Virginia United/2010/Readings/Responses/UVA/Assignment1
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)
Five Hard Truths for Synthetic Biology
1) Many of the parts are undefined -researchers find it unable to characterize all the parts within an engineered biological system -genes being introduced into the system work unpredictably in different configuration and conditions -most of the time, too complex to capture by standardized characterization
2) The circuitry is unpredictable -laborious process of trial and error -Reduce the guesswork by using computer modeling -directed evolution
3)The complexity is unwieldy Solution: -Automated process to combine genetic parts, which might involve assembly using "robots"
4)Many parts are incompatible
-Solutions:
-orthogonal systems that operate independently
-parallel systems which allow tweaking components without disrupting stability of the the biological system
-physically isolate the synthetic network from the rest of the cell
5)Variability crashes the system -Solutions: -Synchronize blinking by relying on cell-cell communication -Use more accurate DNA replication machine
Applications: bio-fuel production
Yong Y. Wu 16:28, 25 January 2010 (EST)