20.20:Advanced topics

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Advanced Topics in Synthetic Biology: reading schedule

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

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

Better odds in Vegas:
DNA elements are modular too, allowing for circuits, but circuits don't always work
Wed Feb 27 2 presenters needed

Combinatorial synthesis of genetic networks. Guet CC, Elowitz MB, Hsing W, Leibler S.Science. 2002 May 24;296(5572):1466-70.
PMID 12029133

Wed Mar 5 NK and DE OoT
Darwin is alive and well:
Directed evolution at the device level
Wed Mar 12 2 presenters needed

Directed evolution of a genetic circuit.Yokobayashi Y, Weiss R, Arnold FH. Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16587-91.
PMID 12451174

Intelligent Design:
Functional composition at the device level
Wed Mar 19 2 presenters needed

A modular and extensible RNA-based gene-regulatory platform for engineering cellular function.Win MN, Smolke CD. Proc Natl Acad Sci U S A. 2007 Sep 4;104(36):14283-8.
PMID 17709748

Spring Break Mar 24-28 No class all week
Writing in genetic code:
DNA construction and editing technologies
Wed Apr 2 presenter
article 1:
article 2:
Article 1:
Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides.Stemmer WP, Crameri A, Ha KD, Brennan TM, Heyneker HL.

Gene. 1995 Oct 16;164(1):49-53.
PMID 7590320
Article 2: genome synthesis

Church automated editing paper, if available.
Also slashdot for genome synthesis
We're only human:
What is the state of the art?
Wed Apr 9 presenter
article 1:
article 2:
Article 1:
In vitro reprogramming of fibroblasts into a pluripotent ES-cell-like state.Wernig M, Meissner A, Foreman R, Brambrink T, Ku M, Hochedlinger K, Bernstein BE, Jaenisch R.Nature. 2007 Jul 19;448(7151):318-24.
PMID 17554336
Article 2:
Environmentally controlled invasion of cancer cells by engineered bacteria.

Anderson JC, Clarke EJ, Arkin AP, Voigt CA.J Mol Biol. 2006 Jan 27;355(4):619-27.
PMID 16330045

Alternative to Article 1: Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors.
Takahashi K, Yamanaka S.Cell. 2006 Aug 25;126(4):663-76. PMID 18035408
(remember to point out that the tumor destroying bacteria do not have epigenetic memory, and perhaps raise the question as to why / how the ES cells do...)
Little Red Corvette:
Once you've got the DNA, where do you put it? Introducing... THE CHASSIS
Wed Apr 16 presenter
article 1:
article 2:
Article 1:
A vesicle bioreactor as a step toward an artificial cell assembly.Noireaux V, Libchaber A.Proc Natl Acad Sci U S A. 2004 Dec 21;101(51):17669-74.
PMID 15591347
Article 2:
The completeness of molecular biology. Morowitz HJ. Isr J Med Sci. 1984 Sep;20(9):750-3.
PMID 6511349
was Article 2:
Irene Chen & Szostak paper, TBD, maybe A kinetic study of the growth of fatty acid vesicles.

Biophys J. 2004 Aug;87(2):988-98.
PMID 15298905

Can we understand it? Can we program it?
Apr 23 presenter
article 1:
article 2:
Article 1:
Identification of an infectious progenitor for the multiple-copy HERV-K human endogenous retroelements.Dewannieux M, Harper F, Richaud A, Letzelter C, Ribet D, Pierron G, Heidmann T. Genome Res. 2006 Dec;16(12):1548-56.

PMID 17077319
Article 2:
Hsp90 as a capacitor for morphological evolution. Rutherford SL, Lindquist S.Nature. 1998 Nov 26;396(6709):336-42.
PMID 9845070

2020: Empire of Reason Wed Apr 30 presenter
article 1:
article 2:
Article 1:
1970 Matt Meselson paper on three pronged approach against bioweapons
maybe PMID 5440151 or PMID 5263755
Article 2:One commentary or piece of fiction... something forward looking, optimistic, The Golden Years
Freshmen Team Presentations (Wed Apr 30,)
Wed May 7,
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