UCSF Sleuths Identify Suspects in Mystery of Vanishing Honeybees

http://pub.ucsf.edu/today/print.php?news_id=200704251


By Wallace Ravven
UCSF scientists have identified two likely suspects in the massive die-off of half a million bee 
colonies in the US. Joe DeRisi, PhD, and Don Ganem, MD, both Howard Hughes Medical Institute 
investigators at UCSF, have used a powerful combination of a "virus chip" — a microarray with 
DNA samples of most known viruses and fungi — and "shotgun" sequencing, which identifies 
telltale DNA from random samples of the biological sample.
The Army's Edgewood Chemical Biological Center at the Aberdeen Proving Ground in Maryland 
sent DeRisi samples to analyze from bees in the Central Valley of California. DeRisi and Ganem 
identified a parasite known to have caused massive bee losses in the last decade in Asia and 
Europe, making it a strong candidate as a culprit responsible for bee collapse in the US. The 
parasite is called Nosema ceranae, a so-called microsporidian fungus — a small, single-celled 
parasite that mainly has been associated with affecting Asian bees, and is thought to have jumped 
to the Western honeybee in the last few years. The shotgun approach succeeded in this search, as 
the microarry does not include this species' DNA.

Joe DeRisi

The lab's search for culprits using the micorarray, however, also netted a second potential killer, a 
virus from the genus Iflavirus, which has been implicated in a number of problems in the bee 
industry.
"The next — and very critical — step is to assay other failing hives around the country and the 
world to measure to what degree these pathogens we have identified are also associated with bee 
collapse elsewhere," DeRisi said. "We can't say that because the bees in Central Valley may have 
fallen to one or both of these pathogens that we have now proven that this is the cause 
throughout the United States."

Don Ganem

The virus chip gene-hunting technique is designed to identify a sample virus by comparing its 
DNA or RNA to more than 20,000 snippets of genetic material derived from all known viruses 
found in humans, animals, plants, fungi and bacteria. The microarry also has gene sequences 
from other microorganisms. The chip draws on computer chip technology, computation and 
bioinformatics, but in essence it is a simple 3 x 1 inch glass microscope slide. Onto the slide the 
scientists robotically deposit 10 to 12 different DNA sequences from all the viruses. Each sample 
appears as a microscopic dot, about a tenth of a millimeter in diameter — giving it the name 
micoroarray. Researchers then wash fluorescently tagged DNA from a sample of interest over the 
slide, and wherever the two sets of nucleic acid match up, they anneal to each other. The slide is 
then rinsed and visualized with a scanning laser microscope. The dots that have found a match 
glow with fluorescent light.
During the SARS scare in 2003, the Centers for Disease Control and Prevention (CDC) turned to 
DeRisi for help in identifying the cause of SARS, or severe acute respiratory syndrome. His lab 
used the virus chip to confirm the culprit, a new form of coronavirus. Last year DeRisi and Ganem, 
in collaboration with scientists at the Cleveland Clinic, discovered a previously unknown human 
virus associated with prostate cancer.
DeRisi is professor of biochemistry, and Ganem is professor of microbiology and immunology at 
UCSF.

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