Systems biology, which presently encompasses transcriptomics, proteomics, and
metabolomics, is a branch of biology whose objective is to discover and elucidate
biological properties that emerge due to interactions of systems elements (Ideker et al.,
2001; Kitano 2002). These new tools, based on high throughput computers, robotics
and new tandem mass spectrometer chemistry have resulted in an explosion of information unparalleled in the history of biology. This information explosion presents new
challenges for gathering and configuring data into interactive models. Thus, the development of predictive models will necessitate strong interactions with other disciplines
such as mathematics, computer sciences, engineering, organic and biochemistry, evolutionary theories and bioinformatics. Perhaps the most important discipline for the
success of system biology to add new and meaningful data will be supplied by the
whole plant biologist who has a thorough knowledge of the growth and development
of plants under natural environments. In studying abiotic stresses such as freezing,
cooling and heating rates must be realistic, light intensities must approach sunlight,
water potential changes should be similar to natural changes, and growth should not be
restricted by the soil mass, etc. What appears to be forgotten is that many abiotic
stresses occur over days to weeks and not in minutes. If experiments do not duplicate
or approach natural conditions it does not make sense to add to the literature erroneous
facts that confuse and retard, rather than advance, scientific truths. Controlled environment studies must be cross-referenced to field studies to obtain meaningful data.
The following sections on transcriptomics, proteomics and metabolomics discuss some recent research on abiotic stress with primary emphasis on cold acclimation.
Due to the limitations of all these methods there will be a need for parallel analyses of
transcripts, protein and metabolic profiles. There will then be a need for comprehensive
identification of protein-coding genes, elucidation of protein structures and identification of protein functions, protein-protein interactions, localization of proteins, knowledge of signal transduction cascades to understand cellular dynamics and differentiation. Since cold acclimations is such a dynamic and complex multi-gene trait it will only
be possible to identify candidate genes as system biology evolves. In all of these
studies morphological and anatomical differences in plant tissues will need to be examined in order to determine their role in ameliorating stresses. Perhaps then it will be
possible to make significant advances in understanding how plants adapt and tolerate
abiotic stress.

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