The study of genomics – of genes and non-coding sequences of DNA in organisms – has been led by those in the medical profession, where it has enabled doctors to understand certain traits and inherited diseases. More recently, it has been used for simultaneously screening thousands of potentially affected indicators and, while the full potential has not yet been harnessed, for bio- marker discovery. Dr Bo Lönnerdal from the University of California Davis provided an introduction to this field and its potential relevance to micronutrient nutri- tion. Dr Lönnerdal co-moderated this session with Professor Xiaoguang Yang from the Chinese CDC. Single nutrients can affect gene transcription, which, in turn, affects protein expression. The use of genomics enables nutrition researchers to identify pathways associated with particular nutrients. For example, what genes are up- or down-regulated by dosing with vitamin A? Genes or groups of genes may be associated with a particular nutrient deficiency. Unfortunately, genetics research requires samples of RNA, which are rarely available from field studies. One potential solution is to use peripheral blood mononuclear cells (PBMC). Even in this case, blood samples need to be processed very quickly and stored at -80 °C to prevent RNA degradation. Sample requirements have thus far restricted the use of genomics in nutrition intervention studies. Genomics alone is insufficient to model and predict biological systems. Post-transcriptional modifications such as phosphorylation often regulate protein activi- ties. Furthermore, the quantity of protein in a cell, tis- sue or organism is not always regulated by mRNA: translation and degradation play critical roles in deter- mining protein abundance. This brought scientists to the study of proteomics, which considers all of the pro- teins present in a cell or sample at a given time. Proteomics can be used for profiling, i.e., the large- scale identification of proteins. Another application, as discussed in Dr Keith West’s presentation, is compar- ative or quantitative proteomics for target identifica- tion and biomarker discovery. Regardless of the appli- cation, there are two routes for proteomic analyses. After sample preparation to remove major proteins (e.g., serum albumin, immunoglobulins, transferrin), a first route involves the use of two-dimensional gels to separate proteins and then mass spectrometry to iden- tify them. In the second route, “shotgun proteomics,” fluids are digested into a large amount of peptides, which are separated and then identified and quantified by mass spectrometry. Either of these options requires complex bioinformatics, but methods and tools have been developed for these purposes.
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