CH391L/S13/Topics

From OpenWetWare

Revision as of 03:24, 1 January 2013 (view source) Jeffrey E. Barrick (Talk | contribs) ← Previous diff		Revision as of 15:38, 5 March 2013 (view source) Evan J. Weaver (Talk | contribs) Next diff →
(21 intermediate revisions not shown.)
Line 4:		Line 4:
	http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0034368		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 ===		=== Recent/Upcoming Meetings ===
Line 10:		Line 20:
	http://sb6.biobricks.org/		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 19:		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 24:		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 54:		Line 92:
	</biblio>		</biblio>
-	=== Gene Therapy ===	+	=== 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 ===
Line 65:		Line 156:
	http://soslab.ee.washington.edu/synthbio/index.php/Main_Page		http://soslab.ee.washington.edu/synthbio/index.php/Main_Page
		+
		+	=== Notable iGEM Projects ===

---

Revision as of 15:38, 5 March 2013

This is a brainstorming page...

Contents 1 What is synthetic biology? 1.1 Videos 2 Recent/Upcoming Meetings 3 New Topics 3.1 Synthetic Biology Part II 3.2 In vitro Biology 3.3 Algal biofuels 3.4 DNA computation / nanomachines 3.5 Spider Goats 3.6 Pathogen synthesis 3.7 Riboswitches / Aptamer Biosensors 3.8 Gene Therapy 3.9 Spermless Mosquitos Mate without Offspring 3.10 Mussel bioadhesives 3.11 Dental Probiotics 3.12 Bioethics 3.13 Biocontainment 3.14 CRISPR Genome Editing 3.15 Gas Vesicles 4 Topic Updates 4.1 Refactoring 4.2 Ancestral Sequence Reconstruction 4.3 Genetic Circuits 5 Other 5.1 Humor 5.2 Software 5.3 Other synthetic biology courses 5.4 Notable iGEM Projects

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. . 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

2. 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

3. Cello J, Paul AV, and Wimmer E. . pmid:12114528. PubMed HubMed [Cello2002]

   Polio virus

4. 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. . pmid:22723413. PubMed HubMed [Herfst2012]

   AIrborne H5N1

5. 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. . pmid:22723414. PubMed 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

5. Davidson ME, Harbaugh SV, Chushak YG, Stone MO, and Kelley-Loughnane N. . pmid:23092157. PubMed HubMed [Russell2012]

   DNT/TNT riboswitch

6. 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

7. Stojanovic MN, de Prada P, and Landry DW. . pmid:11457319. PubMed HubMed [Stojanovic2001]

   Cocaine aptamer biosensor

8. 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

9. 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

5. 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

10. 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

11. 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