Whole Cells - Molecular Theory of the Living Cell - page 407

Examples of the two-dimensional displays of the ViDaExpert results are shown
in Fig. 12.12 . In general, the kinetic patterns of the RNAs belonging to different
metabolic pathways appear more clearly distinguishable in the two-dimensional
counterparts (Fig. 12.12 ) than in the three-dimensional plots (Fig. 12.11 ). For
example, Panels c and d or e and g in Fig. 12.11 are less easily distinguished than
their two-dimensional plots in Fig. 12.12 . Figure 12.12 clearly demonstrates that
each metabolic pathway exhibits a unique RNA spectrum. When the node number
is increased to 100 (as compared to 64 in Fig. 12.12 ), the pathway-specific features
have been found to become even more readily distinguishable (data not shown).
Also, the shapes of the RNA spectra have been found to change dramatically when
RNA trajectories are measured in budding yeast with microarrays under different
experimental conditions, for example, under nitrogen-deficient condition during
alcoholic fermentation (Mendes-Ferreira et al. 2007) (data not shown). In other
words, the RNA spectra (or ribonic spectra ) described in this topic for the first
time (Fig. 12.12 ) are both pathway-specific and cell state-specific , thus suggesting
the possibility that RNA spectroscopy (or ribonoscopy ) may be employed as a
sensitive experimental tool for characterizing living cells in normal and diseased
states (see Chaps. 18 and 19 for further discussions).
The two-dimensional plots in Fig. 12.12 are strikingly similar to molecular
spectra , an example of which is given in Panel a in Fig. 12.13 along with a ribonic
spectrum in Panel b. The molecular spectrum in Panel a (Rold ´ n et al. 2004) depicts
the probability of exciting certain vibrational motions in the inorganic molecule,
tetrachlorophsophonium oxotetrachlorovanadate, as a function of excitation energy
expressed in wavenumbers. This similarity motivated invoking the term “RNA
spectra” introduced in Fig. 12.12 .
The concept of “RNA spectra” (or “ ribonic spectra ”) is compared with that of
molecular spectra in Table 12.5 . One interesting difference between them is that
molecular spectroscopy studies the equilibrium structure of molecules whereas
“RNA spectroscopy” or (“ribonoscopy”) studies the dissipative structures comprised
of the time-dependent RNA concentrations or RNA waves (i.e., ribons) participating
in a common metabolic function (or pathway) (see Row 2, Table 12.5 ). Molecular
spectroscopy allows investigators to probe the internal energy levels of a molecule
available for electronic, vibrational, and rotational excitations . Analogously, it is here
postulated that ribonoscopy allows cell biologists to investigate the internal structures
of the cell consisting of the functional connections (encoded in the genome) among
individual RNA molecules (1), RNA pairs (2), and systems of RNA molecules (

2)
participating in various metabolic pathways. By “functional connections among
individual RNAmolecules,” I mean, for example, the connection between an identical
RNA molecule at two time points, i.e., a temporal autocorrelation.
It is interesting to note that the x -axis of molecular spectra encodes energy levels
expressed in terms of wavenumbers , whereas the x -axis of ribonic spectra encodes
information specifying the shape of RNA trajectories, waves, or ribons expressed in
terms of node numbers :Justas wavenumbers imply the energy of molecular motions,
so node numbers carry the information about RNA trajectories (see Row 4,
Table 12.5 ). The y -axis of molecular spectrum measures the probability of

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