Summary
Whole mount in situ hybridization is a process that allows the visualization of gene expression (mRNA) within the cells of an intact organism. By comparing gene expression domains between organisms that have been subjected to different environmental conditions, an understanding of the cellular and tissue-specific effects of these environmental exposures can be identified. This technique is complementary to gene expression profiling techniques such as DNA microarrays which can usually provide information only on the differential levels of gene expression within an organism or tissue. In the case of whole mount in situ hybridization there is the added ability to detect differences in the distribution of cells, within a whole organism, expressing a particular gene. Subtle changes in the distribution of cells expressing a gene may not be reflected in the overall level of gene expression when RNA samples are retrieved from a whole organism and assayed. Exploitation of automation technology has made whole mount in situ hybridization a procedure that is amiable to high-throughput genomic studies. Combining automation with computer-aided image analysis makes this an efficient strategy for quantifying subtle changes in tissues and genes expression that can result from sublethal exposures to environmental toxins, for example.
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References
Kolpin, D. W., Furlong, E. T., Meyer, M. T., Thurman, E. M., Zaugg, S. D., Barber, L. B., and Buxton, H. T. (2002) Pharmaceuticals, hormones, and other organic wastewater contaiminants in U.S. streams, 1999–2000: a national reconnaissance. Environ. Sci. Technol. 36, 1202–1211.
Mandal, R., Hassan, N. M., Murimboh, J., Chakrabarti, C. L., Back, M. H., Rahayu, U., and Lean, D. R. S. (2002) Chemical speciation and toxicity of nickel species in natural waters from the Sudbury area (Canada). Environ. Sci. Technol. 36, 1477–1484.
Squillace, P. J., Scott, J. C., Moran, M. J., Nolan, B. T., and Kolpin, D. W. (2002) VOCs, pesticides, nitrate, and their mixtures in groundwater used for drinking water in the United States. Environ. Sci. Technol. 36, 1923–1930.
Nagel, R. and Isberner, K. (1998) Testing of chemicals with fish-a critical evaluation of tests with special regard to zebrafish. In: Braunbeck, T., Hinton, D. E. and B. Streit (Eds.) Fish Ecotoxicology, Birkhäuser Verlag Basel/Switzerland, 338–352.
Lele, Z., Hartson, S. D., Martin, C. C., Whitsell, L., Matts, R. L., and Krone, P. H. (1999) Disruption of zebrafish somite development by pharmacologic inhibition of Hsp90. Dev. Biol. 210, 56–70.
Martin, C. C., LaForest, L., Akimenko, M-A., and Ekker, M. (1999) A role for DNA methylation in gastrulation and somite patterning. Dev. Biol. 206, 189–205.
Ellies, D. L., Langille, R. M., Martin, C. C., Akimenko, M-A, and Ekker, M. (1997) Specific craniofacial cartilage dysmorphogenesis coincides with a loss of dlx gene expression in retinoic acid treated zebrafish embryos. Mech. Dev. 61, 23–36.
Coverdale, L. E. and Martin, C. C. (2004) Not just a fishing trip—environmental genomics using zebrafish. Curr. Genom. 5, 299–308.
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© 2008 Humana Press
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Coverdale, L.E., Burton, L.E., Martin, C.C. (2008). High Throughput Whole Mount In Situ Hybridization of Zebrafish Embryos for Analysis of Tissue-Specific Gene Expression Changes After Environmental Perturbation. In: Martin, C.C., Martin, C.C. (eds) Environmental Genomics. Methods in Molecular Biology, vol 410. Humana Press. https://doi.org/10.1007/978-1-59745-548-0_1
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DOI: https://doi.org/10.1007/978-1-59745-548-0_1
Publisher Name: Humana Press
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