CH391L/S13/Assignments
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= For Monday, January 28th, 2013 = | = For Monday, January 28th, 2013 = | ||
| - | * Register to use the OpenWetWare Wiki. | + | * [[OpenWetWare:How_to_join|Register to use the OpenWetWare Wiki.]] |
| - | * Learn how to [[CH391L/ | + | * Learn how to [[CH391L/S13/WikiEditing|edit pages]]. |
* Play around in the [[Sandbox|WIki sandbox]]. | * Play around in the [[Sandbox|WIki sandbox]]. | ||
| + | * Add your name to the [[CH391L/S13/Users|CH391L Users page]]. | ||
* Leave at least one comment on the Talk page or make at least one addition to either [[CH391L/S13/Introduction|Introduction to Synthetic Biology]] or [[CH391L/S13/Ethics|Ethics of synthetic biology]]. | * Leave at least one comment on the Talk page or make at least one addition to either [[CH391L/S13/Introduction|Introduction to Synthetic Biology]] or [[CH391L/S13/Ethics|Ethics of synthetic biology]]. | ||
* Add at least one event to the "Timeline of Synthetic Biology" in the [[CH391L/S13/Introduction|Introduction to Synthetic Biology]] with a link or citation. | * Add at least one event to the "Timeline of Synthetic Biology" in the [[CH391L/S13/Introduction|Introduction to Synthetic Biology]] with a link or citation. | ||
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=== New Topics: === | === New Topics: === | ||
| + | * [[CH391L/S13/Ethics|Ethics of synthetic biology]] ([[User:Neil_R_Gottel|Neil]]) | ||
| + | * [[CH391L/S13/DIY_SyntheticBiology|DIY Biology Movement ]]([[User:John_Hanks|John]]) | ||
* BioBricks and the iGEM registry (Tyler) | * BioBricks and the iGEM registry (Tyler) | ||
| - | |||
| - | |||
= For Monday, February 4th, 2013 = | = For Monday, February 4th, 2013 = | ||
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=== Topic Updates === | === Topic Updates === | ||
| - | + | * [[CH391L/S13/Ethics|Ethics of synthetic biology]] <cite>ethics</cite> | |
| - | * [[CH391L/S13/ | + | * DIY Biology<cite>Kelty2010</cite> |
| - | * | + | * BioBricks and the iGEM registry <cite>Endy2009</cite> |
| - | === | + | ===Papers for Discussion=== |
<biblio> | <biblio> | ||
| - | # | + | #ethics [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2837218/ Playing God in Frankenstein's Footsteps: Synthetic Biology and the Meaning of Life] |
| - | // | + | |
| + | //For Bioethics | ||
| + | #Endy2009 pmid=19298678 | ||
| + | //For BioBricks | ||
| + | #Kelty2010 Outlaw, hackers, victorian amateurs: diagnosing public participation in the life sciences today [http://www.google.com/url?sa=t&rct=j&q=outlaw%2C%20hackers%2C%20victorian%20amateurs%3A%20diagnosing%20public%20participation%20in%20the%20life%20sciences%20today&source=web&cd=1&ved=0CDIQFjAA&url=http%3A%2F%2Fjcom.sissa.it%2Farchive%2F09%2F01%2FJcom0901(2010)C01%2FJcom0901(2010)C03%2FJcom0901(2010)C03.pdf&ei=kxIHUbD2GMy_2QX89YGYAg&usg=AFQjCNEdkOua-21aVHkR2wvRv6SiNrEVMQ&sig2=o5F9qPJQ-os8J49rbAM43A&bvm=bv.41524429,d.b2I pdf] | ||
| + | //For DIY Biology | ||
</biblio> | </biblio> | ||
=== New Topics === | === New Topics === | ||
| - | |||
| - | |||
* CAD for Synthetic Biology (Kevin) | * CAD for Synthetic Biology (Kevin) | ||
| + | * [[CH391L/S13/DnaAssembly | DNA Assembly: From Genes to Genomes]] (Gabe) <cite>Gibson2008</cite> | ||
= For Monday, February 11th, 2013 = | = For Monday, February 11th, 2013 = | ||
| + | |||
| + | === Topic Updates === | ||
| + | * CAD for Synthetic Biology (Kevin) | ||
| + | * Chris Yellman and Randy Hughes will discuss the paper for [[CH391L/S13/DnaAssembly | DNA Assembly: From Genes to Genomes]]<cite>Gibson2008</cite> | ||
| + | |||
| + | ===Papers for Discussion=== | ||
| + | |||
| + | <biblio> | ||
| + | #Gibson2008 pmid=18218864 | ||
| + | //Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. For DNA synthesis and assembly | ||
| + | #iGEMSoftware http://igem.synbioreview.com/ | ||
