20.20:Advanced topics: Difference between revisions
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Part 1: Readings | '''Part 1: Readings''' | ||
*Paper 1 (15%): presented with a partner<br> | *Paper 1 (15%): presented with a partner<br> | ||
*Paper 2 (20%): presented solo<br> | *Paper 2 (20%): presented solo<br> | ||
*Response journal (15%): your thoughts about the papers you don't present. Instructions for this assignment are [https://stellar.mit.edu/S/course/20/sp08/20.902/homework/ here] | *Response journal (15%): your thoughts about the papers you don't present. Instructions for this assignment are [https://stellar.mit.edu/S/course/20/sp08/20.902/homework/ here]<br> | ||
'''Presentation requirements''' are [[20.20:Advanced topics, presentation information| here]] | |||
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Part 2: Team Mentoring | '''Part 2: Team Mentoring''' | ||
*Progress reports (25%): 2x one page summary of your freshman team's work, due Wednesday March 12th, and Wednesday April 9th<br> | *Progress reports (25%): 2x one page summary of your freshman team's work, due Wednesday March 12th, and Wednesday April 9th<br> | ||
*Mentoring journal (10%): 2x one page summary of your freshman team's dynamics, due Wednesday March 12th, and Wednesday April 9th<br> | *Mentoring journal (10%): 2x one page summary of your freshman team's dynamics, due Wednesday March 12th, and Wednesday April 9th<br> | ||
*Team's project average (10%): based on the grade for the 3 major assignments submitted by your freshman team<br> | *Team's project average (10%): based on the grade for the 3 major assignments submitted by your freshman team<br> | ||
*Instructor Leverage (5%): discretionary adjustment by NK and DE<br> | *Instructor Leverage (5%): discretionary adjustment by NK and DE<br> | ||
Revision as of 12:48, 4 February 2008
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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 Ptashne previewed here or Sci Am summary (request from NK or DE) |
| 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. |
David Baker's protein folding game NCBI protein viewer CN3D |
| 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. |
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. |
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| 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. |
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| 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. |
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| 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 | 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. |
Church automated genome editing paper, if available. |
| We're only human: What is the state of the art? |
Wed Apr 9 | presenter article 1: article 2: |
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. |
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. |
| (R)evolution: 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 |
Darwin’s Surprise: Why are evolutionary biologists bringing back extinct deadly viruses? Michael Specter New Yorker article |
| 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 |
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| Freshmen Team Presentations | (Wed Apr 30,) 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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