Virginia United/2010/Readings/Responses/UVA/Assignment1

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Virginia United 2010

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Assignment 1 Responses (Due Jan 25)

Example:

  • Paper title
    • Response
  • Paper 2 title
    • Response

Daniel R Tarjan 21:29, 24 January 2010 (EST)

Building outside of the Box: iGEM and the Biobricks Foundation

Main points:

  • Creating an open sharing platform of DNA constructs
  • Building a Registry of biobrick parts
  • Developing tools to make engineering biological systems easier (BBF & iGEM)

IGEM:

  • Synthetic biology competition held at MIT
  • Teams identify a real world problem and prototype engineered genetic programs as possible solutions

Synthetic Biology:

  • Relies on the decoupling design
  • Uses abstraction to manage biological complexity
  • Limitations:

1) Budget for de novo DNA synthesis -solution: share and reuse parts,Registry of parts 2) Challenges with gene synthesis -solution: optimize variable copy number vectors with enhanced transcriptional insulation 3) Too much time spent trying to understand how systems work -solution: abstraction hierarchy

Registry of Parts

  • Online catalog of parts
  • Purpose-streamline a process that can be used to make the integration of parts more reliable and efficient
  • iGEM competition fosters a quality control check by rewarding teams that contribute parts and improve technical standards

Biobrick Foundation:

  • Provide a legal framework for the collection of functional genetic elements encoding bio parts
  • RFC (request for comment)
  • Develop a contract between the inventor and user (determine terms of use,etc)
  • Reduce legal ambiguity around use and re-use of parts—BPA (Biobrick Public Agreement)


Five Hard Truths for Synthetic Biology

Challenges in the field:

1) Many of the parts are undefined -eliminate variations arising from experimental conditions and instruments by measuring promoter activity relative to a reference promoter (standard)

2) Circuitry is unpredictable -cells integrate genes in their genome unpredictably -requires trial and error process -computational modeling can be used for predictions -optimize the system with directed evolution: mutating DNA sequences, screening their performance, selecting the best candidates, repeat the process

3) Complexity is unwieldy -speed up biobrick assembly with assembler cells, selection cells, enzymes

4) Many parts are incompatible -genetic circuits can have unintended effects on host -solution: develop orthogonal systems that operate independently of the cell’s natural machinery

5) Variability crashes the system -i.e. growth conditions, noise, genetic mutations

Rohini Manaktala 23:59, 24 January 2010 (EST)

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