2. The Toolkit Expanded for Synthetic Biology
   4. Wrap-Up
   5. Additional Reading and Resources
3. 2. Fundamentals of Biodesign
   1. Illustrating a Top-Down Design Approach
   2. From Planning Vacations to Biodesign
      1. From Design to Implementation
   3. Biodesign Process Overview
      1. Identify an Area and Challenge
      2. Brainstorm Solutions to the Challenge
      3. Decide on an Approach
      4. Specify Your System with Devices, Parts, and DNA
   4. What’s Next?
   5. Additional Reading and Resources
4. 3. Fundamentals of DNA Engineering
   1. Framing the Discussion
   2. Standardization of Parts and Measurements
      1. What Is Standardization?
      2. Competing Standards
      3. How Standards Are Established
   3. DNA Engineering in Practice
      1. DNA Assembly Basics
      2. Applying the Basics of DNA Assembly
   4. What’s Next?
   5. Additional Reading and Resources
5. 4. Fundamentals of Bioethics
   1. What Makes “Good Work”?
   2. Regulating for Ethical Research
      1. Scientific Advances Raise Ethical Questions
      2. Public Response
   3. Three Synthetic Biology Case Studies
      1. Grow-Your-Own Glowing Plants
      2. “Creating” Genomes
      3. Biosynthetic Drugs and the Economics of Public Benefit
   4. Group Bioethics Activities
      1. Bioethics Involves a Decision-Making Process
      2. Stakeholder Activity
   5. Additional Reading and Resources
6. 5. Introduction to the BioBuilder Labs
   1. Biological Engineering with Synthetic Biology’s Toolkit
7. 6. Eau That Smell
   1. Inspiration from the Eau d’coli iGEM Project
      1. Identify a Challenge
      2. Brainstorm Solutions
      3. System-Level Design
      4. Device-Level Design
      5. System-Level Design, Revised
      6. Device-Level Design, Revised
      7. Parts-Level Design
      8. Final Device and System-Level Edits
   2. Additional Reading and Resources
   3. Eau That Smell Lab
      1. Design Choices
      2. Experimental Question
      3. Getting Started
      4. Lab Protocol
8. 7. iTune Device
   1. Modularity
   2. Insulation
   3. Principles of Measurement
      1. What’s Normally Measured
      2. Making and Reporting Measurements for Synthetic Biology
   4. Foundational Concepts for the iTune Device Lab
      1. Promoters and RBSs
      2. The Lac Operon
   5. Additional Reading and Resources
   6. iTune Device Lab
      1. Design Choices
      2. Experimental Question
      3. Getting Started
      4. Lab Protocol
9. 8. Picture This
   1. Introduction to Modeling
      1. Computational Modeling
      2. Physical Modeling
   2. Inspiration from the “Coliroid” iGEM Project
      1. Device-Level Design
      2. Parts-Level Design
   3. Additional Reading and Resources
   4. Picture This Lab
      1. Design Choices
      2. Bacterial Photographs
      3. TinkerCell Modeling
      4. Electronic Circuit Modeling
10. 9. What a Colorful World
    1. Introduction to Chassis
       1. Utility, and How to Engineer It
       2. Safety, and How to Engineer It
    2. Background on the E. chromi iGEM Project
       1. About Their Devices
       2. Parts and Devices
    3. Additional Reading and Resources
    4. What a Colorful World Lab
       1. Design Choices
       2. Experimental Question
       3. Getting Started
       4. Lab Protocol
11. 10. Golden Bread
    1. Engineering Reliability
       1. Scheduled Maintenance
       2. Redundancy
       3. Building Robust Systems
    2. Background on the “VitaYeast” iGEM Project
       1. Motivation
       2. Parts-Level and Device-Level Design
    3. Additional Reading and Resources
    4. Golden Bread Lab
       1. Design Choices
       2. Experimental Question
       3. Getting Started
       4. Lab Protocol
       5. Transforming VitaYeast
12. A. Laboratory Reagents and Materials
    1. Equipment
    2. Reagent Preparation and Storage
       1. Solid and Liquid Media
       2. Stock Solutions
       3. Buffers
       4. Miscellaneous
13. Glossary
14. Index