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What is synthetic biology?


Imperial College iGEM team documentary (50 min)

E. chromi

Recent/Upcoming Meetings

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
metabolic engineering
molecular gastronomy
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]

  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 | PubMed ID:23371936 | HubMed [invitro]

    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

DNA computation / nanomachines

  1. 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 | PubMed ID:22722847 | HubMed [Langecker]

    Programmable single-cell mammalian biocomputers

  2. 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 | PubMed ID:23161995 | HubMed [Langecker]

    DNA origami to design functional structures

All Medline abstracts: PubMed | HubMed

Spider Goats

"Spider Goats" - synthetic silk production. Video -

Pathogen synthesis

  1. 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 | PubMed ID:12114528 | HubMed [Cello2002]

    Polio virus

  2. 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 | PubMed ID:22723413 | HubMed [Herfst2012]

    AIrborne H5N1

  3. 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 | PubMed ID:22723414 | HubMed [Russell2012]

    AIrborne H5N1

All Medline abstracts: PubMed | HubMed

Airborne H5N1 publication debate

Riboswitches / Aptamer Biosensors

  1. 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 | PubMed ID:23092157 | HubMed [Russell2012]

    DNT/TNT riboswitch

  2. 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 | PubMed ID:18504560 | HubMed [Ehrentreich2008]

    TNT aptamer

  3. 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 | PubMed ID:11457319 | HubMed [Stojanovic2001]

    Cocaine aptamer biosensor

  4. 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 | PubMed ID:12175205 | HubMed [Stojanovic2002]

    Cocaine aptamer biosensor, next iteration

All Medline abstracts: PubMed | HubMed

Gene Therapy

Spermless Mosquitos Mate without Offspring

  1. 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 | PubMed ID:21825136 | HubMed [Thailayil2011]

Mussel bioadhesives

Dental Probiotics

  1. Hillman JD. Genetically modified Streptococcus mutans for the prevention of dental caries. Antonie Van Leeuwenhoek. 2002 Aug;82(1-4):361-6. PubMed ID:12369203 | HubMed [Russell2012]

    Genetically modified Streptococcus mutans for the prevention of dental caries


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?


  1. 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 | PubMed ID:23355834 | HubMed [Moe-Behrens2013]

    Preparing synthetic biology for the world

CRISPR Genome Editing

Papers described here

Gas Vesicles

Would be a new topic no one has chosen before.

Topic Updates


  1. 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 | PubMed ID:22509035 | HubMed [Temme2012]

    Refactoring Nitrogen fixation gene cluster

Ancestral Sequence Reconstruction

Genetic Circuits

Stuff like oscillators,double negative genetic circuits, etc.




Other synthetic biology courses

Notable iGEM Projects

Ideas for next time

  • Stochasticity / Noise