Difference between revisions of "CH391L/S13/Topics"

From OpenWetWare
Jump to: navigation, search
m
 
(29 intermediate revisions by 4 users not shown)
Line 1: Line 1:
 +
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
 +
 +
http://sb6.biobricks.org/
 +
 +
== New Topics ==
 +
 +
===Synthetic Biology Part II===
 +
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>
 +
bioremediation <br>
 +
metabolic engineering <br>
 +
molecular gastronomy <br>
 +
mechanoreceptors <br>
 +
biomineralization <br>
 +
lab grown meat/organs <br>
 +
cell printing/scaffolding (Evan)<br>
 +
genetic circuits <br>
 +
 +
=== ''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 7: Line 56:
 
#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 12: Line 63:
 
"Spider Goats" - synthetic silk production.  
 
"Spider Goats" - synthetic silk production.  
 
Video - http://www.fieldtest.us/bio.shtml
 
Video - http://www.fieldtest.us/bio.shtml
 
  
 
=== Pathogen synthesis ===
 
=== Pathogen synthesis ===
Line 28: Line 78:
 
http://www.nytimes.com/2011/12/27/science/debate-persists-on-deadly-flu-made-airborne.html?pagewanted=all&_r=0
 
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
 
http://www.sciencemag.org/content/336/6088/1521.full
 +
 +
=== Riboswitches / Aptamer Biosensors ===
 +
 +
<biblio>
 +
#Russell2012 pmid=23092157
 +
//DNT/TNT riboswitch
 +
#Ehrentreich2008 pmid=18504560
 +
//TNT aptamer
 +
#Stojanovic2001 pmid=11457319
 +
//Cocaine aptamer biosensor
 +
#Stojanovic2002 pmid=12175205
 +
//Cocaine aptamer biosensor, next iteration
 +
</biblio>
 +
 +
=== Gene Therapy ===
 +
 +
===Spermless Mosquitos Mate without Offspring===
 +
 +
<biblio>
 +
#Thailayil2011 pmid=21825136
 +
</biblio>
 +
 +
===Mussel bioadhesives===
 +
 +
http://techportal.eere.energy.gov/technology.do/techID=562
 +
 +
===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
 +
 +
===Gas Vesicles===
 +
 +
Would be a new topic no one has chosen before.
 +
 +
== Topic Updates ==
 +
 +
=== Refactoring ===
 +
 +
<biblio>
 +
#Temme2012 pmid=22509035
 +
//Refactoring Nitrogen fixation gene cluster
 +
</biblio>
 +
 +
=== Ancestral Sequence Reconstruction ===
 +
 +
http://fastml.tau.ac.il/
 +
 +
===Genetic Circuits===
 +
 +
Stuff like oscillators,double negative genetic circuits, etc.
 +
 +
== Other ==
  
 
=== Humor ===
 
=== Humor ===
  
 
https://www.facebook.com/IgemMemes
 
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

Latest revision as of 12:49, 15 April 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

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]

  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

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

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 - http://www.fieldtest.us/bio.shtml

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 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. 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. 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. 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

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

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

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. 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 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. 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

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