20.20(S13):Advanced topics: Difference between revisions

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| [[Natalie Kuldell]]
| [[Natalie Kuldell]]
| preview of 20.385
| preview of 20.385
|before next week read
|'''Factory of Life '''<br> Witze A [http://www.sciencenews.org/view/feature/id/347263/description/Factory_of_Life Science News]<br>
#''Factory of Life ''<br>A. Witze<br>Science News (2013) 183:1 [[http://www.sciencenews.org/view/feature/id/347263/description/Factory_of_Life]]
'''Two ‘What if' experiments'''<br> Ptashne M [[PMID: 15055587]]<br>
#''Two ‘What if' experiments''<br>Ptashne, M. <br>[[PMID: 15055587]]
'''Build Artificial''' <br> Brent R [[PMID: 15055588]]   
#''Build Artificial''<br> Brent, R. <br> [[PMID: 15055588]]   
|--
|--
| <b>Parts™</b>
| <b>Parts™</b>
Line 53: Line 52:
| '''Synthetic biology devices as tools for metabolic engineering''' <br>Shiue E, Prather K. ''Biochemical Engineering Journal'' (2012) 65:82–89<br>[[doi:10.1016/j.bej.2012.04.006]]
| '''Synthetic biology devices as tools for metabolic engineering''' <br>Shiue E, Prather K. ''Biochemical Engineering Journal'' (2012) 65:82–89<br>[[doi:10.1016/j.bej.2012.04.006]]
|--
|--
| ''' DNA fine-tuning + evolution '''<br>  
|'''Transcription-based Logic Devices'''<br>
| Week 3: <br>Wed Feb 20   
| Week 3: <br>Wed Feb 20   
|  
| Paula + NK <br> [[Media:Journal Club 1 slides NK PCT.pdf| ppt is here]]
|'''Genetic programs constructed from layered logic gates in single cells'''<br>  Moon TS, Lou C, Tamsir A, Stanton BC, Voigt CA ''Nature'' (2012) 491: 249–253 <br>[[doi:10.1038/nature11516]]
|'''Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology '''<br> Wang B, et al. ''Nat. Commun.'' (2011) 2 : 508 <br>[[doi: 10.1038/ncomms1516]]  
|'''Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology '''<br> Wang B, et al. ''Nat. Commun.'' (2011) 2 : 508 <br>[[doi: 10.1038/ncomms1516]]  
|'''A synthetic oscillatory network of transcriptional regulators'''<br>Elowitz, MB, and Leibler, S. ''Nature'' (2000) 403:335–338 <br>[[PMID: 10659856]] <br>'''Construction of a genetic toggle switch in Escherichia coli'''<br> Gardner TS, et al.''Nature''(2000) 403:339–342 <br>[[PMID: 10659857]]<br>
|--  
|--  
|'''Transcription-based Logic Devices'''<br>  
| ''' DNA fine-tuning + evolution '''<br>  
| Week 4:<br> Wed Feb 27
| Week 4:<br> Wed Feb 27
|  
| Jessica + NK <br> [[Media:20.385(S13) JC1 JL NK 022713.pdf| ppt is here]]
|'''Direct and specific chemical control of eukaryotic translation with a synthetic RNA–protein interaction'''<br> Goldfless SJ, et al. ''NAR'' (2012) 1-12<br>[[DOI: 10.1093/nar/gks028]]
|'''Rational Diversification of a Promoter Providing Fine-Tuned Expression and Orthogonal Regulation for Synthetic Biology'''<br> Blount BA, Weenink T, Vasylechko S, Ellis T.<br>PLoS ONE (2012) 7(3): e33279.<br> [[doi:10.1371/journal.pone.0033279]]
|'''Versatile RNA-sensing transcriptional regulators for engineering genetic networks''' <br>Lucks JB, et al. ''PNAS'' (2011) 108(21): 8617-8622 <br> [[DOI: 10.1073/pnas.1015741108]]
|'''Directed evolution as a powerful synthetic biology tool'''<br>Cobb RE, Sun N, Zhao H. ''Methods'' (2012) Mar 23. <br>[[PMID: 22465795]] <br>
|-
|-
|'''RNA Engineering'''<br>  
|'''RNA Engineering'''<br>  
| Week 5: <br>Wed Mar 6
| Week 5: <br>Wed Mar 6
|  
| Kristine + Ryan <br> [[Media:De novo automated d---mall RNA circuits.pdf| ppt is here]]
