Unmixing of fluorescence spectra to resolve quantitative time-series measurements of gene expression in plate readers

BMC Biotechnology

Volumn 14, Issue , 2014, Pages

  Lichten, Catherine A ^a,b   White, Rachel ^a   Clark, Ivan B N ^a   Swain, Peter S ^a  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

^b MCGILL UNIVERSITY   (Canada)

Author keywords

Budding yeast; Fluorescence; Gene expression; High throughput measurements; Plate readers; Spectral unmixing; Systems biology

Indexed keywords

BUDDING YEASTS; FLUORESCENCE SPECTRA; GREEN FLUORESCENT PROTEIN; HIGH THROUGHPUT STUDIES; HIGH-THROUGHPUT MEASUREMENTS; QUANTITATIVE MEASUREMENT; SPECTRAL UNMIXING; SYSTEMS BIOLOGY;

CELLS; CYTOLOGY; DIGITAL STORAGE; GENE EXPRESSION; GENES; POPULATION STATISTICS; PROTEINS; THROUGHPUT; TRANSCRIPTION; YEAST;

FLUORESCENCE;

1,4 ALPHA GLUCAN BRANCHING ENZYME; ACETYL COENZYME A HYDROLASE; ACETYL COENZYME A SYNTHETASE; GLUCOSE 6 PHOSPHATE; GLYCOGEN PHOSPHORYLASE; HEAT SHOCK PROTEIN 30; MESSENGER RNA; PHOSPHOGLUCOMUTASE;

ARTICLE; AUTOFLUORESCENCE; BINDING AFFINITY; CARBON SOURCE; CELL DENSITY; FLUORESCENCE SPECTROSCOPY; FUNGAL GENE; FUNGUS GROWTH; GENE EXPRESSION; MICROFLUIDICS; MICROPLATE READER; NEGATIVE FEEDBACK; NONHUMAN; POSITIVE FEEDBACK; SACCHAROMYCES CEREVISIAE; YEAST;

SACCHAROMYCES CEREVISIAE; SACCHAROMYCETALES;

CULTURE MEDIA; FLUORESCENCE; GENE EXPRESSION; GREEN FLUORESCENT PROTEINS; IMAGE PROCESSING, COMPUTER-ASSISTED; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SOFTWARE; SPECTROMETRY, FLUORESCENCE;

EID: 84893166001     PISSN: None     EISSN: 14726750     Source Type: Journal    
DOI: 10.1186/1472-6750-14-11     Document Type: Article

References (40)

