CH391L/S13/Assignments

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* [[OpenWetWare:How_to_join|Register to use the OpenWetWare Wiki.]]
* [[OpenWetWare:How_to_join|Register to use the OpenWetWare Wiki.]]
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* Learn how to [[CH391L/S12/WikiEditing|edit pages]].
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* 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)
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* [[CH391L/S13/DnaAssembly | DNA Assembly: From Genes to Genomes]] (Gabe)
 
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* Ethics/DIY Biology Movement (????)
 
= For Monday, February 4th, 2013 =
= For Monday, February 4th, 2013 =
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=== Topic Updates ===
=== Topic Updates ===
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* BioBricks and the iGEM registry
+
* [[CH391L/S13/Ethics|Ethics of synthetic biology]] <cite>ethics</cite>
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* [[CH391L/S13/DnaAssembly | DNA Assembly: From Genes to Genomes]] <cite>Gibson2008</cite>
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* DIY Biology<cite>Kelty2010</cite>
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* Ethics/DIY Biology Movement
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* BioBricks and the iGEM registry <cite>Endy2009</cite>
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===Highlighted Papers===
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===Papers for Discussion===
<biblio>
<biblio>
-
#Gibson2008 pmid=18218864
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#ethics [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2837218/ Playing God in Frankenstein's Footsteps: Synthetic Biology and the Meaning of Life]
-
//For DNA Assembly
+
 +
//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 ===
-
* Refactoring (Neil)
 
-
* Minimal / "clean" genomes (Evan)
 
* 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 ===
-
* Ancestral sequence reconstruction (Aurko)
+
* Minimal / "clean" genomes (Evan)
-
* Directed protein evolution (Max)
+
* [[CH391L/S13/Functional Nucleic Acids | Functional Nucleic Acids]] --[[User:Alvaro E. Rodriguez M.|Alvaro E. Rodriguez M.]] 21:50, 27 January 2013 (EST)
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* In vitro nucleic acid selection (Alvaro)
+
= 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 ===
-
* Biocontainment (Thomas)
+
* [[Ancestral sequence reconstruction]] (Aurko)
* Bioprospecting / Metagenomics (Andre)
* Bioprospecting / Metagenomics (Andre)
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* New Marker Genes (Ben)
+
 
 +
= 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 19:16, 3 March 2013


Contents

For Monday, January 28th, 2013

New Topics:

For Monday, February 4th, 2013

Topic Updates

Papers for Discussion

  1. Playing God in Frankenstein's Footsteps: Synthetic Biology and the Meaning of Life [ethics]
    For Bioethics

  2. Outlaw, hackers, victorian amateurs: diagnosing public participation in the life sciences today pdf [Kelty2010]
    For DIY Biology

  3. 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. PubMed HubMed [Endy2009]
    For BioBricks

New Topics

For Monday, February 11th, 2013

Topic Updates

Papers for Discussion

  1. 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. PubMed HubMed [Gibson2008]
    Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. For DNA synthesis and assembly

  2. http://igem.synbioreview.com/ [iGEMSoftware]
  3. http://2011.igem.org/Jamboree/Team_Abstracts [iGEMAbstracts]
    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

For Monday, February 18th, 2013

Topic Updates

  • Minimal / "clean" genomes (Evan)
  • Functional Nucleic Acids (Alvaro)

Papers for Discussion

  1. 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. PubMed HubMed [Posfai2006]
    Emergent properties of reduced-genome Escherichia coli. For minimal genomes.

  2. Ohuchi M, Murakami H, and Suga H. . pmid:17884697. PubMed HubMed [Ohuchi2007]
    The flexizyme system: a highly flexible tRNA aminoacylation tool for the translation apparatus. For in vitro selection.

  3. Murakami H, Ohta A, Goto Y, Sako Y, and Suga H. . pmid:17150804. PubMed HubMed [Murakami2006]
    Flexizyme as a versatile tRNA acylation catalyst and the application for translation. For in vitro selection.

All Medline abstracts: PubMed HubMed

New Topics

For Monday, February 25th, 2013

Papers for Discussion

  1. Risso VA, Gavira JA, Mejia-Carmona DF, Gaucher EA, and Sanchez-Ruiz JM. . pmid:23394108. PubMed HubMed [Risso2013]
    Hyperstability and substrate promiscuity in laboratory resurrections of Precambrian β-lactamases. For Ancestral protein reconstruction.

  2. 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. PubMed HubMed [Beja2000]
    Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. For Metagenomic bioprospecting.

All Medline abstracts: PubMed HubMed

New Topics

  • Directed protein evolution (Max)
  • Riboswitches (Kate)
  • Optogenetics (Sid)

For Monday, March 4th, 2013

Papers for Discussion

  1. Giver L, Gershenson A, Freskgard PO, and Arnold FH. . pmid:9788996. PubMed HubMed [Giver1998]
    Directed evolution of a thermostable esterase. For directed protein evolution.

  2. Davidson ME, Harbaugh SV, Chushak YG, Stone MO, and Kelley-Loughnane N. . pmid:23092157. PubMed HubMed [Davidson2012]
    Development of a 2,4-dinitrotoluene-responsive synthetic riboswitch in E. coli cells. For riboswitches.

All Medline abstracts: PubMed HubMed

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.

For Monday, April 1st, 2013

For Monday, April 8th, 2013

For Monday, April 15th, 2013

For Monday, April 22nd, 2013

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