Sinha Studies Genetic Foundation of Honeybee Behavior Using Supercomputers
by Vince Dixon, NCSA
In a typical honey bee colony, young worker bees are responsible for attending to the queen and her larvae. As the worker bee ages, it progresses through different roles, ultimately landing the job of forager bee. Under irregular conditions, this natural succession can be disrupted causing the bee to prematurely adopt an advanced position within the hive. A nurse bee, for instance, will suddenly become a forager if for some reason there are not enough foragers bees in the hive. The genetic explanation for such socially regulated behavior in bees can also help in understanding the rules that influence behavior in other species, including humans.
"That's remarkable, and that's the reason that we are studying this behavior," said Saurabh Sinha, a University of Illinois assistant professor of computer science and 2007-2008 NCSA Faculty Fellow. Sinha, in collaboration with Illinois entomology professor Gene Robinson, set out to explore the molecular basis for social behavior in honey bees. They wanted to study what in a bee's DNA causes certain social responses.
Following Robinson's discovery of the genes responsible for the bee's activity, Sinha and his lab began locating the genomic regulatory sequences that turn on the genes.
These sequences regulate when and where a gene becomes active. They are what tell genes that produce organ-specific molecules to do so in the correct organ's cells.
Sinha and team developed statistics to predict which sequences are responsible for the socially regulated behavior in bees and where the sequences may be located. The process is long and complicated.
"Because of the sophisticated nature of those statistical procedures, it takes time and it takes a lot of computing power," Sinha said.
As an NCSA Faculty Fellow, Sinha was able to access NCSA supercomputing power for his research.
Sinha's lab used its own genomic analysis software on NCSA computers. The software scanned genomes for patterns and formed statistics from the data. Sinha said without NCSA computing power, the scanning process would have been very slow.
Much of this procedure was repeated with the newly sequenced wasp genome. Evolutionarily, the wasp is the closest sequenced insect to the honey bee, but is not a social insect. If sequences found in the honey bee are also found in the wasp, the sequences can be ruled out as an influence on honey bee social habits. In this manner, the wasp genome acts as a filter for possible regulatory sequences for honey bee behavior.
This illustrates the power of comparative genomics, Sinha said. Comparing and contrasting genomes across species can lead to a greater understanding of human biology and can point to evolutionary innovations.
In addition to high-powered computer access, NCSA provided funding for two graduate students involved with the project. The students were able to assist the professor for one semester testing different statistical procedures and developing methods to apply to various elements of the research. The findings of the project were submitted for peer review.
The Faculty Fellows program allowed Sinha to form a relationship with NCSA and its staff.
"It has built a dialog between me and the appropriate researchers at NCSA," Sinha said. He added that he hopes to continue the relationship for future projects.