20.109(F14):Journal club II (Day8)

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#''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]]
#''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]]
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#''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]]
+
#''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]]  
-
#''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
+
#''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]]
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#''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]]
+
#''Engineering a Direct and Inducible Protein−RNA Interaction To Regulate RNA Biology''Belmont, B., Niles, J.'''ACS Chem. Biol.,''' 2010; 5 (9): 851–861 [[DOI: 10.1021/cb100070j]]
#''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]]  
#''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]]  
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# ''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 ]]  
# ''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 ]]  
# ''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]]
# ''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]]
-
#''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]]
+
#''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]]
-
#''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]]
+
-
#''Engineering a Direct and Inducible Protein−RNA Interaction To Regulate RNA Biology''Belmont, B., Niles, J.'''ACS Chem. Biol.,''' 2010; 5 (9): 851–861 [[DOI: 10.1021/cb100070j]]
+
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#<font color="purple"><b>"Construction of a genetic toggle switch" Gardner, T. S., C. R. Cantor, and J. J. Collins, 2000, Nature (London) 403, 520.
#<font color="purple"><b>"Construction of a genetic toggle switch" Gardner, T. S., C. R. Cantor, and J. J. Collins, 2000, Nature (London) 403, 520.

Revision as of 11:43, 16 August 2014

20.109(F14): Laboratory Fundamentals of Biological Engineering

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Contents

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. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  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. 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
  11. 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
  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. 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
  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. Standard biological parts knowledgebaseGaldzicki M, Rodriguez C, Chandran D, Sauro HM, Gennari JH. PLoS One 2011 Feb 24;6(2):e17005 PMID: 21390321
  18. 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
  19. Design and construction of "synthetic species" Moreno E. PLoS One2012;7(7):e39054.PMID: 22848349
  20. 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
  21. Expanding the Genetic Code of an AnimalS Greiss, and J Chin. J. Am. Chem. Soc.(2011) 133(36):14196-9.DOI: 10.1021/ja2054034
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. Precise Manipulation of Chromosomes in Vivo Enables Genome-Wide Codon Replacement Isaacs et al. Science (2011) 333(348)DOI: 10.1126/science.1205822
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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
  37. 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
  38. 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
  39. 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
  40. 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
  41. 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
  42. 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
  43. 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
  44. 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
  45. 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
  46. 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
  47. 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

  1. "Construction of a genetic toggle switch" Gardner, T. S., C. R. Cantor, and J. J. Collins, 2000, Nature (London) 403, 520.

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