| '''De Novo Designed Proteins from a Library of Artificial Sequences Function in Esherichia Coli and Enable Cell Growth''' <br>Fisher MA, et al. ''PLoS One'' (2011)6(1):e15364<br>[[DOI: 10.1371/journal.pone.0015364]]
| '''De novo automated design of small RNA circuits for engineering synthetic riboregulation in living cells.''' <br>Rodrigo G, Landrain TE, Jaramillo A. ''PNAS''(2012) 109(38):15271-6.<br> [[PMID: 22949707]]
| '''Directed evolution of recombinase specificity by split gene reassembly''' <br>Gersbach, CA, et al. ''NAR'' (2010) 38(12): 4198-4206-1543 <br> [[DOI: 10.1093/nar/gkq125]]
| '''RNA synthetic biology''' <br>Isaacs FJ, Dwyer DJ, Collins JJ. ''Nat Biotechnol.'' (2006) 24(5):545-54. <br> [[PMID: 16680139]]
|--
|--
| '''Modularity''' <br>  
| '''Engineering Biology''' <br>  
| Week 6:<br> <font color = blue> Wed Mar 13</font color> <br>before 3 ideas presentations
| Week 6:<br> <font color = blue> Wed Mar 13</font color> <br>before 3 ideas presentations
|  
| Divya + NK<br> [[Media:20.385(S13)Journal Club 1 DC NK.pdf| ppt is here]]
|'''Modularity of a carbon-fixing protein organelle'''<br> Bonacci W et al. ''PNAS'' (2012)109(2):478-483<br>[[DOI: 10.1073/pnas.1108557109]]
|'''Towards practical, high-capacity, low-maintenance information storage in synthesized DNA'''<br> Goldman N et al.     ''Nature'' (2013)<br> [[doi:10.1038/nature11875]]  
| '''A modular positive feedback-based gene amplifier''' <br>Nistala GJ et al. ''JBE'' (2010) 4:4<br>[[DOI: 10.1186/1754-1611-4-4]]]
| '''A fully decompressed synthetic bacteriophage øX174 genome assembled and archived in yeast''' <br>Jaschke PR et al. ''Virology''(2012)434(2):278-84. <br> [[doi: 10.1016/j.virol.2012.09.020]]  
|--
|--
| '''(re)Programming Systems''' <br>  
| '''SynBio for Science''' <br>  
| Week 7:<br> Wed Mar 20  
| Week 7:<br> Wed Mar 20  
|
| Holly + Gonzo<br> [[Media:20.385 Gonzo and Holly Journal Club.pptx.pdf| ppt is here]]
| '''Reprogramming bacteria to seek and destroy an herbicide''' <br>Sinha, J. et al. ''Nature Chemical Biology'' (2010)6: 464–470<br>[[doi:10.1038/nchembio.369]]
| '''Synthetic biology challenges long-held hypotheses in translation, codon bias and transcription''' <br>Forster AC. ''Biotechnol J.'' (2012) 7(7):835-45.<br> [[doi: 10.1002/biot.201200002]]
|'''Scaling up synthetic biology: Do not forget the chassis'''<br> A Danchin ''FEBS letters'' (2012)<br>[[Media:Don'tForgetChassis FEBSLett12.pdf| pdf here]]
|'''Five hard truths for synthetic biology'''<br> Kwok R. ''Nature''(2010) 463(7279):288-90.<br>[[doi: 10.1038/463288a]]
|--
|--
! colspan="3" | Spring Break Mar 26-30
! colspan="3" | Spring Break Mar 26-30
Line 89: Line 88:
| '''DNA construction and editing technologies'''<br>  
| '''DNA construction and editing technologies'''<br>  
| Week 8:<br> Wed Apr 3
| Week 8:<br> Wed Apr 3
|  
| Jessica (Sung et al paper)<br> [[Media:Jessica Journal presentation 2.pdf| ppt is here]]
| '''Precise Manipulation of Chromosomes in Vivo Enables Genome-Wide Codon Replacement'''<br>Isaacs FJ et al. ''Science'' (2011) 333(6040):348-353 <br>[[DOI: 10.1126/science.1205822]]
| '''Knockout mice created by TALEN-mediated gene targeting.'''<br>Sung YH et al. ''Nat Biotechnol'' (2013) 31(1):23-4. <br> [[doi: 10.1038/nbt.2477]]
| '''Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting.'''<br>Cermak T et al. ''NAR'' (2011) 39(12):7879 <br>[[PMID: 21493687]] <br>
