20.20:Advanced topics: Difference between revisions

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PMID 3907859
PMID 3907859


|Ptashne “Two ‘What if” experiments”
|Ptashne “Two ‘What if” experiments” PMID 15055587<br>
[http://www.ncbi.nlm.nih.gov/pubmed/15055587?ordinalpos=12&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum]<br>
Brent “Build Artificial”
Brent “Build Artificial”
[http://www.ncbi.nlm.nih.gov/pubmed/15055588?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVAbstractPlus]<br>
PMID 15055588  
 
 
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| Natural systems are noisy
| Natural systems are noisy

Revision as of 20:21, 23 January 2008

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Advanced Topics in Synthetic Biology: reading schedule

Discussions will be 1 hour long during Wednesday 2-5 studio block
26-152

TOPIC DATE Discussion leader(s) Discussion paper(s) Related paper(s) to enjoy
A Voyage To Lilliput:
How a small number of AA substitution change activity of a protein 		Wed Feb 6 Natalie Kuldell and Drew Endy

Turning lambda Cro into a transcriptional activator
Bushman FD, Ptashne M.
Cell. 1988 Jul 15;54(2):191-7.
PMID 2968842

Slide rule optional:
Computational design of novel protein activities 		Wed Feb 13 2 presenters needed

Computational design of receptor and sensor proteins with novel functions
Looger LL, Dwyer MA, Smith JJ, Hellinga HW.
Nature. 2003 May 8;423(6936):185-90.
PMID 12736688

Nature heart Legos™:
Proteins are modular too 		Wed Feb 20 2 presenters needed

A eukaryotic transcriptional activator bearing the DNA specificity of a prokaryotic repressor.
Brent R, Ptashne M.
Cell. 1985 Dec;43(3 Pt 2):729-36.
PMID 3907859

Ptashne “Two ‘What if” experiments” PMID 15055587

Brent “Build Artificial” PMID 15055588

Natural systems are noisy Wed Feb 27 Hysteresis and noise
Wed Mar 5 NK and DE OoT
Natural systems can be intentionally changed to be useful Wed Mar 12 Protein induction systems
Natural systems can offer improved chassis Wed Mar 19 Metabolic engineering
Minimal genomes

Artificial cells [1]
Spring Break Mar 24-28 No class all week
Computational design of unnatural systems Wed Apr 2 Dwyer, Looger, Hellinga “Computational design of active enzyme”

Some ex of directed evolution
Building Logic gates
Expanding Nature’s Genetic Programming Language Wed Apr 9 Chin Schultz “expanded genetic code”

[2]
BK Davis commentary [3]
Recoli
Tx’l of polymers [4]

Programming artificial life Wed Apr 16 2 genomes 1 cell
1 cell to new cell
Populations of cells communicate Apr 23
Populations of cells make patterns Wed Apr 30
Freshmen Team Presentations Wed Apr 30, Wed May 7, Wed May 14

Grades for 20.902/20.947

Part 1: Readings

  • Paper 1 (15%): presented with a partner
  • Paper 2 (20%): presented solo
  • Response journal (15%): your thoughts about the papers you don't present. [link here]

Part 2: Team Mentoring

  • Progress reports (25%): 2x one page summary of your freshman team's work, [due x, and y]
  • Mentoring journal (10%): 2x one page summary of your freshman team's dynamics, [due x, and y]
  • Team briefing average (10%): based on the grade for your freshman team
  • Instructor Leverage (5%): discretionary adjustment by NK and DE
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