CH391L/S12/Assignments: Difference between revisions
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== Other topic ideas == | == Other topic ideas == | ||
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* Computer-Aided Design (CAD) systems for synthetic biology - OPEN | * Computer-Aided Design (CAD) systems for synthetic biology - OPEN | ||
== For Monday, April | == Final Project Groups == | ||
{| border=1 cellpadding=3 cellspacing=0 | |||
!Project | |||
!Group | |||
|- | |||
|Caffeine | |||
| Erik, Brian, Midhat, Peter | |||
|- | |||
|Spinach | |||
|Mike, Jon, Logan, Jeremy | |||
|- | |||
|Snow Globe | |||
|Adam, Yi, Razan, Ben, (Jeff) | |||
|- | |||
|Zombie Apocalypse | |||
| David, Joe, Jared | |||
|} | |||
== For Monday, April 30, 2012 == | |||
Final project presentations! | |||
== For Monday, April 23, 2012 == | == For Monday, April 23, 2012 == | ||
As a group we will read three papers | As a group we will all read these three papers and discuss them in class on April 23 in detail. | ||
=== Nominated Papers === | === Papers to Read === | ||
<biblio> | |||
#Gallivan pmid=20453864 | |||
//Atrazine seek and destroy | |||
Votes: Barrick, Meyer, Truong, Yi, Bachman | |||
#Chin pmid=20154731 | |||
//Encoding multiple unnatural amino acids via evolution of a quadruplet-decoding ribosome | |||
Votes: Meyer, Truong, Yi, Barrick | |||
#Chang pmid=21847113 | |||
//Engineering microbes to sense and eradicate ''Pseudomonas aeruginosa'', a human pathogen | |||
Votes: Meyer, Truong, Patel | |||
</biblio> | |||
=== Other Nominated Papers === | |||
(Vote by placing your name in the comments after a paper. You can vote for as many as you would like). | (Vote by placing your name in the comments after a paper. You can vote for as many as you would like). | ||
''Voting is over --April 16''' | |||
<biblio> | <biblio> | ||
# | #Voigt pmid=21035461 | ||
// | //Multichromatic Control of Gene Expression in ''Escherichia coli'' | ||
Votes: | Votes: Meyer (vote retracted, Jared covered this) | ||
#Danino pmid=20090747 | |||
//A synchronized quorum of genetic clocks. This is a very nice paper featuring logic circuits, oscillators, and quorum sensing. | |||
Votes: Meyer | |||
</biblio> | </biblio> | ||
== For Monday, April 16, 2012 == | == For Monday, April 16, 2012 == | ||
* Guest topic | Smell (or maybe magnetic yeast? Huh?) - Joe Hanson | ||
* Guest topic (2 PM) - Dr. Hal Alper (Chemical Engineering) | |||
Paper discussions. | |||
== For Monday, April 9, 2012 == | == For Monday, April 9, 2012 == | ||
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=== New Topics: Systems II === | === New Topics: Systems II === | ||
*Artemisinic acid engineering- | *Artemisinic acid engineering- Peter Otoupal | ||
*MAGE lycopene production - | *MAGE lycopene production, CAGE "Amberless" E. coli - Logan Bachman | ||
* | *Synthetic Cooperation - Jeremy McLain | ||
== For Monday, April 2, 2012 == | == For Monday, April 2, 2012 == | ||
Line 54: | Line 86: | ||
=== New Topics: Systems I === | === New Topics: Systems I === | ||
*Repressilator, counter, toggle swtich - | *Repressilator, counter, toggle swtich - Razan Alnahhas | ||
*Edge detection ''E. coli'' - | *Edge detection ''E. coli'' - Jared Ellefson | ||
*Refactored T7 and yeast - | *Refactored T7 and yeast - Jon Laurent | ||
== For Monday, March 26, 2012 == | == For Monday, March 26, 2012 == | ||
Line 65: | Line 97: | ||
*Quorum sensing - Brian Renda | *Quorum sensing - Brian Renda | ||
*Locomotion - | *Locomotion - Erik Quandt | ||
*Unnatural amino acids - Michael Hammerling | *Unnatural amino acids - Michael Hammerling | ||
Line 74: | Line 106: | ||
=== New Topics: Reporter Genes === | === New Topics: Reporter Genes === | ||
* Guest topic (2 PM) - Dr. Andy Ellington (Chemistry and Biochemistry) | |||
* Fluorescent/luminescent proteins (GFP, lux, variants) - Midhat Patel | * Fluorescent/luminescent proteins (GFP, lux, variants) - Midhat Patel | ||
* Pigments - | * Pigments - Yi Kou | ||
== For Monday, March 5, 2012 == | == For Monday, March 5, 2012 == |
Latest revision as of 08:01, 16 April 2012
Other topic ideas
- Riboswitches (synthetic and natural) - OPEN
- Directed evolution (plasmid-based in vivo evolution of thermostability, altered substrate specificity, etc) and/or phage display. - OPEN
- Possible reference [1]
- Gupta RD, Goldsmith M, Ashani Y, Simo Y, Mullokandov G, Bar H, Ben-David M, Leader H, Margalit R, Silman I, Sussman JL, and Tawfik DS. Directed evolution of hydrolases for prevention of G-type nerve agent intoxication. Nat Chem Biol. 2011 Feb;7(2):120-5. DOI:10.1038/nchembio.510 |
- Computer-Aided Design (CAD) systems for synthetic biology - OPEN
Final Project Groups
Project | Group |
---|---|
Caffeine | Erik, Brian, Midhat, Peter |
Spinach | Mike, Jon, Logan, Jeremy |
Snow Globe | Adam, Yi, Razan, Ben, (Jeff) |
Zombie Apocalypse | David, Joe, Jared |
For Monday, April 30, 2012
Final project presentations!
