CH391L/S13/Assignments

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* [[CH391L/S13/Ethics|Ethics of synthetic biology]] <cite>ethics</cite>
* [[CH391L/S13/Ethics|Ethics of synthetic biology]] <cite>ethics</cite>
-
* DIY Biology<cite>19298678</cite>
+
* DIY Biology<cite>Kelty2010</cite>
* BioBricks and the iGEM registry <cite>Endy2009</cite>
* BioBricks and the iGEM registry <cite>Endy2009</cite>
Line 39: Line 39:
=== New Topics ===
=== New Topics ===
-
* 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>
* [[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)
* [[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 ===
-
* Biocontainment (Thomas)
+
* [[Ancestral sequence reconstruction]] (Aurko)
* Bioprospecting / Metagenomics (Andre)
* Bioprospecting / Metagenomics (Andre)
-
* New Marker Genes  (Ben)
 
= For Monday, February 25th, 2013 =
= 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 ===
=== New Topics ===
-
* Optogenetics (Sid)
+
* Directed protein evolution (Max)
-
* TBD (Larry)
+
* Riboswitches (Kate)
* Riboswitches (Kate)
 +
* [[CH391L/S13/Optogenetics | Optogenetics]] (Sid)
= For Monday, March 4th, 2013 =
= For Monday, March 4th, 2013 =
-
* TBD (Jeremy)
+
 
-
* Biological material assembly and patterning - Belcher virus work (Marco)
+
===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 =
 +
 
 +
===Paper for Discussion===
 +
<biblio>
 +
#Prindle2011 pmid=22178928
 +
//A sensing array of radically coupled genetic 'biopixels'.
 +
</biblio>
 +
 
 +
===New Topics===
 +
* [http://openwetware.org/wiki/CH391L/S13/Algal_Biofuels Algal Biofuels] (Aurko)
 +
* Probiotics (Alvaro)
 +
* Brainstorm ideas for final projects!
 +
 
 +
= For Monday, March 25th, 2013 =
 +
 
 +
Discuss preliminary research into topics for final projects. Decide on topics and groups.
 +
 
 +
===Papers for Discussion===
 +
<biblio>
 +
#Hillman2002 pmid=12369203
 +
//Genetically modified Streptococcus mutans for the prevention of dental caries.
 +
#Tran2013 pmid=23236148
 +
//Production of unique immunotoxin cancer therapeutics in algal chloroplasts
 +
</biblio>
 +
 
 +
===New Topics===
 +
* Synthetic Meat/Organs (Sid)
 +
* Phage Therapy (Neil)
 +
 
 +
= For Monday, April 1st, 2013 =
 +
 
 +
===Papers for Discussion===
 +
<biblio>
 +
#Ott2008 pmid=18193059
 +
//Perfusion-decellularized matrix: using nature's platform to engineer a bioartificial heart.
 +
#Lu2009 pmid=19255432
 +
//Engineered bacteriophage targeting gene networks as adjuvants for antibiotic therapy.
 +
</biblio>
 +
 
 +
===New Topics===
 +
* Gas Vesicles (Larry)
 +
* DNA Computation (Tyler)
 +
* Operon Refactoring (Max)
 +
 
 +
= For Monday, April 8th, 2013 =
 +
 
 +
===Papers for Discussion===
 +
<biblio>
 +
#Bonnet2013 pmid=23539178
 +
//Amplifying genetic logic gates
 +
#Temme2012 pmid=22509035
 +
//Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca.
 +
</biblio>
 +
 
 +
===New Topics===
 +
* Biomaterials (Gabe)
 +
* Cell Printing / Scaffolding (Evan)
 +
* Genome Editing (Ben)
 +
 
 +
= For Monday, April 15th, 2013 =
 +
 
 +
===Papers for Discussion===
 +
<biblio>
 +
#Lazaris2002 pmid=11799236
 +
//Spider silk fibers spun from soluble recombinant silk produced in mammalian cells
 +
 
 +
#Jiang2013 pmid=23360965
 +
//RNA-guided editing of bacterial genomes using CRISPR-Cas systems
 +
</biblio>
 +
 
 +
===New Topics===
 +
* Metabolic Engineering (Thomas)
 +
* Genetic Circuits / Single-Molecule / Single-Cell / something  (Andre)
 +
 
 +
= For Monday, April 22nd, 2013 =
 +
 
 +
===Papers for Discussion===
 +
<biblio>
 +
#Keller2013 pmid=23530213
 +
//Exploiting microbial hyperthermophilicity to produce an industrial chemical, using hydrogen and carbon dioxide
 +
 
 +
#Elowitz2000 pmid=10659856
 +
//A synthetic oscillatory network of transcriptional regulators
 +
</biblio>
 +
 
 +
===New Topics===
 +
* Molecular Gastronomie (Kate)
 +
* Mechanosensing (Kevin)
 +
 
 +
= For Monday, April 29th, 2013 =
 +
 
 +
===Papers for Discussion===
 +
<biblio>
 +
#Boyle2012 pmid=23530213
 +
//A BioBrick compatible strategy for genetic modification of plants
 +
#Assadi-Porter2008 pmid=18221889
 +
// Efficient and rapid protein expression and purification of small high disulfide containing sweet protein brazzein in ''E. coli''
 +
#Follonier2012 pmid=22290643
 +
//Pressure to kill or pressure to boost: a review on the various effects and applications of hydrostatic pressure in bacterial biotechnology
 +
</biblio>

Revision as of 09:37, 24 April 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

Paper for Discussion

  1. Prindle A, Samayoa P, Razinkov I, Danino T, Tsimring LS, and Hasty J. . pmid:22178928. PubMed HubMed [Prindle2011]
    A sensing array of radically coupled genetic 'biopixels'.

