20.109(F14):Journal club II (Day8)

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20.109(F14): Laboratory Fundamentals of Biological Engineering

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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 (according to your lab section), 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 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. Heuristic for Maximizing DNA Reuse in Synthetic DNA Library AssemblyJonathan Blakes, Ofir Raz, Uriel Feige, Jaume Bacardit, Paweł Widera, Tuval Ben-Yehezkel, Ehud Shapiro, and Natalio Krasnogor. ACS Synth Biol February 20, 2014 pp 529–542 DOI: 10.1021/sb400161v
  2. Optimal Part and Module Selection for Synthetic Gene Circuit Design Automation Linh Huynh and Ilias Tagkopoulos. ACS Synth Biol January 28, 2014 pp 556–564 DOI: 10.1021/sb400139h
  3. Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains. Kyrpides NC, et al. PLoS Biol. 2014 Aug 5;12(8):e1001920. PMID: 25093819
  4. Negative Autoregulation Matches Production and Demand in Synthetic Transcriptional Networks Elisa Franco, Giulia Giordano, Per-Ola Forsberg, and Richard M. Murray. ACS Synth Biol. February 26, 2014 pp 589–599 DOI: 10.1021/sb400157z
  5. Dual-selection for evolution of in vivo functional aptazymes as riboswitch parts. Goler JA, Carothers JM, Keasling JD. Methods Mol Biol. 2014;1111:221-35. PMID: 24549623
  6. The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology. Galdzicki M, et al. Nat Biotechnol. 2014 Jun;32(6):545-50. PMID: 24911500 [BW/WF/Purple]
  7. Composability of regulatory sequences controlling transcription and translation in Escherichia coli. Kosuri S, Goodman DB, Cambray G, Mutalik VK, Gao Y, Arkin AP, Endy D, Church GM. Proc Natl Acad Sci U S A. 2013 Aug 20;110(34):14024-9. PMID: 23924614 [LS/WF/Purple]
  8. Tunable and multifunctional eukaryotic transcription factors based on CRISPR/Cas.' ' Farzadfard F, Perli SD, Lu TK. ACS Synth Biol. 2013, 2(10):604-13. PMID: 23977949 [LK/TR/Blue]
  9. Modular control of multiple pathways using engineered orthogonal T7 polymerasesTemme K, Hill R, Segall-Shapiro TH, Moser F, Voigt CA. Nucleic Acids Res. 2012 Jun 28. PMID: 22743271
  10. Design and construction of "synthetic species" Moreno E. PLoS One 2012, 7(7):e39054.PMID: 22848349 [RR/TR/Green]
  11. 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 [DA/TR/Cherries]
  12. 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
  13. 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
  14. Refactored M13 bacteriophage as a platform for tumor cell imaging and drug delivery.Ghosh D, Kohli AG, Moser F, Endy D, Belcher AM. ACS Synth Biol. 2012 Dec 21;1(12):576-82. PMID: 23656279 [MA/TR/Green]
  15. 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
  16. 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
  17. 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
  18. Standard biological parts knowledgebaseGaldzicki M, Rodriguez C, Chandran D, Sauro HM, Gennari JH. PLoS One 2011, 6(2):e17005 PMID: 21390321
  19. 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
  20. 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
  21. 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 [RL/TR/Purple]
  22. Expanding the Genetic Code of an AnimalS Greiss, and J Chin. J. Am. Chem. Soc.2011, 133(36):14196-9.DOI: 10.1021/ja2054034
  23. 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
  24. 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
  25. Precise Manipulation of Chromosomes in Vivo Enables Genome-Wide Codon Replacement Isaacs et al. Science 2011, 333(348)DOI: 10.1126/science.1205822
  26. 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
  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
  30. 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
  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 [AS/WF/PINKLE]
  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 [AO/WF/Blue]
  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[JS/TR/Purple]
  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 [JY/TR/Yellow]
  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 [GDS/WF/Green]
  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. 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 [KR/TR/Pink] [CAR/WF/Green]
  39. 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 [VW/TR/Purple]
  40. 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
  41. 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
  42. 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
  43. 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
  44. 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
  45. 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
  46. 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

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