AGCI research programme: Risk Analysis, Chemistry and Genomics

AGCI postdoc: Tjalf de Boer

Establishing common gene expression patterns for biomarker development in ecotoxicological research


This postdoc project aims to investigate the practical and economic feasibility of using gene expression measurements in ecotoxicological testing in general and more specifically to develop a set or panel of genes that may be used in multiple species of test animals to determine the impact of polluting chemicals on animal, human and ecosystem health. Organisms respond to abiotic stress by altering the expression of stress responsive genes. These genes may act as biomarkers to detect and determine the impact of effects caused by anthropogenic stress such as polluting chemicals. Measuring the expression patterns of thousands of genes at once, more commonly known as genomics, is a faster and more sensitive way of determining the impact of polluting chemicals than only using more traditional ecotoxicological endpoints such as survival and fecundity.

In this project we plan to establish a large database containing all gene expression profiles generated in the last years by the department of Animal Ecology and the Institute for Environmental Studies (IVM). With this database it should be possible to look for common expression patterns and filter out those genes that can act as biomarkers to detect anthropogenic stress.

Short CV

Tjalf de Boer is a post-doctoral researcher at the Amsterdam Global Change Institute (AGCI) and in the Ecolinc consortium. He obtained his PhD in December 2010 after defending his thesis which was called “Stress-free Springtails”. His PhD project was situated in the Dutch Ecogenomics Consortium and focused on the genomic response of relevant ecological test animals when exposed to natural Dutch soils. The goal was to use data from this project, together with the data from other PhD research projects, to develop a genomics based soil quality test that can be used for fast and sensitive soil quality assessment. Trained as a molecular biologist and biochemist, Tjalf holds a Master of Science degree in Biomolecular Sciences from the University of Amsterdam and a Bachelor in Applied Science degree in biochemistry from the Hogeschool Inholland. During his MSc and BSc training he performed internships at the Dutch Cancer Institute, Academic Medical Centre Amsterdam, and the University of Amsterdam.

Academic training

2010PhD, Faculty of Earth and Life Sciences, VU University Amsterdam
2005MSc, Biomolecular Sciences, Universiteit van Amsterdam
2003BSc, Biochemistry, Hogeschool Inholland

Professional employment history

2011Post-doc, Department of Animal Ecology, VU University Amsterdam
2006 - 2010PhD researcher, Department of Animal Ecology, VU University Amsterdam
2005Intern, Department of Epigenetics, Universiteit van Amsterdam
2003Intern, Department of Molecular Genetics, Dutch Cancer Institute (NKI)

Selected publications

de Boer, T.E., Taş, N., Braster, M., Temminghoff, E.J.M., Röling, W.F.M., and Roelofs, D. (2011). Systems ecology of microbial communities and springtail responses to a long-term copper contaminated agricultural soil at different pH levels. Environmental Science & Technology, DOI: 10.1021/es2013598.

de Boer, T.E., Birlutiu, A., Bochdanovits, Z., Timmermans, M.J.T.N., Dijkstra, T., van Straalen, N.M.,  Ylstra, B., and Roelofs, D. (2011). Transcriptional plasticity of a soil arthropod across different ecological conditions. Molecular Ecology. 20(6), 1144-1154.

van Straalen, N.M., Roelofs, D., van Gestel, C.A.M., and de Boer, T.E. (2010). Fitness-neutral gene expression and the importance of defining a normal operating range. Environmental Science & Technology, 44, 4328-4333.

de Boer, T.E., Holmstrup, M., van Straalen, N.M., and Roelofs, D. (2010). The effect of soil pH and temperature on Folsomia candida transcriptional regulation. Journal of Insect Physiology, 56, 350-355.

de Boer, M.E., de Boer, T.E., Mariën, J., Timmermans, M.J.T.N., Nota, B., van Straalen, N.M., Ellers, J., and Roelofs, D. (2009). Reference genes for QRT-PCR tested under various stress conditions in Folsomia candida and Orchesella cincta (Insecta, Collembola). BMC Molecular Biology, 10, 54.