Sequencing Success

UF researchers have stayed ahead of the biotech curve for 25 years with help from the Interdisciplinary Center for Biotechnology Research

by Donna Hesterman

Doug and Pam Soltis began their journey as botanical researchers in the 1980s when biotechnology was still young.

The human genome had not yet been sequenced, but the first genetically engineered “human” insulin was on the market, and researchers working on techniques for recombining segments of DNA had just won the Nobel Prize in chemistry.

“Doug and I were the DNA sequencing facility back then,” Pam Soltis says of their work at Washington State University. “It took us 6 months just to get eight sequences that were maybe 1,600 bases long.”

Today she’s a distinguished professor of molecular systematics and evolutionary genetics at the Florida Museum of Natural History. Her husband, Doug is a distinguished professor in UF’s biology department. And the two can now sequence millions of DNA bases in a single day — thanks to a multi-million-dollar facility at UF called the Interdisciplinary Center for Biotechnology Research.

“Most of what we are doing now, we could never have dreamed possible when we were getting started,” she says. “To think about how much things have changed over the span of our career is really mind-boggling.”

ICBR is housed in the Cancer and Genetics Research Complex south of UF’s main campus. A shared resource available to all UF researchers, it has all the latest equipment for sequencing DNA, analyzing proteins, cellular imaging and data management.

A staff of 60 experts specializing in four different branches of biotechnology runs the facility.

Their mission?

To make biotech laboratory support available to researchers in every college of the university — even those that aren’t traditionally associated with biotech.

“Honestly,” Pam says. “It’s one of the reasons we came here.”
 

Common Thread

Connie Mulligan, professor of anthropology and an associate director of the UF Genetics Institute, has used ICBR services in her research for more than a decade. One ongoing project began in 2007 when she travelled to the deserts of Yemen to study what was thought to be the migration route used by prehistoric man on his way out of Africa.

She used the traditional tools of anthropology — oral histories and artifacts — but she also used DNA analysis to look for patterns of relatedness that could tell her about the ancestral roots of the Yemeni people. Standard DNA sequencing techniques at ICBR provided her with an inexpensive data set that she could not have produced in her own lab.

DNA analysis is now a staple of Mulligan’s anthropological work. She and her students are currently using DNA analysis to examine the effects of prenatal maternal stress on unborn babies.

“We’re conducting that research in the Democratic Republic of the Congo,” she says. “Where ongoing civil war and the use of rape as a weapon has created one of the most stressful environments for mothers imaginable.

“We know that maternal stress affects the health of an unborn child,” Mulligan says. “But we don’t know the physiological mechanisms that translate that stress into problems for the fetus.”

She suspects that signals for gene expression in the developing fetus are modified by the mother’s physiological responses to stress. The changes can result in an increased risk for disease later in the child’s life.

ICBR staff scientists analyze the DNA in blood samples Mulligan and her students collect at a women’s clinic in the Democratic Republic of the Congo. Next-generation sequencing techniques and cutting-edge instrumentation enable ICBR to measure the biochemical status of more than 500,000 sites throughout the genome in each of her samples.

Mulligan and other scientists from all academic disciplines at UF are able to capitalize on ICBR’s expertise because of the center’s un

ique standing as an independent entity within the university.

“ICBR is part of the Office of Research,” says Rob Ferl, ICBR’s director. “We don’t belong to any one department or college at the university, and that keeps us available to everyone.”

By everyone he means researchers from any college at UF, scientists from various governmental agencies across the state and a handful of researchers working for privately owned businesses that pay a fee for ICBR’s services.

 

Ginger Clark, the scientific director for genotyping at ICBR, has probably provided laboratory services for the 

most diverse group of clients. She’s known for her work in wildlife forensics and has sequenced DNA from endangered sea turtles, timber rattlers and black bears in the course of her duties.

When she came to ICBR as a student worker in 1992, she mostly provided mitochondrial DNA analysis for biologists doing research on various types of wildlife, including venomous snakes. However, when state officials started allowing the sale of farm-raised exotic venison in Florida grocery stores, her phone began to ring for another reason.

Florida Fish and Wildlife Conservation Commission officers wanted to know if Clark would be able to tell if meat in the grocer’s freezer was the farm-raised venison or local white-tailed deer. White-tailed deer are a carefully managed resource in the Southeast, and the officers were keen to make sure that poachers didn’t hunt them illegally for sale to retail grocers.

Of course, Clark was able to help them and soon began analyzing DNA from other animals, helping officers bust poachers as well as restaurateurs who served mystery meat to unsuspecting customers.

Today Clark spends much of her time generating genetic profiles of plants and animals being studied by ecologists. She also provides DNA analyses on genetically modified mice that are used as test subjects in medical research.

“It used to be that there was a steady stream of wildlife officers walking in here with little brown bags of God-knows-what,” she says. “Today it’s mostly medical researchers bringing in samples from their study subjects.”

 

Human Hope

Indeed, human medicine has been a major beneficiary of biotech’s boom over the last quarter century. Gene therapies and personalized medicine that were the stuff of science fiction are now a reality, and UF’s medical researchers have played a big part in advancing those innovations.

