20.109(F09): Journal Club II: Difference between revisions

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==Synthetic Biology==
==Synthetic Biology==
===Programming Cells===
===Programming Cells===
# ''Why are cellular switches Boolean? General conditions for multistable genetic circuits.''Macía J, Widder S, Solé R. '''J Theor Biol.''' 2009 Jul 24. [[PMID: 19632240]]
# ''Why are cellular switches Boolean? General conditions for multistable genetic circuits.''Macía J, Widder S, Solé R. '''J Theor Biol.''' 2009 Jul 24. [[PMID: 19632240]] <font color = orange><b>[SAA/TR/Orange]</b></font color>
#''A yeast synthetic network for in vivo assessment of reverse-engineering and modeling approaches.'' Cantone I, Marucci L, Iorio F, Ricci MA, Belcastro V, Bansal M, Santini S, di Bernardo M, di Bernardo D, Cosma MP. '''Cell.''' 2009 Apr 3;137(1):172-81. [[PMID: 19327819]]
#''A yeast synthetic network for in vivo assessment of reverse-engineering and modeling approaches.'' Cantone I, Marucci L, Iorio F, Ricci MA, Belcastro V, Bansal M, Santini S, di Bernardo M, di Bernardo D, Cosma MP. '''Cell.''' 2009 Apr 3;137(1):172-81. [[PMID: 19327819]]
#''A synthetic mammalian gene circuit reveals antituberculosis compounds.'' Weber W, Schoenmakers R, Keller B, Gitzinger M, Grau T, Daoud-El Baba M, Sander P, Fussenegger M. '''Proc Natl Acad Sci U S A.''' 2008 Jul 22;105(29):9994-8. [[PMID: 18621677]]<font color=green><b>[RA/WF/Green]</b></font color>
#''A synthetic mammalian gene circuit reveals antituberculosis compounds.'' Weber W, Schoenmakers R, Keller B, Gitzinger M, Grau T, Daoud-El Baba M, Sander P, Fussenegger M. '''Proc Natl Acad Sci U S A.''' 2008 Jul 22;105(29):9994-8. [[PMID: 18621677]]<font color=green><b>[RA/WF/Green]</b></font color><font color=purple><b>[RAH/TR/Purple]</b></font color>
# ''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]]
# ''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]]
#''Programming cells by multiplex genome engineering and accelerated evolution.'' Wang HH, Isaacs FJ, Carr PA, Sun ZZ, Xu G, Forest CR, Church GM. '''Nature.''' 2009 Jul 26. [[PMID: 19633652]] <font color = orange><b>[JGP/TR/Orange]</b></font color>
#''Programming cells by multiplex genome engineering and accelerated evolution.'' Wang HH, Isaacs FJ, Carr PA, Sun ZZ, Xu G, Forest CR, Church GM. '''Nature.''' 2009 Jul 26. [[PMID: 19633652]] <font color = orange><b>[JGP/TR/Orange]</b></font color>
#''A synthetic genetic edge detection program.'' Tabor JJ, Salis HM, Simpson ZB, Chevalier AA, Levskaya A, Marcotte EM, Voigt CA, Ellington AD. '''Cell.''' 2009 Jun 26;137(7):1272-81. [[PMID: 19563759]]
#''A synthetic genetic edge detection program.'' Tabor JJ, Salis HM, Simpson ZB, Chevalier AA, Levskaya A, Marcotte EM, Voigt CA, Ellington AD. '''Cell.''' 2009 Jun 26;137(7):1272-81. [[PMID: 19563759]]<font color = pink><b>[HHC/TR/Pink]</b></font color>
#''Synthetic gene networks that count.'' Friedland AE, Lu TK, Wang X, Shi D, Church G, Collins JJ. '''Science.''' 2009 May 29;324(5931):1199-202. [[PMID: 19478183]]<font color = yellow><b>[DLG/TR/Yellow]</b></font color>
#''Synthetic gene networks that count.'' Friedland AE, Lu TK, Wang X, Shi D, Church G, Collins JJ. '''Science.''' 2009 May 29;324(5931):1199-202. [[PMID: 19478183]]<font color = yellow><b>[DLG/TR/Yellow]</b></font color>
#''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]]
#''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]]<font color = pink><b>[HC/TR/Pink]</b></font color>
#''Using two-component systems and other bacterial regulatory factors for the fabrication of synthetic genetic devices.'' Ninfa AJ, Selinsky S, Perry N, Atkins S, Xiu Song Q, Mayo A, Arps D, Woolf P, Atkinson MR. '''Methods Enzymol.''' 2007;422:488-512. [[PMID: 17628156]]
