20.20:Advanced topics
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| 20.902/20.947 | Student Resources | Teacher Resources |
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. |
Genetic Switch: Phage Lambda and Higher Organisms Mark Ptashnepreviewed here or Sci Am summary (request from NK or DE) |
| Slide rule optional: Computational design of novel protein activities |
Wed Feb 13 | Stephanie Nix and Matt Gethers |
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. |
David Baker's protein folding game NCBI protein viewer CN3D |
| Nature heart Legos™: Proteins are modular too |
Wed Feb 20 | Kay Aull + Jessica Keenan |
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. |
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 | Angi Wu and Robbie Barbero | Combinatorial synthesis of genetic networks.Guet CC, Elowitz MB, Hsing W, Leibler S.Science. 2002 May 24;296(5572):1466-70. PMID 12029133 |
Ultrasensitivity and noise propagation in a synthetic transcriptional cascade.Hooshangi S, Thiberge S, Weiss R.Proc Natl Acad Sci U S A. 2005 Mar 8;102(10):3581-6. PMID 15738412 |
| Darwin is alive and well: Directed evolution at the device level |
Wed Mar 5 | Mike Lee and Stephen Payne | 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 |
NK and DE OoT |
| I demand the cone of silence: nature's constraints on genetic circuit design |
Wed Mar 12 | Roshini Zachariah and Han Zhu | Design of molecular control mechanisms and the demand for gene expression. Savageau MA.Proc Natl Acad Sci U S A. 1977 Dec;74(12):5647-51. PMID 271992 |
Rules for biological regulation based on error minimization.Shinar G, Dekel E, Tlusty T, Alon U.Proc Natl Acad Sci U S A. 2006 Mar 14;103(11):3999-4004. PMID 16537475 |
| Intelligent Design: Functional composition at the device level |
Wed Mar 19 | Kate Broadbent and Mike Oh | 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. |
Golden year: the gift of memoriesIgor Teper Nature 2006 July 27; 442: 484 doi 10.1038/442484a |
| presentation to 20.020 students | Thursday Mar 20 | 3 presenters Aditya Kohli, Sophia Roosth and Neelima Yeddanapudi |
possibly: Lessons from the 1918 influenza.Zambon M. Nat Biotechnol. 2007 Apr;25(4):433-4. PMID 17420751 |
should also include: A two-aa change in the hemagglutinin of the 1918 influenza virus abolishes transmission.Science. 2007 Feb 2;315(5812):655-9. PMID 17272724 as well as original synthesis article PMID 16210530 and any editorial comments you deem relevant |
| Spring Break Mar 24-28 | No class all week | |||
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| Writing in genetic code: DNA construction and editing technologies |
Wed Apr 2 | article 1: Robbie Barbero article 2: Mike Lee |
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. |
Church automated genome editing paper, if available. |
| We're only human: What is the state of the art? |
Wed Apr 9 | article 1: Mike Oh article 2: Angi Wu |
Article 1: Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Takahashi K, Tanabe K, Ohnuki M, Narita M, Ichisaka T, Tomoda K, Yamanaka S.Cell. 2007 Nov 30;131(5):861-72. PMID 18035408 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. |
Editorial: "A reprogramming rush" Nature 452, 388 (27 March 2008) doi:10.1038/452388a |
| Little Red Corvette: Once you've got the DNA, where do you put it? Introducing... THE CHASSIS |
Wed Apr 16 | article 1: Matt Gethers article 2: Sophia Roosth |
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: Emergent properties of reduced-genome Escherichia coli.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, Blattner FR. Science. 2006 May 19;312(5776):1044-6. PMID 16645050 |
The completeness of molecular biology. Morowitz HJ. Isr J Med Sci. 1984 Sep;20(9):750-3. PMID 6511349 |
| (R)evolution: Can we understand it? Can we program it? |
Wed Apr 23 | article 1: Stephanie Nix article 2: Kate Broadbent |
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 |
Darwin’s Surprise: Why are evolutionary biologists bringing back extinct deadly viruses? Michael Specter New Yorker article |
| On your mark, get set, go: System dynamics | Wed Apr 30 | article 1: Kay Aull |
Article 1: Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells. Arkin A, Ross J, McAdams HH. Genetics. 1998 Aug;149(4):1633-48. PMID 9691025 |
note: article 2 presentation will take place during 20.020 lecture time |
| Tuesday May 6 | article 2: Han Zhu |
Article 2: Synchronizing genetic relaxation oscillators by intercell signaling. McMillen D, Kopell N, Hasty J, Collins JJ. Proc Natl Acad Sci U S A. 2002 Jan 22;99(2):679-84. PMID 11805323 |
Modeling a synthetic multicellular clock: repressilators coupled by quorum sensing.Garcia-Ojalvo J, Elowitz MB, Strogatz SH.Proc Natl Acad Sci U S A. 2004 Jul 27;101(30):10955-60. PMID 15256602 | |
| Rough consensus and running code: building patterns and memories | Wed May 7 | article 1: Aditya Kohli |
article 1: Small regulatory RNAs may sharpen spatial expression patterns.Levine E, McHale P, Levine H. PLoS Comput Biol. 2007 Nov;3(11):e233. PMID 18052540 |
note: article 2 presentation will take place during 20.020 lecture time |
| Thursday May 8 | article 2: Neelima Yeddanapudi |
article 2: Rational design of memory in eukaryotic cells. Ajo-Franklin CM, Drubin DA, Eskin JA, Gee EP, Landgraf D, Phillips I, Silver PA. Genes Dev. 2007 Sep 15;21(18):2271-6. PMID 17875664 |
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| mine mine mine: property rights in synthetic biology | Tue May 13 | Jessica L Keenan | Synthetic biology: caught between property rights, the public domain, and the commons.Rai A, Boyle J. PLoS Biol. 2007 Mar;5(3):e58 PMID 17355173 |
note that this presentation will take place during the 20.020 lecture time |
| 2020: Empire of Reason | Tues May 13 | Article 1: Stephen Payne |
Article 1: Chemical and biological weapons. Matt Meselson, Sci Am. 1970 May;222(5):15-25. PMID 5440151 |
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| drop it like it's hot: safety! | Wed May 14 | Article 2: Roshini Zachariah |
Article 2: The Pandora's Box Congress. Michael Rogers, Rolling Stone 1975 June 19 page 37 |
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| Team Presentations | Wed May 7, May 14 |
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Grades for 20.902/20.947
All assignments should be dropped into the homework drop-box, found here
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Part 2: Team Mentoring
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