CH391L/S13/Topics

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(Synthetic Biology Part II)
Line 30: Line 30:
gas vesicles <br>
gas vesicles <br>
dental probiotics (Al) <br>
dental probiotics (Al) <br>
-
mussel protein bioadhesive <br>
+
mussel protein bioadhesive (Neil) <br>
bioremediation <br>
bioremediation <br>
metabolic engineering <br>
metabolic engineering <br>

Revision as of 15:00, 18 March 2013

This is a brainstorming page...

Contents

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 (Neil)
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]

  1. Chappell J, Jensen K, and Freemont PS. . pmid:23371936. PubMed 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

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

DNA computation / nanomachines

  1. Ausländer S, Ausländer D, Müller M, Wieland M, and Fussenegger M. . pmid:22722847. PubMed 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. . pmid:23161995. PubMed HubMed [Langecker]
    DNA origami to design functional structures

All Medline abstracts: PubMed HubMed

Spider Goats

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

Pathogen synthesis

Error fetching PMID 12114528:
Error fetching PMID 22723413:
Error fetching PMID 22723414:
  1. Error fetching PMID 12114528: [Cello2002]
    Polio virus

  2. Error fetching PMID 22723413: [Herfst2012]
    AIrborne H5N1

  3. Error fetching PMID 22723414: [Russell2012]
    AIrborne H5N1

All Medline abstracts: PubMed HubMed

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

  1. Davidson ME, Harbaugh SV, Chushak YG, Stone MO, and Kelley-Loughnane N. . pmid:23092157. PubMed 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. . pmid:18504560. PubMed HubMed [Ehrentreich2008]
    TNT aptamer

  3. Stojanovic MN, de Prada P, and Landry DW. . pmid:11457319. PubMed HubMed [Stojanovic2001]
    Cocaine aptamer biosensor

  4. Stojanovic MN and Landry DW. . pmid:12175205. PubMed 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. . pmid:21825136. PubMed HubMed [Thailayil2011]

Mussel bioadhesives

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

Dental Probiotics

  1. Hillman JD. . pmid:12369203. PubMed HubMed [Russell2012]
    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

  1. Moe-Behrens GH, Davis R, and Haynes KA. . pmid:23355834. PubMed HubMed [Moe-Behrens2013]
    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

  1. Temme K, Zhao D, and Voigt CA. . pmid:22509035. PubMed HubMed [Temme2012]
    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

Software

Other synthetic biology courses

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

Notable iGEM Projects

Personal tools