![Page 1: NATIONAL ENVIRONMENTAL RESEARCH INSTITUTE AARHUS UNIVERSITY Write or delete: DATE GENEPEASE From ecotoxicogenomics to a soil ecological model system](https://reader035.vdocument.in/reader035/viewer/2022070308/551c5c6f550346a5458b529c/html5/thumbnails/1.jpg)
NATIONAL ENVIRONMENTAL RESEARCH INSTITUTEAARHUS UNIVERSITY Write or delete: DATE
GENEPEASE
From ecotoxicogenomics to a soil ecological model system
![Page 2: NATIONAL ENVIRONMENTAL RESEARCH INSTITUTE AARHUS UNIVERSITY Write or delete: DATE GENEPEASE From ecotoxicogenomics to a soil ecological model system](https://reader035.vdocument.in/reader035/viewer/2022070308/551c5c6f550346a5458b529c/html5/thumbnails/2.jpg)
NATIONAL ENVIRONMENTAL RESEARCH INSTITUTEAARHUS UNIVERSITY Jan. 7, 2011Paul Henning Krogh
Lars Henrik Heckmann Jesper Givskov Sørensen
GENEPEASE collembolan studies› WP 2.2 Transcript response to stress in F.
candida
› WP2.2.1 Microarrays
› WP2.2.2 temporal qPCR of selected genes at EC10 and EC50 effect levels
› WP3 Transcripts in a long-term mesocosm field model system
![Page 3: NATIONAL ENVIRONMENTAL RESEARCH INSTITUTE AARHUS UNIVERSITY Write or delete: DATE GENEPEASE From ecotoxicogenomics to a soil ecological model system](https://reader035.vdocument.in/reader035/viewer/2022070308/551c5c6f550346a5458b529c/html5/thumbnails/3.jpg)
NATIONAL ENVIRONMENTAL RESEARCH INSTITUTEAARHUS UNIVERSITY Jan. 7, 2011Paul Henning Krogh
Lars Henrik Heckmann Jesper Givskov Sørensen
Microarray and qPCR of a collembolan
› iSQ Chip Folsomia candida Collembola VU version 1.0 for gene expression analysis (Dick Roelofs, VU Amsterdam)
› Microarray overview of the genes that are differentially expressed in control and pesticide exposed F. candida
› The temporal expression of selected target genes will be monitored, using real-time quantitative PCR (qPCR),
› Selected target genes should preferably respond to many pesticides
![Page 4: NATIONAL ENVIRONMENTAL RESEARCH INSTITUTE AARHUS UNIVERSITY Write or delete: DATE GENEPEASE From ecotoxicogenomics to a soil ecological model system](https://reader035.vdocument.in/reader035/viewer/2022070308/551c5c6f550346a5458b529c/html5/thumbnails/4.jpg)
NATIONAL ENVIRONMENTAL RESEARCH INSTITUTEAARHUS UNIVERSITY Jan. 7, 2011Paul Henning Krogh
Lars Henrik Heckmann Jesper Givskov Sørensen
Transcriptomic responses in Folsomia candida – potential outcome
› ≈ 100 transcripts may be differential in response to the EC10
and EC50
› Upregulation of transcripts encoding for xenobiotic
detoxification and biotransformation enzymes (phases I, II,
and III)
› General stress response
› Oxidative stress – antioxidant transcripts
› Chitin metabolism
› Suppression of protein translation (allocating energy to
detoxification!)
› Immune responses
Nota, B., Bosse, M., Ylstra, B., van Straalen, N.M., Roelofs, D., 2009. Transcriptomics reveals extensive inducible biotransformation in the soil-dwelling invertebrate Folsomia candida exposed to phenanthrene. BMC Genomics 10:236.
Yuan, Y., Ke, X., Chen, F., Krogh, P.H., Ge, F., 2011. Decrease in catalase activity of Folsomia candida fed a Bt rice diet. Subm. to Enviromental Pollution.
![Page 5: NATIONAL ENVIRONMENTAL RESEARCH INSTITUTE AARHUS UNIVERSITY Write or delete: DATE GENEPEASE From ecotoxicogenomics to a soil ecological model system](https://reader035.vdocument.in/reader035/viewer/2022070308/551c5c6f550346a5458b529c/html5/thumbnails/5.jpg)
NATIONAL ENVIRONMENTAL RESEARCH INSTITUTEAARHUS UNIVERSITY Jan. 7, 2011Paul Henning Krogh
Lars Henrik Heckmann Jesper Givskov Sørensen
What is a microarray?
