53a sufficient condition for high in vivo protein production. Regulation of translation,
RNA and protein stability, and posttranslational modifications can alter the linear
relationship between the message and the corresponding protein. Additionally, a
protein could be present in high concentration, but it may lack the requisite con-
ditions (substrate concentration, cofactors, etc.) for activity in the actual cellular
environment. Moreover, in the context of the regulatory networks, a modification in
the expression levels of a gene is not expected to alter only the concentration of the
corresponding protein and the activity of the corresponding biochemical reaction,
but it would also affect other parts of the cellular networks depending on the role of
this gene in cellular function. Therefore, it is the integration of all of these molecu-
lar profiles for a systematically perturbed cellular system that can provide insight
about the function of unknown genes, the relationship between gene and metabolic
regulation, and even the reconstruction of the gene regulation network (Klapa and
Quackenbush 2003 ; Vidal 2009 ). To succeed in the challenge of quantitative sys-
tems biology, however, major issues concerning the quantification capabilities and
sources of biases of these multistep molecular analyses (Fig. 3.1) need to be thor-
oughly resolved for each level of molecular function and for the specific needs of
each investigated biological system. They range from limitations in the available
experimental protocols, to lack of data analysis and visualization techniques for
upgrading the information content of the acquired measurements.
Fig. 3.1 Omic profiling analyses are multistep procedures with potential sources of systematic
biases at any stage
3 Investigating the Effect of Elevated CO 2 in the Growth Environment ...