1. Nurse P. Life logic and information Nature. 2008, 454(7203):424-426.
2. Locke JCW, Elowitz MB. Using movies to analyse gene circuit dynamics in single cells. 2009, 7(5):383-392.
3. Bennett MR, Hasty J. Microfluidic devices for measuring gene network dynamics in single cells. Nat Rev Genet 2009, 10(9):628-638. 10.1038/nrg2625, 2931582, 19668248.
4. Kalir S, McClure J, Pabbaraju K, Southward C, Ronen M, Leibler S, Surette MG, Alon U. Ordering genes in a flagella pathway by analysis of expression kinetics from living bacteria. Science 2001, 292(5524):2080-2083. 10.1126/science.1058758, 11408658.
5. Chen WW, Niepel M, Sorger PK. Classic and contemporary approaches to modeling biochemical reactions. Genes Dev 2010, 24(17):1861-1875. 10.1101/gad.1945410, 2932968, 20810646.
6. Dalgaard P, Ross T, Kamperman L, Neumeyer K, McMeekin TA. 1994, 23:391-404.
7. Warringer J, Blomberg A. Automated screening in environmental arrays allows analysis of quantitative phenotypic profiles in Saccharomyces cerevisiae. Yeast 2003, 20(1):53-67. 10.1002/yea.931, 12489126.
8. de Jong H, Ranquet C, Ropers D, Pinel C, Geiselmann J. Experimental and computational validation of models of fluorescent and luminescent reporter genes in bacteria. BMC Syst Biol 2010, 4:55. 10.1186/1752-0509-4-55, 2877006, 20429918.
9. Berthoumieux S, de Jong H, Baptist G, Pinel C, Ranquet C, Ropers D, Geiselmann J. Shared control of gene expression in bacteria by transcription factors and global physiology of the cell. Mol Syst Biol 2013, 9:634. 3564261, 23340840.
10. Stagoj MN, Comino A, Komel R. Fluorescence based assay of GAL system in yeast Saccharomyces cerevisiae. FEMS Microbiol Lett 2005, 244(1):105-110. 10.1016/j.femsle.2005.01.041, 15727828.
11. Ghaemmaghami S, Huh W-K, Bower K, Howson RW, Belle A, Dephoure N, O'Shea EK, Weissman JS. Global analysis of protein expression in yeast. Nature 2003, 425(6959):737-741. 10.1038/nature02046, 14562106.
12. Sellick CA, Campbell RN, Reece RJ. Galactose metabolism in yeast-structure and regulation of the leloir pathway enzymes and the genes encoding them. Int Rev Cell Mol Biol 2008, 269:111-150.
13. Zimmermann T, Rietdorf J, Pepperkok R. Spectral imaging and its applications in live cell microscopy. FEBS Lett 2003, 546(1):87-92. 10.1016/S0014-5793(03)00521-0, 12829241.
14. Garini Y, Young IT, McNamara G. Spectral imaging: principles and applications. Cytometry A 2006, 69(8):735-747.
15. Gordon A, Colman-Lerner A, Yu RC, Brent R. Single-cell quantification of molecules and rates using open-source microscope-based cytometry. Nat Methods 2007, 4(2):175-181. 10.1038/nmeth1008, 17237792.
16. Douglas HC, Hawthorne DC. Enzymatic expression and genetic linkage of genes controlling galactose utilization in Saccharomyces. Genetics 1964, 49:837-844. 1210618, 14158615.
17. Bar-Even A, Paulsson J, Maheshri N, Carmi M, O'Shea E, Pilpel Y, Barkai N. Noise in protein expression scales with natural protein abundance. Nat Genet 2006, 38(6):636-643. 10.1038/ng1807, 16715097.
18. Dénervaud N, Becker J, Delgado-Gonzalo R, Damay P, Rajkumar AS, Unser M, Shore D, Naef F, Maerkl SJ. A chemostat array enables the spatio-temporal analysis of the yeast proteome. Proc Nat Acad Sci USA 2013, 110(39):15842-15847. 10.1073/pnas.1308265110, 3785771, 24019481.
19. Wang Y, Pierce M, Schneper L, Güldal CG, Zhang X, Tavazoie S, Broach JR. Ras and Gpa2 mediate one branch of a redundant glucose signaling pathway in yeast. PLoS Biol 2004, 2(5):128.
20. Gygi SP, Rochon Y, Franza BR, Aebersold R. Correlation between protein and mRNA abundance in yeast. Mol Cell Biol 1999, 19(3):1720-1730. 83965, 10022859.
21. Rodriguez A, De La C, Herrero P, Moreno F. The hexokinase 2 protein regulates the expression of the GLK1, HXK1 and HXK2 genes of Saccharomyces cerevisiae. Biochem J 2001, 355:625-631. 1221776, 11311123.
22. de Jong-Gubbels P, van den B, Steensma HY, van Dijken JP, Pronk JT. The Saccharomyces cerevisiae acetyl-coenzyme a synthetase encoded by the ACS1 gene, but not the ACS2-encoded enzyme, is subject to glucose catabolite inactivation. FEMS Microbiol Lett 1997, 153:75-81. 10.1016/S0378-1097(97)00236-X, 9252575.
