20.20:Advanced topics: Difference between revisions
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| '''I demand the cone of silence:''' <br> nature's constraints on genetic circuit design | | '''I demand the cone of silence:''' <br> nature's constraints on genetic circuit design | ||
| Wed Mar 12 | | Wed Mar 12 | ||
| Roshini Zachariah and | | 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.<br> | |'''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 | PMID 271992 | ||
Line 72: | Line 72: | ||
PMID 17709748 | PMID 17709748 | ||
|'''Golden year: the gift of memories'''Igor Teper ''Nature'' 2006 July 27; 442: 484 <br> doi 10.1038/442484a | |'''Golden year: the gift of memories'''Igor Teper ''Nature'' 2006 July 27; 442: 484 <br> doi 10.1038/442484a | ||
|-- | |||
| presentation to 20.020 students | |||
| Thursday Mar 20 | |||
| '''3 presenters''' <br>Aditya Kohli, Sophia Roosth and Neelima Yeddanapudi | |||
| possibly: '''Lessons from the 1918 influenza.'''Zambon M. ''Nat Biotechnol.'' 2007 Apr;25(4):433-4. <br> 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. <br>PMID 17272724 <br> as well as original synthesis article <br>PMID 16210530 <br>and any editorial comments you deem relevant | |||
|-- | |-- | ||
! colspan="3" | Spring Break Mar 24-28 | ! colspan="3" | Spring Break Mar 24-28 | ||
Line 90: | Line 96: | ||
| Wed Apr 9 | | Wed Apr 9 | ||
| '''article 1:'''<br> Mike Oh<br> '''article 2:'''<br> Angi Wu | | '''article 1:'''<br> Mike Oh<br> '''article 2:'''<br> Angi Wu | ||
|'''Article 1:''' <br>'''Induction of pluripotent stem cells from | |'''Article 1:''' <br>'''Induction of pluripotent stem cells from adult human fibroblasts by defined factors.'''<br> Takahashi K, Tanabe K, Ohnuki M, Narita M, Ichisaka T, Tomoda K, Yamanaka S.''Cell.'' 2007 Nov 30;131(5):861-72.<br> PMID 18035408<br> '''Article 2:''' <br>'''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. <br> | Anderson JC, Clarke EJ, Arkin AP, Voigt CA.''J Mol Biol.'' 2006 Jan 27;355(4):619-27. <br> | ||
PMID 16330045 | PMID 16330045 | ||
| | |Editorial: "A reprogramming rush" <br>'''Nature''' 452, 388 (27 March 2008) <br> doi:10.1038/452388a | ||
|-- | |-- | ||
| '''Little Red Corvette:'''<br> Once you've got the DNA, where do you put it? Introducing... THE CHASSIS | | '''Little Red Corvette:'''<br> Once you've got the DNA, where do you put it? Introducing... THE CHASSIS | ||
Line 100: | Line 107: | ||
| '''Article 1:''' <br>'''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. <br> PMID 15591347<br> '''Article 2:'''<br> '''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. <br> | | '''Article 1:''' <br>'''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. <br> PMID 15591347<br> '''Article 2:'''<br> '''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. <br> | ||
PMID 16645050 | PMID 16645050 | ||
| | | '''The completeness of molecular biology.''' Morowitz HJ. ''Isr J Med Sci.'' 1984 Sep;20(9):750-3. <br> PMID 6511349 | ||
|-- | |-- | ||
| '''(R)evolution:'''<br> Can we understand it? Can we program it? | | '''(R)evolution:'''<br> Can we understand it? Can we program it? | ||
| Apr 23 | | Wed Apr 23 | ||
| '''article 1:'''<br>Stephanie Nix <br> '''article 2:'''<br>Kate Broadbent | | '''article 1:'''<br>Stephanie Nix <br> '''article 2:'''<br>Kate Broadbent | ||
|'''Article 1:''' <br>'''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. <br> | |'''Article 1:''' <br>'''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. <br> | ||
Line 112: | Line 119: | ||
| '''On your mark, get set, go:''' System dynamics | | '''On your mark, get set, go:''' System dynamics | ||
| Wed Apr 30 | | Wed Apr 30 | ||
| '''article 1:''' <br> | | '''article 1:''' <br> Kay Aull<br> | ||
|'''Article 1:''' <br> '''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.<br> | |'''Article 1:''' <br> '''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.<br> | ||
PMID 9691025<br> ''' | PMID 9691025<br> | ||
| note: '''article 2''' presentation will take place during 20.020 lecture time | |||
|-- | |||
| | | | ||
| Tuesday May 6 | |||
| '''article 2:'''<br> Han Zhu | |||
|'''Article 2:''' <br> '''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. <br>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. <br>PMID 15256602 | |||
|-- | |-- | ||
