20.902(S09):Advanced topics in synthetic biology: Difference between revisions

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=20.902/20.947: Advanced Topics in Synthetic Biology=
=20.902: Advanced Topics in Synthetic Biology=
==Assignments==
==Assignments==
Homework dropbox is [http://stellar.mit.edu/S/course/20/sp09/20.902/homework/index.html here]
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'''Part 1: Readings'''
'''Part 1: Readings'''
*Paper 1 (15%): presented with a partner
*Paper 1 (10%): presented with a partner
*Paper 2 (20%): presented solo
*Paper 2 (15%): 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 record (25%): your thoughts about the papers you don't present.  
'''Presentation requirements''' are [[20.20:Advanced topics, presentation information| here]]
Instructions for these assignment are [[20.902(S09):Assignments on readings| 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 11th, and Wednesday April 8th
*Progress reports (15%): one page summaries of your freshman team's work
*Mentoring journal (10%): 2x one page summary of your freshman team's dynamics, due Wednesday March 11th, and Wednesday April 8th
*Mentoring journal(15%): one page summary of your freshman team's dynamics
*Team's project average (10%): based on the grade for the 3 major assignments submitted by your freshman team
*Team's project average (15%): based on the grade for the 3 major assignments submitted by your freshman team
*Instructor Leverage (5%): discretionary adjustment by NK  
*Instructor Leverage (5%): discretionary adjustment by NK  
Instructions for these assignments are [[20.902(S09): Team mentoring assignments| here]]
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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>ppt [[Media:Cro2activator.ppt| here]]
[[PMID: 2968842]]<br> <br>ppt [[Media:2020(S09) 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 '''Sci Am''' summary (request from NK)
Line 46: Line 49:
| Wed Feb 11
| Wed Feb 11
|  
|  
| '''Design of multi-specificity in protein interfaces'''Humphris, EL; Kortemme, T. ''PLoS computational biology'' (2007) 3(8):e164<br>[[DOI : 10.1371/journal.pcbi.0030164]]
|  
|  
<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
| David Baker's [http://game.bakerlab.org/portal/video_intro protein folding game]<br>NCBI protein viewer [http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml CN3D]<br>
|--
|--
| '''Nature heart Legos™''':<br> Proteins are modular too
| '''Nature heart Legos™''':<br> Proteins are modular too
| Wed Feb 18
| Wed Feb 18
|  
|  
|  
|'''Ligand binding to the receptor domain regulates the ratio of kinase to phosphatase activities of the signaling domain of the hybrid Escherichia coli transmembrane receptor, Taz1.'''Jin T, Inouye M.''J Mol Biol.'' (1993)232(2):484-92.<br>[[PMID: 8393937]]
'''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.<br>
PMID 3907859
 
