20.20:Advanced topics: Difference between revisions
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| <b>Slide rule optional:</b><br>Computational design of novel protein activities | | <b>Slide rule optional:</b><br>Computational design of novel protein activities | ||
| Wed Feb 13 | | Wed Feb 13 | ||
| | | Stephanie Nix and Matt Gethers | ||
| | | | ||
<b>Computational design of receptor and sensor proteins with novel functions.</b>Looger LL, Dwyer MA, Smith JJ, Hellinga HW.''Nature.'' 2003 May 8;423(6936):185-90.<br> PMID 12736688 | <b>Computational design of receptor and sensor proteins with novel functions.</b>Looger LL, Dwyer MA, Smith JJ, Hellinga HW.''Nature.'' 2003 May 8;423(6936):185-90.<br> PMID 12736688 | ||
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| '''Nature heart Legos™''':<br> Proteins are modular too | | '''Nature heart Legos™''':<br> Proteins are modular too | ||
| Wed Feb 20 | | Wed Feb 20 | ||
| | | Kay Aull + one more presenter needed | ||
| | | | ||
'''A eukaryotic transcriptional activator bearing the DNA specificity of a prokaryotic repressor.''' | '''A eukaryotic transcriptional activator bearing the DNA specificity of a prokaryotic repressor.''' | ||
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| '''Better odds in Vegas:'''<br>DNA elements are modular too, allowing for circuits, but circuits don't always work | | '''Better odds in Vegas:'''<br>DNA elements are modular too, allowing for circuits, but circuits don't always work | ||
| Wed Feb 27 | | Wed Feb 27 | ||
| | | Angi Wu and Robbie Barbero | ||
| | | | ||
'''Combinatorial synthesis of genetic networks.''' | '''Combinatorial synthesis of genetic networks.''' | ||
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| Wed Mar 5 | | Wed Mar 5 | ||
| NK and DE OoT | | NK and DE OoT | ||
| | | articles to be added here for Sophia and Neelima | ||
| | | | ||
|-- | |-- | ||
| '''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 12 | | Wed Mar 12 | ||
| | | Mike Lee and Stephen Payne | ||
| | | | ||
'''Directed evolution of a genetic circuit.'''Yokobayashi Y, Weiss R, Arnold FH. | '''Directed evolution of a genetic circuit.'''Yokobayashi Y, Weiss R, Arnold FH. | ||
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| '''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 | ||
| | | | ||
'''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. | ||
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| '''Writing in genetic code:'''<br> DNA construction and editing technologies | | '''Writing in genetic code:'''<br> DNA construction and editing technologies | ||
| Wed Apr 2 | | Wed Apr 2 | ||
| | | '''article 1:'''<br> Robbie Barbero<br> '''article 2:'''<br> Mike Lee | ||
| '''Article 1:''' <br>'''Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides.'''Stemmer WP, Crameri A, Ha KD, Brennan TM, Heyneker HL. | | '''Article 1:''' <br>'''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.<br> | ''Gene.'' 1995 Oct 16;164(1):49-53.<br> | ||
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| '''We're only human:''' <br>What is the state of the art? | | '''We're only human:''' <br>What is the state of the art? | ||
| Wed Apr 9 | | Wed Apr 9 | ||
| | | '''article 1:'''<br> Mike Oh<br> '''article 2:'''<br> Angi Wu | ||
|'''Article 1:''' <br>'''Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors.'''<br>Takahashi K, Yamanaka S.''Cell.'' 2006 Aug 25;126(4):663-76.<br> PMID 18035408<br> '''Article 2:''' <br>'''Environmentally controlled invasion of cancer cells by engineered bacteria.''' | |'''Article 1:''' <br>'''Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors.'''<br>Takahashi K, Yamanaka S.''Cell.'' 2006 Aug 25;126(4):663-76.<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> | ||
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| '''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 | ||
| Wed Apr 16 | | Wed Apr 16 | ||
| | | '''article 1:'''<br> Matt Gethers<br> '''article 2:'''<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> '''The completeness of molecular biology.''' Morowitz HJ. ''Isr J Med Sci.'' 1984 Sep;20(9):750-3. <br> PMID 6511349 | | '''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> '''The completeness of molecular biology.''' Morowitz HJ. ''Isr J Med Sci.'' 1984 Sep;20(9):750-3. <br> PMID 6511349 | ||
| was '''Article 2:''' <br>Irene Chen & Szostak paper, TBD, maybe '''A kinetic study of the growth of fatty acid vesicles.''' | | was '''Article 2:''' <br>Irene Chen & Szostak paper, TBD, maybe '''A kinetic study of the growth of fatty acid vesicles.''' | ||
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| '''(R)evolution:'''<br> Can we understand it? Can we program it? | | '''(R)evolution:'''<br> Can we understand it? Can we program it? | ||
| Apr 23 | | Apr 23 | ||
| | | '''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> | ||
PMID 17077319 <br> | PMID 17077319 <br> | ||
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| '''2020:''' Empire of Reason | | '''2020:''' Empire of Reason | ||
| Wed Apr 30 | | Wed Apr 30 | ||
| | | '''article 1:''' <br>Stephen Payne<br> '''article 2:'''<br> | ||
|'''Article 1:''' <br>1970 Matt Meselson paper on three pronged approach against bioweapons<br> maybe PMID 5440151 or PMID 5263755 <br> '''Article 2:'''One commentary or piece of fiction... something forward looking, optimistic, The Golden Years | |'''Article 1:''' <br>1970 Matt Meselson paper on three pronged approach against bioweapons<br> maybe PMID 5440151 or PMID 5263755 <br> '''Article 2:'''One commentary or piece of fiction... something forward looking, optimistic, The Golden Years | ||
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Revision as of 11:28, 6 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 | 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 + one more presenter 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 | 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. |
|
Wed Mar 5 | NK and DE OoT | articles to be added here for Sophia and Neelima | ||
Darwin is alive and well: Directed evolution at the device level |
Wed Mar 12 | 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. |
|
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. |
|
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 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: |
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: |
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 |
|
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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