Comparative transcriptomics: are transcriptional stress responses comparable among distantly related species?

Background

Comparative analysis is a fundamental tool in Biology. Conservation among species greatly assists the detection and characterization of functional elements such as protein coding regions in genomes. This is also true for gene expression programs: comparison of distantly related organisms is important for identifying biological processes essential for life.

All living organisms need to cope with stress and recent studies indicate that the important stress response pathways are phylogenetically highly conserved.  We want to apply this in an environmental context in order to extrapolate environmental test results in a single species to potential environmental-induced risks relevant for invertebrate communities in whole ecosystems.

Within an existing research program we focus on comparative analysis of metal stress in invertebrates. In this context we have already generated expression profiles of metal stress in Folsomia candida, an ecologically relevant indicator species for soil quality. The eventual goal is to compare these transcriptional responses to the aquatic ecotoxicological model Daphnia magna.

The aim of this study is to investigate if F. candida and D. magna share evolutionary conserved stress response pathways. We hypothesize that both species will show comparable transcriptional responses to identical effect concentrations of toxic metals.

Approach

First, D. magna will be subjected an ecotoxicological test to assess the concentration of the heavy metal Zinc that exert 50% decrease in reproduction (EC50). Then, microarray experiments with animals exposed to EC50 concentrations will be conducted to study and compare transcriptional responses with existing microarray data generated with Zn exposed F. candida. Bioinformatics and gene annotation information available in public databases, will be used to interpret shared and species-specific transcriptional responses.

Supervision and information

Dr. Ir. Dick Roelofs (Room H147, W&N building, Vrije Universiteit)
E-mail:   dick.roelofs@vu.nl
Phone: +31 (0)20 – 59 87078