LANL team banking on bioinformation

Joel Berendzen, left, and a team from Los Alamos have developed new genome sequencing software called Sequedex.

Roger Snodgrass

Don’t blame your toothache on germs, says Joel Berendzen, who works in the theoretical division at Los Alamos National Laboratory and happens to play chamber music in his spare time.

“Instead, blame yourself for living a lifestyle that allows bacteria to make an honest living doing harmful things,” he said.

Berendzen sees the day when you’ll rinse and spit into a cup that will let you know confidentially how bad your breath is and whether you should rethink the date you planned that night. While you’re on the subject, the cup’s sensors might issue a follow-up report on your gingivitis and oral health in general, measure your progress, throw in some encouragement and then make a dental appointment for you with ticklers as reminders.

Berendzen works with a group of scientists at Los Alamos National Laboratory who have developed what they believe is an ideal tool for the oncoming biological age. The innovation is not the cup; that’s still down the road. The enabler is a software package called Sequedex, which is capable of rapid sequencing of a snippet of genetic material or multiple organisms from microbial communities.

Sequedex was one of three inventions by the laboratory that won an R&D 100 award this year from the leading research and development magazine. A journal article on the project just passed through peer review and was accepted for future publication in the open-access journal BMC Bioinformatics

The team claims their program, which runs on a laptop, is 250,000 times faster than the most commonly used approach — the Basic Local Alignment Search Tool (BLAST), which was developed for the Human Genome Project — and 50 times faster than the fastest commercial rival. At $2,000 per license, it’s also cheaper than the competition that runs from $3,500 to $11,000, according to the team’s entry form for the R&D 100 competition.

A recent announcement by the White House on new initiatives supporting the “bioeconomy,” estimated current revenues from bioinformation and industrial biology at $180 billion a year in 2010. Berendzen believes the biological revolution in the global economy will continue to advance, driven by limited energy supplies and resources and mounting health needs that will require both efficiencies and advances in the life sciences.

Health-based consumer products, such as a device for home-monitoring of oral care are possible avenues for the future, but Sequedex is expected to have a variety of far reaching applications — like cultivating the ideal algae for biofuel or helping doctors distinguish between a viral and a bacterial disease. Or on a larger scale, rapid analysis tools can be useful in monitoring environmental health or measuring climate effects. When people need to know what kind of organism is present in a particular sample of DNA and how the fragment functions in life, Sequedex answers the preliminary questions about what it is and what it does.

Berendzen and theoretical biologist Ben McMahon went to the Gulf of Mexico after the Deepwater Horizon oil spill to collect soil samples. They were looking for evidence of environmental impacts on the microbial communities, but also testing some of the boundaries for an oil spill analysis. “We saw differences,” said McMahon, ‘but it brought up a whole slew of interpretation problems.” The scientists found changes, but without a history of soil sampling that would provide baselines from before and during the earlier oil-drilling impacts, it was hard to draw a valid comparison. “So what you really want to do in some ways is sample in the Arctic now and then sample after there is a major oil spill” he said.

The software is a work in progress with a patent pending and a variety of approaches under investigation.

“We are starting to make contacts with venture capital,” Berendzen said. “We’re moving from being a research tool to something that would go into a doctor’s office.”

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