by Sharon J. proctor, Ph.D
Photography by Greg Ehlers
Dr. Fiona Brinkman, award-winning leader
in bioinformatics research, encapsulates a rare combination of computer
programming and microbiology.
Dr. Fiona Brinkman’s campus office is nearly empty!
There are virtually no journals, reports, or other papers on her
shelves. Her desktop is clean, holding only framed family photos.
Yet she teaches, does research, oversees graduate students, heads
up projects, reads scientific articles, and has a family. What gives?
She points to her PC. “I prefer receiving everything online.”
An appropriate answer – as Brinkman is one of North America’s
top young researchers in the field of bioinformatics (the use of
computers to solve biological problems). She uses a powerful PC,
linked to a network of other computers, to study DNA and protein
sequences in bacteria that cause disease.
Brinkman is a microbiologist and a computer scientist –
a rare combination. “My parents were both involved in science
(chemistry). I became interested in living things early on, because
I was outdoors a lot as a child. Then, when I was 14, my mom bought
a VIC20 computer and I started playing computer games. I became
familiar with all aspects of the computer and programmed my first
simple computer game a year later.
“In college I majored in general biochemistry, for it allowed
me to study biology, chemistry, physics, math, and computer science.
I was drawn to microbiology during my undergraduate years.”
In graduate school, while she was working on a PhD in microbiology,
her interest in computers grew.
“I realized what a powerful tool a computer could be for studying
bacterial gene sequences.” Today, she pursues her two favourite
subjects in SFU’s department of molecular biology and biochemistry.
Bioinformatics is a new discipline. It combines biology, biochemistry,
and computer science. In Brinkman’s case, she’s using
the computer to gather, store, organize, and analyze enormous amounts
of data relating to bacterial gene sequences and protein sequences.
Her background in biology enables her to relate the computer results
to real life. “Bacteria aren’t actually out to get us,”
she notes. “They’re one-celled opportunists. Why sit on
a handrail with fluctuating temperatures and no food, when one can
enjoy a warm, constant temperature in a nutrient-rich human being?”
Bacteria are everywhere, including on and in our bodies. Some have
always caused disease. Others have become a problem only recently.
Most are totally harmless. “We have more bacteria in us than
human cells,” says Brinkman. “And there are more bacteria
in one person’s mouth than there are people on Earth.”
Some bacteria are kept in check by our immune system. Others quietly
grow on the surface of our cells, minding their own business.
Certain disease-causing infectious agents have come to us from animals.
The AIDS virus, for instance, came from monkeys, SARS from civet
cats, and tuberculosis (possibly) from Pleistocene bison. Cholera
we get by drinking contaminated water. “Actually cholera bacteria
don’t appear to like living in us,” explains Brinkman.
“They get our intestine to release water and flush them out
(causing fatal diarrhea).”
Brinkman's goal is to develop a through understanding
of gene and protein events important to disease-causing bacteria.
Bacteria can also become human pathogens through “gene exchange.”
This occurs when one bacterium passes a few genes to another. Mostly
it’s harmless. But sometimes a novel gene or two can give individual
bacteria the ability to attack our cells and cause disease. As well,
gene exchange can lead to antibiotic resistance. If antibiotics
are not taken properly (correct dose for the full length of prescribed
time) a few bacteria may survive the inadequate treatment and become
resistant to the drug. They pass this resistance to their offspring.
The way Brinkman studies bacteria is reminiscent of how large store
chains study shoppers’ buying habits. You’ve seen, of
course, the ubiquitous computerized cash registers. They record
what you buy, the time, date, cost, and how you pay. If you have
a special store card, this information is linked to your name and
address. All is then added to data accumulated from hundreds of
thousands of other transactions. Computer analysis can find hidden
trends and patterns in this mass of data. And it can create models
that predict where, when, and which people are likely to buy new
products. This extraction of predictable patterns from large amounts
of data is called “data mining.”
Brinkman uses data mining to study how bacterial genomes work. A
genome is the biological blueprint of a species. “It’s
like an encyclopedia,” she says. “Each word in it is a
gene.” In real life, of course, genes are made of DNA and strung
together in long chains. A gene is a specific word-like sequence
of chemical “letters” (nucleotides). It oversees the production
of a specific protein that
plays a vital role in the life of the cell. Proteins, too, are sequences
of chemical letters (amino acids). In fact, protein sequences reflect
the “letter” sequences of the genes that produce them.
Brinkman’s goal is to develop a thorough understanding of gene
and protein events important to disease-causing bacteria.
Through computer analysis of gene and protein sequences, she and
her team are learning what goes on inside disease-causing bacteria.
One project focuses on the mechanisms and consequences of gene exchange
– how and when it occurs, its effect on bacterial proteins,
and its role in creating new strains of bacteria. Another focus
is the outer membrane of individual bacterial cells.
Vaccines are often made up of outer membrane proteins. Vaccines
train our immune system to recognize these proteins and
to attack the associated disease-causing bacteria. Previously, identifying
such proteins in the lab was slow. Brinkman is now speeding up this
process, using her computer analyses (the most precise worldwide
to date) to identify them. This computer-based approach is cutting
decades from the time it takes to develop a new vaccine.
And that is being noted. Brinkman’s recent awards include a
Science Council of B.C.’s Young Innovator Award and a Michael
Smith Foundation for Health Research Award for career achievement,
and the Massachusetts Institute of Technology named her one of the
world’s top 100 young innovators (see aq, Nov. ’02).
In addition to doing research, teaching classes, and advising students,
Brinkman is a sought-after conference speaker. How does she balance
work and family?
“I have a work-hard, play-hard mentality,” she answers.
“I concentrate on work at work, and on family at home.”
That’s not entirely true, however. Her computer desktop, which
displays her program icons, features a large photo of her happy,
smiling one-year-old! aq
