a special program of the National Emergency Medicine Association (NEMA)
Transcripts: 548.4 and 548.5
Week: 548.4 Guest: Dr. Mark Boguski, contributing developer, NIH Gene Map Project Topic: Bio-informatics speeds research, Part one of Two Producer/Host: Steve Girard
NEMA: The melding of biology and computer technology is a wonder in its beauty and productivity. Today, we're talking with Dr. Mark Boguski, and medical doctor with a Ph.D. in molecular biology...one of a group of people working within a special biotechnology branch of the National institutes of Health in Washington, D.C. And it's called the National Center for Biotechnology Information...or NCBI....
BOGUSKI: ...And it's devoted to, not only collecting biotechnology information in the form of DNA and protein sequence data worldwide, but we also distribute it and develop tools that allow researchers and the public to gain access to it. In addition to providing this database service function, we also have a research group, which I'm a member of, that does research into what we call computational molecular biology...also sometimes known as Bio-informatics.
NEMA: When you're trying to put together a document as complex as one describing the gene structure in our cells, the computer is the key unlocking greater progress...
BOGUSKI: You know the first place to look when you're contemplating a new research project is computerized databases, that often times you could save yourself a lot of work, or come up with things you didn't know about before, just by searching the on-line databases. For instance, Gen-Bank, the largest, most comprehensive public DNA sequence database in the world, which NCBI builds and produces, has about a million sequences in it from about 18 thousand different biological organisms.
NEMA: Scientists around the world are using their computers to come up with information on their own gene sequencing projects...do they use the same databases...do they share what they find with a central database such as GenBank?
BOGUSKI: There are counterparts of Gen-Bank both in the United Kingdom and Japan. So, these three sites gather data from all over the world, and then we synchronize our collections on a nightly basis, so at any one point in time, data is flowing into these nodes', if you will, but it's immediately made available to the other partners. It was realized very early on when DNA sequences started to become plentiful, that it really would have an impact if it was available at a centralized location that everyone would have access to it, and that everyone who was doing this kind of research contributed to it.
NEMA: You were telling me a story about a project looking into a rare disease called ataxia telangictasia, which alerts a doctor to a carrier's predisposition to certain other diseases...
BOGUSKI: I was talking to the principal investigator on the project, a scientist in Israel named Yosi Shiloh, and he told me that from the time he set out to clone the a-t gene, to the time he got a DNA sequence, it took him 18 years to do that. However, once he had the DNA sequence in hand, he was able to figure out its probable function in only five minutes, by sending that sequence over the Internet from Tel Aviv to our computers in Bethesda, and receiving a report back from us, literally in minutes, showing him what other previously determined DNA sequences it was similar to, and therefore what its presumed function was. So, these kind of discoveries occur every day, in fact, Gen-Bank services on the order of 25 or 30 thousand of these homology searches a day.
NEMA: Dr. Mark Boguski of the National Institutes of Health...he says a link from Gen-Bank sends a researcher right to the Medline database at the National Library of Medicine for information...progressing research on genetic traits and problems. I'm Steve Girard.
Week: 548.5 Guest: Dr. Mark Boguski, contributing developer, NIH Gene Map Project Topic: Gene mapping-understandable/ accessible to everyone- Part Two of Two Producer/Host: Steve Girard
NEMA: I always wondered, when I looked at ancient maps, how they figured out how to put the mountains, plains and oceans in perspective to make an accurate tool for travel and exploration. Well, I've got my thinking cap on again, as I gaze at the newly released gene map at the National Institutes of Health Internet site. We're with Dr. Mark Boguski of the NIH...a molecular biologist working on mapping out the genes responsible for the traits and tendencies of our bodies and health...
BOGUSKI: There are somewhere between 50 thousand and 100 thousand human genes, and we will, by the year 2005 or so, know all those genes, and exactly where they are in our gnome, or arranged on our chromosomes. However, because of a historic convergence of rapid sequencing technology, and rapid mapping technology, we were able to put together kind of an intermediate gene map of the gnome, containing 16 thousand genes, or perhaps 20% of the total...which is being used as we speak by gene hunters all over the world, in attempting to isolate the genes responsible for human disease. Anyway, this gene map was a remarkable project, because it brought together 104 scientists from five countries on three continents, and about 18 different scientific institutions...using the Internet and world wide web technology to collaborate on a global scale.
NEMA: Seems what was once miraculous is now becoming commonplace...
BOGUSKI: What biotechnology has allowed us to do, combined with computer technology, is to dramatically speed up this process, and make it more accurate at the same time. So, for instance, when this gene map project got started, at the end of 1994, there had previously been mapped about five thousand genes, but these had been mapped over the previous 20 years with various, different kinds of technologies that differed in accuracy and precision. So, in the course of only 18 months after that, we were able to triple the number of genes mapped, and place them with high accuracy on a common framework.
NEMA: It seems part of the reason behind the release of the partial gene map to the general public, to educators, and students of all ages is to get them more familiar with the entire field of genetics....with likely benefits to the field down the line....
BOGUSKI: The construction of this gene map is very special, because it allows anyone to take a look at the gene map, or our world wide web page behind it, and get the big picture. So, for instance, though we've mapped 16 thousand or more genes on this map, we've picked 50 or so genes to illustrate in more detail, representing different aspects of biology or human disease, that common people get. And anyone from a cutting edge scientist, down to a middle school student can appreciate this. In fact, about three days after the gene map was published on the world wide web, we got an e-mail from a sixth grader on Long Island who told us that, for the first time, he really had an idea of what the gnome was all about, and they thought this was magnificent. Now, they spelled magnificent wrong, but the point is that this kid, who's 11 years old, was able to log into the world wide web from his home computer, and have a snapshot of the entire human gnome at a glance, but also able, using this Internet site, to navigate right down...with a few mouse clicks...to the actual underlying raw data that a cutting edge scientist would use.
NEMA: Dr. Mark Boguski of the National Institutes of Health...he's looking forward to seeing how students make use of the gene map, how educators use it in their courses, and how the public taps into it to get an idea of what this is all about. Check it out yourself at the NIH Internet site, use your search engine, or go to www.nih.gov. I'm Steve Girard.