20.20:Advanced topics: Difference between revisions
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<b>Turning lambda Cro into a transcriptional activator.</b>Bushman FD, Ptashne M.''Cell.'' 1988 Jul 15;54(2):191-7.<br> | <b>Turning lambda Cro into a transcriptional activator.</b>Bushman FD, Ptashne M.''Cell.'' 1988 Jul 15;54(2):191-7.<br> | ||
PMID 2968842<br> <br>DENK ppt [[Media:Cro2activator.ppt| here]] | PMID 2968842<br> <br>DENK ppt [[Media:Cro2activator.ppt| here]] | ||
|'''Genetic Switch: Phage Lambda and Higher Organisms''' Mark Ptashne [http://www.amazon.com/Genetic-Switch-Lambda-Higher-Organisms/dp/0865422095 previewed here]<br> | |'''Genetic Switch: Phage Lambda and Higher Organisms''' Mark Ptashne[http://www.amazon.com/Genetic-Switch-Lambda-Higher-Organisms/dp/0865422095 previewed here]<br> | ||
or '''Sci Am''' summary (request from NK or DE) | or '''Sci Am''' summary (request from NK or DE) | ||
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| Wed Feb 27 | | Wed Feb 27 | ||
| Angi Wu and Robbie Barbero | | 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.<br> | ||
'''Combinatorial synthesis of genetic networks.''' | |||
Guet CC, Elowitz MB, Hsing W, Leibler S.''Science.'' 2002 May 24;296(5572):1466-70.<br> | |||
PMID 12029133 | 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.<br> | ||
PMID 15738412 | |||
|-- | |-- | ||
| '''Darwin is alive and well:''' <br>Directed evolution at the device level | | '''Darwin is alive and well:''' <br>Directed evolution at the device level | ||
| Wed Mar | | Wed Mar 5 | ||
| Mike Lee and Stephen Payne | | 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.<br> | ||
'''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. <br> | |||
PMID 12451174 | PMID 12451174 | ||
| | | NK and DE OoT | ||
|-- | |||
| '''I demand the cone of silence:''' <br> nature's constraints on genetic circuit design | |||
| Wed Mar 12 | |||
| Roshini Zachariah and another presenter | |||
|'''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.<br> | |||
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. <br> | |||
PMID 16537475 | |||
|-- | |-- | ||
| '''Intelligent Design:'''<br> Functional composition at the device level | | '''Intelligent Design:'''<br> Functional composition at the device level | ||
| Wed Mar 19 | | Wed Mar 19 | ||
| Kate Broadbent and Mike Oh | | Kate Broadbent and Mike Oh | ||
| | | '''A modular and extensible RNA-based gene-regulatory platform for engineering cellular function.'''Win MN, Smolke CD. | ||
'''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. <br> | ''Proc Natl Acad Sci U S A.'' 2007 Sep 4;104(36):14283-8. <br> | ||
PMID 17709748 | PMID 17709748 | ||
| | |'''Golden year: the gift of memories'''Igor Teper ''Nature'' 2006 July 27; 442: 484 <br> doi 10.1038/442484a | ||
|-- | |-- | ||
! colspan="3" | Spring Break Mar 24-28 | ! colspan="3" | Spring Break Mar 24-28 |
Revision as of 05:09, 9 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 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 another presenter | 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 |
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. |
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 | 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: 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 | 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 |
2020: Empire of Reason | Wed Apr 30 | 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: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 |
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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