Unraveling the Host-Pathogen Interaction
Ruy Ribeiro (right) is the principal investigator on a project funded by the Laboratory Directed Research and Development program to find genetic markers, in both influenza and humans, that correlate with highand low-virulence viruses. Says Ribeiro, “Our goal is to develop the knowledge and tools necessary to predict the pandemic potential of any influenza virus.”
Figure A shows one approach—whole-genome microarray experiments. Each of the more than 30,000 spots in the microarray image corresponds to a human gene, and the spot brightness indicates the degree to which that gene was turned on 24 hours after a cell was infected with a high-virulence strain of influenza. The “hit” pattern changes with virus strain, type of cell, and time after infection. Through pattern comparison, a set of genes might be found that would correlate with virulent viruses, but it takes sophisticated tools to extract information from the complex images.
One of those techniques is shown in Figure B on the facing page. Numerous experiments similar to those described in Figure A were conducted, and pairwise comparisons of the results were reduced by an algorithm to a single value. The values are plotted as a “tree.” Each experiment, represented by a color, was repeated three times. Data were taken after 8 hours (open circles) and 24 hours (closed circles). A short line between two dots indicates the two experimental resuls are very similar, a longer line less similar. The “tree” suggests that the cellular response to different strains of influenza cluster into characteristic patterns; for example, the highvirulence strains (red) and low-virulence strains (yellow) form distinct groups.
The figure to the left shows a more quantitative assay. A matrix is constructed with cellular or immunesystem genes as column elements and viral strains as row elements. The color of each matrix element shows the degree to which that gene turned on or off when the cell was infected with that virus. The matrix was analyzed and rearranged as per the two “trees” on the right and top of the matrix. There is a clear distinction between high- and low-virulence strains; namely, the gene expression for high-virulence strains was greatly reduced, which may be related to the ability of those strains to minimize the immune response.
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