Cell Language Theory, The: Connecting Mind And Matter

Applications of the Cell Language Theory to Biomedical Sciences 295

“6x9” b2861 The Cell Language Theory: Connecting Mind and Matter

1. Isolate mRNA from broken cells.


2. Synthesize fluorescently labeled cDNA from mRNA using reverse
   transcriptase and fluorescent nucleotides.


3. Prepare a microarray either with DNA fragments or oligonucleotides
   synthesized on the microarray surface.


4. Pour the fluorescently labeled cDNA preparations over the microar-
   ray surface to effect hybridization. Wash off excess debris.


5. Measure fluorescently labeled cDNA using a computer-assisted fluo-
   rescence microscope.


6. The final result is a table of numbers, each number registering the
   fluorescent intensity which is in turn assumed to be proportional to
   the concentration of cDNA (and ultimately mRNA in the cell) located
   at row x and column y, the row indicating the identity of genes, and
   y the conditions under which the mRNA levels are measured (see
   Table 7.2).

Another example of microarray measurements of RNA is shown in

Figure 7.4. The term RNA here refers to not only mRNA, but all other

forms of RNA including RNA complementary to the introns, promoters,

ribosomal RNA, small interfering RNA, and non-coding RNA. The data

in Figure 7.4 were measured by Garcia-Martinez et al. [315] from bud-

ding yeast Saccharomyces cerevisiae undergoing glucose–galactose shift

at six time points: 0, 5, 120, 360, 450, and 850 min after the nutritional

shift. Each data point is the average of three measurements. The overall

quality of the kinetic data, as evident in the smooth and coherent trajectory

exhibited by each gene, increases our confidence in the microarray experi-

mental method.

Figure 7.3 down-regulated mRNA levels. The image is adopted from [305]. (c) The mRNA

fold changes (y-axis) in breast tumor tissues of 20 patients (x-axis) before (BE) treatment

relative to control (N). Each profile represents the mRNA level changes encoded by one

gene. The figure contains 50 genes out of ~5000 genes analyzed. (d) The mRNA fold

changes of tumor in 20 breast cancer patients before (BE) and after (AF) treating with doxo-

rubicin for 16 weeks. RAT2N indicates mRNA level ratio with red channel (or channel 2)

normalized [306].

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