Midweek Article “Retired” bacteriologist keeps working on her unique role in genetic research

Stanford University-educated Patricia Vary is a Renaissance woman. She sings in the chorus Bread and Roses, she plays violin in the Kishwaukee Symphony, she is a member of the DeKalb County Board, she is grandmother and a Texan, she is an NIU presidential research professor, and she has spent much of her life with a little thing called Bacillus megaterium (B. meg).

It’s much friendlier than Bacillus anthracis — the bug that causes anthrax, which resulted in several deaths and a national panic in the fall of 2001.

Vary’s research and manipulation of B. meg, which has about 5,000 genes, has played a significant role in genetic research and in development of tests for HIV.

The same woman, one of three principal investigators who recently received a $630,000 National Science Foundation (NSF) grant for continuing genetic research, is also an NIU faculty retiree who has fed dolphins from the porch of her sister’s home in Rockport, Texas

Vary is an illustration of what can happen when a woman leaves her field during nest-building, child-rearing time—not that she regrets the latter. But during the eight years Vary was an at-home mom, researchers in her field, bacteriology, had begun the techniques of gene cloning that bring both benefits and concerns to the human race. They learned to replicate a piece of spliced DNA inside a bacterial cell. “For example, they can clone genes for the production of human insulin by putting that gene into the bacterium E. coli and it produces it,” she explained.

Vary worked several years to understand the genetics of B. meg, which forms spores as anthrax does. The NSF wanted to sequence it because it is one of the major producers of Vitamin B-12 and it also produces an enzyme that makes the synthetic penicillin.

To make B. meg easier to work with, Vary withdrew seven types of “plasmids” from the cell and her newly created strain of the bacterium was named PV361.

“I gave a talk about it to the American Chemical Society in the mid-1980s and Abbott Labs called me and said they’d like to work with it. If anything commercial came out of it, I could renegotiate later. They also recommended that I patent it,” Vary said.

“Abbott inserted a gene they were interested in, and they found that B. meg produced the product with no degradation. Then Abbott took the HIV virus coat protein which is what they make antibiotic to, and put it in PV361—and that is the basis for the diagnostic tests from Abbott for AIDS.”

“I just gave them the host, the factory to produce the protein,” Vary said.

The “retired” bacteriologist is now working with the plasmids she removed from B. meg, which have a lot of DNA, and the work will constitute four papers for publishing.

She and other scientists The Institute for Genomic Research (TIGR) tried to make a case for a grant and approached TIGR. Vary said the institute managed to sequence 90 percent of the human genome in two years, whereas it took the rest of the world much longer; the work sequencing the human genome is now complete.

The research journal Nature published sequencing results of the National Institutes of Health (NIH) research, and the journal Science published TIGR’s sequencing.

An international effort succeeded in gene sequencing the bacterium E. coli within the last 10 years.

“The human genome is 1,000 times bigger than a bacterium genome,” Vary explained.

“In 2000, there was an attempt to sequence all disease-carrying bacteria.” The work is extremely dangerous, considering the”materials” used.

“I have a friend who works on the anthrax bacterium and during the anthrax incidents (in 2001), the FBI was in her lab checking to see” if the product used in the letters came from that lab.

“TIGR sequenced many of the pathogens,” Vary said

She and two scientists at TIGR applied for a grant to sequence PV361 which “went down in flames,” Vary said. Then she received two calls—one from a German lab that wanted her to help in the sequencing of another strain of B. meg. and another from TIGR, who wanted to try again to sequence her strain. They were interested, which resulted in Vary becoming one of the three P.I.s on the project.

“My job was to give them the strain, and they would do all the gene sequencing,” Vary said. TiGR gets most of the money, but $41,000 goes to NIU.

“It has now been sequenced—there are only a few gaps,” she said. ” The machine (computer) has done what’s called annotation (to determine where the genes are in the sequence and what they do).”

For those who lament that computers have completely taken over, they may take heart from the fact that the computer’s work now must be checked manually.

She had taken six faculty members and four graduate students to TIGR to learn how to use their software.

“Most of us will be doing the analysis this summer and fall,” Vary said.

“I spend most of the time on the computer putting sequences into a genetic bank of all sequences in the world, the NIH Gene Bank. When I do a search, it takes from 30 seconds to four minutes for the computer to respond, ‘Yes, there is a gene like mine, sometimes several.’”

“We will set up a web site at NIU and the whole B. meg sequence will be transferred to NIU from TIGR for us to do the manual analysis.”

Indicating some of the links that hold creation together, Vary said many times the bacterial gene is similar to genes in humans, dogs, mice, fruit flies and alfalfa.