For Monday, April 23, 2012
As a group we will all read these three papers and discuss them in class on April 23 in detail.
Papers to Read
- Sinha J, Reyes SJ, and Gallivan JP. Reprogramming bacteria to seek and destroy an herbicide. Nat Chem Biol. 2010 Jun;6(6):464-70. DOI:10.1038/nchembio.369 |
Atrazine seek and destroy
Votes: Barrick, Meyer, Truong, Yi, Bachman
- Neumann H, Wang K, Davis L, Garcia-Alai M, and Chin JW. Encoding multiple unnatural amino acids via evolution of a quadruplet-decoding ribosome. Nature. 2010 Mar 18;464(7287):441-4. DOI:10.1038/nature08817 |
Encoding multiple unnatural amino acids via evolution of a quadruplet-decoding ribosome
Votes: Meyer, Truong, Yi, Barrick
- Saeidi N, Wong CK, Lo TM, Nguyen HX, Ling H, Leong SS, Poh CL, and Chang MW. Engineering microbes to sense and eradicate Pseudomonas aeruginosa, a human pathogen. Mol Syst Biol. 2011 Aug 16;7:521. DOI:10.1038/msb.2011.55 |
Engineering microbes to sense and eradicate Pseudomonas aeruginosa, a human pathogen
Votes: Meyer, Truong, Patel
Other Nominated Papers
(Vote by placing your name in the comments after a paper. You can vote for as many as you would like). Voting is over --April 16'
- Tabor JJ, Levskaya A, and Voigt CA. Multichromatic control of gene expression in Escherichia coli. J Mol Biol. 2011 Jan 14;405(2):315-24. DOI:10.1016/j.jmb.2010.10.038 |
Multichromatic Control of Gene Expression in Escherichia coli
Votes: Meyer (vote retracted, Jared covered this)
- Danino T, Mondragón-Palomino O, Tsimring L, and Hasty J. A synchronized quorum of genetic clocks. Nature. 2010 Jan 21;463(7279):326-30. DOI:10.1038/nature08753 |
A synchronized quorum of genetic clocks. This is a very nice paper featuring logic circuits, oscillators, and quorum sensing.
Votes: Meyer
For Monday, April 16, 2012
Smell (or maybe magnetic yeast? Huh?) - Joe Hanson
- Guest topic (2 PM) - Dr. Hal Alper (Chemical Engineering)
Paper discussions.
For Monday, April 9, 2012
New Topics: Systems II
- Artemisinic acid engineering- Peter Otoupal
- MAGE lycopene production, CAGE "Amberless" E. coli - Logan Bachman
- Synthetic Cooperation - Jeremy McLain
For Monday, April 2, 2012
- Comment on or add to old topics.
New Topics: Systems I
- Repressilator, counter, toggle swtich - Razan Alnahhas
- Edge detection E. coli - Jared Ellefson
- Refactored T7 and yeast - Jon Laurent
For Monday, March 26, 2012
- Comment on or add to old topics.
New Topics: Complex Parts
- Quorum sensing - Brian Renda
- Locomotion - Erik Quandt
- Unnatural amino acids - Michael Hammerling
For Monday, March 19, 2012
- Comment on or add to old topics.
New Topics: Reporter Genes
- Guest topic (2 PM) - Dr. Andy Ellington (Chemistry and Biochemistry)
- Fluorescent/luminescent proteins (GFP, lux, variants) - Midhat Patel
- Pigments - Yi Kou
For Monday, March 5, 2012
- Comment on or add to old topics.
New Topics: Gene Regulation
- Origins of Replication - Adam Meyer
- Protein regulators of transcription (Lac, Ara, etc) - Ben Slater
- Light sensing. Two-component systems - David Truong
For Monday, February 27, 2012
- Comment on or add to old topics.
New Topics: Basic Gene Construction
- Transcription: initiation and termination - Logan Bachman
- Spinach RNA - Jon Laurent
- Translation. Ribosome binding sites and codon optimization - Jeremy McLain
For Monday, February 20, 2012
- Comment on or add to old topics.
New Topics: Chassis and Backbones
- Selectable genetic markers (Ab resistance, etc.) - Peter Otoupal
- Toxin/anti-toxins, plasmid addiction systems - Brian Renda
- Counter-selectable genetic markers - Erik Quandt
For Monday, February 13, 2012
- Comment on or add to old topics.
New Topics: Optimizing Parts and their Interactions
- Gene/genome synthesis/Gibson assembly - Joe Hanson
- Host organisms (general properties of common ones, new ones that are being developed) - Michael Hammerling
- Metabolic engineering - Razan Alnahhas
For Monday, February 6, 2012
- Add a link to your user page to the CH391L Users Page.
- Add something to your user page.
- Comment on or add to old topics.
New Topics: Assembling Biological Parts
- Restriction enzyme cloning & BioBricks/BglBricks assembly - Ben Slater
- Advanced PCR techniques - Yi Kou
For Monday, January 30, 2012
- Register to use the OpenWetWare Wiki.
- Learn how to edit pages.
- Play around in the WIki sandbox.
- Leave at least one comment on the Talk page or make at least one addition to Introduction to Synthetic Biology
- Read the review article:
New Topics: Finding Biological Parts
- iGEM registry - Midhat Patel
- bioprospecting / metagenomics - David Truong
- directed evolution / in vitro selection - Adam Meyer
- ancestral protein construction - Jared Ellefson