20.20:Advanced topics

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
Current revision (20:57, 6 May 2008) (view source)
 
(38 intermediate revisions not shown.)
Line 19: Line 19:
|  
|  
<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
+
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)
|--
|--
| <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
-
| 2 presenters needed
+
| 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
-
|
+
| 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 20
| Wed Feb 20
-
| 2 presenters needed
+
| Kay Aull + Jessica Keenan
|  
|  
'''A eukaryotic transcriptional activator bearing the DNA specificity of a prokaryotic repressor.'''
'''A eukaryotic transcriptional activator bearing the DNA specificity of a prokaryotic repressor.'''
Line 44: Line 44:
| '''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
-
| 2 presenters needed
+
| 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
-
|
+
-
| Wed Mar 5
+
-
| NK and DE OoT
+
-
|
+
-
|
+
|--
|--
| '''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 5
-
| 2 presenters needed
+
| 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 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>
 +
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
-
| 2 presenters needed
+
| 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
 +
|--
 +
| 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 81: Line 85:
| '''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
-
| presenter<br>article 1: <br> article 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>
Line 91: Line 95:
| '''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
-
| presenter<br>article 1: <br> article 2:  
+
| '''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 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
-
|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...
+
|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  
| Wed Apr 16
| Wed Apr 16
-
| presenter<br>article 1: <br> article 2:
+
| '''article 1:'''<br> Matt Gethers<br> '''article 2:'''<br>Sophia Roosth
-
| '''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> '''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>
-
| was '''Article 2:''' <br>Irene Chen & Szostak paper, TBD, maybe '''A kinetic study of the growth of fatty acid vesicles.'''
+
PMID 16645050
-
Biophys J. 2004 Aug;87(2):988-98. <br>PMID 15298905
+
| '''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
-
| presenter<br>article 1: <br> article 2:
+
| '''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>
Line 112: Line 117:
|'''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]
|'''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]
|--
|--
-
| '''2020:''' Empire of Reason
+
| '''On your mark, get set, go:''' System dynamics
| Wed Apr 30  
| Wed Apr 30  
-
| presenter<br>article 1: <br> article 2:
+
| '''article 1:''' <br> Kay Aull<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> '''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>  
 +
| 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
 +
|'''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
 +
|
|--
|--
-
| Freshmen Team Presentations  
+
| Team Presentations  
|  
|  
|  
|  
-
| (Wed Apr 30,) <br>Wed May 7,<br> May 14
+
| Wed May 7,<br> May 14
|
|
|--
|--
|}
|}
 +
===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 color>[https://stellar.mit.edu/S/course/20/sp08/20.902/homework/ here]
+
<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]
{| cellspacing="2"  
{| cellspacing="2"  
|- valign="top"
|- valign="top"
|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="clear: right; text-align: left; float: left; padding: .4em .9em .9em">
+
<div style="padding: .4em .9em .9em">
-
Part 1: Readings
+
'''Part 1: Readings'''
-
*Paper 1 (15%): presented with a partner<br>
+
*Paper 1 (15%): presented with a partner
-
*Paper 2 (20%): presented solo<br>
+
*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]]
 +
</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<br>
+
*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<br>
+
*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<br>
+
*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<br>
+
*Instructor Leverage (5%): discretionary adjustment by NK and DE
 +
</div>
 +
|}

Current revision

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.
PMID 2968842

DENK ppt here

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.
PMID 12736688

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.
PMID 3907859

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.
PMID 17709748

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.
PMID 7590320
Article 2:
Complete Chemical Synthesis, Assembly, and Cloning of a Mycoplasma genitalium Genome. Gibson et al. Science. 2008 Jan 24; [Epub ahead of print]
PMID 18218864

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.
PMID 16330045

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
Article 2:
Hsp90 as a capacitor for morphological evolution. Rutherford SL, Lindquist S.Nature. 1998 Nov 26;396(6709):336-42.
PMID 9845070

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 1: Readings

  • Paper 1 (15%): presented with a partner
  • Paper 2 (20%): presented solo
  • Response journal (15%): your thoughts about the papers you don't present. Instructions for this assignment are here

Presentation requirements are here

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
  • 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
  • Instructor Leverage (5%): discretionary adjustment by NK and DE
Personal tools