Biology Reference
In-Depth Information
distance between two sequences. Furthermore, some changes may yield a bend
in the DNA molecule, resulting in a disproportionate change in gel mobility.
Further analysis of this method will resolve its value for molecular ecology.
13.5.6 Microarrays
DNA microarrays (also known as gene chips, genome chips, and gene arrays)
are a technology that began to be used in the mid-1990s to analyze genome-
wide patterns of gene expression within and among species (
Gibson 2002
, see
Chapter 6). Initial applications of microarrays involved gene discovery, disease
diagnosis, drug discovery, and toxicological analyses comparing tissues or cells.
However, this technology provides a tool that allows entomologists to move
beyond the one-gene-one experiment paradigm.
Microarrays allow the researcher to measure the relative quantities of specific
mRNAs in two or more samples for hundreds or thousands of genes simultane-
ously. When a sample containing bits of fluorescently labeled cDNA is added
to the chip containing spotted samples of DNA or cDNA, the labeled samples
(e.g., one may be labeled green and one red) will anneal to the DNA on the chip
that has complementary sequences. The chip contains known DNA sequences
in a specific array. After complementary base pairing, the chip can be scanned
and the colors will tell you which genes have hybridized with the sample DNA
by complementary base pairing. Intermediate colors indicate those genes were
active in both samples. When one sample contains cDNA but the other sample
does not, the sample will fluoresce either red or green. If the same genes are
turned on in both insects, both red and green dyes will be present on the micro-
array “dot” and appear as yellow (
Figure 13.1
). Thus, DNA microarrays can pro-
vide information on the transcriptional changes (transcriptomics) that occur in
specific cells, tissues, or whole organisms under specific conditions.
DNA microarrays provide a way to analyze ecological interactions between
plants and arthropod pests. For example, microarrays were used to assess the
multiple transcriptional changes that occur after plants are attacked by insects
(see case study below on insect-plant interactions). DNA microarrays should be
useful for other ecological analyses. Scientists could use microarrays to evaluate
the major events that occur during parasitism of insects by pathogens or nema-
todes or to evaluate the role of symbionts or what genes are involved in dia-
pause induction and termination. DNA microarrays might be applied to DNA
profiling to characterize genetic differences among biotypes or closely related
species (
Gibson 2002
). Limitations to the application of microarrays to ecological
problems currently include their perceived expense and lack of availability for
nonmodel insect species (
Gibson 2002
). As with DNA sequencing, however, the