#''Using two-component systems and other bacterial regulatory factors for the fabrication of synthetic genetic devices.'' Ninfa AJ, Selinsky S, Perry N, Atkins S, Xiu Song Q, Mayo A, Arps D, Woolf P, Atkinson MR. '''Methods Enzymol.''' 2007;422:488-512. [[PMID: 17628156]]
#''Synthetic cooperation in engineered yeast populations.''Shou W, Ram S, Vilar JM. '''Proc Natl Acad Sci U S A.''' 2007 Feb 6;104(6):1877-82. [[PMID: 17267602]]
#''Synthetic cooperation in engineered yeast populations.''Shou W, Ram S, Vilar JM. '''Proc Natl Acad Sci U S A.''' 2007 Feb 6;104(6):1877-82. [[PMID: 17267602]]
#''Rewiring the specificity of two-component signal transduction systems.'' Skerker JM, Perchuk BS, Siryaporn A, Lubin EA, Ashenberg O, Goulian M, Laub MT. '''Cell.''' 2008 Jun 13;133(6):1043-54. [[PMID: 18555780]]
#''Rewiring the specificity of two-component signal transduction systems.'' Skerker JM, Perchuk BS, Siryaporn A, Lubin EA, Ashenberg O, Goulian M, Laub MT. '''Cell.''' 2008 Jun 13;133(6):1043-54. [[PMID: 18555780]]<font color="red"><b>[SLB/WF/Red]</b></font color>
#''Synthetic protein scaffolds provide modular control over metabolic flux.'' Dueber JE, Wu GC, Malmirchegini GR, Moon TS, Petzold CJ, Ullal AV, Prather KL, Keasling JD. '''Nat Biotechnol.''' 2009 Aug;27(8):753-9. [[PMID: 19648908]]
#''Synthetic protein scaffolds provide modular control over metabolic flux.'' Dueber JE, Wu GC, Malmirchegini GR, Moon TS, Petzold CJ, Ullal AV, Prather KL, Keasling JD. '''Nat Biotechnol.''' 2009 Aug;27(8):753-9. [[PMID: 19648908]] <font color="green"><b>[KAD/TR/Green]</b></font>
#''Engineering alternative butanol production platforms in heterologous bacteria.'' Nielsen DR, Leonard E, Yoon SH, Tseng HC, Yuan C, Prather KL. '''Metab Eng.''' 2009 Jul-Sep;11(4-5):262-73. [[PMID: 19464384]]
#''Engineering alternative butanol production platforms in heterologous bacteria.'' Nielsen DR, Leonard E, Yoon SH, Tseng HC, Yuan C, Prather KL. '''Metab Eng.''' 2009 Jul-Sep;11(4-5):262-73. [[PMID: 19464384]]
#''Creating bacterial strains from genomes that have been cloned and engineered in yeast.'' Lartigue, C. et al. '''Science''' 20 Aug 2009 [[doi: 10.1126/science.1173759]]
#''Creating bacterial strains from genomes that have been cloned and engineered in yeast.'' Lartigue, C. et al. '''Science''' 20 Aug 2009 [[doi: 10.1126/science.1173759]]<font color = pink><b>[KMT/WF/Pink]</b></font color>  <font color = purple><b>[SBP/TR/Purple]</b></font color>
#''Single-molecule sequencing of an individual human genome.'' Pushkarev, D., Neff, N. F. & Quake, S. R.  '''Nature Biotech.''' 10 Aug 2009 [[doi: 10.1038/nbt.1561]]
#''Single-molecule sequencing of an individual human genome.'' Pushkarev, D., Neff, N. F. & Quake, S. R.  '''Nature Biotech.''' 10 Aug 2009 [[doi: 10.1038/nbt.1561]]
#''A switchable light-input, light-output system modelled and constructed in yeast.'' Sorokina, O et al., '''Journal of Biological Engineering''' 2009, 3:15 [[doi:10.1186/1754-1611-3-15]]
#''A switchable light-input, light-output system modelled and constructed in yeast.'' Sorokina, O et al., '''Journal of Biological Engineering''' 2009, 3:15 [[doi:10.1186/1754-1611-3-15]]
# ''Induction of protein-protein interactions in live cells using light'' Masayuki Yazawa, Amir M Sadaghiani, Brian Hsueh and Ricardo E Dolmetsch '''Nature Biotechnology.''' 2009 Oct;27(1):941-945 [[doi:10.1038/nbt.1569 ]] <font color = green><b>[IPB/WF/Green]</b></font color>
# ''Automated design of synthetic ribosome binding sites to control protein expression'' Howard M Salis, Ethan A Mirsky and Christopher A Voigt '''Nature Biotechnology''' 2009 Oct;27(1):946 - 950  [[doi:10.1038/nbt.1568]]