| '''Multiplex Genome Engineering Using CRISPR/Cas Systems'''<br>Cong L et al. ''Science'' (2013) Jan 3. <br>[[PMID: 23287718]] <br>
|--
|--
| '''Feedback and Insulation''' <br>
| '''Cell Physiology''' <br>
| Week 9:<br> <font color = blue> Wed Apr 10 </font color><br> before tech spec review  
| Week 9:<br> <font color = blue> Wed Apr 10 </font color><br> before tech spec review  
|  
| No presentations this week (response record for one or the other paper due)
| '''A yeast synthetic network for in vivo assessment of reverse-engineering and modeling approaches'''<br>Cantone I et al''Cell'' (2009)137(1):172-181<br> [[PMID: 19327819]]  
| '''Shared control of gene expression in bacteria by transcription factors and global physiology of the cell'''<br>Berthoumieux S et al''Mol Syst Biol'' (2013) 9:634 <br> [[doi: 10.1038/msb.2012.70]]
|'''In silico feedback for in vivo regulation of a gene expression circuit''' <br> Milias-Argeitis A et al.''Nature BioTech'' (2011) 29(12):1114–1116<br> [[doi:10.1038/nbt.2018]]
|'''A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis''' <br> Picotti P et al.''Nature'' (2013) Jan 20. <br> [[doi: 10.1038/nature11835]]
|-
|-
| '''Chassis''' <br>  
| '''Chassis''' <br>  
| Week 10: <br> Wed Apr 17  
| Week 10: <br> Wed Apr 17  
|
| Kristine (Woodruff paper)[[Media:WoodruffPaper KristineKim.pdf| ppt is here]]<br> Ryan (Cardinale paper)[[Media:CardinalePaper Keating.pdf| ppt is here]]
|'''An E. coli Cell-Free Expression Toolbox: Application to Synthetic Gene Circuits and Artificial Cells'''<br> Shin J, and Noireaux, V. ''ACS Synthetic Biology'' (2012) 1(1):29–41<br> [[DOI: 10.1021/sb200016s]]
|'''Towards a metabolic engineering strain "commons": An Escherichia coli platform strain for ethanol production'''<br> Woodruff LB, May BL, Warner JR, Gill RT. ''Biotechnol Bioeng'' (2013) Jan 15.<br> [[doi: 10.1002/bit.24840]]
| '''Low-mutation-rate, reduced-genome Escherichia coli: An improved host for faithful maintenance of engineered genetic constructs''' <br> Csorgo B et al. ''Microbial Cell Factories'' (2012)11:11<br> [[doi:10.1186/1475-2859-11-11]]
| '''Contextualizing context for synthetic biology--identifying causes of failure of synthetic biological systems''' <br> Cardinale S, Arkin AP.''Biotechnol J''(2012) 7(7):856-66. <br> [[doi: 10.1002/biot.201200085]]  
|--
|--
| '''Programming with Models & Noise'''<br>
| '''Programming in the Noise'''<br>
| Week 11:<br> Wed Apr 24
| Week 11:<br> Wed Apr 24
|  
| Divya (Litcofsky paper)<font color= red> May 1st</font color><br> Gonzo (Prindle paper)<font color= red> May 8th</font color>
|'''Model-Driven Engineering of RNA Devices to Quantitatively Program Gene Expression'''<br>Carothers JM et al. ''Science'' (2011)334(6063):1716-1719 <br>[[DOI: 10.1126/science.1212209 ]]
|'''Iterative plug-and-play methodology for constructing and modifying synthetic gene networks'''<br>Litcofsky KD et al. ''Nat Methods''(2012) 9(11):1077-80.<br> [[doi: 10.1038/nmeth.2205]]
|'''A sensing array of radically coupled genetic ‘biopixels’''' <br>Prindle A et al. ''Nature''(2012)481:39–44<br>[[doi:10.1038/nature10722]]
|'''A sensing array of radically coupled genetic ‘biopixels’''' <br>Prindle A et al. ''Nature''(2012)481:39–44<br>[[doi:10.1038/nature10722]]
|--
|--
| '''Metabolic Engineering'''  
| '''Property rights in synthetic biology'''  
| Week 12:<br> Wed May 1
| Week 12:<br> Wed May 1
|  