| + | #iGEMAbstracts 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 | ||
| + | </biblio> | ||
=== New Topics === | === New Topics === | ||
| - | * | + | * Minimal / "clean" genomes (Evan) |
| - | * | + | * [[CH391L/S13/Functional Nucleic Acids | Functional Nucleic Acids]] --[[User:Alvaro E. Rodriguez M.|Alvaro E. Rodriguez M.]] 21:50, 27 January 2013 (EST) |
| - | + | ||
= For Monday, February 18th, 2013 = | = For Monday, February 18th, 2013 = | ||
| + | |||
| + | === Topic Updates === | ||
| + | * Minimal / "clean" genomes (Evan) | ||
| + | * Functional Nucleic Acids (Alvaro) | ||
| + | |||
| + | ===Papers for Discussion=== | ||
| + | |||
| + | <biblio> | ||
| + | #Posfai2006 pmid=16645050 | ||
| + | //Emergent properties of reduced-genome Escherichia coli. For minimal genomes. | ||
| + | #Ohuchi2007 pmid=17884697 | ||
| + | //The flexizyme system: a highly flexible tRNA aminoacylation tool for the translation apparatus. For in vitro selection. | ||
| + | #Murakami2006 pmid=17150804 | ||
| + | //Flexizyme as a versatile tRNA acylation catalyst and the application for translation. For in vitro selection. | ||
| + | </biblio> | ||
=== New Topics === | === New Topics === | ||
| - | * | + | * [[Ancestral sequence reconstruction]] (Aurko) |
* Bioprospecting / Metagenomics (Andre) | * Bioprospecting / Metagenomics (Andre) | ||
| - | * New Marker Genes | + | |
| + | = For Monday, February 25th, 2013 = | ||
| + | |||
| + | ===Papers for Discussion=== | ||
| + | <biblio> | ||
| + | #Risso2013 pmid=23394108 | ||
| + | //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. For Metagenomic bioprospecting. | ||
| + | </biblio> | ||
| + | |||
| + | === New Topics === | ||
| + | * Directed protein evolution (Max) | ||
| + | * Riboswitches (Kate) | ||
| + | * [[CH391L/S13/Optogenetics | Optogenetics]] (Sid) | ||
| + | |||
| + | = For Monday, March 4th, 2013 = | ||
| + | |||
| + | ===Papers for Discussion=== | ||
| + | <biblio> | ||
| + | #Giver1998 pmid=9788996 | ||
| + | //Directed evolution of a thermostable esterase. For directed protein evolution. | ||
| + | #Davidson2012 pmid=23092157 | ||
| + | //Development of a 2,4-dinitrotoluene-responsive synthetic riboswitch in ''E. coli'' cells. For riboswitches. | ||
| + | </biblio> | ||
| + | |||
| + | ===New Topics=== | ||
| + | * [[CH391L/S13/QuorumSensing | Quorum Sensing (Larry)]] | ||
| + | * Biocontainment (Thomas) | ||
| + | * New Marker Genes (Ben) | ||
| + | * Optional: Biological material assembly and patterning - Belcher virus work (Marco) | ||
| + | |||
| + | = For Monday, March 18th, 2013 = | ||
| + | |||
| + | Brainstorm ideas for final projects. | ||
| + | |||
| + | = For Monday, March 25th, 2013 = | ||
| + | |||
| + | Topics and groups for final projects due. | ||
| + | |||
| + | = For Monday, April 1st, 2013 = | ||
| + | |||
| + | = For Monday, April 8th, 2013 = | ||
| + | |||
| + | = For Monday, April 15th, 2013 = | ||
| + | |||
| + | = For Monday, April 22nd, 2013 = | ||
Revision as of 20:16, 3 March 2013
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
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 Metagenomic bioprospecting.
New Topics
- Directed protein evolution (Max)
- Riboswitches (Kate)
- Optogenetics (Sid)
For Monday, March 4th, 2013
Papers for Discussion
- Giver L, Gershenson A, Freskgard PO, and Arnold FH. . pmid:9788996.
Directed evolution of a thermostable esterase. For directed protein evolution. - Davidson ME, Harbaugh SV, Chushak YG, Stone MO, and Kelley-Loughnane N. . pmid:23092157.
Development of a 2,4-dinitrotoluene-responsive synthetic riboswitch in E. coli cells. For riboswitches.
New Topics
- Quorum Sensing (Larry)
- Biocontainment (Thomas)
- New Marker Genes (Ben)
- Optional: Biological material assembly and patterning - Belcher virus work (Marco)
For Monday, March 18th, 2013
Brainstorm ideas for final projects.
For Monday, March 25th, 2013
Topics and groups for final projects due.
