Health and Science: New DNA sequencing machine advancing genome research

Humans, check. Fruit flies, check. Honeybees, check.

No, this is not some weird Christmas shopping list, it's a list of the some of the organisms whose genomes have already been mapped out by scientists.

With scientists rapidly completing the decoding of the genomes of so many species, I wondered where the field of genetics is heading in the upcoming new year. Can firefly light illuminate the mysteries of the Neanderthals? Did the Neanderthals speak? What was their hair and skin color? Did they interbreed with modern humans or become extinct without leaving behind any kind of genetic legacy?

A new DNA sequencing machine that utilizes the firefly enzyme luciferase as one of its main features is helping scientists reconstruct the Neanderthal genome and tap the surface of unanswered questions about this ancient species.

Known as pyrosequencing, it uses flashes of light to determine a DNA sequence. The amount of light equals how many base pairs are incorporated into that sequence.

Dr. Clare O'Connor, assistant chair of Boston College's biology department, explained that because pyrosequencing is very rapid, it is only effective for stretches of about 100 base pairs at a time.

This makes it perfect for examining Neanderthal DNA, which has experienced fragmentation because it is so ancient.

So far about one million units of Neanderthal DNA have been analyzed, according to The New York Times article "New DNA Test is Yielding Clues to Neanderthals" by Nicholas Wade. Dr. Svante Paabo, the leader of this research project, estimates that the draft of the entire genome should be ready within two years.

Paabo had been searching for a source of Neanderthal DNA for over a decade. His main obstacle was finding uncontaminated DNA. According to O'Connor, this is not an uncommon problem.

Two of the major problems when working with ancient DNA are (1) contamination with modern DNA, and (2) chemical damage and fragmentation.

In 1997, Paabo finally successfully analyzed part of the mitochondrial DNA of Neanderthals.

His search for uncontaminated DNA involved evaluating 70 bones from various museums all over Europe, and turned up only one bone as a source of DNA that comes from the Vindija cave in Croatia.

Paabo hopes to find other Neanderthal bones containing usable DNA. Even if more is not found, he believes that the full Neanderthal genome should be able to be completed.

Once the Neanderthal genome is completed, scientists hope to begin other projects.

One project that would develop, according to The New York Times article, is to discover if the Neanderthals had language by evaluating FOXP2, their analogous version of the human gene for modern human language.

This gene underwent marked differences from when humans and chimps split evolutionarily.

If the Neanderthal version of the gene is closer to that of the chimps, then it would be unlikely that their language was similar to humans.

David Burgess, a professor in the biology department, and other researchers from Massachusetts' universities collaborated as part of an international conglomerate to sequence the sea urchin genome.

Burgess's group was responsible for decoding the genome of Strongylocentrotus purpuratus, a male California purple sea urchin.

The Human Genome Sequencing Center of Baylor College of Medicine and scientists at Cal Tech in Pasadena headed The Sea Urchin Genome Sequencing Project (SUGSP) Consortium.

For two years, 240 scientists in 11 countries analyzed the genome of this marine species.

The SUGSP was divided into teams; Burgess's group was responsible for understanding the sea urchin's cytoskeleton genome, which is in charge of cell division and cell movements.

The sea urchin's genome is of particular interest to scientists because of how humans share a common ancestor with the species.

Because of their evolutionary proximity to vertebrates, researchers can develop a greater comprehension of the evolution of genes responsible for encoding various cytoskeletal proteins.

"Understanding the genome will allow us to develop better experiments. Having sequence of genes of the protein [of interest] will allow us to make probes, such as antibodies, to affect the function of these proteins: with homologous proteins in other species the probes may not work across species," said Burgess.

Besides Neanderthals and sea urchins, what other genomic projects are out there?

Perhaps the most famous is the International HapMAP project. Started in 2002, the goal of the project is to develop a haplotype (the genetic make-up of an individual chromosome) map of the human genome that will describe patterns of variation in it.

O'Connor is hopeful that it will eventually simplify identification of the multifactorial origin of a disease, the multiple genes that are responsible for the onset of an illness.

"I think we're going to come away with a more complex understanding of human genomes," said O'Connor.

Alexis Mark is a staff columnist for The Heights. She welcomes comments at marka@bcheights.com.