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First published online May 26, 2006
Journal of Experimental Biology 209, 2328-2336 (2006)
Published by The Company of Biologists 2006
doi: 10.1242/jeb.02256

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Review Article: Molecular Mechanisms of Phenotypic Plasticity

Post-genomic approaches to understanding the mechanisms of environmentally induced phenotypic plasticity

Andrew Cossins^1,*, Jane Fraser¹, Margaret Hughes¹ and Andrew Gracey²

¹ School of Biological Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
² Marine Environmental Biology, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA 90089, USA

^* Author for correspondence (e-mail: cossins{at}liv.ac.uk)

Accepted 5 April 2006

Summary

Post-genomic techniques offer new and detailed insights into the mechanisms underpinning all biological processes, including phenotypic plasticity and environmentally relevant phenotypes. Although they require access to genomic resources it is now possible to create these for species of comparative or environmental interest even within a modest research project. Here we describe an open transcript screen for genes responding to environmental cold that might account for the acquired cold-specific phenotype in all its complex manifestations. Construction of a cDNA microarray led to a survey of transcript expression levels in seven tissues of carp, as a function of time, and three different extents of cooling. The resulting data delineated a common stress response found in all tissues that comprises genes involved in cellular homeostasis, including energy charge, ATP turnover, protein turnover and stress protein production. These genes respond to kinds of perturbation other than cold and probably form part of a more general stress response common to other species. We also defined tissue-specific response patterns of transcript regulation whose main characteristics were investigated by a profiling technique based on categorisation of gene function. These genes underpin the highly tissue-specific pattern of physiological adaptations observed in the cold-acclimated fish. As a result we have identified a large number of candidate gene targets with which to investigate adaptive responses to environmental challenge.

Key words: transcriptomics, microarray, cDNA, carp, Cyprinus carpio

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