Omics

Genomics, proteomics and metabolomics ("omics") are extremely valuable tools in studying biological processes, in bio- and disease marker discovery, in drug discovery, in nutrition and toxicology. Generally, cells, plants or animals are exposed and divided into a treated and an untreated group. Following the experiment both groups are analysed at the mRNA, the protein or the metabolite level using DNA microarrays, 2D-gel electrophoresis plus MALDI/TOFMS or LC/MS, NMR plus GC- or LC/MS, respectively. Next the differential regulation of thousands of targets is assessed using appropriate statistics. Usually both experimental groups are well-defined and identical, except for the treatment, and the dose of exposure is relatively high as compared to levels normally encountered in food contaminant and residue analysis. On the other hand, biomarkers thus obtained might be used for the development of dedicated screening assays based on PCR, tailored DNA microarrays, receptor or immunoassays. Assuming that such screening assays will be developed at least two scenarios can be distinguished: (i) exposure of a standard cell system or organism to the food sample extract of interest followed by isolation of mRNA, proteins or metabolites from the cells and analysis using the developed dedicated screening assay and (ii) isolation of mRNA, proteins or metabolites directly from biofluids in the food sample, usually restricted to farm animals and crops. A major challenge would be to obtain, purify and maintain the integrity of a representative isolate. But most important of all will be the validation of the biomarker targets versus their natural background variability in food, feed and biofluid matrices: real-life is quite different from standard cells or organisms! The on-going European project on new technologies to screen multiple chemical contaminants in food, acronym BioCop, has taken this challenge and is studying both transcriptomics and proteomics for chemical food contaminant analysis [20]. An MCF-7 standard cell line is used and exposed with food sample extracts for phytoestrogen and mycotoxin analysis, next the extracted mRNA from the cells is analysed by tailored DNA microarrays. In the proteomics topic of BioCop a multiplex SPR biosensor immunoassay is being developed to analyse protein biomarkers in blood of bovines for the screening of steroid abuse in cattle fattening.

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