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Introduction to Synthetic Biology
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  1. Introduction to Synthetic Biology Dannenberg and Purdy 2012 (Tokos edits 2012)

  2. What is Synthetic Biology? • https://www.youtube.com/watch?v=rD5uNAMbDaQ

  3. ELECTRICAL engineering solution

  4. water = weight water<weight MECHANICAL engineering solution

  5. BIOLOGICAL engineering solution

  6. BIOLOGICAL engineering solution

  7. Genetic Engineering rDNA Sequencing PCR

  8. A LIVING HOUSE - Terreform’s Fab Tree Hab

  9. How is Synthetic Biology Different? Synthetic biology uses four principles not typically found in genetics, genomics, or molecular biology: abstraction, modularity, standardization, and design and modeling.

  10. Abstraction: • Abstraction - you can use parts/devices/systems without having to worry about how they work. • DNA makes parts. • Parts into devices. • Devices connected to make systems.

  11. Modularity: • parts, devices and systems - connected as self-contained units and combined in any combination you want

  12. Standardization: • All the “Tab A’s” fit into all the “Slot B’s.” • An everyday example - all light bulbs fit into any socket!

  13. Designing and modeling • build a model • test the devices capacity • improves design • tests basic biological assumptions that could be false

  14. Registry of Standard biological Parts • http://partsregistry.org/Main_Page

  15. DNA is DNA • E. Coli is our chassis • Can use parts from any organism • Can use parts made by a computer

  16. Abstraction Hierarchy a human invention designed to assist people in engineering complex systems Assemblies of devices make a system Assemblies of parts make up devices Sequences of DNA encode “parts”

  17. “Part” – sequence of DNA with human defined function AAAATGCACCCGCTGTCGATCAAACGCGCGGTGGCGAATATGGTGGTCAACGCCGCCCGTTATGGCAATGGCTGGGTCAAAGTCAGCAGCGGAACGGAGCCGAATCGCGCCTGGTTCCAGGTGGAAGATGACGGTCCGGGAATTGCGCCGGAACAACGTAAGCACCTGTTCCAGCCGTTTGTCCGCGGCGACAGTGCGCGCACCATTAGCGGCACGGGATTAGGGCTGGCAATTGTGCAGCGTATCGTGGATAACCATAACGGGATGCTGGAGCTTGGCACCAGCGAGCGGGGCGGGCTTTCCATTCGCGCCTGGCTGCCAGTGCCGGTAACGCGGGCGCAGGGCATGACAAAAGAAGGGTAATCTAGAGGCATCAAATAAAACGAAAGGCTCAGTCGAAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCCTGAGTAGGACAAATCCGCCGCC

  18. Parts assembled into Devices AAAATGCACCCGCTGTCGATCAAACGCGCGGTGGCGAATATGGTGGTCAACGCCGCCCGTTATGGCAATGGCTGGGTCAAAGTCAGCAGCGGAACGGAGCCGAATCGCGCCTGGTTCCAGGTGGAAGATGACGGTCCGGGAATTGCGCCGGAACAACGTAAGCACCTGTTCCAGCCGTTTGTCCGCGGCGACAGTGCGCGCACCATTAGCGGCACGGGATTAGGGCTGGCAATTGTGCAGCGTATCGTGGATAACCATAACGGGATGCTGGAGCTTGGCACCAGCGAGCGGGGCGGGCTTTCCATTCGCGCCTGGCTGCCAGTGCCGGTAACGCGGGCGCAGGGCATGACAAAAGAAGGGTAATCTAGAGGCATCAAATAAAACGAAAGGCTCAGTCGAAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCCTGAGTAGGACAAATCCGCCGCC

  19. Parts assembled into Devices AAAATGCACCCGCTGTCGATCAAACGCGCGGTGGCGAATATGGTGGTCAACGCCGCCCGTTATGGCAATGGCTGGGTCAAAGTCAGCAGCGGAACGGAGCCGAATCGCGCCTGGTTCCAGGTGGAAGATGACGGTCCGGGAATTGCGCCGGAACAACGTAAGCACCTGTTCCAGCCGTTTGTCCGCGGCGACAGTGCGCGCACCATTAGCGGCACGGGATTAGGGCTGGCAATTGTGCAGCGTATCGTGGATAACCATAACGGGATGCTGGAGCTTGGCACCAGCGAGCGGGGCGGGCTTTCCATTCGCGCCTGGCTGCCAGTGCCGGTAACGCGGGCGCAGGGCATGACAAAAGAAGGGTAATCTAGAGGCATCAAATAAAACGAAAGGCTCAGTCGAAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCCTGAGTAGGACAAATCCGCCGCC

  20. Device to System Plasmids and Transformation

  21. Now for the Good Part(2009 Cambridge iGEM Team)

  22. The Problem • Toxins contaminate the environment • Detection can be expensive and complicated • Can cheap bacteria be used as toxin indicators that change color in response to toxin levels?

  23. The Color-Generating Device • Contain violacein pigment devices (ORF from Chromobacterium violacein) Genes re-engineered to produce purple and green in E. Coli • If all 5 genes in the ORF are expressed - purple pigment produced • If third gene in ORF sequence is removed - green pigment produced

  24. The Chassis • To a Synthetic Biologist = Escherichia coli

  25. Bacterial transformation of Escherichia coli • Two different strains of E. coli (4-1 & 4-2) • Two different plasmids (pPRL & pGRN) • Can we expect the devices to behave the same in each strain, or will the chassis have an effect on the intensity of color produced?

  26. Creation of a Bacterial Cell Controlledby a Chemically Synthesized Genome Dan Gibson, +21, Ham Smith and Craig Venter Science (2010) 329: 52 M. mycoides genome transplanted to M. capricolum PCR for watermarks

  27. Creation of a Bacterial Cell Controlledby a Chemically Synthesized Genome Dan Gibson, +21, Ham Smith and Craig Venter Science (2010) 329: 52 Presidential Commission for the Study of Bioethical Issues New Directions: The Ethics of Synthetic Biology and Emerging Technologies December 2010