|Ptashne “Two ‘What if” experiments” PMID 15055587<br>
Brent “Build Artificial” PMID 15055588
|--
|--
| '''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 25
| Wed Feb 25
|  
|  
|'''Combinatorial synthesis of genetic networks.'''Guet CC, Elowitz MB, Hsing W, Leibler S.''Science.'' 2002 May 24;296(5572):1466-70.<br>
|'''Environmental signal integration by a modular AND gate.'''Anderson JC, Voigt C, Arkin, AP ''Molecular systems biology''3 133 2007<br>[[DOI : 10.1038/msb4100173]]
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 parts and device level
| Wed Mar 4  
| Wed Mar 4  
|  
|  
|'''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>
|'''RNA and RNP as new molecular parts in synthetic biology.'''Saito H, Inoue, T ''Journal of biotechnology''(2007)132(1):1-7<br>[[doi:10.1016/j.jbiotec.2007.07.952]]
PMID 12451174
|
|
|--
|--
Line 80: Line 73:
| <font color = blue> Thursday Mar 12</font color>
| <font color = blue> Thursday Mar 12</font color>
|  
|  
|'''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>
|'''Phenotypic consequences of promoter-mediated transcriptional noise.''' Blake WJ, Balazsi G, Kohanski MA, Isaacs FJ, Murphy KF, Kuang Y, Cantor CR, Walt DR, Collins JJ, ''Molecular cell''(2006) 24(6):853-65<br>[[DOI : 10.1016/j.molcel.2006.11.003]]
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<br><font color = blue>note that this presentation will take place during the 20.020 lecture time</font color>
|--
|--
| '''Intelligent Design:'''<br> Functional composition at the device level
| '''Intelligent Design:'''<br> Functional composition at the device level
| Wed Mar 18
| Wed Mar 18
|
|
| '''A modular and extensible RNA-based gene-regulatory platform for engineering cellular function.'''Win MN, Smolke CD.
| '''Rapid "open-source" engineering of customized zinc-finger nucleases for highly efficient gene modification.''' Maeder ML, et. al.  ''Mol Cell.'' (2008)31(2):294-301<br>[[DOI : 10.1016/j.molcel.2008.06.016]]
''Proc Natl Acad Sci U S A.'' 2007 Sep 4;104(36):14283-8. <br>
|
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
Line 99: Line 88:
| '''Writing in genetic code:'''<br> DNA construction and editing technologies
| '''Writing in genetic code:'''<br> DNA construction and editing technologies
| Wed Apr 1
| Wed Apr 1
| '''article 1:'''<br> <br> '''article 2:'''<br>  
|
| '''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.
| '''DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways.'''<br> Shao Z, Zhao H, Zhao H. Nucleic Acids Res. 2008 Dec 12<br>[[PMID: 19074487]]<br> '''Article 2:''' <br>  
''Gene.'' 1995 Oct 16;164(1):49-53.<br>
| '''Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides.'''<br>Stemmer WP, Crameri A, Ha KD, Brennan TM, Heyneker HL. Gene. 1995 Oct 16;164(1):49-53.<br> [[PMID: 7590320]]
PMID 7590320 <br>
'''Article 2:''' <br>'''Complete Chemical Synthesis, Assembly, and Cloning of a Mycoplasma genitalium Genome. '''Gibson et al. ''Science.'' 2008 Jan 24; [Epub ahead of print]<br>
PMID 18218864<br>
| Church automated genome editing paper, if available. <br>
|--
|--
| '''We're only human:''' <br>What is the state of the art?   
| '''We're only human:''' <br>What is the state of the art?   
| <font color = blue> Thursday Apr 9 </font color>
| <font color = blue> Thursday Apr 9 </font color>
| '''article 1:'''<br> <br> '''article 2:'''<br>
|  
|'''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.'''
|'''Rewiring the specificity of two-component signal transduction systems.''' Skerker JM, et al. ''Cell'' (2008)133(6):1043-54.<br>[[DOI: 10.1016/j.cell.2008.04.040]]
Anderson JC, Clarke EJ, Arkin AP, Voigt CA.''J Mol Biol.'' 2006 Jan 27;355(4):619-27. <br>
|
PMID 16330045
|Editorial: "A reprogramming rush" <br>'''Nature''' 452, 388 (27 March 2008) <br> doi:10.1038/452388a<br>
<font color = blue>note that this presentation will take place during the 20.020 lecture time</font color>
