Reproducibility and consistency of proteomic experiments on natural populations of a non-model aquatic insect.

Amparo Hidalgo-Galiana,Marta Monge,Francesc Canals,Alexandra Cieslak,Ignacio Ribera,David G Biron

doi:10.1371/journal.pone.0104734

Abstract

Population proteomics has a great potential to address evolutionary and ecological questions, but its use in wild populations of non-model organisms is hampered by uncontrolled sources of variation. Here we compare the response to temperature extremes of two geographically distant populations of a diving beetle species (Agabus ramblae) using 2-D DIGE. After one week of acclimation in the laboratory under standard conditions, a third of the specimens of each population were placed at either 4 or 27°C for 12 h, with another third left as a control. We then compared the protein expression level of three replicated samples of 2–3 specimens for each treatment. Within each population, variation between replicated samples of the same treatment was always lower than variation between treatments, except for some control samples that retained a wider range of expression levels. The two populations had a similar response, without significant differences in the number of protein spots over- or under-expressed in the pairwise comparisons between treatments. We identified exemplary proteins among those differently expressed between treatments, which proved to be proteins known to be related to thermal response or stress. Overall, our results indicate that specimens collected in the wild are suitable for proteomic analyses, as the additional sources of variation were not enough to mask the consistency and reproducibility of the response to the temperature treatments.

Highlights

The comparison of natural populations using proteomic methods, which has been termed ‘‘population proteomics’’ [1,2] has a high potential to address fundamental questions in ecology and evolutionary biology, as it allows us to directly link environmental conditions to changes in protein expression [3,4,5,6]
Proteomic methods are especially suited to understanding phenotypic changes induced by the environment, since they enable detection of alterations affecting physiologically significant protein expression and modification, rather than changes in mRNA expression levels [7,8,9]
Proteomic studies of non-model organisms are increasingly common, in most cases specimens are kept in the laboratory under controlled conditions, as the use of specimens directly taken from their natural environment poses an additional challenge [12]

Summary

Introduction

[8] for review), in most cases specimens are kept in the laboratory under controlled conditions, as the use of specimens directly taken from their natural environment poses an additional challenge [12]. Many unknown factors, such as the genetic background of the individuals, their age, the physiological state, the presence of parasites or other pathogens may introduce variation of unpredictable importance [13,14,15]. It seems that previous to any comparative study of wild populations it is necessary to estimate the degree of variability due to unknown or unforeseeable sources of variation, and to assess both the reproducibility and consistency of the protein expression data

Methods

Results

Conclusion