The Norwegian Zebrafish Platform at the Norwegian School of Veterinary Science was established as a National Technology Platform under the Functional Genomics Program, Research Council of Norway.

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December 17th, 2009

Genome-wide Gene Expression Profiling in the Zebrafish Model

We congratulate Dr. Rasoul Nourizadeh-Lillabadi who successfully defended his PhD on the 14th of December at the Norwegian School of Veterinary Science.

Rasoul has during his PhD performed a Genome-wide Gene expression Profiling in the Zebrafish Model with focus on eco-toxicology and functional genomics by using microarrays and bioinformatics tools.

 

 

Summary of thesis

 

The zebrafish model is increasingly used for many applications, spanning from basic biology, via human disease models to industrial drug screening and recently in eco-toxicology. For several of these applications, genome wide transcriptomics analyses with high precision and reproducibility are required. One of the aims of this study was to establish a robust microarray platform. Based on a commercial 16k oligonucelotide probe library a microarray platform was established in collaboration with the Norwegian Microarray Consortium ( NMC). A bioinformatics processing pipeline for the analysis of microarray raw data using a R-based bioconductor software package, linear models for microarray data analyses (Limma) , was established. The microarray platform protocol was optimised with respect to technical (random noise and systematic error) and biological variation. Random noise for this platform was not detectable and minor systematic variation was normalized before statistical analyses. Biological individual variation was estimated to be 1-1,5% of the total number of gene probes in the library, demonstrating the necessity of biological replicates for each experiment.

 

Downstream bioinformatics approaches using BioArray Software Environment (BASE) from NMC and Ingenuity Pathway analysis (IPA), were applied to characterize effects on the transcriptome after treatment of zebrafish with two different types of environmental pollutant mixtures and a prion (prp-2) gene knock-down morpholino (prp-2 MO) reagent. The first study was exposure to synthetic mixtures of polyaromatic hydrocarbons (PAHs) and alkylphenols (APs) in produced water (PW) as is generated by the offshore oil industry. The second study was exposure of zebrafish to natural mixtures of POPs (persistent organic pollutants) from Norwegian lakes Mjøsa and Losna. Demographics effects ( mortality, malformation, body weight, sex ratio and puberty) from these two exposure studies were correlated with the observed altered gene expression profiles proving the power of toxicogenomics in eco-toxicological studies. The functional cluster analyses of the altered genes revealed effects on the reproductive system and the lipid/carbohydrate metabolism of zebrafish in both exposure studies. 

The effects of prp-2MO on zebrafish embryos were studied using the established microarray pipeline. From the transcriptomics data generated, the patterns of differentially expressed genes could link the prp2 gene  to biological processes like apoptosis, embryo development and neurogenesis, suggesting that the zebrafish can be useful for elucidating the biological function of the prion protein.

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