| Holly (Rai paper) [[Media:Holly Week 12 Journal Club - Rai Paper.pdf| ppt is here]]<br>+ Divya [[Media:Divya Journal Club 2.pdf| ppt is here]]
| '''Use of modular, synthetic scaffolds for improved production of glucaric acid in engineered E. coli.'''Moon TS et al. ''Metabolic Engineering'' (2010) 12: 298-305 <br>[[PMID: 20117231]]
|''' Synthetic biology: caught between property rights, the public domain, and the commons''' <br>Rai A, Boyle ''J. PLoS Biol.'' (2007)5(3):e58<br>[[PMID: 17355173]] <br>
|'''Organization of Intracellular Reactions with Rationally Designed RNA Assemblies'''<br>Delebecqu CJ et al. ''Science'' (2011) 333:470 <br>[[DOI: 10.1126/science.1206938 ]]
|'''Preparing synthetic biology for the world'''<br>Moe-Behrens GH, Davis R, Haynes KA. ''Front Microbiol'' (2013) 4:5 <br> [[doi: 10.3389/fmicb.2013.00005]]
|--
|--
|'''Systems & System Ecology'''  
|'''Systems & Communities'''  
| Week 13:<br> Wed May 8  
| Week 13:<br> Wed May 8  
|  
| Paula (Oritz paper) [[Media:Paula Trepman Journal Club Final.pdf| ppt is here]]<br>+ Gonzo (Prindle paper)[[Media:Gonzo Presentation2 20385(13).pdf| ppt is here]]
|'''Synthetic chromosome arms function in yeast and generate phenotypic diversity by design'''<br>Dymond JS et al. ''Nature'' (2011) 477: 471–476<br>[[doi:10.1038/nature10403]]
|'''Engineered cell-cell communication via DNA messaging'''<br>Ortiz ME, Endy D. ''JBE'' (2012) 6(1):16. <br> [[doi: 10.1186/1754-1611-6-16]]
| ''' Engineered bidirectional communication mediates a consensus in a microbial biofilm consortium''' <br> Brenner K ''PNAS'' (2007) 104(44):17300-17304<br>[[DOI: 10.1073/pnas.0704256104]]
| ''' Autonomous bacterial localization and gene expression based on nearby cell receptor density''' <br> Wu HC et al. ''Mol Syst Biol'' (2013) 9:636.<br> [[doi: 10.1038/msb.2012.71]]
|--
|--
| '''Property rights in synthetic biology'''  
| '''Metabolic Engineering'''  
| Week 14: <br><font color = blue> Wed May 15 </font color><br> before final presentations  
| Week 14: <br><font color = blue> Wed May 15 </font color><br> before final presentations  
|  
| no presentations this week (response record only if you've missed a different discussion this term)
|''' Synthetic biology: caught between property rights, the public domain, and the commons''' <br>Rai A, Boyle ''J. PLoS Biol.'' (2007)5(3):e58<br>[[PMID: 17355173]] <br>
| '''Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs''' Na D et al. ''Nat Biotechnol'' (2013) Jan 20. <br> [[doi: 10.1038/nbt.2461]]
|'''Patents and Translational Research in Genomics'''<br>Kaye J, Hawkins N, and Taylor J. ''Nature Biotech'' (2007) 25(7): 739–741.[[doi: 10.1038/nbt0707-739.]]
| '''Synthetic protein scaffolds provide modular control over metabolic flux'''Dueber JE et al. ''Nat Biotechnol'' (2009) 27(8):753-9. <br> [[doi: 10.1038/nbt.1557]]
|--
|'''Safety!'''  
| Week 14: <br><font color = blue> Wed May 16 </font color> <br> before final presentations
|
| '''Managing the unimaginable. Regulatory responses to the challenges posed by synthetic biology and synthetic genomics.''' <br>Samuel GN, Selgelid MJ, Kerridge I. ''EMBO reports'' (2009) 10(1):7-11.<br>[[DOI: 10.1038/embor.2008.232]]<br>
|'''Darwin’s Surprise: Why are evolutionary biologists bringing back extinct deadly viruses?''' <br>Michael Specter [http://www.newyorker.com/reporting/2007/12/03/071203fa_fact_specter New Yorker article]
|}
|}