Latest revision as of 20:19, 5 November 2009


20.109(F09): Laboratory Fundamentals of Biological Engineering

Home        People        Schedule Fall 2009        Assignments        Lab Basics        OWW Basics       
DNA Engineering        System Engineering        Biomaterials Engineering              

Focus: Synthetic Biology

Paper Options

The list of papers below is provided as a guideline for the types of papers that might be relevant for your presentation. You are not limited to the primary research articles on this list. The list is provided simply to give you an idea of the kinds of subjects that could make suitable presentations for the class. Search pubmed yourself to find articles of interest to you.

Note: If you have trouble accessing your article directly, go to http://libraries.mit.edu/vera, which is MIT's collection of journals online. Try selecting "exact title" from the search pulldown menu if the name of your journal is a common word such as Science. For older articles, you need to choose the JSTOR rather than Highwire interface.

Logistics of Paper Selection

  • Once you have decided on a paper for your presentation, please email it to 20.109.f09.talks AT gmail DOT com, and also "reserve" it by putting your (initials/lab section/team color) next to the listing here.
  • For visibility, please use the following format to sign up if possible, substituting in your own initials and team color: [ANS/WF/Purple]. Thanks!
  • The same paper may be presented by a T/R and a W/F student, but may only be presented once per section.

As you prepare your talk be sure to follow the specific guidelines for oral presentations in this class.

  • Please email your finished journal club presentation to the Stellar site associated with our subject no later than 1 pm on the day of your presentation. The order in which your presentations are uploaded to Stellar will determine the order of speakers.
  • Presentations will take place in room 16-336.

Synthetic Biology

Programming Cells

  1. Why are cellular switches Boolean? General conditions for multistable genetic circuits.Macía J, Widder S, Solé R. J Theor Biol. 2009 Jul 24. PMID: 19632240 [SAA/TR/Orange]
  2. A yeast synthetic network for in vivo assessment of reverse-engineering and modeling approaches. Cantone I, Marucci L, Iorio F, Ricci MA, Belcastro V, Bansal M, Santini S, di Bernardo M, di Bernardo D, Cosma MP. Cell. 2009 Apr 3;137(1):172-81. PMID: 19327819
  3. A synthetic mammalian gene circuit reveals antituberculosis compounds. Weber W, Schoenmakers R, Keller B, Gitzinger M, Grau T, Daoud-El Baba M, Sander P, Fussenegger M. Proc Natl Acad Sci U S A. 2008 Jul 22;105(29):9994-8. PMID: 18621677[RA/WF/Green][RAH/TR/Purple]
  4. 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
  5. Programming cells by multiplex genome engineering and accelerated evolution. Wang HH, Isaacs FJ, Carr PA, Sun ZZ, Xu G, Forest CR, Church GM. Nature. 2009 Jul 26. PMID: 19633652 [JGP/TR/Orange]
  6. A synthetic genetic edge detection program. Tabor JJ, Salis HM, Simpson ZB, Chevalier AA, Levskaya A, Marcotte EM, Voigt CA, Ellington AD. Cell. 2009 Jun 26;137(7):1272-81. PMID: 19563759[HHC/TR/Pink]
  7. Synthetic gene networks that count. Friedland AE, Lu TK, Wang X, Shi D, Church G, Collins JJ. Science. 2009 May 29;324(5931):1199-202. PMID: 19478183[DLG/TR/Yellow]
  8. 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[HC/TR/Pink]
  9. Using two-component systems and other bacterial regulatory factors for the fabrication of synthetic genetic devices. Ninfa AJ, Selinsky S, Perry N, Atkins S, Xiu Song Q, Mayo A, Arps D, Woolf P, Atkinson MR. Methods Enzymol. 2007;422:488-512. PMID: 17628156
  10. Synthetic cooperation in engineered yeast populations.Shou W, Ram S, Vilar JM. Proc Natl Acad Sci U S A. 2007 Feb 6;104(6):1877-82. PMID: 17267602
  11. Rewiring the specificity of two-component signal transduction systems. Skerker JM, Perchuk BS, Siryaporn A, Lubin EA, Ashenberg O, Goulian M, Laub MT. Cell. 2008 Jun 13;133(6):1043-54. PMID: 18555780[SLB/WF/Red]
  12. Synthetic protein scaffolds provide modular control over metabolic flux. Dueber JE, Wu GC, Malmirchegini GR, Moon TS, Petzold CJ, Ullal AV, Prather KL, Keasling JD. Nat Biotechnol. 2009 Aug;27(8):753-9. PMID: 19648908 [KAD/TR/Green]
  13. Engineering alternative butanol production platforms in heterologous bacteria. Nielsen DR, Leonard E, Yoon SH, Tseng HC, Yuan C, Prather KL. Metab Eng. 2009 Jul-Sep;11(4-5):262-73. PMID: 19464384
  14. Creating bacterial strains from genomes that have been cloned and engineered in yeast. Lartigue, C. et al. Science 20 Aug 2009 doi: 10.1126/science.1173759[KMT/WF/Pink] [SBP/TR/Purple]
  15. Single-molecule sequencing of an individual human genome. Pushkarev, D., Neff, N. F. & Quake, S. R. Nature Biotech. 10 Aug 2009 doi: 10.1038/nbt.1561
  16. A switchable light-input, light-output system modelled and constructed in yeast. Sorokina, O et al., Journal of Biological Engineering 2009, 3:15 doi:10.1186/1754-1611-3-15
  17. Induction of protein-protein interactions in live cells using light Masayuki Yazawa, Amir M Sadaghiani, Brian Hsueh and Ricardo E Dolmetsch Nature Biotechnology. 2009 Oct;27(1):941-945 doi:10.1038/nbt.1569 [IPB/WF/Green]
  18. Automated design of synthetic ribosome binding sites to control protein expression Howard M Salis, Ethan A Mirsky and Christopher A Voigt Nature Biotechnology 2009 Oct;27(1):946 - 950 doi:10.1038/nbt.1568
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