Plants help scholars understand DNA

by Peter Kauffner

Mustard weed may be an annoyance for farmers, but a group of University researchers hope to use the plant to unravel genetic mysteries.
Its fast rate of growth makes the weed, known scientifically as Arabidopsis, a relatively easy plant for biologists to work with. Researchers at University’s Arabidopsis cDNA Sequence Analysis Project are mapping the plant’s genome to create a model to better understand genetic data from other plants. The work is funded by a $900,000 grant from the National Science Foundation.
Every cell in a living organism contains a genome, which consists of genetic information coded in a double helix strand of the chemical DNA.
“One strand of DNA is used to create RNA, which is in turn used to create proteins. We take the RNA and use that create cDNA,” said Ed Chi, a computer science research assistant who is working on the project.
The chemical complement of DNA is cDNA. A group of biologists at Michigan State University develop the cDNA sequences and send them to the University.
“We use cDNA because a lot of the original DNA is just junk and this process allows us analyze only the parts used to make protein,” Chi said.
Chi has written a computer program called the alignment viewer, which allows researchers to view their results in graphical form.
“The alignment viewer is very powerful. It takes a 3,000 page (text representation of a genetic sequence) and displays it as a single image. It can manipulate in three dimensions and pick things out,” said Ernest Retzel, a research associate in the medical school.
The project uses computerized tests to compare sequences in order to find similarities. If a sequence of code’s function is unknown and found to be similar to a sequence that has a known function, a “putative function” can be assigned.
“We are guessing we now have about 60 percent of the genes that are present and expressed in Arabidopsis,” Retzel said. The project has produced genetic data for the past four years.
“We take data from the rice genome sequencing project (in Tsukuba, Japan) and map this on the Arabidopsis genome. The ordering of that information on the Arabidopsis genome tells that rice community something about their data,” Retzel said.
Besides rice, the project also focuses on data gathered from pine trees. The forest industry has offered funding for such work in hope that such information will help them grow improved, genetically engineered trees.
The project’s most surprising result so far is a preliminary finding that only 35 to 40 percent of the cDNA sequences for Arabidopsis match those for rice, corn and the lobolly pine, said Elizabeth Shoop, a research assistant in the computer science department.
About 35 percent cDNA sequences for plants match those for animals. Geneticists had expected that there would be 60 percent match rate among plants.
The project’s findings have since attracted considerable attention in the genetics community. “The entire rest of the world knows we’re here, but no one (at the University) knows we are here,” Retzel said.