Geneticist George Vandemark isolates a DNA sample
for identification using polymerase chain reaction and other genetic
fingerprinting methods. Click the image for more information about
Pathogen Monitoring Made Easier With Paint Can
By Jan Suszkiw
June 27, 2005
Vandemark likes his DNA (deoxyribonucleic acid) "shaken, not
stirred"--recalling the fictional British secret agent James Bond.
Stirring, or centrifugation, is a key step by which diagnostic labs genetically
identify crop pathogens inhabiting farmers' soils.
But shaking, not stirring, the DNA may give farmers more bang for their
diagnostic buck, reports Vandemark, an Agricultural Research Service geneticist in
Normally, diagnosticians use centrifugation to separate pathogen DNA from
other soil sample debris. Polymerase chain reaction and other so-called
fingerprinting steps then determine whether the DNA's genetic patterns match
those of a particular crop pathogen. The problem is, today's DNA extraction
kits only work with 10-gram soil samples. And at around $15 per test, such
extraction can become prohibitive for field-wide surveys--for example, to
choose appropriate fungicides or resistant crop varieties, according to
Vandemark, in ARS'
and Forage Crop Research Unit in Prosser.
His solution was to use paint can shakers, like those used in hardware
stores. Instead of paint, though, he modified the shakers to hold test tubes
capable of storing 70 grams of soil. To the tubes, he adds small glass beads
and a buffer. The beads smash the cells of pathogens in the sample while the
buffer protects their escaping DNA from damage by enzymes. After extraction,
Vandemark uses PCR-based fingerprinting to determine the pathogen's genetic
He began experimenting with the paint can shaker idea in 2004, and has used
it to extract miscellaneous DNA from three different soil types in the Columbia
Basin. His chief targets are Verticillium, Phytophthora and
Fusarium fungi that plague Pacific Northwest potatoes, which comprise
over half the nation's $3 billion tuber crop. Detecting DNA of soil-borne
roundworms that cause disease of potatoes is another goal.
Vandemark plans more tests using different soil types and welcomes
commercial interest in refining the modification, which he estimates could save
farmers hundreds of dollars per field in disease-diagnostic costs.
ARS is the U.S. Department of
Agriculture's chief scientific research agency.