By David N. Leff

When a lone serial killer goes to ground, law-enforcement elements organize a search party made up of local cops from the crime scene, county sheriffs, state constabulary, U.S. marshals and the FBI. Once they hunt down and catch the suspect, forensic DNA tests help nail down the culprit's identity, and evidence linking him to his victims.

Now a multinational posse of genomicists is hot on the trail of the world's largest-scale killer, most of whose victims are children. Their quarry is the mosquito-borne parasite, Plasmodium falciparum, which takes the lives of some 2 million people a year, most of them in the world's tropical areas.

While other task forces have been striving for decades to develop anti-malarial drugs and vaccines, the U.S.-UK Malaria Genome Consortium came into existence a few years ago to sequence P. falciparum's entire 24.6 megabase genome.

"The consortium," said genomicist David Schwartz, at the University of Wisconsin-Madison, "is funded by the U.S. National Institutes of Health, and Britain's Wellcome Trust plus the Burroughs-Wellcome Fund. The major sequencing efforts," he added, include labs from Stanford University; TIGR (The Institute for Genomic Research, in Rockville, Md.); and the UK's Sanger Institute. "Those people have divvied up the parasite's 14 chromosomes," Schwartz observed.

"The consortium's goals," he pointed out, "are first completely analyzing the genome, in terms of getting its sequence. That should take about a year from now, maybe a little bit longer. Then, secondly, making sense of that sequence."

Schwartz himself is making some of that sense at a pre-sequencing stage of the consortium's progress. He is senior author of an article in the November 1999 issue of Nature Genetics, titled, "A shotgun optical map of the entire Plasmodium falciparum genome."

"Optical mapping," Schwartz explained, "is a new technology, which colleagues and I invented and patented 10 or 11 years ago. It maps an organism's entire genome from single DNA molecules, provides reliable landmarks, and could ratchet up the race to decipher complete genomes - from food crops to human beings.

"One can picture optical mapping as an entire map of the United States," he suggested, "whereas conventional genome sequencing would be thousands of detailed maps of every city in the nation. Optical mapping data works in concert with high-resolution DNA sequence data, linking both together in a complete and seamless description of a genome."

Consortium laboratories, Schwartz told BioWorld Today, "are already incorporating our optical scanning of P. falciparum into their total-sequencing modus operandi. They are relying on us to do the optical mapping, and they do the sequencing."

Parasite's Map - From Bottle To Data

The 15 co-authors of his Nature Genetics report reflect the assembly-line procedure of optically mapping the parasite's genome. "At the U.S. Naval Medical Research Center's malaria program," Schwartz recounted, "Daniel Carucci and his colleagues were able to grow the single-cell parasite, put it into a bottle, then simply extract DNA from these bottled pathogens."

"Then he sent the DNA to us - just long strands, millions of bases in length. We simply pinned them down on glass surfaces, to which they stick through electrostatic forces. It's very much like rubbing a balloon on a wool sweater; then you're able to stick it to a wall. Basically, the DNA molecules stick to our glass surface, and elongate.

"Next," Schwartz went on, "we took two restriction enzymes, and cut the DNA strands. Wherever an enzyme recognizes its cognate site, it cuts the molecule. And we can see that it cuts because that's where a gap forms - visible enough so that we can see it through a light microscope. We have software that automatically goes in there and finds the cleaved fragments, and measures their mass, their size, according to how much fluorescence is associated with each fragment.

"When you have an ordered restriction map," he went on, "a single molecule that's been cut, it generates a series of daughter fragments, which constitute a single ordered restriction map. Then software puts together many such maps that have overlaps of commonality with one another, at least in part - and that did it. We then had a physical map of an entire P. falciparum genome, generated without clones or PCR or electrophoresis."

For purposes of genome sequencing, Schwartz pointed out, "these maps serve as a scaffold to tell you very concisely how to align small snippets of sequence with a whole chromosome. Also, to know if your sequence is correct, this is a way of error-checking it."

Anti-Malarial Drugs, Vaccines, Therapies?

"The fact that optical mapping can facilitate sequencing," Schwartz pointed out, "and be sure about it, provides the stuff that people are going to be looking at to develop new anti-malarial therapies, new vaccines, new drugs and so on. By comparing maps of hundreds of individual human genomes, for example," he added, "scientists could pinpoint the origin of genetic diseases, understand the complexities of trait inheritance, examine the process behind DNA repair. This is like the Periodic Table."

Having wrapped up P. falciparum - which took them five months - he and his co-authors are now tackling the genome of Trypanosoma brucei, the pathogen of African sleeping sickness. And he has just received a grant to take on the genome of rice, the world's No. 1 food crop.

"What we've been in the process of doing for the past three or four years," Schwartz said, "is trying to harden the optical mapping system so that it will have a very very high throughput, and be very cheap to do. Right now, we're looking for industrial partners to do that, because this sort of development work doesn't go that well in a university environment. Originally we got a lot of funding from Chiron and Novartis. So now," he concluded, "we're thinking about trying to put together our own company."