New Topics

  • Algal Biofuels (Aurko)
  • Probiotics (Alvaro)
  • Brainstorm ideas for final projects!

For Monday, March 25th, 2013

Discuss preliminary research into topics for final projects. Decide on topics and groups.

Papers for Discussion

  1. Hillman JD. . pmid:12369203. PubMed HubMed [Hillman2002]
    Genetically modified Streptococcus mutans for the prevention of dental caries.

  2. Tran M, Van C, Barrera DJ, Pettersson PL, Peinado CD, Bui J, and Mayfield SP. . pmid:23236148. PubMed HubMed [Tran2013]
    Production of unique immunotoxin cancer therapeutics in algal chloroplasts

All Medline abstracts: PubMed HubMed

New Topics

  • Synthetic Meat/Organs (Sid)
  • Phage Therapy (Neil)

For Monday, April 1st, 2013

Papers for Discussion

  1. Ott HC, Matthiesen TS, Goh SK, Black LD, Kren SM, Netoff TI, and Taylor DA. . pmid:18193059. PubMed HubMed [Ott2008]
    Perfusion-decellularized matrix: using nature's platform to engineer a bioartificial heart.

  2. Lu TK and Collins JJ. . pmid:19255432. PubMed HubMed [Lu2009]
    Engineered bacteriophage targeting gene networks as adjuvants for antibiotic therapy.

All Medline abstracts: PubMed HubMed

New Topics

  • Gas Vesicles (Larry)
  • DNA Computation (Tyler)
  • Operon Refactoring (Max)

For Monday, April 8th, 2013

Papers for Discussion

  1. Bonnet J, Yin P, Ortiz ME, Subsoontorn P, and Endy D. . pmid:23539178. PubMed HubMed [Bonnet2013]
    Amplifying genetic logic gates

  2. Temme K, Zhao D, and Voigt CA. . pmid:22509035. PubMed HubMed [Temme2012]
    Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca.

All Medline abstracts: PubMed HubMed

New Topics

  • Biomaterials (Gabe)
  • Cell Printing / Scaffolding (Evan)
  • Genome Editing (Ben)

For Monday, April 15th, 2013

Papers for Discussion

  1. Lazaris A, Arcidiacono S, Huang Y, Zhou JF, Duguay F, Chretien N, Welsh EA, Soares JW, and Karatzas CN. . pmid:11799236. PubMed HubMed [Lazaris2002]
    Spider silk fibers spun from soluble recombinant silk produced in mammalian cells

  2. Jiang W, Bikard D, Cox D, Zhang F, and Marraffini LA. . pmid:23360965. PubMed HubMed [Jiang2013]
    RNA-guided editing of bacterial genomes using CRISPR-Cas systems

All Medline abstracts: PubMed HubMed

New Topics

  • Metabolic Engineering (Thomas)
  • Genetic Circuits / Single-Molecule / Single-Cell / something (Andre)

For Monday, April 22nd, 2013

Papers for Discussion

  1. Keller MW, Schut GJ, Lipscomb GL, Menon AL, Iwuchukwu IJ, Leuko TT, Thorgersen MP, Nixon WJ, Hawkins AS, Kelly RM, and Adams MW. . pmid:23530213. PubMed HubMed [Keller2013]
    Exploiting microbial hyperthermophilicity to produce an industrial chemical, using hydrogen and carbon dioxide

  2. Elowitz MB and Leibler S. . pmid:10659856. PubMed HubMed [Elowitz2000]
    A synthetic oscillatory network of transcriptional regulators

All Medline abstracts: PubMed HubMed

New Topics

  • Molecular Gastronomie (Kate)
  • Mechanosensing (Kevin)

For Monday, April 29th, 2013

Papers for Discussion

  1. Keller MW, Schut GJ, Lipscomb GL, Menon AL, Iwuchukwu IJ, Leuko TT, Thorgersen MP, Nixon WJ, Hawkins AS, Kelly RM, and Adams MW. . pmid:23530213. PubMed HubMed [Boyle2012]
    A BioBrick compatible strategy for genetic modification of plants

  2. Assadi-Porter FM, Patry S, and Markley JL. . pmid:18221889. PubMed HubMed [Assadi-Porter2008]
    Efficient and rapid protein expression and purification of small high disulfide containing sweet protein brazzein in E. coli

  3. Follonier S, Panke S, and Zinn M. . pmid:22290643. PubMed HubMed [Follonier2012]
    Pressure to kill or pressure to boost: a review on the various effects and applications of hydrostatic pressure in bacterial biotechnology

All Medline abstracts: PubMed HubMed
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