Profiling Techniques
also see: Food Safety
Issues in food safety usually concern the presence of contaminants, chemical residues, food additives, the influence of storage, spoilage or effects of preparation. Since the introduction of genetically modified plants in agriculture and the food chain, it became important to also analyse less obvious differences in crops and foods. Detailed studies on the exact composition of unprocessed foods, like shown in the film "What is in my potato", are the result of a long debate on substantial equivalence of conventional, organic and novel crops and foods.
Substantial equivalence
The determination of substantial equivalence would indicate whether a new food shares similar health and nutritional characteristics with an existing, familiar food with an established history of safe use. In order to do such an analysis researchers now make use of a range of biochemical techniques to determine a spectrum (total fingerprint) of cellular molecules and metabolic compounds present in a food or crop. Novel foods are considered to be substantially equivalent if their biochemical profile fall within the range of natural variation already exhibited by biochemical profiles of existing foods or crops. If a novel food (for instance genetically modified) was found to be substantially equivalent to its nearest existing counterpart by careful compositional analysis, it can be argued that it is at least as safe as that conventional counterpart.
Profiling technologies
State of the art biochemical, bioinformatics and statistical methods are used to unravel the complex relationships between genes, messengers, proteins and metabolites. Basically three types of studies are at the researcher's disposal to elucidate what changes may occur as the result of for instance the introduction of new genes (so a change in the genome) or an altered environment (the use of organic agricultural methods, the influence of location / climate).
The figure below shows the interrelation of such studies with the machinery and molecules in living cells:
Transcriptomics
The study of transcriptomics examines the expression level of mRNAs in cells, often using high-throughput techniques based on DNA microarray technology. Unlike the genome, which is basically fixed when for instance a potato variety is studied, the transcriptome (the set of all messenger RNA -mRNA- molecules, or transcripts in a particular cell) can vary with external environmental conditions. The levels of mRNA are not directly proportional to the expression level of the proteins they code for, which are measured using:
Proteomics
The study of proteomics involves the qualitative and quantitative comparison of the entire complement of proteins (proteomes) by separating and identifying these proteins using two dimensional gel electrophoresis techniques.
The comparison of proteomes, from for instance different potato varieties, yields more information than knowledge of their genome or transcriptome only. Messenger RNA may be degraded rapidly or translated inefficiently, resulting in a small amount of protein, or transcripts may give rise to more than one type of protein, through alternative splicing or alternative post-translational modifications. Also proteins may be subjected to (in)activation through post-translational modification or may only function when complexes are formed with other proteins or RNA molecules. By using proteomics techniques it is expected that such cellular reactions can be detected in comparative analyses.
Metabolomics
The study of the metabolome refers to the determination of the complete set of small-molecule metabolites, such as metabolic intermediates, signalling molecules and secondary metabolites, to be found within a certain cell type, tissue or organism. Such an entire range of small molecules are determined by a combination of analytical methods. Gas chromatography and capillary electrophoresis are mainly used for separating the molecules, while mass spectrometry and nuclear magnetic resonance spectroscopy are the prime methods for their detection and identification.
In the figure below typical outputs from the three 'omics' profiling techniques are shown:
Results
When profiling techniques were used in a comparative analysis of genetically modified potatoes and their parents, no consistent differences could be detected. The reason that differences were detected were contributed to the fact that random, but statistically significant differences were also found between wildtype controls and tubers derived from for instance tissue culture. Even greater differences can be detected between potato varieties, or when similar varieties are grown under different circumstances, such as conventional agriculture versus organic methods.
Supporting materials
Plant metabolomics: Addressing the scientific concerns and uncertainties of genetic modification: a poster from the Scottish Crop Research Institute.