|--
|--
| '''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 15
| Wed Apr 15
| '''article 1:'''<br> <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> '''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>
|'''Reconstitution of contractile FtsZ rings in liposomes.''' Osawa M, Anderson DE, Erickson HP.''Science'' (2008)320(5877):792-4.<br>[[DOI: 10.1126/science.1154520]]
PMID 16645050
| '''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)312(5776):1044-6.<br> [[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?
| '''Secret map hidden in the peg-leg:'''<br> getting DNA to speak in binary
| Wed Apr 22
| Wed Apr 22
| '''article 1:'''<br><br> '''article 2:'''<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>
|'''Length-based encoding of binary data in DNA.''' Portney NG, Wu Y, Quezad, LK, Lonardi S, Ozkan M.
PMID 17077319 <br>
''Langmuir'' (2008) 24(5):1613-6.<br>[[DOI: 10.1021/la703235y]]
'''Article 2:''' <br>'''Hsp90 as a capacitor for morphological evolution.''' Rutherford SL, Lindquist S.''Nature.'' 1998 Nov 26;396(6709):336-42.<br> PMID 9845070
|
|'''Darwin’s Surprise: Why are evolutionary biologists bringing back extinct deadly viruses?''' Michael Specter [http://www.newyorker.com/reporting/2007/12/03/071203fa_fact_specter New Yorker article]
|--
|--
| '''On your mark, get set, go:''' System dynamics
| '''On your mark, get set, go:''' System dynamics
| Wed Apr 29  
| Wed Apr 29
| '''article 1:''' <br> <br>'''article 2:'''<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>
|'''Using Engineered Scaffold Interactions to Reshape MAP Kinase Pathway Signaling Dynamics''' Bashor CJ, Helman NC, Yan S, Lim, WA ''Science'' (2008)319: 1539-1543 <br> [[DOI: 10.1126/science.1151153]]
PMID 9691025<br>
|  
'''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
|'''Rough consensus and running code:''' building patterns and memories
|Wed May 6
| <font color = blue>Tue May 5</font color>  
|'''article 1:''' <br><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>
|'''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):21(18):2271-6.<br> [[DOI: 10.1101/gad.1586107]]
|  
|  
|--
|--
| '''mine mine mine:''' property rights in synthetic biology
|  <font color = blue> Tue May 12 </font color>
|
|
|<font color = blue> Thur May 7 </font color>
| '''Synthetic biology: caught between property rights, the public domain, and the commons''' Rai A, Boyle ''J. PLoS Biol.'' (2007)5(3):e58<br>[[PMID: 17355173]]
|'''article 2:'''<br><br>
|'''Patents and Translational Research in Genomics'''Kaye J, Hawkins N, and Taylor J. ''Nature Biotech'' (2007) 25(7): 739–741.[[doi: 10.1038/nbt0707-739.]]
|'''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
| <font color= blue>note that this presentation will take place during the 20.020 lecture time</font color>
|--
|--
| '''mine mine mine:''' property rights in synthetic biology
|'''drop it like it's hot:''' safety!
| <font color = blue> Tue May 12 </font color>  
| <font color = blue> Tue May 12 </font color>  
| '''Article 1:'''<br><br>
| '''Article 1:'''<br>'''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
| <font color = blue> note that this presentation will take place during the 20.020 lecture time</font color>
|--
|'''2020:''' Empire of Reason
| Wed May 13
| '''Article 2:'''<br><br>
| '''Article 2:'''<br>'''Chemical and biological weapons.''' Matt Meselson, Sci Am. 1970 May;222(5):15-25. PMID 5440151<br>
|  
|  
|--
| '''Managing the unimaginable. Regulatory responses to the challenges posed by synthetic biology and synthetic genomics.''' Samuel GN, Selgelid MJ, Kerridge I. ''EMBO reports'' (2009) 10(1):7-11.<br>[[DOI: 10.1038/embor.2008.232]]
|'''drop it like it's hot:''' safety!
|
| Wed May 13
| '''Article 2:'''<br>  
| '''Article 2:'''<br>'''The Pandora's Box Congress.''' Michael Rogers, Rolling Stone 1975 June 19 page 37
| Alternative article
|--
|--
|}
|}

