Validation of promising gene expression assays for improved soil quality assessment

Chen-1                                Chen-3                                 Chen-2

Background

Increasing environmental contamination of potentially toxic chemicals and heavy metals is becoming a severe risk for ecological systems, agricultural functions and human health for the global human community in the modern society. These chemicals and heavy metals are tending to accumulate in soils and sediments, because of the slow degradation pace. The collembolan Folsomia candida is a soil-dwelling arthropod, abundant in soil, and has a detritivores role in territorial ecosystem. F. candida is often used as a model organism for soil toxicology. Recently, our ecotoxicogenomics studies on environmental soil samples have discovered gene sets that show highly significant does-dependent gene expression patterns and thus were tightly linked with adverse effect exerted by contaminants from soil samples. By measuring gene expression profiles of this animal, this group of genes can be used for fast screening soil quality assessment. The aim of this project is to validate whether particular gene sets are dose-dependent in environmental samples with a known level of metal contamination. This result will support this gene set as a new sensitive and quick tool to assess the soil quality.

Approaches

F. candida will be exposed in environmental samples for 2 days. Then the RNA of these animals will be extracted. These RNA will be used for QPCR (quantitative PCR) to check single gene’s expression patterns among different soil samples. Then correlation analysis will be done to validate the significant does-dependent expression patterns of genes.

Methods

  • Culturing animals (F. candida)
  • RNA extractions and QPCR
  • Learning data analysis about QPCR and how to do correlation analysis with permutation in R

Supervision and information

Guangquan Chen (room H157, W&N building, Vrije Universiteit)
E-mail: G.Chen@vu.nl
Phone: +31 (0)20 – 59 87068

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