Use of fluorescence microscopy to analyze genetic circuit dynamics

Methods in Enzymology

Volumn 497, Issue , 2011, Pages 275-293

  Süel, Gürol ^a  

^a UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FLUORESCENT DYE;

ARTICLE; BACTERIUM; CELL DIFFERENTIATION; FLUORESCENCE MICROSCOPY; GENE EXPRESSION; GENE INTERACTION; IMAGE ANALYSIS; MOLECULAR DYNAMICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN INTERACTION; PROTEIN LOCALIZATION; PROTEIN STABILITY; SYSTEMS BIOLOGY; TRANSCRIPTION REGULATION;

FLUORESCENT DYES; GENE REGULATORY NETWORKS; GENES, REPORTER; IMAGE PROCESSING, COMPUTER-ASSISTED; LUMINESCENT PROTEINS; MICROSCOPY, FLUORESCENCE; PROMOTER REGIONS, GENETIC; PROTEIN BIOSYNTHESIS; TIME-LAPSE IMAGING; TRANSCRIPTION, GENETIC;

EID: 79957445743     PISSN: 00766879     EISSN: 15577988     Source Type: Book Series    
DOI: 10.1016/B978-0-12-385075-100013-5     Document Type: Article

References (27)

1. U. Alon An Introduction to Systems Biology: Design Principles of Biological Circuits. 2007 Chapman & Hall/CRC Boca Raton
2. Bradley J. Feilmeir Green fluorescent protein function as a reporter for protein localization in Escherichia coli J. Bact. 182 14 2000 4068 4076
3. T. Cagatay Architecture-dependent noise discriminates functionally analogous differentiation circuits Cell 139 3 2009 512 522
4. H.Y. Chen Determination of the optimal aligned spacing between the ShineDalgarno Sequence and the translation initiation codon of Escherichia coli Messenger-Rnas Nucleic Acids Res. 22 23 1994 4953 4957
5. P.J. Choi, X.S. Xie, and E.I. Shakhnovich Stochastic switching in gene networks can occur by a single-molecule event or many molecular steps J. Mol. Biol. 396 1 2010 230 244
6. M.B. Elowitz, and S. Leibler A synthetic oscillatory network of transcriptional regulators Nature 403 6767 2000 335 338 (Pubitemid 30062393)
7. M.B. Elowitz Stochastic gene expression in a single cell Science 297 5584 2002 1183 1186 (Pubitemid 36193353)
8. R. Heim, and R.Y. Tsien Engineering green fluorescent protein for improved brightness, longer wavelengths and fluorescence resonance energy transfer Curr. Biol. 6 2 1996 178 182
9. D. Kim Improved mammalian expression systems by manipulating transcriptional termination regions Biotechnol. Prog. 19 5 2003 1620 1622 (Pubitemid 37250056)
10. J.R. Lakowicz Principles of Fluorescence Spectroscopy. 2006 Springer Science & Business Media Baltimore
11. A. Miyawaki, T. Nagai, and H. Mizuno Mechanisms of protein fluorophore formation and engineering Curr. Opin. Chem. Biol. 7 5 2003 557 562 (Pubitemid 37315790)
12. T. Nagai A variant of yellow fluorescent protein with fast and efficient maturation for cell-biological applications Nat. Biotechnol. 20 1 2002 87 90 (Pubitemid 34044921)
13. T. Nishihara, T. Iwabuchi, and T. Nohno A T7 promoter vector with a transcriptional terminator for stringent expression of foreign genes Gene 145 1 1994 145 146 (Pubitemid 24224979)
14. J.M. Pedraza, and A. van Oudenaarden Noise propagation in gene networks Science 307 5717 2005 1965 1969
15. H.M. Salis, E.A. Mirsky, and C.A. Voigt Automated design of synthetic ribosome binding sites to control protein expression Nat. Biotechnol. 27 10 2009 946 950
16. I. Sastalla Codon-optimized fluorescent proteins designed for expression in low-GC gram-positive bacteria Appl. Environ. Microbiol. 75 7 2009 2099 2110
17. D.A. Shagin GFP-like proteins as ubiquitous metazoan superfamily: Evolution of functional features and structural complexity Mol. Biol. Evol. 21 5 2004 841 850 (Pubitemid 38529726)
18. D. Sprinzak, and M.B. Elowitz Reconstruction of genetic circuits Nature 438 7067 2005 443 448 (Pubitemid 41742009)
19. S.H. Strogatz Nonlinear Dynamics and Chaos: With Appliations to Physics, Biology, Chemistry, and Engineering 1994 Perseus Books Publishing, LLC Cambridge
20. G.M. Suel An excitable gene regulatory circuit induces transient cellular differentiation Nature 440 7083 2006 545 550
21. G.M. Suel Tunability and noise dependence in differentiation dynamics Science 315 5819 2007 1716 1719 (Pubitemid 46515626)
22. Jared E. Toettcher The promise of optogenetics in cell biology: interrogating molecular circuits in space and time Nature Methods. 8 2011 35 38
23. R.Y. Tsien The green fluorescent protein Annu. Rev. Biochem. 67 1998 509 544 (Pubitemid 28411137)
24. G.S. Waldo Rapid protein-folding assay using green fluorescent protein Nat. Biotechnol. 17 7 1999 691 695 (Pubitemid 29316148)
25. A.J. Whitmarsh, and R.J. Davis Regulation of transcription factor function by phosphorylation Cell. Mol. Life Sci. 57 89 2000 1172 1183 (Pubitemid 30663475)
26. J. Zhang Creating new fluorescent probes for cell biology Nat. Rev. Mol. Cell Biol. 3 12 2002 906 918 (Pubitemid 35477369)
27. D. Zhuravel Phenotypic impact of regulatory noise in cellular stress-response pathways Syst. Synth. Biol. 4 2010 105 106