Keck Subbasement:Reading

From OpenWetWare
Jump to: navigation, search

Home        References        Reading List        Members        Contact       


Oscillators

  1. Elowitz MB and Leibler S. A synthetic oscillatory network of transcriptional regulators. Nature. 2000 Jan 20;403(6767):335-8. DOI:10.1038/35002125 | PubMed ID:10659856 | HubMed [Elowitz2000]
  1. Vilar JM, Kueh HY, Barkai N, and Leibler S. Mechanisms of noise-resistance in genetic oscillators. Proc Natl Acad Sci U S A. 2002 Apr 30;99(9):5988-92. DOI:10.1073/pnas.092133899 | PubMed ID:11972055 | HubMed [Vilar2002]
  1. Tsai TY, Choi YS, Ma W, Pomerening JR, Tang C, and Ferrell JE Jr. Robust, tunable biological oscillations from interlinked positive and negative feedback loops. Science. 2008 Jul 4;321(5885):126-9. DOI:10.1126/science.1156951 | PubMed ID:18599789 | HubMed [Ferrell2008]

Delays

This theory paper investigates how delays destabilize fixed points. This is a fundamentally different analysis, quite the opposite of trying to use delays to make limit cycles more attractive.

  1. Bratsun D, Volfson D, Tsimring LS, and Hasty J. Delay-induced stochastic oscillations in gene regulation. Proc Natl Acad Sci U S A. 2005 Oct 11;102(41):14593-8. DOI:10.1073/pnas.0503858102 | PubMed ID:16199522 | HubMed [Bratsun2002]

This is not transcriptional delay, but rather delay through intermediate species, which is the principle that dominates previous delay studies.

  1. Monk NA. Oscillatory expression of Hes1, p53, and NF-kappaB driven by transcriptional time delays. Curr Biol. 2003 Aug 19;13(16):1409-13. PubMed ID:12932324 | HubMed [Monk2003]

This experimental paper uses a plasmid that effectively contains a delay, used for another purpose entirely, but might be a good starting point for design.

  1. Golding I, Paulsson J, Zawilski SM, and Cox EC. Real-time kinetics of gene activity in individual bacteria. Cell. 2005 Dec 16;123(6):1025-36. DOI:10.1016/j.cell.2005.09.031 | PubMed ID:16360033 | HubMed [Golding2005]

Plasmid Design

  1. Lutz R and Bujard H. Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements. Nucleic Acids Res. 1997 Mar 15;25(6):1203-10. PubMed ID:9092630 | HubMed [Lutz1997]

Testing delays

This paper measures transfer curves and dynamics of a simple circuit

  1. Canton B, Labno A, and Endy D. Refinement and standardization of synthetic biological parts and devices. Nat Biotechnol. 2008 Jul;26(7):787-93. DOI:10.1038/nbt1413 | PubMed ID:18612302 | HubMed [Endy2008]

Metastable hairpins

  1. Bois JS, Venkataraman S, Choi HM, Spakowitz AJ, Wang ZG, and Pierce NA. Topological constraints in nucleic acid hybridization kinetics. Nucleic Acids Res. 2005;33(13):4090-5. DOI:10.1093/nar/gki721 | PubMed ID:16043632 | HubMed [Pierce2005]