Synthetic Biology

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Synthetic Biology

• Lecture 1 Introduction to Synthetic Biology

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What is Synthetic Biology?

• Genetic Manipulation?
• Genetic selection carried out for millenia
  (domestication of animals)
• Mendelian selection rationalized process.
• Recombinant DNA

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Engineering Goal To build components that can
be reliably and predictably assembled into ever
more complicated systems
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Fumbling Around

• Current Systems are Art

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Recombinant DNA
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Genetic Tools
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Scissors
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Glue
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Vectors
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Synthesizing DNA
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These are Tools, but
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We want to create complex systems
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EE in the beginning
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How useful is Maxwell?
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Abstraction Works for EM
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Composability

• OK - suppose we have individual parts that work,
  can we actually put them together such that they
  work in a well-defined/predictable way?

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Standardization

• Assembly
• Part Definition
• Interactions
• Load
• Input/Output
• Stability

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Standardizing a Part

• BioBrick - standard ends, restrictions on
  internal sequence

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Standard Assembly
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Standard Assembly
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Now we can share!
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What constitutes a part?

• The DNA Sequence?
• The function?

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Parts Basic biological functions encoded as DNA
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DNA Sequence

• TAATACGACTCACTATAGGGAGA
• (T7 promoter)

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Load Imposing on our Hosts

• Parts dont exist in a vacuum.
• Cells may dislike the parts, resulting in
  mutation or rejection
• Too much modification may result in cells that
  just give up and die

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Standard Measurement
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Our Parts arent necessarily Stable

• Anything that adds load to a cell reduces its
  fitness vs. cells that lose the part
• Mutations Losing a plasmid, alteration of
  promoters to not work as efficiently (or not at
  all)
• Antibiotic resistance, dependence

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Application Goals

• Bacterial robotics
• Microbial factories
• Adding features to plants to reduce environmental
  requirements/impact

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Cancer Destroying Robot
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Adding Computation to Cells
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Bacterial Communication Networks
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Artemisinin
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Public Policy
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gmo.jpg
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Is the fear so Irrational?

• We claim we can make all sorts of cool things,
  why not something evil?

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Major Risks
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What is different now?

• Rapid Sequencing
• Lots of sequence data on the internet
• Protocols available online
• Fedex Synthesis
• Data on Pathogens?

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The good news

• Major weaponized biological agents have existed
  for decades
• Virulence, resistance, transmissibility were all
  enhanced prior to SB.
• The major advantage of our approach is putting
  together well characterized components.
• Creating new pathogens would require a full scale
  research effort

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Summary

• Engineering instead of Science
• Modularity and Abstraction are powerful
  techniques
• Mechanical Engineering, Electrical Engineering
  were all at the stage where it was too
  complicated.