CH391L/S13/Topics

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== New Topics ==
== New Topics ==
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===Synthetic Biology Part II===
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Algae/Biofuels (aurko) <br>
 +
DNA computation/fabrication (Tyler) <br>
 +
Spider goats <br>
 +
CRISPR genome editing (Ben) <br>
 +
gas vesicles <br>
 +
dental probiotics (Al) <br>
 +
mussel protein bioadhesive <br>
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bioremediation <br>
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metabolic engineering <br>
 +
molecular gastronomy <br>
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mechanoreceptors <br>
 +
biomineralization <br>
 +
lab grown meat/organs <br>
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cell printing/scaffolding (Evan)<br>
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genetic circuits <br>
=== ''In vitro'' Biology ===
=== ''In vitro'' Biology ===
Line 123: Line 140:
http://fastml.tau.ac.il/
http://fastml.tau.ac.il/
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===Genetic Circuits===
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Stuff like oscillators,double negative genetic circuits, etc.
== Other ==
== Other ==
Line 137: Line 158:
=== Notable iGEM Projects ===
=== Notable iGEM Projects ===
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 +
=== Ideas for next time ===
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 +
* Stochasticity / Noise

Current revision

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
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]

Error fetching PMID 23371936:
  1. Error fetching PMID 23371936: [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

Error fetching PMID 23161995:
Error fetching PMID 22722847:
  1. Error fetching PMID 22722847: [Langecker]
    Programmable single-cell mammalian biocomputers

  2. Error fetching PMID 23161995: [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

Error fetching PMID 23092157:
Error fetching PMID 18504560:
Error fetching PMID 11457319:
Error fetching PMID 12175205:
  1. Error fetching PMID 23092157: [Russell2012]
    DNT/TNT riboswitch

  2. Error fetching PMID 18504560: [Ehrentreich2008]
    TNT aptamer

  3. Error fetching PMID 11457319: [Stojanovic2001]
    Cocaine aptamer biosensor

  4. Error fetching PMID 12175205: [Stojanovic2002]
    Cocaine aptamer biosensor, next iteration

All Medline abstracts: PubMed HubMed

Gene Therapy

Spermless Mosquitos Mate without Offspring

Error fetching PMID 21825136:
  1. Error fetching PMID 21825136: [Thailayil2011]

Mussel bioadhesives

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

Dental Probiotics

Error fetching PMID 12369203:
  1. Error fetching PMID 12369203: [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

Error fetching PMID 23355834:
  1. Error fetching PMID 23355834: [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

Error fetching PMID 22509035:
  1. Error fetching PMID 22509035: [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

Ideas for next time

  • Stochasticity / Noise
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