Latest revision as of 18:16, 8 May 2013

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20.385: Advanced Topics in Synthetic Biology

Assignments

Homework dropbox is here

Part 1: Readings

  • Paper 1 (10%)
  • Paper 2 (15%)
  • Response record (20%): your thoughts about the papers you don't present.
  • Participation in class discussions (5%): your thoughtful questions and ideas during the presentations of others

Instructions for these assignment are here

Part 2: Team Mentoring

  • Progress and Mentoring Reports (30%): one page summaries of your freshman team's work and 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

16-220

TOPIC DATE Discussion leader(s) Discussion paper(s) Related paper(s) to enjoy
Preview of 20.385 Week 1:
Wed Feb 6 		Natalie Kuldell preview of 20.385 Factory of Life
Witze A Science News

Two ‘What if' experiments
Ptashne M PMID: 15055587
Build Artificial
Brent R PMID: 15055588

Parts™ Week 2:
Wed Feb 13 		Natalie Kuldell
ppt is here 		Turning lambda Cro into a transcriptional activator
Bushman FD, Ptashne M.Cell. (1988) Jul 15;54(2):191-7.
PMID: 2968842
 Synthetic biology devices as tools for metabolic engineering
Shiue E, Prather K. Biochemical Engineering Journal (2012) 65:82–89
doi:10.1016/j.bej.2012.04.006
Transcription-based Logic Devices
 Week 3:
Wed Feb 20 		Paula + NK
ppt is here 		Genetic programs constructed from layered logic gates in single cells
Moon TS, Lou C, Tamsir A, Stanton BC, Voigt CA Nature (2012) 491: 249–253
doi:10.1038/nature11516 		Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology
Wang B, et al. Nat. Commun. (2011) 2 : 508
doi: 10.1038/ncomms1516
DNA fine-tuning + evolution
Week 4:
Wed Feb 27 		Jessica + NK
ppt is here 		Rational Diversification of a Promoter Providing Fine-Tuned Expression and Orthogonal Regulation for Synthetic Biology
Blount BA, Weenink T, Vasylechko S, Ellis T.
PLoS ONE (2012) 7(3): e33279.
doi:10.1371/journal.pone.0033279 		Directed evolution as a powerful synthetic biology tool
Cobb RE, Sun N, Zhao H. Methods (2012) Mar 23.
PMID: 22465795
RNA Engineering
 Week 5:
Wed Mar 6 		Kristine + Ryan
ppt is here 		De novo automated design of small RNA circuits for engineering synthetic riboregulation in living cells.
Rodrigo G, Landrain TE, Jaramillo A. PNAS(2012) 109(38):15271-6.
PMID: 22949707 		RNA synthetic biology
Isaacs FJ, Dwyer DJ, Collins JJ. Nat Biotechnol. (2006) 24(5):545-54.
PMID: 16680139
Engineering Biology
Week 6:
Wed Mar 13
before 3 ideas presentations 		Divya + NK
ppt is here 		Towards practical, high-capacity, low-maintenance information storage in synthesized DNA
Goldman N et al. Nature (2013)
doi:10.1038/nature11875 		A fully decompressed synthetic bacteriophage øX174 genome assembled and archived in yeast
Jaschke PR et al. Virology(2012)434(2):278-84.
doi: 10.1016/j.virol.2012.09.020
SynBio for Science
Week 7:
Wed Mar 20 		Holly + Gonzo
ppt is here 		Synthetic biology challenges long-held hypotheses in translation, codon bias and transcription
Forster AC. Biotechnol J. (2012) 7(7):835-45.
