Difference between revisions of "CH391L/S13/Assignments"

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= For Monday, March 18th, 2013 =
 
= For Monday, March 18th, 2013 =
  
===Papers for Discussion===
+
===Paper for Discussion===
 
<biblio>
 
<biblio>
 
#Prindle2011 pmid=22178928
 
#Prindle2011 pmid=22178928
Line 123: Line 123:
  
 
===New Topics===
 
===New Topics===
* Algal Biofuels (Aurko)
+
* [http://openwetware.org/wiki/CH391L/S13/Algal_Biofuels Algal Biofuels] (Aurko)
 
* Probiotics (Alvaro)
 
* Probiotics (Alvaro)
 
* Brainstorm ideas for final projects!
 
* Brainstorm ideas for final projects!
Line 129: Line 129:
 
= For Monday, March 25th, 2013 =
 
= For Monday, March 25th, 2013 =
  
Topics and groups for final projects due.
+
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 =
 
= 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 =
 
= For Monday, April 8th, 2013 =
 +
 +
===Papers for Discussion===
 +
<biblio>
 +
#Bonnet2013 pmid=23539178
 +
//Amplify 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 =
 
= For Monday, April 15th, 2013 =
 +
 +
===New Topics===
 +
* Metabolic Engineering (Thomas)
 +
* Genetic Circuits / Single-Molecule / Single-Cell / something  (Andre)
  
 
= For Monday, April 22nd, 2013 =
 
= For Monday, April 22nd, 2013 =
 +
 +
===New Topics===
 +
* Molecular Gastronomie (Kate)
 +
* Mechanosensing (Kevin)

Revision as of 07:17, 4 April 2013


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. Measuring the activity of BioBrick promoters using an in vivo reference standard. J Biol Eng. 2009 Mar 20;3:4. DOI:10.1186/1754-1611-3-4 | PubMed ID:19298678 | 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. Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science. 2008 Feb 29;319(5867):1215-20. DOI:10.1126/science.1151721 | PubMed ID:18218864 | 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. Emergent properties of reduced-genome Escherichia coli. Science. 2006 May 19;312(5776):1044-6. DOI:10.1126/science.1126439 | PubMed ID:16645050 | HubMed [Posfai2006]
    Emergent properties of reduced-genome Escherichia coli. For minimal genomes.
  2. Ohuchi M, Murakami H, and Suga H. The flexizyme system: a highly flexible tRNA aminoacylation tool for the translation apparatus. Curr Opin Chem Biol. 2007 Oct;11(5):537-42. DOI:10.1016/j.cbpa.2007.08.011 | PubMed ID:17884697 | 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. Flexizyme as a versatile tRNA acylation catalyst and the application for translation. Nucleic Acids Symp Ser (Oxf). 2006(50):35-6. DOI:10.1093/nass/nrl018 | PubMed ID:17150804 | 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. Hyperstability and substrate promiscuity in laboratory resurrections of Precambrian β-lactamases. J Am Chem Soc. 2013 Feb 27;135(8):2899-902. DOI:10.1021/ja311630a | PubMed ID:23394108 | 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. Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science. 2000 Sep 15;289(5486):1902-6. PubMed ID:10988064 | 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. Directed evolution of a thermostable esterase. Proc Natl Acad Sci U S A. 1998 Oct 27;95(22):12809-13. PubMed ID:9788996 | 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. Development of a 2,4-dinitrotoluene-responsive synthetic riboswitch in E. coli cells. ACS Chem Biol. 2013 Jan 18;8(1):234-41. DOI:10.1021/cb300274g | PubMed ID:23092157 | 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. A sensing array of radically coupled genetic 'biopixels'. Nature. 2011 Dec 18;481(7379):39-44. DOI:10.1038/nature10722 | PubMed ID:22178928 | 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. Genetically modified Streptococcus mutans for the prevention of dental caries. Antonie Van Leeuwenhoek. 2002 Aug;82(1-4):361-6. PubMed ID:12369203 | 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. Production of unique immunotoxin cancer therapeutics in algal chloroplasts. Proc Natl Acad Sci U S A. 2013 Jan 2;110(1):E15-22. DOI:10.1073/pnas.1214638110 | PubMed ID:23236148 | 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. Perfusion-decellularized matrix: using nature's platform to engineer a bioartificial heart. Nat Med. 2008 Feb;14(2):213-21. DOI:10.1038/nm1684 | PubMed ID:18193059 | HubMed [Ott2008]
    Perfusion-decellularized matrix: using nature's platform to engineer a bioartificial heart.
  2. Lu TK and Collins JJ. Engineered bacteriophage targeting gene networks as adjuvants for antibiotic therapy. Proc Natl Acad Sci U S A. 2009 Mar 24;106(12):4629-34. DOI:10.1073/pnas.0800442106 | PubMed ID:19255432 | 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. Amplifying genetic logic gates. Science. 2013 May 3;340(6132):599-603. DOI:10.1126/science.1232758 | PubMed ID:23539178 | HubMed [Bonnet2013]
    Amplify Genetic Logic Gates
  2. Temme K, Zhao D, and Voigt CA. Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca. Proc Natl Acad Sci U S A. 2012 May 1;109(18):7085-90. DOI:10.1073/pnas.1120788109 | PubMed ID:22509035 | 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

New Topics

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

For Monday, April 22nd, 2013

New Topics

  • Molecular Gastronomie (Kate)
  • Mechanosensing (Kevin)