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 May 20 | need 3 presenters (Aditya, Sophia and Neelima?) | possibly: Lessons from the 1918 influenza.Zambon M. Nat Biotechnol. 2007 Apr;25(4):433-4. PMID 17420751 |
should also include: A two-amino acid change in the hemagglutinin of the 1918 influenza virus abolishes transmission.Tumpey TM, Maines TR, Van Hoeven N, Glaser L, Solórzano A, Pappas C, Cox NJ, Swayne DE, Palese P, Katz JM, García-Sastre A. 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 mouse embryonic and adult fibroblast cultures by defined factors. Takahashi K, Yamanaka S.Cell. 2006 Aug 25;126(4):663-76. 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. |
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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? |
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: article 2: Han Zhu |
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 |
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Rough consensus and running code: building patterns and memories | Wed May 7 | Article 1: Aditya Kohli Article 2: |
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 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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2020: Empire of Reason | Wed May 14 | article 1: Stephen Payne article 2: Roshini Zachariah |
Article 1: 1970 Matt Meselson paper on three pronged approach against bioweapons maybe PMID 5440151 or PMID 5263755 Article 2:Sydney Brenner lab safety or Bio/Techniques environmental safety |
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Freshmen Team Presentations | Wed Apr 30, Wed May 7, May 14 |
Grades for 20.902/20.947
All assignments should be dropped into the homework drop-box, found here
Part 2: Team Mentoring
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