Latest revision as of 05:30, 3 February 2009

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20.902: Advanced Topics in Synthetic Biology

Assignments

Homework dropbox is here

Part 1: Readings

  • Paper 1 (10%): presented with a partner
  • Paper 2 (15%): presented solo
  • Response record (25%): your thoughts about the papers you don't present.

Instructions for these assignment are here

Part 2: Team Mentoring

  • Progress reports (15%): one page summaries of your freshman team's work
  • Mentoring journal(15%): one page summary of your freshman team's dynamics
  • Team's project average (15%): based on the grade for the 3 major assignments submitted by your freshman team
  • Instructor Leverage (5%): discretionary adjustment by NK

Instructions for these assignments are here

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 4 Natalie Kuldell

Turning lambda Cro into a transcriptional activator.Bushman FD, Ptashne M.Cell. 1988 Jul 15;54(2):191-7.
PMID: 2968842

ppt here

Genetic Switch: Phage Lambda and Higher Organisms Mark Ptashnepreviewed here

or Sci Am summary (request from NK)

Slide rule optional:
Computational design of novel protein activities 		Wed Feb 11 Design of multi-specificity in protein interfacesHumphris, EL; Kortemme, T. PLoS computational biology (2007) 3(8):e164
DOI : 10.1371/journal.pcbi.0030164
Nature heart Legos™:
Proteins are modular too 		Wed Feb 18 Ligand binding to the receptor domain regulates the ratio of kinase to phosphatase activities of the signaling domain of the hybrid Escherichia coli transmembrane receptor, Taz1.Jin T, Inouye M.J Mol Biol. (1993)232(2):484-92.
PMID: 8393937
Better odds in Vegas:
DNA elements are modular too, allowing for circuits, but circuits don't always work 		Wed Feb 25 Environmental signal integration by a modular AND gate.Anderson JC, Voigt C, Arkin, AP Molecular systems biology3 133 2007
DOI : 10.1038/msb4100173
Darwin is alive and well:
Directed evolution at the parts and device level 		Wed Mar 4 RNA and RNP as new molecular parts in synthetic biology.Saito H, Inoue, T Journal of biotechnology(2007)132(1):1-7
doi:10.1016/j.jbiotec.2007.07.952
I demand the cone of silence:
nature's constraints on genetic circuit design 		Thursday Mar 12 Phenotypic consequences of promoter-mediated transcriptional noise. Blake WJ, Balazsi G, Kohanski MA, Isaacs FJ, Murphy KF, Kuang Y, Cantor CR, Walt DR, Collins JJ, Molecular cell(2006) 24(6):853-65
DOI : 10.1016/j.molcel.2006.11.003
Intelligent Design:
Functional composition at the device level 		Wed Mar 18 Rapid "open-source" engineering of customized zinc-finger nucleases for highly efficient gene modification. Maeder ML, et. al. Mol Cell. (2008)31(2):294-301
DOI : 10.1016/j.molcel.2008.06.016
Spring Break Mar 24-28 No class all week
Writing in genetic code:
DNA construction and editing technologies 		Wed Apr 1 DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways.
Shao Z, Zhao H, Zhao H. Nucleic Acids Res. 2008 Dec 12
PMID: 19074487
Article 2:
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.
PMID: 7590320
We're only human:
What is the state of the art? 		Thursday Apr 9 Rewiring the specificity of two-component signal transduction systems. Skerker JM, et al. Cell (2008)133(6):1043-54.
DOI: 10.1016/j.cell.2008.04.040
Little Red Corvette:
Once you've got the DNA, where do you put it? Introducing... THE CHASSIS 		Wed Apr 15 Reconstitution of contractile FtsZ rings in liposomes. Osawa M, Anderson DE, Erickson HP.Science (2008)320(5877):792-4.
DOI: 10.1126/science.1154520 		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)312(5776):1044-6.
PMID: 16645050
Secret map hidden in the peg-leg:
getting DNA to speak in binary 		Wed Apr 22 Length-based encoding of binary data in DNA. Portney NG, Wu Y, Quezad, LK, Lonardi S, Ozkan M.

Langmuir (2008) 24(5):1613-6.
DOI: 10.1021/la703235y

On your mark, get set, go: System dynamics Wed Apr 29 Using Engineered Scaffold Interactions to Reshape MAP Kinase Pathway Signaling Dynamics Bashor CJ, Helman NC, Yan S, Lim, WA Science (2008)319: 1539-1543
DOI: 10.1126/science.1151153
Rough consensus and running code: building patterns and memories Tue May 5 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):21(18):2271-6.
DOI: 10.1101/gad.1586107
mine mine mine: property rights in synthetic biology Tue May 12 Synthetic biology: caught between property rights, the public domain, and the commons Rai A, Boyle J. PLoS Biol. (2007)5(3):e58
PMID: 17355173 		Patents and Translational Research in GenomicsKaye J, Hawkins N, and Taylor J. Nature Biotech (2007) 25(7): 739–741.doi: 10.1038/nbt0707-739.
drop it like it's hot: safety! Tue May 12 Managing the unimaginable. Regulatory responses to the challenges posed by synthetic biology and synthetic genomics. Samuel GN, Selgelid MJ, Kerridge I. EMBO reports (2009) 10(1):7-11.
DOI: 10.1038/embor.2008.232
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