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
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]
- Chappell J, Jensen K, and Freemont PS. Validation of an entirely in vitro approach for rapid prototyping of DNA regulatory elements for synthetic biology. Nucleic Acids Res. 2013 Mar 1;41(5):3471-81. DOI:10.1093/nar/gkt052 |
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. Programmable single-cell mammalian biocomputers. Nature. 2012 Jul 5;487(7405):123-7. DOI:10.1038/nature11149 |
Programmable single-cell mammalian biocomputers
- Langecker M, Arnaut V, Martin TG, List J, Renner S, Mayer M, Dietz H, and Simmel FC. Synthetic lipid membrane channels formed by designed DNA nanostructures. Science. 2012 Nov 16;338(6109):932-6. DOI:10.1126/science.1225624 |
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. Chemical synthesis of poliovirus cDNA: generation of infectious virus in the absence of natural template. Science. 2002 Aug 9;297(5583):1016-8. DOI:10.1126/science.1072266 |
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. Airborne transmission of influenza A/H5N1 virus between ferrets. Science. 2012 Jun 22;336(6088):1534-41. DOI:10.1126/science.1213362 |
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. The potential for respiratory droplet-transmissible A/H5N1 influenza virus to evolve in a mammalian host. Science. 2012 Jun 22;336(6088):1541-7. DOI:10.1126/science.1222526 |
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. Development of a 2,4-dinitrotoluene-responsive synthetic riboswitch in E. coli cells. ACS Chem Biol. 2013 Jan 18;8(1):234-41. DOI:10.1021/cb300274g |
DNT/TNT riboswitch
- Ehrentreich-Förster E, Orgel D, Krause-Griep A, Cech B, Erdmann VA, Bier F, Scheller FW, and Rimmele M. Biosensor-based on-site explosives detection using aptamers as recognition elements. Anal Bioanal Chem. 2008 Jul;391(5):1793-800. DOI:10.1007/s00216-008-2150-5 |
TNT aptamer
- Stojanovic MN, de Prada P, and Landry DW. Aptamer-based folding fluorescent sensor for cocaine. J Am Chem Soc. 2001 May 30;123(21):4928-31. DOI:10.1021/ja0038171 |
Cocaine aptamer biosensor
- Stojanovic MN and Landry DW. Aptamer-based colorimetric probe for cocaine. J Am Chem Soc. 2002 Aug 21;124(33):9678-9. DOI:10.1021/ja0259483 |
Cocaine aptamer biosensor, next iteration
Gene Therapy
Spermless Mosquitos Mate without Offspring
- Thailayil J, Magnusson K, Godfray HC, Crisanti A, and Catteruccia F. Spermless males elicit large-scale female responses to mating in the malaria mosquito Anopheles gambiae. Proc Natl Acad Sci U S A. 2011 Aug 16;108(33):13677-81. DOI:10.1073/pnas.1104738108 |
Mussel bioadhesives
http://techportal.eere.energy.gov/technology.do/techID=562
Dental Probiotics
- Hillman JD. Genetically modified Streptococcus mutans for the prevention of dental caries. Antonie Van Leeuwenhoek. 2002 Aug;82(1-4):361-6.
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. Preparing synthetic biology for the world. Front Microbiol. 2013;4:5. DOI:10.3389/fmicb.2013.00005 |
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
- Temme K, Zhao D, and Voigt CA. Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca. Proc Natl Acad Sci U S A. 2012 May 1;109(18):7085-90. DOI:10.1073/pnas.1120788109 |
Refactoring Nitrogen fixation gene cluster
Ancestral Sequence Reconstruction
Genetic Circuits
Stuff like oscillators,double negative genetic circuits, etc.
Other
Humor
https://www.facebook.com/IgemMemes
Software
Other synthetic biology courses
http://soslab.ee.washington.edu/synthbio/index.php/Main_Page
Notable iGEM Projects
Ideas for next time
- Stochasticity / Noise