Microarrays provide a global overview of the genes that are induced/suppressed in a model organism in a specific biological context
![Page 6: NATIONAL ENVIRONMENTAL RESEARCH INSTITUTE AARHUS UNIVERSITY Write or delete: DATE GENEPEASE From ecotoxicogenomics to a soil ecological model system](https://reader035.vdocument.in/reader035/viewer/2022070308/551c5c6f550346a5458b529c/html5/thumbnails/6.jpg)
NATIONAL ENVIRONMENTAL RESEARCH INSTITUTEAARHUS UNIVERSITY Jan. 7, 2011Paul Henning Krogh
Lars Henrik Heckmann Jesper Givskov Sørensen
How does a microarray work?
Exposed F. candida
![Page 7: NATIONAL ENVIRONMENTAL RESEARCH INSTITUTE AARHUS UNIVERSITY Write or delete: DATE GENEPEASE From ecotoxicogenomics to a soil ecological model system](https://reader035.vdocument.in/reader035/viewer/2022070308/551c5c6f550346a5458b529c/html5/thumbnails/7.jpg)
NATIONAL ENVIRONMENTAL RESEARCH INSTITUTEAARHUS UNIVERSITY Jan. 7, 2011Paul Henning Krogh
Lars Henrik Heckmann Jesper Givskov Sørensen
Real-time quantitative PCR (QPCR)
To estimate the initial quantity of a specific DNA sequence (target gene)
![Page 8: NATIONAL ENVIRONMENTAL RESEARCH INSTITUTE AARHUS UNIVERSITY Write or delete: DATE GENEPEASE From ecotoxicogenomics to a soil ecological model system](https://reader035.vdocument.in/reader035/viewer/2022070308/551c5c6f550346a5458b529c/html5/thumbnails/8.jpg)
NATIONAL ENVIRONMENTAL RESEARCH INSTITUTEAARHUS UNIVERSITY Jan. 7, 2011Paul Henning Krogh
Lars Henrik Heckmann Jesper Givskov Sørensen
Principles of QPCR
![Page 9: NATIONAL ENVIRONMENTAL RESEARCH INSTITUTE AARHUS UNIVERSITY Write or delete: DATE GENEPEASE From ecotoxicogenomics to a soil ecological model system](https://reader035.vdocument.in/reader035/viewer/2022070308/551c5c6f550346a5458b529c/html5/thumbnails/9.jpg)
NATIONAL ENVIRONMENTAL RESEARCH INSTITUTEAARHUS UNIVERSITY Jan. 7, 2011Paul Henning Krogh
Lars Henrik Heckmann Jesper Givskov Sørensen
Principles of QPCR
![Page 10: NATIONAL ENVIRONMENTAL RESEARCH INSTITUTE AARHUS UNIVERSITY Write or delete: DATE GENEPEASE From ecotoxicogenomics to a soil ecological model system](https://reader035.vdocument.in/reader035/viewer/2022070308/551c5c6f550346a5458b529c/html5/thumbnails/10.jpg)
NATIONAL ENVIRONMENTAL RESEARCH INSTITUTEAARHUS UNIVERSITY Jan. 7, 2011Paul Henning Krogh
Lars Henrik Heckmann Jesper Givskov Sørensen
Principles of QPCR
Baseline (threshold)
Cycle threshold (Ct)
3 cycles difference between green and blue sample= 23 = 8 fold difference
![Page 11: NATIONAL ENVIRONMENTAL RESEARCH INSTITUTE AARHUS UNIVERSITY Write or delete: DATE GENEPEASE From ecotoxicogenomics to a soil ecological model system](https://reader035.vdocument.in/reader035/viewer/2022070308/551c5c6f550346a5458b529c/html5/thumbnails/11.jpg)
NATIONAL ENVIRONMENTAL RESEARCH INSTITUTEAARHUS UNIVERSITY Jan. 7, 2011Paul Henning Krogh
Lars Henrik Heckmann Jesper Givskov Sørensen
Detoxification phases› In phase I
toxic compounds are modified resulting in more reactive
› metabolites (cytochrome P450s)
› phase IIreactive metabolites are conjugated by transferases with chemical groups such as glutathione or glucuronic acid
› phase III specialized transporters recognize the conjugates, and expel them out of the cell
Nota et al. 2009