Title: Stress-based expression profiles in arthropods

Primary Researcher: Ben Nota
Email address: ben.nota@falw.vu.nl
Submitted on: October 4, 2005

Start date: 01 October 2005
End date: 01 October 2009

Introduction:

In laboratory set up, the invertebrate soil organism Folsomia candida can be used in bioassays to evaluate soil quality (whether it contains pollutants). These bioassays are often time consuming. New genomic techniques, like microarray gene expression profiling, may help making these bioassays more sensitive and rapid. F. candida is an ecological relevant soil organism and is therefore a better choice for using in genomics-based bioassays than the standard genomic model organisms.

At the moment the complete transcriptome of F. candida is being characterized (sequenced) and a freely accessible EST database (Collembase) is being developed. These EST sequences in the database will be annotated using possible homologous sequences available in other public databases. The ESTs will also be used to design a microarray, or DNA chip: the Invertebrate Soil Quality (ISQ) chip.

Aim:

Develop ISQ chip with all available ESTs present in the database

Translate gene expression profiles to defined ecotoxicological endpoints of contaminated soils

Research:

The ISQ chip will be constructed using synthesized oligos (~65 mers). Each of these oligos will be uniquely designed to represent one of the ESTs available from the database. RNA will be isolated from F. candida exposed to different test soils spiked with pollutants. Pollutants of interest are: metals, polycyclic aromatic hydrocarbons, pesticides, and mineral oil. RNA extracted from F. candida exposed to pollutants will be compared with reference RNA, which is extracted from F. candida not exposed to pollutants. Microarray data analysis will be done using bioinformatics and statistical tools, like hierarchical clustering and Principal Component Analysis.

External funding

Yes

External Funding Sponsors

Ecogenomics

Research Group

VU - Animal Ecology

FTE

1.00