CLASI-FISH: Principles of combinatorial labeling and spectral imaging

Systematic and Applied Microbiology

Volumn 35, Issue 8, 2012, Pages 496-502

  Valm, Alex M ^a,b   Mark Welch, Jessica L ^a   Borisy, Gary G ^a,b  

^a MARINE BIOLOGICAL LABORATORY   (United States)

^b BROWN UNIVERSITY   (United States)

Author keywords

Combinatorial labeling; FISH; Fluorescence in situ hybridization; Microbial diversity; Spectral imaging

Indexed keywords

ARTICLE; AUTOFLUORESCENCE; CHEMICAL LABELING; CLINICAL PROTOCOL; COMBINATORIAL LABELING AND SPECTRAL IMAGING; FLUORESCENCE IN SITU HYBRIDIZATION; MOLECULAR PROBE; NONHUMAN; PRACTICE GUIDELINE; PRIORITY JOURNAL; STANDARD;

BIODIVERSITY; IN SITU HYBRIDIZATION, FLUORESCENCE; SPECTRUM ANALYSIS;

EID: 84870353180     PISSN: 07232020     EISSN: 16180984     Source Type: Journal    
DOI: 10.1016/j.syapm.2012.03.004     Document Type: Article

References (18)

1. Abramoff M., Magalhaes P., Ram S. Image processing with ImageJ. Biophotonics 2004, 11:36-42.
2. Amann R.I., Krumholz L., Stahl D.A. Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology. J. Bacteriol. 1990, 172:762-770.
3. Ashby M.N., Rine J., Mongodin E.F., Nelson K.E., Dimster-Denk D. Serial analysis of rRNA genes and the unexpected dominance of rare members of microbial communities. Appl. Environ. Microbiol. 2007, 73:4532-4542.
4. Bäckhed F., Ley R.E., Sonnenburg J.L., Peterson D.A., Gordon J.I. Host-bacterial mutualism in the human intestine. Science 2005, 307:1915-1920.
5. Daims H., Lücker S., Wagner M. daime, a novel image analysis program for microbial ecology and biofilm research. Environ. Microbiol. 2006, 8:200-213.
6. DeLong E.F., Wickham G.S., Pace N.R. Phylogenetic stains: ribosomal RNA-based probes for the identification of single cells. Science 1989, 243:1360-1363.
7. Fazi S., Amalfitano S., Pizzetti I., Pernthaler J. Efficiency of fluorescence in situ hybridization for bacterial cell identification in temporary river sediments with contrasting water content. Syst. Appl. Microbiol. 2007, 30:463-470.
8. Garini Y., Young I.T., McNamara G. Spectral imaging: principles and applications. Cytometry 2006, 69A:735-747.
9. Neher R., Neher E. Optimizing imaging parameters for the separation of multiple labels in a fluorescence image. J. Microsc. 2004, 213:46-62.
10. Pernthaler A., Pernthaler J., Amann R. Fluorescence in situ hybridization and calalyzed reporter deposition for the identification of marine bacteria. Appl. Environ. Microbiol. 2002, 86:3094-3101.
11. Pernthaler J., Glöckner F.-O., Schönhuber W., Amann R. Methods in Microbiology 2001, 207-226. Academic Press, Ltd., London. J. Paul (Ed.).
12. Quevedo B., et al. Phylogenetic group- and species-specific oligonucleotide probes for single-cell detection of lactic acid bacteria in oral biofilms. BMC Microbiol. 2011, 11:14.
13. Raes J., Bork P. Molecular eco-systems biology: towards an understanding of community function. Nat. Rev. Microbiol. 2008, 6:693-699.
14. Sogin M.L., et al. Microbial diversity in the deep sea and the underexplored " rare biosphere". Proc. Natl. Acad. Sci. U.S.A. 2006, 103:12115-12120.
15. Thurnheer T., Gmür R., Guggenheim B. Multiplex FISH analysis of a six-species bacterial biofilm. J. Microbiol. Methods 2004, 56:37-47.
16. Valm A.M., et al. Systems-level analysis of microbial community organization through combinatorial labeling and spectral imaging. Proc. Natl. Acad. Sci. U.S.A. 2011, 108:4152-4157.
17. Yilmaz L.S., Okten H.E., Noguera D.R. Making all parts of the 16S rRNA of Escherichia coli accessible in situ to single DNA oligonucleotides. Appl. Environ. Microbiol. 2006, 72:733-744.
18. Zimmermann T. Spectral imaging and its applications in live cell microscopy. FEBS Lett. 2003, 546:87-92.