Reprinted with permission from Biohawk, December 2002
Anybody reading this in Overland Park might want to watch out for northern snakeheads on the lawn. You Goodland readers can rest easy, however.
The snakehead was the Asian walking fish pulled out of a Maryland pond this summer. Wildlife officials openly worried about snakeheads marching across the landscape, devouring native fish. As it turns out, a snakehead invasion might jeopardize ponds in eastern Kansas, but the fish in western Kansas would be safe. Snakeheads cannot make it past Hays. How do we know? Ed Wiley’s computer said so.
Dr. Wiley is one of several University of Kansas biologists harnessing information technology to create the discipline of bioinformatics. Bioinformaticians combine powerful computers with the Internet to quickly comb through dozens or even hundreds of databases spread throughout the globe. This ability allows bioinformaticians to analyze unprecedented amounts of data and to collaborate more easily with chemists, medical doctors, meteorologists, geologists, geographers and other scientists in the relentless effort to reveal the mysterious workings of the world.
Wiley’s research on how far snakeheads might spread in North America is a good example of bioinformatics at work. The research started with an analysis of the snakehead threat done by Greg Vorontsov of KU’s Biodiversity Research Center. Vorontsov did his work with the help of Lifemapper. Lifemapper is an on-line, collaborative project spearheaded by KU and available to anyone curious about where organisms live (see sidebar). It allows scientists to scan the collection records of any of its member-museums, currently about 100 and growing, and to cross-reference those records with environmental databases.
Wiley then followed-up with a more detailed analysis using tools similar to those used by Lifemapper. He did a computer search of museum records to find where members captured all the snakeheads in their collections. He then combined that information with data on things like climate and altitude in the snakehead’s home range and fed it all to GARP. GARP is a “smart” computer program that created models of the conditions in which snakeheads like to live in their native habitats. Wiley finished by finding everyplace in North America with similar conditions. The resulting map showed Wiley the places at risk for a snakehead invasion.
Capabilities like this have drawn the attention of government agencies. The U.S. Geological Survey has identified 50-70 species they think pose a great risk of invading North America. To help plan their defenses against these species, the USGS has asked Wiley to develop maps of where the invaders might spread.
“This technology allows them to be proactive, rather than reactive,” Wiley said, “It will show politicians the damage that these species might do.”
Organismal biologists do not have all the fun, and molecular biologists like Dr. Kathy Suprenant have been in on bioinformatics for some time. Suprenant studies hollow intra-cellular filaments called microtubules. Microtubules pull chromosomes into the daughter cells during cell division, and also help nerve cells create extensions to their neighbors so nerve impulses can travel between cells. Suprenant first used bioinformatics 14 years ago after discovering a unique protein in the microtubules of sea urchins. She found the DNA responsible for the unique protein, and then searched databases around the world looking for DNA coding for similar proteins in other organisms. She found such DNA in creatures ranging from protozoans to people. Comparisons of the proteins coded for by the DNA revealed that they shared a motif, which is a unique amino acid sequence, that united them into a protein family called ELP. Now she wants to know what the motif does.
“We think the motif has an important function. Why else would it be conserved in all these organisms?” she said.
Understanding the motif’s workings has special importance for people with Usher syndrome. This genetic disorder causes blindness and deafness in about 8,000 Americans. Researchers have found a locus for Usher and it includes a gene coding for a protein with Suprenant’s motif. Furthermore, one of her graduate students found that an ELP-family protein called ELP-1 appears in the sensory neurons of the flatworm Caenorhabditis elegans. All this evidence is very suggestive to Suprenant.
“I think that a study of ELP-1 function in the worm will lead to an understanding of Usher syndrome in humans,” she said.
Dr. Jianwen Fang, bioinformatics resource manager for the Division of Biological Sciences, sees other ways for bioinformatics to help medicine. For instance, it may help researchers figure out if a treatment for one disease could also help another. Imagine that researchers find a drug that cures a disease caused by a malfunction in a protein called PRO-1. That drug, or a variation of it, would also be a good candidate to cure diseases caused by proteins that looked like PRO-1, according to Fang. Before bioinformatics, searching for the protein look-alikes among the thousands of known proteins would have required months of work. Now researchers can conduct such a search in a matter of hours.
Fang thinks that the ability to match proteins with drugs may even make personalized medicine possible.
“Right now, we have the have the same medicines for all people. Maybe in the future, we will be able to design a medicine specifically for one patient,” he said.
Bioinformatics may have a lot of possibilities in its future, but planning for that future will be a great challenge. James Beach, assistant director of informatics for the Museum of Natural History, says that bioinformaticians must anticipate the questions that researchers may ask in the future.
“We can’t design our systems for current research needs, we have to design for the next thing,” he said, “It’s like planning for a city’s sewer system. What you need now will be obsolete in five years.”
In Beach’s case, planning includes figuring out what information the Museum should attach to all the specimens it collects. Traditionally, a biologist would record the date, time, and location for every specimen collected. Now that technology allows scientists to plow through much larger mountains of data, Beach wonders about other tidbits of
information that might interest researchers in the future. Should the collector record other species they see in the area? How about the soil type? Maybe somebody will want to know if roads are a good invasion pathway for alien species to follow. Structuring the databases so somebody with a computer and an interesting question can find the answer without ever leaving their office is Beach’s challenge.
“We want to extract as much knowledge out of the data as we can,” he said.
Spoken like a true bioinformatician.