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

From OpenWetWare
Jump to navigationJump to search
Line 23: Line 23:
#''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]]
#''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]]
#''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 synthetic biology framework for programming eukaryotic transcription functions'' Khalil AS, Lu TK, Bashor CJ, Ramirez CL, Pyenson NC, Joung JK, Collins JJ. '''Cell''' 2012 Aug 3;150(3):647-58. [[PMID: 22863014]]
#''Modular Design of Artificial Tissue Homeostasis: Robust Control through Synthetic Cellular Heterogeneity''Miller M, Hafner M, Sontag E, Davidsohn N, Subramanian S, Purnick PE, Lauffenburger D, Weiss R. '''PLoS Comput Biol.''' 2012 Jul;8(7):e1002579.[[PMID: 22829755]]
#''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]]
#''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]]
#''PGASO: A synthetic biology tool for engineering a cellulolytic yeast''Chang JJ, Ho CY, Ho FJ, Tsai TY, Ke HM, Wang CH, Chen HL, Shih MC, Huang CC, Li WH.'''Biotechnol Biofuels.''' 2012 Jul 27;5(1):53.[[PMID: 22839502]]
#''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]]
#''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]]
#''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]]
#''Design and construction of "synthetic species"'' Moreno E. '''PLoS One'''2012;7(7):e39054.[[PMID: 22848349]]
# ''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]]  
#''Expanding the Genetic Code of an Animal''S Greiss, and J Chin. '''J. Am. Chem. Soc.'''(2011) 133(36):14196-9.[[DOI: 10.1021/ja2054034]]  
#''Expanding the Genetic Code of an Animal''S Greiss, and J Chin. '''J. Am. Chem. Soc.'''(2011) 133(36):14196-9.[[DOI: 10.1021/ja2054034]]  

Revision as of 04:08, 18 August 2012


20.109(F12): Laboratory Fundamentals of Biological Engineering

Home        People        Schedule Fall 2012        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 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 synthetic biology framework for programming eukaryotic transcription functions Khalil AS, Lu TK, Bashor CJ, Ramirez CL, Pyenson NC, Joung JK, Collins JJ. Cell 2012 Aug 3;150(3):647-58. PMID: 22863014
  4. Modular Design of Artificial Tissue Homeostasis: Robust Control through Synthetic Cellular HeterogeneityMiller M, Hafner M, Sontag E, Davidsohn N, Subramanian S, Purnick PE, Lauffenburger D, Weiss R. PLoS Comput Biol. 2012 Jul;8(7):e1002579.PMID: 22829755
  5. 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
  6. PGASO: A synthetic biology tool for engineering a cellulolytic yeastChang JJ, Ho CY, Ho FJ, Tsai TY, Ke HM, Wang CH, Chen HL, Shih MC, Huang CC, Li WH.Biotechnol Biofuels. 2012 Jul 27;5(1):53.PMID: 22839502
  7. 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
  8. Standard biological parts knowledgebaseGaldzicki M, Rodriguez C, Chandran D, Sauro HM, Gennari JH. PLoS One 2011 Feb 24;6(2):e17005 PMID: 21390321
  9. 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
  10. Design and construction of "synthetic species" Moreno E. PLoS One2012;7(7):e39054.PMID: 22848349
  11. 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
  12. Expanding the Genetic Code of an AnimalS Greiss, and J Chin. J. Am. Chem. Soc.(2011) 133(36):14196-9.DOI: 10.1021/ja2054034
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. Precise Manipulation of Chromosomes in Vivo Enables Genome-Wide Codon Replacement Isaacs et al. Science (2011) 333(348)DOI: 10.1126/science.1205822
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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
  37. 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
  38. 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
  39. 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
  40. 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
Retrieved from "https://openwetware.org/mediawiki/index.php?title=20.109(F12):_Journal_Club_II&oldid=618761"