20.20(S13):Advanced topics: Difference between revisions
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| [[Natalie Kuldell]] | | [[Natalie Kuldell]] | ||
| preview of 20.385 | | preview of 20.385 | ||
| | |'''Factory of Life '''<br> Witze A [http://www.sciencenews.org/view/feature/id/347263/description/Factory_of_Life Science News]<br> | ||
'''Two ‘What if' experiments'''<br> Ptashne M [[PMID: 15055587]]<br> | |||
'''Build Artificial''' <br> Brent R [[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]] | ||
|-- | |-- | ||
|'''Transcription-based Logic Devices'''<br> | |||
| 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]] | |||
|-- | |||
| ''' DNA fine-tuning + evolution '''<br> | | ''' DNA fine-tuning + evolution '''<br> | ||
| Week | | Week 4:<br> Wed Feb 27 | ||
| | | Jessica + NK <br> [[Media:20.385(S13) JC1 JL NK 022713.pdf| ppt is here]] | ||
|'''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]] | |'''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]] | ||
|'''Directed evolution as a powerful synthetic biology tool'''<br>Cobb RE, Sun N, Zhao H. ''Methods'' (2012) Mar 23. <br>[[PMID: 22465795]] <br> | |'''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 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]] | | '''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]] | ||
| '''RNA synthetic biology''' <br>Isaacs FJ, Dwyer DJ, Collins JJ. ''Nat Biotechnol.'' (2006) 24(5):545-54. <br> [[PMID: 16680139]] | | '''RNA synthetic biology''' <br>Isaacs FJ, Dwyer DJ, Collins JJ. ''Nat Biotechnol.'' (2006) 24(5):545-54. <br> [[PMID: 16680139]] | ||
|-- | |-- | ||
| ''' | | '''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]] | ||
|''' | |'''Towards practical, high-capacity, low-maintenance information storage in synthesized DNA'''<br> Goldman N et al. ''Nature'' (2013)<br> [[doi:10.1038/nature11875]] | ||
| '''A | | '''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]] | ||
|-- | |-- | ||
| ''' | | '''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]] | ||
| ''' | | '''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]] | ||
|''' | |'''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]] | ||
| ''' | | '''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]] | ||
| ''' | | '''Multiplex Genome Engineering Using CRISPR/Cas Systems'''<br>Cong L et al. ''Science'' (2013) Jan 3. <br>[[PMID: 23287718]] <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) | ||
| ''' | | '''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]] | ||
|''' | |'''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 | |'''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]] | ||
| ''' | | '''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 | | '''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> | ||
|''' | |'''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]] | ||
|-- | |-- | ||
| ''' | | '''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]] | ||
| ''' | |''' 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> | ||
|''' | |'''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 & | |'''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]] | ||
|''' | |'''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]] | ||
| ''' | | ''' 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]] | ||
|-- | |-- | ||
| ''' | | '''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) | ||
| '''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]] | |||
|''' | | '''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]] | ||
|''' | |||
|} | |} |
Latest revision as of 18:16, 8 May 2013
20.385: Advanced Topics in Synthetic Biology
Assignments
Homework dropbox is here
Part 1: Readings
Instructions for these assignment are here |
Part 2: Team Mentoring
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 |
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 |