| ''' | |'''Rough consensus and running code:''' building patterns and memories | ||
| Wed May 7 | |Wed May 7 | ||
| '''article 1:''' <br> | |'''article 1:''' <br>Aditya Kohli<br> | ||
|''' | |'''article 1:''' <br> '''Small regulatory RNAs may sharpen spatial expression patterns.'''Levine E, McHale P, Levine H. ''PLoS Comput Biol.'' 2007 Nov;3(11):e233. <br>PMID 18052540<br> | ||
| note: '''article 2''' presentation will take place during 20.020 lecture time | |||
|-- | |||
| | |||
|Thursday May 8 | |||
|'''article 2:'''<br>Neelima Yeddanapudi<br> | |||
|'''article 2:'''<br> '''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.<br>PMID 17875664 | |||
| | | | ||
|-- | |-- | ||
| | | '''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<br>PMID 17355173 | |||
| note that this presentation will take place during the 20.020 lecture time | |||
|-- | |||
|'''2020:''' Empire of Reason | |||
| Tues May 13 | |||
| '''Article 1:'''<br>Stephen Payne<br> | |||
| '''Article 1:'''<br>'''Chemical and biological weapons.''' Matt Meselson, Sci Am. 1970 May;222(5):15-25. PMID 5440151<br> | |||
| | |||
|-- | |||
|'''drop it like it's hot:''' safety! | |||
| Wed May 14 | |||
| '''Article 2:'''<br> Roshini Zachariah | |||
| '''Article 2:'''<br>'''The Pandora's Box Congress.''' Michael Rogers, Rolling Stone 1975 June 19 page 37 | |||
| | | | ||
|-- | |||
| Team Presentations | |||
| | | | ||
| | | | ||
| Wed May 7,<br> May 14 | |||
| | | | ||
|-- | |-- | ||
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===Grades for 20.902/20.947=== | ===Grades for 20.902/20.947=== | ||
<font color = red> All assignments should be dropped into the homework drop-box, found </font | <font color = red> All assignments should be dropped into the homework drop-box, found </font>[https://stellar.mit.edu/S/course/20/sp08/20.902/homework/ here] | ||
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|width="400px" class="MainPageBG" style="border: 1px solid #336600; color: #000; background-color: #CCCCFF"| | |width="400px" class="MainPageBG" style="border: 1px solid #336600; color: #000; background-color: #CCCCFF"| | ||
<div style=" | <div style="padding: .4em .9em .9em"> | ||
'''Part 1: Readings''' | '''Part 1: Readings''' | ||
*Paper 1 (15%): presented with a partner | *Paper 1 (15%): presented with a partner | ||
*Paper 2 (20%): presented solo | *Paper 2 (20%): presented solo | ||
*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] | ||
'''Presentation requirements''' are [[20.20:Advanced topics, presentation information| here]] | '''Presentation requirements''' are [[20.20:Advanced topics, presentation information| here]] | ||
</div> | |||
|width="400px" class="MainPageBG" style="border: 1px solid #336600; color: #000; background-color: #9999FF"| | |width="400px" class="MainPageBG" style="border: 1px solid #336600; color: #000; background-color: #9999FF"| | ||
<div style="padding: .4em .9em .9em"> | <div style="padding: .4em .9em .9em"> | ||
'''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 | *Progress reports (25%): 2x one page summary of your freshman team's work, due Wednesday March 12th, and Wednesday April 9th | ||
*Mentoring journal (10%): 2x one page summary of your freshman team's dynamics, due Wednesday March 12th, and Wednesday April 9th | *Mentoring journal (10%): 2x one page summary of your freshman team's dynamics, due Wednesday March 12th, and Wednesday April 9th | ||
*Team's project average (10%): based on the grade for the 3 major assignments submitted by your freshman team | *Team's project average (10%): based on the grade for the 3 major assignments submitted by your freshman team | ||
*Instructor Leverage (5%): discretionary adjustment by NK and DE< | *Instructor Leverage (5%): discretionary adjustment by NK and DE | ||
</div> | |||
|} |
Latest revision as of 18:57, 6 May 2008
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Home | Lecture schedule |
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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 | |||
---|---|---|---|---|
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 |
||
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 |
|
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 |
|
Team Presentations | 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
|