23. Lee FJ, Lin LW, Smith JA. A glucose-repressible gene encodes acetyl-CoA hydrolase from Saccharomyces cerevisiae. J Biol Chem 1990, 265:7413-7418.
24. Navarro-Avino JP, Prasad R, Miralles VJ, Benito RM, Serrano R. A proposal for nomenclature of aldehyde dehydrogenases in Saccharomyces cerevisiae and characterization of the stress-inducible ALD2 and ALD3 genes. Yeast 1999, 15:829-842. 10.1002/(SICI)1097-0061(199907)15:10A<829::AID-YEA423>3.0.CO;2-9, 10407263.
25. Hohmann S. Characterization of PDC6, a third structural gene for pyruvate decarboxylase in Saccharomyces cerevisiae. J Bacteriol 1991, 173:7963-7969. 212591, 1744053.
26. Hedges D, Proft M, Entian KD. CAT8, a new zinc cluster-encoding gene necessary for derepression of gluconeogenic enzymes in the yeast Saccharomyces cerevisiae. Mol Cell Biol 1995, 15:1915-1922. 230417, 7891685.
27. Fu L, Bounelis P, Dey N, Browne BL, Marchase RB, Bedwell DM. The posttranslational modificaon of phosphoglucomutase is regulated by galactose induction and glucose repression in Saccharomyces cerevisiae. J Bacteriol 1995, 177:3087-3094. 176997, 7768805.
28. Panaretou B, Piper PW. The plasma membrane of yeast acquires a novel heat-shock protein (Hsp30) and displays a decline in proton-pumping ATPase levels in response to both heat shock and the entry to stationary phase. Eur J Biochem 1992, 206:635-640. 10.1111/j.1432-1033.1992.tb16968.x, 1535043.
29. Parrou JL, Enjalbert B, Plourde L, Bauche A, Gonzalez B, Francois JW. Dynamic responses of reserve carbohydrate metabolism under carbon and nitrogen limitations in Saccharomyces cerevisiae. Yeast 1999, 15:191-203. 10.1002/(SICI)1097-0061(199902)15:3<191::AID-YEA358>3.0.CO;2-O, 10077186.
30. Hwang PK, Tugendreich S, Fletterick RJ. Molecular analysis of GPH1, the gene encoding glycogen phosphorylase in Saccharomyces cerevisiae. Mol Cell Biol 1989, 9:1659-1666. 362584, 2657401.
31. Steinkamp JA, Stewart CC. Dual-laser, differential fluorescence correction method for reducing cellular background autofluorescence. Cytometry 1986, 7:566-574. 10.1002/cyto.990070611, 3780360.
32. Roederer M, Murphy RF. Cell-by-cell autofluorescence correction for low signal-to-noise systems: application to epidermal growth factor endocytosis by 3T3 fibroblasts. Cytometry 1986, 7(6):558-565. 10.1002/cyto.990070610, 3096673.
33. Brown KS, Sethna JP. Statistical mechanical approaches to models with many poorly known parameters. Phys Rev E 2003, 68(2 Pt 1):021904.
34. Finkenstädt B, Heron EA, Komorowski M, Edwards K, Tang S, Harper CV, Davis JRE, White MRH, Millar AJ, Rand DA. Reconstruction of transcriptional dynamics from gene reporter data using differential equations. Bioinformatics 2008, 24(24):2901-2907. 10.1093/bioinformatics/btn562, 2639297, 18974172.
35. Sheff MA, Thorn KS. Optimized cassettes for fluorescent protein tagging in Saccharomyces cerevisiae. Yeast 2004, 21(8):661-670. 10.1002/yea.1130, 15197731.
36. Janke C, Magiera MM, Rathfelder N, Taxis C, Reber S, Maekawa H, Moreno-Borchart A, Doenges G, Schwob E, Schiebel E, Knop M. A versatile toolbox for PCR-based tagging of yeast genes: new fluorescent proteins, more markers and promoter substitution cassettes. Yeast 2004, 21(11):947-962. 10.1002/yea.1142, 15334558.
37. Knop M, Siegers K, Pereira G, Zachariae W, Winsor B, Nasmyth K, Schiebel E. Epitope tagging of yeast genes using a PCR-based strategy: more tags and improved practical routines. Yeast 1999, 15(10B):963-972. 10.1002/(SICI)1097-0061(199907)15:10B<963::AID-YEA399>3.0.CO;2-W, 10407276.
38. Rasmussen CE, Williams CKI. Gaussian Process for Machine Learning 2006, Cambridge, Massachusetts: MIT Press.
39. Sivia D, Skilling J. Data Analysis a Bayesian Tutorial 2006, Cambridge, UK: Cambridge University Press.
40. MacKay DJC. Information Theory, Inference, and Learning Algorithms; 2003, Oxford, UK: Oxford University Press.