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Bee Gene Expression Study Yields Marker for Colony Collapse Disorder

NEW YORK (GenomeWeb News) – Honey bees from colonies affected by colony collapse disorder, or CCD, harbor ribosomal RNA fragments that may be useful for early CCD detection, according to a study appearing online this week in the Proceedings of the National Academy of Sciences.

Researchers from the University of Illinois and the US Department of Agriculture's Bee Research Laboratory used microarrays to compare gene expression patterns in the guts of honey bees from CCD-affected colonies on the East and West Coast with samples collected before CCD emerged in the US. They found expression differences between both bees with or without CCD and bees from different geographic areas.

Unexpectedly, though, the team also found that bees from colonies with CCD tended to harbor high levels of fragmented ribosomal RNA in their guts. Those involved say such rRNA patterns could offer a method for early identification of colonies undergoing CCD — as well as insights into the underlying cause of the disorder.

"The one consistent indicator of CCD across samples collected at multiple times and in multiple places was the overabundance of ribosomal fragments," senior author May Berenbaum, head of entomology at the University of Illinois, said in a statement.

Over the past several years, CCD has been linked to dramatic declines in honey bee numbers across the US. Among the first pathogens implicated in CCD was a picorna-like virus called Israeli acute paralysis virus that wasn't thought to infect American bees.

But subsequent studies suggested the Israeli acute paralysis virus had actually been in the country before CCD was recognized, Berenbaum and her co-authors noted. And additional research indicated that CCD was more complex than initially believed, involving several pathogens and/or other factors affecting bee immunity.

To further explore the intricacies of CCD, the researchers compared adult worker bees from CCD-affected colonies on the East and West coasts of the US with bee samples collected from the same regions prior to the identification of CCD.

After extracting DNA from the bee guts, the team used a custom microarray to evaluate 9,867 honey bee genes. Overall, the researchers identified more than 1,300 probes that showed expression differences between the CCD affected and unaffected colonies.

These expression patterns varied depending on both CCD and geography, with the team detecting differential expression for genes involved in everything from transcription factor to metabolic enzyme activity.

But there was relatively little overlap between differentially expressed genes in severely affected and moderately affected colonies from the East and West coast.

Because their microarray contained probes recognizing eight bee pathogens, the researchers were also able to get hints about what sorts of creatures were infecting bees in each colony. They identified three different pathogens in the bees tested: the chalkbrood-causing fungus Ascosphaera apis (found in East coast bees with CCD as well as colonies with severe CCD), the black queen cell virus (found more often in CCD affected than unaffected colonies), and deformed wing virus (in East coast bees and bees with severe CCD).

While the researchers did not see dramatic increases in the expression of bee genes involved in apoptosis, immune response, or pesticide exposure in the CCD colonies, they did see an unusually high number of polyadenylated, fragmented ribosomal RNA in these bees.

Based on that pattern, they speculated that picorna-like viral infection might upend ribosome function making bees less capable of dealing with other stressors such as pesticides, the varroa mite that carry picorna-like viruses, and pathogenic fungi such as Nosema ceranae.

"If your ribosome is compromised, then you can't respond to pesticides, you can't respond to fungal infections or bacteria or inadequate nutrition because the ribosome is central to the survival of any organism," Berenbaum said in a statement. "You need proteins to survive."

Based on their findings, the researchers argued that the rRNA fragments may prove useful for diagnosing colonies that are at risk of succumbing to CCD. And, they noted, given the differences in CCD severity and expression profiles between colonies in California and those in Pennsylvania and Florida, additional research should provide a better understanding of genetic variation in bees from different parts of the country.

"This variation provides insight into the different stresses facing bees and clearly demonstrates that diagnostic surveys must sample extensively across numerous bee populations," the researchers concluded. "Colony surveillance via assay of rRNA-like transcript abundance may provide an earlier indication of CCD status than has hitherto been available and allow beekeepers to take actions to reduce losses."

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