Difference between revisions of "20.109(F11): Journal Club II"

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==<center>Focus: Synthetic Biology</center>==
 
==<center>Focus: Synthetic Biology</center>==
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# ''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]]   
 
#''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]]
 +
#''Programmable Ligand Detection System in Plants through a Synthetic Signal Transduction Pathway''Antunes MS, Morey KJ, Smith JJ, Albrecht KD, Bowen TA, et al.'''PLoS ONE''' 6(1): e16292. [[doi:10.1371/journal.pone.0016292]]
 +
#''Precise Manipulation of Chromosomes in Vivo Enables Genome-Wide Codon Replacement'' Isaacs et al. '''Science''' (2011) 333(348)[[DOI: 10.1126/science.1205822]]
 +
#''Towards a Synthetic Chloroplast'' Agapakis CM, Niederholtmeyer H, Noche RR, Lieberman TD, Megason SG, et al. '''PLoS ONE''' (2011) 6(4): e18877. [[doi:10.1371/journal.pone.0018877]]
 
#''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]]  
 
#''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]]  
−
# ''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]] <font color = yellow>'''[AT/YELLOW]'''</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]]  
 
#''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]]   
 
#''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]]   
 
#''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]]
Line 38: Line 41:
 
#''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]]
 
#''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]]  
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#''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]]<font color = green> '''[SK/Green]'''</font color>
+
#''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]]
 
#''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]]

Revision as of 18:15, 14 August 2011


20.109(F11): Laboratory Fundamentals of Biological Engineering

20.109(F11) homepage.jpg

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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 nkuldell or astachow AT mit DOT edu, 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 only 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 11 AM 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. Expanding the Genetic Code of an AnimalS Greiss, and J Chin. J. Am. Chem. Soc.DOI: 10.1021/ja2054034
  2. GoldenBraid: An Iterative Cloning System for Standardized Assembly of Reusable Genetic Modules Alejandro Sarrion-Perdigones, Erica Elvira Falconi, Sara I. Zandalinas, Paloma Jua´ rez, Asun Ferna´ndez-del-Carmen, Antonio Granell, Diego Orzaez PLoS ONE2011 6(7):e21622 doi:10.1371/journal.pone.0021622
  3. Characterization of a synthetic bacterial self-destruction device for programmed cell death and for recombinant proteins releaseLorenzo Pasotti, Susanna Zucca, Manuel Lupotto, Maria Gabriella Cusella De Angelis and Paolo Magni1Journal of Biological Engineering 2011, 5:8 doi:10.1186/1754-1611-5-8
  4. Designing and engineering evolutionary robust genetic circuitsSleight SC, Bartley BA, Lieviant JA, Sauro HMJournal of Biological Engineering 2010, 4:12 (1 November 2010)doi:10.1186/1754-1611-4-12
  5. 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
  6. 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
  7. Programmable Ligand Detection System in Plants through a Synthetic Signal Transduction PathwayAntunes MS, Morey KJ, Smith JJ, Albrecht KD, Bowen TA, et al.PLoS ONE 6(1): e16292. doi:10.1371/journal.pone.0016292
  8. Precise Manipulation of Chromosomes in Vivo Enables Genome-Wide Codon Replacement Isaacs et al. Science (2011) 333(348)DOI: 10.1126/science.1205822
  9. Towards a Synthetic Chloroplast Agapakis CM, Niederholtmeyer H, Noche RR, Lieberman TD, Megason SG, et al. PLoS ONE (2011) 6(4): e18877. doi:10.1371/journal.pone.0018877
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. Defining Network Topologies that Can Achieve Biochemical Adaptation. Ma W, Trusina A, El-Samad H, Lim W, Tang C. Cell. 2009 Aug 21. 138:760-773
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. Tracking, tuning, and terminating microbial physiology using synthetic riboregulators. Callura JM, Dwyer DJ, Isaacs FJ, Cantor CR, Collins JJ. Proc Natl Acad Sci U S A. 2010 Aug 16. PMID: 20713708
  28. A synthetic three-color scaffold for monitoring genetic regulation and noise. Cox RS 3rd, Dunlop MJ, Elowitz MB. J Biol Eng. 2010 Jul 21;4:10.PMID: 20646328
  29. Engineering a Direct and Inducible Protein−RNA Interaction To Regulate RNA BiologyBelmont, B., Niles, J.ACS Chem. Biol., 2010; 5 (9): 851–861 DOI: 10.1021/cb100070j
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