Tjalf E. de Boer

Research interests

 
My research interest is in how organisms respond on a molecular level when exposed to external stimuli such as abiotic stress or polluting chemicals.

By using gene expression techniques such as microarrays or RNAseq we can measure the genomic response of an organism exposed to stress. These gene expression measurements can be used as biomarkers to determine the impact of pollutants and chemicals on an organism’s fitness, its population size and eventually ecosystem health. We use the genomic response in soil dwelling animals such as Folsomia candida, which are relevant ecological test animals, to develop a new soil quality test

Other research interests include how different species respond to stress and if these responses are canalized along conserved pathways.

Selected Publications

de Boer T.E., N. Taş, M. Braster, E.J.M. Temminghoff, W.F.M. Röling & D. Roelofs. 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., A. Birlutiu, Z. Bochdanovits, M.J.T.N. Timmermans, T. Dijkstra, N.M. van Straalen, B. Ylstra & D. Roelofs. 2011. Transcriptional plasticity of a soil arthropod across different ecological conditions. Molecular Ecology. 20;6, 1144-54

van Straalen N.M., D. Roelofs, C.A.M. van Gestel & T.E. de Boer. 2010. Fitness-neutral gene expression and the importance of defining a normal operating range. Environmental Science & technology.44, 4328-33.

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

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

Research project

Animals and plants respond to external stress by altering the expression levels of their genes. It is believed that specific genomic responses to similar stressors are conserved within species and are canalized in similar pathways. By analyzing these pathways we can link genomic responses to physiological effects according to the Adverse Outcome Pathway (AOP) principle and determine a set of common genes that are stressor specific and may be used in multiple species to determine the ecotoxicological effects of chemicals.

This post-doc project is situated within the Amsterdam Global Change Institute (AGCI) and focuses on the identification of gene expression pathways and aims to select a set of genes that can act as biomarkers in multiple species to assess the impact of polluting chemicals. To do this we plan to collect gene expression data of multiple species which was generated by other research projects such as the Ecogenomics project (www.ecogenomics.nl) and generate a gene expression profile database. With this database we can then look for ortholog genes and pathways that respond in a similar way to stress.

These genes, together with physiological data, can then be assembled into AOP’s which are multilevel indicators (from gene expression all the way up to population density) that should be universal for all used test species. AOP’s can be used for risk assessment and to determine the economic feasibility for using gene expression measurements in ecological testing.

Participants:
Tjalf de Boer, Juliette Legler, Nico van Straalen