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BMC Research Notes

, 2:43

First Online: 19 March 2009Received: 29 January 2009Accepted: 19 March 2009DOI: 10.1186-1756-0500-2-43

Cite this article as: Callister, S.J., Parnell, J.J., Pfrender, M.E. et al. BMC Res Notes 2009 2: 43. doi:10.1186-1756-0500-2-43

Abstract

BackgroundMost transcriptional activity is a result of environmental variability. This cause environment and effect gene expression relationship is essential to survival in any changing environment. The specific relationship between environmental perturbation and gene expression – and stability of the response – has yet to be measured in detail. We describe a method to quantitatively relate perturbation magnitude to response at the level of gene expression. We test our method using Saccharomyces cerevisiae as a model organism and osmotic stress as an environmental stress.

ResultsPatterns of gene expression were measured in response to increasing sodium chloride concentrations 0, 0.5, 0.7, 1.0, and 1.2 M for sixty genes impacted by osmotic shock. Expression of these genes was quantified over five time points using reverse transcriptase real-time polymerase chain reaction. Magnitudes of cumulative response for specific pathways, and the set of all genes, were obtained by combining the temporal response envelopes for genes exhibiting significant changes in expression with time. A linear relationship between perturbation magnitude and response was observed for the range of concentrations studied.

ConclusionThis study develops a quantitative approach to describe the stability of gene response and pathways to environmental perturbation and illustrates the utility of this approach. The approach should be applicable to quantitatively evaluate the response of organisms via the magnitude of response and stability of the transcriptome to environmental change.

Electronic supplementary materialThe online version of this article doi:10.1186-1756-0500-2-43 contains supplementary material, which is available to authorized users.

Stephen J Callister, J Jacob Parnell contributed equally to this work.

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Author: Stephen J Callister - J Jacob Parnell - Michael E Pfrender - Syed A Hashsham

Source: https://link.springer.com/







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