Maureen Goodenow, a professor of pathology at UF, uses the labs at ICBR to sequence and analyze DNA for her research on HIV/AIDS. The analysis gives her a profile of how the virus changes as it moves through a population and even how it mutates over the course of a lifetime within the cells of an AIDS patient. That information, she says, is crucial for developing treatments and strategies to prevent its spread.

John Aris, an associate professor in anatomy and cell biology at UF, studies cellular aging. He says that he has probably worked with staff in every division of the ICBR over the course of his career.

He is interested in how genes control biological processes that effect longevity in cells, the building blocks of every living organism. He experiments with yeast cells because they have a relatively simple genetic makeup and a short lifespan that allows for observation over many generations of cells.

“To make a hybridoma, we put about 100 million disease-fighting immune cells from an immunized mouse together in a tube with about 100 million specially engineered tumor cells and zap them with electricity.”
—Linda Green

 Aris’ experiments require the use of special antibody-producing cells called hybridomas that are created in an ICBR laboratory.

“To make a hybridoma, we put about 100 million disease-fighting immune cells from an immunized mouse together in a tube with about 100 million specially engineered tumor cells and zap them with electricity,” says Linda Green, manager of the hybridoma laboratory at ICBR.

She and her staff sift through the fused concoction to select the most viable hybrid cells and then spend the next 3 to 4 weeks watching and caring for them as they develop.

The resulting hybridoma cells can live forever and secrete antibodies that can be used to target certain proteins in other organisms, depending on what was used to immunize the mouse.

The ICBR hybridoma laboratory has developed hundreds of different kinds of hybridomas over the years and maintains an impressive array of frozen hybridomas that have been used to research population health issues in everything from manatee to flying foxes.

In human medicine, the antibodies secreted by hybridoma cells are used to treat and diagnose disease, but Aris uses the mouse version as sort of a tracer to help him ferret out biological processes that cause his yeast cells to age and die.

He relies on the proteomics division at ICBR to analyze the proteins at work as the cell goes through its various stages of decline during the normal aging process.

Proteomics is a relatively new technique of microanalysis that uses mass spectrometers to identify the proteins present in a sample the way a sequencer reveals genetic code.

Think of it as a quality assurance check that verifies the instructions coded in DNA are carried out as written.

The proteomics lab at ICBR houses an assortment of multi-million-dollar mass spectrometers engineered to sift through organic materials and identify the protein ingredients. Proteomics division Director Sixue Chen, an associate professor of biology, uses the equipment in his research with tomato and canola plants. He studies the function of plant stomata, the tiny pores on leaves that control gas exchange between the plant and the atmosphere.

“Leaves are protected by a waxy coating on the epidermis, so stomata are like a gateway into the plant’s body,” Chen says. “We are looking for molecular switches that can control that gateway.”

The gateway allows carbon dioxide, a necessary ingredient for photosynthesis, to enter the plant. However, while the gateway is open, precious moisture can escape and dangerous pathogens can enter.

Chen says that protein analysis is the perfect tool for his research because the new generation of technology allows him to monitor how proteins change during different stages of stomata operations.

Older tools for protein analysis were too slow to keep track of a changing protein landscape in real time.

“In the old days we could only get a series of snapshots of one or two proteins at a time,” he says. “But now we can track what hundreds of proteins are doing at once.”

It is proving to be a useful tool for research across many disciplines. Chen is proud of the fact that the proteomics facility has been used by faculty to analyze a wide variety of samples, including viruses, manatee neurons, frog eggs, cow embryos, cancerous tumors and human saliva.

“We’ve focused on genetic analysis for a long time,” Chen says. “Now we are realizing that DNA and RNA do not always translate into the proteins that we expect.”
 

Crunching the Numbers

Proteomics, like DNA analysis, generates bigger and bigger data sets as the machines used for research grow in sophistication. It’s creating a challenge for biotech research groups everywhere, according to Aaron Gardner, ICBR’s cyberinfrastructure director. His job for the past 11 years has been to make sure that ICBR stays ahead of the game.

“If you think about data storage as a water reservoir, we’ve gone from the capacity to contain the Great Lakes to the capacity to contain the world’s oceans with room to spare.”
— Aaron Gardner

“In 2000, we could fit a year’s worth of experimental results on a central computer that had less computational power and storage space than today’s average smartphone,” Gardner says. The requirements for storage have grown dramatically since then. “If you think about data storage as a water reservoir, we’ve gone from the capacity to contain the Great Lakes to the capacity to contain the world’s oceans with room to spare.”

That capacity to adapt and grow with the times is at the heart of ICBR’s success over the last 25 years, says ICBR’s director.

“One of the things we’ve been able to do here is maintain a corps of dedicated experts who keep a finger to the wind and make sure that we have the latest and greatest tools available to support our researchers,” Ferl says. “We keep good people here because we believe that a sound intellectual core is every bit as important as having the latest gear.”

Ferl is quick to acknowledge that ICBR’s might is an inheritance from a previous generation — a small group of faculty who fought hard in the 1980s to convince the university to “go big” when it came to biotech.

“The investment has paid off,” he says. “ICBR has an impressive record of enabling 25 years of truly interdisciplinary research. But more importantly, we know we’re ready for the next 25 years.”

 

Rob Ferl
Director, Interdisciplinary Center for Biotechnology Research
(352) 273-8029
robferl@ufl.edu
Related website:
www.biotech.ufl.edu