CH391L/S13/Topics

This is a brainstorming page...

What is synthetic biology?

http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0034368

http://www.buzzfeed.com/atmccann/how-to-code-a-life

Videos

Imperial College iGEM team documentary (50 min) http://www.youtube.com/watch?v=ushmgPM7HT8

E. chromi http://vimeo.com/19759432

Recent/Upcoming Meetings

http://www.keystonesymposia.org/index.cfm?e=web.Meeting.Program&meetingid=1238

http://sb6.biobricks.org/

New Topics

Synthetic Biology Part II

Algae/Biofuels (aurko)
DNA computation/fabrication (Tyler)
Spider goats
CRISPR genome editing (Ben)
gas vesicles
dental probiotics (Al)
mussel protein bioadhesive
bioremediation
metabolic engineering
molecular gastronomy
mechanoreceptors
biomineralization
lab grown meat/organs
cell printing/scaffolding (Evan)
genetic circuits

In vitro Biology

Validation of an entirely in vitro approach for rapid prototyping of DNA regulatory elements for synthetic biology[1]

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1. Using cell-free extracts of E. coli to eliminate transformation/selection/culturing/purification steps when testing new DNA parts and genetic circuits. Additionally, In vitro performance of the tested parts had a clear correlation to in vivo performance.

Algal biofuels

http://joulefuels.com/how-it-works

DNA computation / nanomachines

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2. Ausländer S, Ausländer D, Müller M, Wieland M, and Fussenegger M. Programmable single-cell mammalian biocomputers. Nature. 2012 Jul 5;487(7405):123-7. DOI:10.1038/nature11149 |

   Programmable single-cell mammalian biocomputers

2. DNA origami to design functional structures

Spider Goats

"Spider Goats" - synthetic silk production. Video - http://www.fieldtest.us/bio.shtml

Pathogen synthesis

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3. Polio virus

4. AIrborne H5N1

5. AIrborne H5N1

Airborne H5N1 publication debate http://www.nytimes.com/2011/12/27/science/debate-persists-on-deadly-flu-made-airborne.html?pagewanted=all&_r=0 http://www.sciencemag.org/content/336/6088/1521.full

Riboswitches / Aptamer Biosensors

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5. DNT/TNT riboswitch

6. TNT aptamer

7. Cocaine aptamer biosensor

8. Cocaine aptamer biosensor, next iteration

Spermless Mosquitos Mate without Offspring

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Mussel bioadhesives

http://techportal.eere.energy.gov/technology.do/techID=562

Dental Probiotics

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5. Genetically modified Streptococcus mutans for the prevention of dental caries

Bioethics

Asilomar:This likely fits into some ethics section. But would be useful to get a nice, reasonably detailed overview of this conference. It is referenced often in synthetic biology circles as a model for public disclosure and internal consistency within a field. Would be nice to understand where/how the analogy fits and maybe where it doesn't?

Biocontainment

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10. Preparing synthetic biology for the world

CRISPR Genome Editing

Papers described here http://www.sciencemag.org/content/339/6121/768.summary

Gas Vesicles

Would be a new topic no one has chosen before.

Topic Updates

Refactoring

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11. Refactoring Nitrogen fixation gene cluster

Ancestral Sequence Reconstruction

http://fastml.tau.ac.il/

Genetic Circuits

Stuff like oscillators,double negative genetic circuits, etc.

Other

Humor

https://www.facebook.com/IgemMemes

Other synthetic biology courses

http://soslab.ee.washington.edu/synthbio/index.php/Main_Page

Ideas for next time

• Stochasticity / Noise