20.109(F12): Journal Club II: Difference between revisions

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==Synthetic Biology==
==Synthetic Biology==
===Programming Cells===
===Programming Cells===
#''Rewritable digital data storage in live cells via engineered control of recombination directionality''Bonnet J, Subsoontorn P, Endy D. '''PNAS''' 2012 Jun 5;109(23):8884-9. [[PMID: 22615351]]
#''Towards a synthetic chloroplast'' Agapakis CM, Niederholtmeyer H, Noche RR, Lieberman TD, Megason SG, Way JC, Silver PA. '''PLoS One'''2011 Apr 20;6(4):e18877. [[PMID: 21533097]]
#''A modular cloning system for standardized assembly of multigene constructs'' Weber E, Engler C, Gruetzner R, Werner S, Marillonnet S. '''PLoS One''' 2011 Feb 18;6(2):e16765.[[PMID: 21364738]]
#''The bacterial nanorecorder: engineering E. coli to function as a chemical recording device'' Bhomkar P, Materi W, Wishart DS. '''PLoS One''' 2011;6(11):e27559. [[PMID: 22132112]]
#''Standard biological parts knowledgebase''Galdzicki M, Rodriguez C, Chandran D, Sauro HM, Gennari JH. '''PLoS One''' 2011 Feb 24;6(2):e17005 [[PMID: 21390321]]
#''Construction of a Genetic Multiplexer to Toggle between Chemosensory Pathways in Escherichia coli'' Moon, et. al. '''Journal of Molecular Biology''' (2011) 406(2): 215-227 [[doi:10.1016/j.jmb.2010.12.019]]
#''Construction of a Genetic Multiplexer to Toggle between Chemosensory Pathways in Escherichia coli'' Moon, et. al. '''Journal of Molecular Biology''' (2011) 406(2): 215-227 [[doi:10.1016/j.jmb.2010.12.019]]
# ''Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology'' Baojun Wang, Richard I Kitney, Nicolas Joly, Martin Buck. '''Nat. Commun.'''(2011) 2 : 508 [[doi: 10.1038/ncomms1516]]  
# ''Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology'' Baojun Wang, Richard I Kitney, Nicolas Joly, Martin Buck. '''Nat. Commun.'''(2011) 2 : 508 [[doi: 10.1038/ncomms1516]]  

Revision as of 03:55, 18 August 2012


20.109(F12): Laboratory Fundamentals of Biological Engineering

Home        People        Schedule Fall 2012        Assignments        Lab Basics        OWW Basics       
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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 skalford 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. Rewritable digital data storage in live cells via engineered control of recombination directionalityBonnet J, Subsoontorn P, Endy D. PNAS 2012 Jun 5;109(23):8884-9. PMID: 22615351
  2. Towards a synthetic chloroplast Agapakis CM, Niederholtmeyer H, Noche RR, Lieberman TD, Megason SG, Way JC, Silver PA. PLoS One2011 Apr 20;6(4):e18877. PMID: 21533097
  3. A modular cloning system for standardized assembly of multigene constructs Weber E, Engler C, Gruetzner R, Werner S, Marillonnet S. PLoS One 2011 Feb 18;6(2):e16765.PMID: 21364738
  4. The bacterial nanorecorder: engineering E. coli to function as a chemical recording device Bhomkar P, Materi W, Wishart DS. PLoS One 2011;6(11):e27559. PMID: 22132112
  5. Standard biological parts knowledgebaseGaldzicki M, Rodriguez C, Chandran D, Sauro HM, Gennari JH. PLoS One 2011 Feb 24;6(2):e17005 PMID: 21390321
  6. Construction of a Genetic Multiplexer to Toggle between Chemosensory Pathways in Escherichia coli Moon, et. al. Journal of Molecular Biology (2011) 406(2): 215-227 doi:10.1016/j.jmb.2010.12.019
  7. Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology Baojun Wang, Richard I Kitney, Nicolas Joly, Martin Buck. Nat. Commun.(2011) 2 : 508 doi: 10.1038/ncomms1516
  8. Expanding the Genetic Code of an AnimalS Greiss, and J Chin. J. Am. Chem. Soc.(2011) 133(36):14196-9.DOI: 10.1021/ja2054034
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. Precise Manipulation of Chromosomes in Vivo Enables Genome-Wide Codon Replacement Isaacs et al. Science (2011) 333(348)DOI: 10.1126/science.1205822
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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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