CH391L/S13/Topics
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== New Topics == | == New Topics == | ||
| + | |||
| + | === ''In vitro'' Biology === | ||
| + | |||
| + | [http://www.ncbi.nlm.nih.gov/pubmed?term=Validation%20of%20an%20entirely%20in%20vitro%20approach%20for%20rapid%20prototyping%20of%20DNA%20regulatory%20elements%20for%20synthetic%20biology Validation of an entirely in vitro approach for rapid prototyping of DNA regulatory elements for synthetic biology]<cite>invitro</cite> | ||
| + | <biblio> | ||
| + | #invitro pmid=23371936 | ||
| + | // 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. | ||
| + | </biblio> | ||
=== Algal biofuels === | === Algal biofuels === | ||
| Line 31: | Line 39: | ||
#Langecker pmid=23161995 | #Langecker pmid=23161995 | ||
// DNA origami to design functional structures | // DNA origami to design functional structures | ||
| + | #Langecker pmid=22722847 | ||
| + | // Programmable single-cell mammalian biocomputers | ||
</biblio> | </biblio> | ||
| Line 78: | Line 88: | ||
===Dental Probiotics=== | ===Dental Probiotics=== | ||
| + | |||
| + | <biblio> | ||
| + | #Russell2012 pmid=12369203 | ||
| + | //Genetically modified Streptococcus mutans for the prevention of dental caries | ||
| + | </biblio> | ||
| + | |||
| + | ===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? <br> | ||
| + | |||
| + | ===Biocontainment=== | ||
| + | <biblio> | ||
| + | #Moe-Behrens2013 pmid=23355834 | ||
| + | //Preparing synthetic biology for the world | ||
| + | </biblio> | ||
| + | |||
| + | ===CRISPR Genome Editing=== | ||
| + | Papers described here | ||
| + | http://www.sciencemag.org/content/339/6121/768.summary | ||
== Topic Updates == | == Topic Updates == | ||
Revision as of 19:46, 17 February 2013
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
New Topics
In vitro Biology
Validation of an entirely in vitro approach for rapid prototyping of DNA regulatory elements for synthetic biology[1]
- Chappell J, Jensen K, and Freemont PS. . pmid:23371936.
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
- Ausländer S, Ausländer D, Müller M, Wieland M, and Fussenegger M. . pmid:22722847.
Programmable single-cell mammalian biocomputers - Langecker M, Arnaut V, Martin TG, List J, Renner S, Mayer M, Dietz H, and Simmel FC. . pmid:23161995.
DNA origami to design functional structures
Spider Goats
"Spider Goats" - synthetic silk production. Video - http://www.fieldtest.us/bio.shtml
Pathogen synthesis
- Cello J, Paul AV, and Wimmer E. . pmid:12114528.
Polio virus - Herfst S, Schrauwen EJ, Linster M, Chutinimitkul S, de Wit E, Munster VJ, Sorrell EM, Bestebroer TM, Burke DF, Smith DJ, Rimmelzwaan GF, Osterhaus AD, and Fouchier RA. . pmid:22723413.
AIrborne H5N1 - Russell CA, Fonville JM, Brown AE, Burke DF, Smith DL, James SL, Herfst S, van Boheemen S, Linster M, Schrauwen EJ, Katzelnick L, Mosterín A, Kuiken T, Maher E, Neumann G, Osterhaus AD, Kawaoka Y, Fouchier RA, and Smith DJ. . pmid:22723414.
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
- Davidson ME, Harbaugh SV, Chushak YG, Stone MO, and Kelley-Loughnane N. . pmid:23092157.
DNT/TNT riboswitch - Ehrentreich-Förster E, Orgel D, Krause-Griep A, Cech B, Erdmann VA, Bier F, Scheller FW, and Rimmele M. . pmid:18504560.
TNT aptamer - Stojanovic MN, de Prada P, and Landry DW. . pmid:11457319.
Cocaine aptamer biosensor - Stojanovic MN and Landry DW. . pmid:12175205.
Cocaine aptamer biosensor, next iteration
Gene Therapy
Spermless Mosquitos Mate without Offspring
Mussel bioadhesives
http://techportal.eere.energy.gov/technology.do/techID=562
Dental Probiotics
- Hillman JD. . pmid:12369203.
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
- Moe-Behrens GH, Davis R, and Haynes KA. . pmid:23355834.
Preparing synthetic biology for the world
CRISPR Genome Editing
Papers described here http://www.sciencemag.org/content/339/6121/768.summary
Topic Updates
Refactoring
- Temme K, Zhao D, and Voigt CA. . pmid:22509035.
Refactoring Nitrogen fixation gene cluster
Ancestral Sequence Reconstruction
Other
Humor
https://www.facebook.com/IgemMemes
Software
Other synthetic biology courses
http://soslab.ee.washington.edu/synthbio/index.php/Main_Page
