High throughput nano-liter RT-qPCR to classify soil contamination using a soil arthropod |
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Authors: | Muriel E de Boer Sandra Berg Martijn JTN Timmermans Johan T den Dunnen Nico M van Straalen Jacintha Ellers Dick Roelofs |
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Institution: | (1) Department of Ecological Science, VU University Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands;(2) Faculty of Natural Sciences, Department of Ecology & Evolution, Imperial College London, Exhibition Road, SW7 2AZ London, UK;(3) LUMC, Leiden Genome Technology Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands |
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Abstract: | Background To incorporate genomics data into environmental assessments a mechanistic perspective of interactions between chemicals and
induced biological processes needs to be developed. Since chemical compounds with structural similarity often induce comparable
biological responses in exposed animals, gene expression signatures can serve as a starting point for the assessment of chemicals
and their toxicity, but only when relevant and stable gene panels are available. To design such a panel, we isolated differentially
expressed gene fragments from the soil arthropod Folsomia candida, a species often used for ecotoxicological testing. Animals were exposed to two chemically distinct compounds, being a metal
(cadmium) and a polycyclic aromatic hydrocarbon (phenanthrene). We investigated the affected molecular responses resulting
from either treatment and developed and validated 44 qPCR assays for their responses using a high throughput nano-liter RT-qPCR
platform for the analysis of the samples. |
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