CH391L/S13/Assignments
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=== New Topics === | === New Topics === | ||
* [[Ancestral sequence reconstruction]] (Aurko) | * [[Ancestral sequence reconstruction]] (Aurko) | ||
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* Bioprospecting / Metagenomics (Andre) | * Bioprospecting / Metagenomics (Andre) | ||
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=== New Topics === | === New Topics === | ||
| - | * | + | * Directed protein evolution (Max) |
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* Riboswitches (Kate) | * Riboswitches (Kate) | ||
| + | * [[CH391L/S13/Optogenetics | Optogenetics]] (Sid) | ||
===Papers for Discussion=== | ===Papers for Discussion=== | ||
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#Risso2013 pmid=23394108 | #Risso2013 pmid=23394108 | ||
//Hyperstability and substrate promiscuity in laboratory resurrections of Precambrian β-lactamases. For Ancestral protein reconstruction. | //Hyperstability and substrate promiscuity in laboratory resurrections of Precambrian β-lactamases. For Ancestral protein reconstruction. | ||
| + | #Beja2000 pmid=10988064 | ||
| + | //Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. | ||
</biblio> | </biblio> | ||
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* TBD (Jeremy) | * TBD (Jeremy) | ||
* Biological material assembly and patterning - Belcher virus work (Marco) | * Biological material assembly and patterning - Belcher virus work (Marco) | ||
| + | * Quorum Sensing (Larry) | ||
| + | * Biocontainment (Thomas) | ||
| + | * New Marker Genes (Ben) | ||
Revision as of 19:44, 20 February 2013
Contents |
For Monday, January 28th, 2013
- Register to use the OpenWetWare Wiki.
- Learn how to edit pages.
- Play around in the WIki sandbox.
- Add your name to the CH391L Users page.
- Leave at least one comment on the Talk page or make at least one addition to either Introduction to Synthetic Biology or Ethics of synthetic biology.
- Add at least one event to the "Timeline of Synthetic Biology" in the Introduction to Synthetic Biology with a link or citation.
- Read articles for discussion:
New Topics:
- Ethics of synthetic biology (Neil)
- DIY Biology Movement (John)
- BioBricks and the iGEM registry (Tyler)
For Monday, February 4th, 2013
Topic Updates
- Ethics of synthetic biology [1]
- DIY Biology[2]
- BioBricks and the iGEM registry [3]
Papers for Discussion
- Playing God in Frankenstein's Footsteps: Synthetic Biology and the Meaning of Life
For Bioethics - Outlaw, hackers, victorian amateurs: diagnosing public participation in the life sciences today pdf
For DIY Biology - Kelly JR, Rubin AJ, Davis JH, Ajo-Franklin CM, Cumbers J, Czar MJ, de Mora K, Glieberman AL, Monie DD, and Endy D. . pmid:19298678.
For BioBricks
New Topics
- CAD for Synthetic Biology (Kevin)
- DNA Assembly: From Genes to Genomes (Gabe) [4]
For Monday, February 11th, 2013
Topic Updates
- CAD for Synthetic Biology (Kevin)
- Chris Yellman and Randy Hughes will discuss the paper for DNA Assembly: From Genes to Genomes[4]
Papers for Discussion
- Gibson DG, Benders GA, Andrews-Pfannkoch C, Denisova EA, Baden-Tillson H, Zaveri J, Stockwell TB, Brownley A, Thomas DW, Algire MA, Merryman C, Young L, Noskov VN, Glass JI, Venter JC, Hutchison CA 3rd, and Smith HO. . pmid:18218864.
Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. For DNA synthesis and assembly - http://igem.synbioreview.com/
- http://2011.igem.org/Jamboree/Team_Abstracts
Find a useful or neat tool from a past iGEM software competition using one of these links. Test drive it if possible. Be able to briefly describe what it does to class. For CAD
New Topics
- Minimal / "clean" genomes (Evan)
- Functional Nucleic Acids --Alvaro E. Rodriguez M. 21:50, 27 January 2013 (EST)
For Monday, February 18th, 2013
Topic Updates
- Minimal / "clean" genomes (Evan)
- Functional Nucleic Acids (Alvaro)
Papers for Discussion
- Pósfai G, Plunkett G 3rd, Fehér T, Frisch D, Keil GM, Umenhoffer K, Kolisnychenko V, Stahl B, Sharma SS, de Arruda M, Burland V, Harcum SW, and Blattner FR. . pmid:16645050.
Emergent properties of reduced-genome Escherichia coli. For minimal genomes. - Ohuchi M, Murakami H, and Suga H. . pmid:17884697.
The flexizyme system: a highly flexible tRNA aminoacylation tool for the translation apparatus. For in vitro selection. - Murakami H, Ohta A, Goto Y, Sako Y, and Suga H. . pmid:17150804.
Flexizyme as a versatile tRNA acylation catalyst and the application for translation. For in vitro selection.
New Topics
- Ancestral sequence reconstruction (Aurko)
- Bioprospecting / Metagenomics (Andre)
For Monday, February 25th, 2013
New Topics
- Directed protein evolution (Max)
- Riboswitches (Kate)
- Optogenetics (Sid)
Papers for Discussion
- Risso VA, Gavira JA, Mejia-Carmona DF, Gaucher EA, and Sanchez-Ruiz JM. . pmid:23394108.
Hyperstability and substrate promiscuity in laboratory resurrections of Precambrian β-lactamases. For Ancestral protein reconstruction. - Béjà O, Aravind L, Koonin EV, Suzuki MT, Hadd A, Nguyen LP, Jovanovich SB, Gates CM, Feldman RA, Spudich JL, Spudich EN, and DeLong EF. . pmid:10988064.
Bacterial rhodopsin: evidence for a new type of phototrophy in the sea.
For Monday, March 4th, 2013
- TBD (Jeremy)
- Biological material assembly and patterning - Belcher virus work (Marco)
- Quorum Sensing (Larry)
- Biocontainment (Thomas)
- New Marker Genes (Ben)