doi: 10.1002/biot.201200002 		Five hard truths for synthetic biology
Kwok R. Nature(2010) 463(7279):288-90.
doi: 10.1038/463288a
Spring Break Mar 26-30 No class all week
DNA construction and editing technologies
 Week 8:
Wed Apr 3 		Jessica (Sung et al paper)
ppt is here 		Knockout mice created by TALEN-mediated gene targeting.
Sung YH et al. Nat Biotechnol (2013) 31(1):23-4.
doi: 10.1038/nbt.2477 		Multiplex Genome Engineering Using CRISPR/Cas Systems
Cong L et al. Science (2013) Jan 3.
PMID: 23287718
Cell Physiology
Week 9:
Wed Apr 10
before tech spec review 		No presentations this week (response record for one or the other paper due) Shared control of gene expression in bacteria by transcription factors and global physiology of the cell
Berthoumieux S et alMol Syst Biol (2013) 9:634
doi: 10.1038/msb.2012.70 		A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis
Picotti P et al.Nature (2013) Jan 20.
doi: 10.1038/nature11835
Chassis
Week 10:
Wed Apr 17 		Kristine (Woodruff paper) ppt is here
Ryan (Cardinale paper) ppt is here 		Towards a metabolic engineering strain "commons": An Escherichia coli platform strain for ethanol production
Woodruff LB, May BL, Warner JR, Gill RT. Biotechnol Bioeng (2013) Jan 15.
doi: 10.1002/bit.24840 		Contextualizing context for synthetic biology--identifying causes of failure of synthetic biological systems
Cardinale S, Arkin AP.Biotechnol J(2012) 7(7):856-66.
doi: 10.1002/biot.201200085
Programming in the Noise
 Week 11:
Wed Apr 24 		Divya (Litcofsky paper) May 1st
Gonzo (Prindle paper) May 8th 		Iterative plug-and-play methodology for constructing and modifying synthetic gene networks
Litcofsky KD et al. Nat Methods(2012) 9(11):1077-80.
doi: 10.1038/nmeth.2205 		A sensing array of radically coupled genetic ‘biopixels’
Prindle A et al. Nature(2012)481:39–44
doi:10.1038/nature10722
Property rights in synthetic biology Week 12:
Wed May 1 		Holly (Rai paper) ppt is here
+ Divya ppt is here 		Synthetic biology: caught between property rights, the public domain, and the commons
Rai A, Boyle J. PLoS Biol. (2007)5(3):e58
PMID: 17355173
Preparing synthetic biology for the world
Moe-Behrens GH, Davis R, Haynes KA. Front Microbiol (2013) 4:5
doi: 10.3389/fmicb.2013.00005
Systems & Communities Week 13:
Wed May 8 		Paula (Oritz paper) ppt is here
+ Gonzo (Prindle paper) ppt is here 		Engineered cell-cell communication via DNA messaging
Ortiz ME, Endy D. JBE (2012) 6(1):16.
doi: 10.1186/1754-1611-6-16 		Autonomous bacterial localization and gene expression based on nearby cell receptor density
Wu HC et al. Mol Syst Biol (2013) 9:636.
doi: 10.1038/msb.2012.71
Metabolic Engineering Week 14:
Wed May 15
before final presentations 		no presentations this week (response record only if you've missed a different discussion this term) Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs Na D et al. Nat Biotechnol (2013) Jan 20.
doi: 10.1038/nbt.2461 		Synthetic protein scaffolds provide modular control over metabolic fluxDueber JE et al. Nat Biotechnol (2009) 27(8):753-9.
doi: 10.1038/nbt.1557
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