Monday, October 27, 2008

The Battle Against Viruses Heats Up

Viruses are nasty opponents, as anyone who has followed the battles against influenza, SARs and HIV/AIDS can attest. They are diverse and in many cases evolve at rates that confound efforts to contain them. Anyone who has gotten a flu shot, and then came down with the flu a few months later because the “strain” of virus that the vaccine was not the same as the “strain” that they were infected with, knows just how fast viruses can evolve. In many cases, medical professional never really know which virus has caused the symptoms in their patients, and this complicates treatment and often leads to the misuse of antibiotics, which, of course, are never effective against viruses.

At the ScienceWriters 2008 New Horizons in Science meeting at Stanford University (sponsored by CASW) this week, Dr. Joseph DeRisi of UCSF presented an interesting talk on his research to develop a new form of “chip” as a diagnostic tool for identifying the viral contributions to diseases. Gene chips are often used by molecular biologists to determine the relationship between a gene and an observed condition. Dr DeRisi's work takes this approach one step further.

What is interesting here is Dr. DeRisi’s application of evolutionary genomics to his work. Like microbiologists, virologists recognize that they have only identified a small fraction of the diversity of viruses that are out there in the natural world. Despite advances in sequencing technology, the ability to sequence every virus in a given environment, such as a fecal or nasal sample, is still not cost effective. However, what Dr DeRisi has done is to develop a “viral chip” that contains not the entire sequences of every virus, but rather the sequences of key genes that are evolutionarily important to certain families of viruses. When one of these viral chips is exposed to a sample, a computer program determines the level of similarity between the DNA (or RNA) in a virus and the sequence on the chip. For previously unknown viruses, this can allow a quick classification of the virus to a certain group, and has been proven to be very successful by Dr. DeRisi’s team in diagnosing diseases for which no known cause could be determined by diagnostic tools.

Furthermore, Dr DeRisi has proposed making these chips available at cost to the medical community through a non-profit organization. The availability of a new technology at an inexpensive cost would represent an important new development in the war against viruses, and would rapidly generate an increase in data for public health officials.

Additional Links

DeRisi Lab at UCSF

Saturday, October 25, 2008

Fruit Flies Enter the Political Battle

The political fray has entered into the world of genetics, and as usual, our politicians have no real idea what they are talking about. In an October 24th speech about children with special needs, Sarah Palin, the Republican nominee for Vice-President, made the following statement about funding for IDEA, or the Individuals with Disabilities Education Act.

“This is a matter of how we prioritize the money that we spend. We've got a three trillion dollar budget, and Congress spends some 18 billion dollars a year on earmarks for political pet projects. That's more than the shortfall to fully fund the IDEA. And where does a lot of that earmark money end up? It goes to projects having little or nothing to do with the public good -- things like fruit fly research in Paris, France, or a public policy center named for the guy who got the earmark. In our administration, we're going to reform and refocus. We're going to get our federal priorities straight, and fulfill our country's commitment to give every child opportunity and hope in life” (Oct 24, 2008 speech)

There is no doubt that more money needs to be spent on research and education of people with disabilities. However, the assumption here is that fruit fly research is a waste of time and money. Nothing could be further from the truth. The simple fact that we have an understanding of genetics can be traced back to Thomas Hunt Morgan and the first use of fruit flies.Since then, four Nobel Prizes, including one to Thomas Hunt Morgan (1933), have gone to "fruit-fly" researchers. Obviously the scientific community values the contributions of the fruit fly to the study of genetics.

The fruit fly Drosophila melanogaster has around 19,000 genes. In humans, if a disease is linked to a specific gene, there is around a 70% chance that a similar gene exists in Drosophila. Drosophila is a model organism for the study of many human-releated diseases, including behavior, aging disorders, Parkinson's, and Alzheimers

Research into Drosophila genomics paved the way for the Human Genome Project. In other words, research using fruit flies, and other model organisms such as the mouse, nematode (C. elegans), and weed (Arabidopsis thaliana) are critical towards our understanding of the molecular world of inheritance and disease.

Time to get some Straight Talk. We owe thanks to geneticists who use this model organism, not ridicule.

Additional links:

A Brief History of Drosophila’s Contributions to Genome Research

A Systematic Analysis of Human Disease-Associated Gene Sequences In Drosophila melanogaster

Homophila: human disease gene cognates in Drosophila

Thursday, October 9, 2008

2008 Nobel Prize in Chemistry

The Nobel Prize in Chemistry has been announced, and this year, three scientists received the Nobel Prize for their work on green fluorescent protein (GFP).The three were Martin Chalfie (Columbia University), Roger Y. Tsien (UC - San Diego) and Osamu Shimomura (Marine Biological Laboratory, Woods Hole, MA). Anyone who has watched the Discovery Channel has seen the images of jellyfish glowing in the depths of the ocean. These scientists not only isolated the fluorescent protein from the jellyfish Aequorea victoria, but found a way to link it to an antibody to identify other proteins in a cell. When the cell is exposed to a certain wavelength of light, the tagged protein fluoresces, showing the location of the tagged protein.

Aequorea victoria

An image of a GFP labeled cell from the website of
Dr. Robert S. McNeil at the Baylor College of Medicine

As an interesting coincidence, I had the opportunity yesterday to attend a seminar at Appalachian State University given by Dr. John Henson of Dickinson College, PA. His area of expertise is cell biology, and specifically the structure and function of the cytoskeleton in sea urchin cells. What made his work truly impressive were the images. The detail and resolution that the GFP provided in the images was astounding. I can't imagine Dr Henson being able to present his findings without the use of GFP. I am sure that researchers and educators around the world would agree that Nobel Prize in chemistry was justly awarded.

Additional Links:

New Scientist's slideshow of how GFP has been used in research.

Announcement from the Nobel Foundation.

Tuesday, October 7, 2008

Good News, and Old News, about HIV

There were several important announcements in the HIV/AIDS battle this week. First was the awarding of the Nobel Prize in physiology or medicine to two French virologists,Françoise Barré-Sinoussi and Luc Montagnier, for discovering that the HIV virus causes AIDS. The side story here is the controversy that the American scientist Robert Gallo is credited by some as being the "first" to discover the virus. "First" is very important to scientists, therefore, there have been some pretty heated exchanges between Montagnier and Gallo in the past. If you are interested in some good drama, there are some decent books out there on the subject, including opposing views written by both Gallo and Montagnier.

The Nobel committee has attempted to end the dispute by announcing that Montagnier was the discoverer, a fact that is widely accepted by the scientific community, but given that there is no love lost between the Americans and the French, it is doubtful that this will die down soon.

The second announcement was that the HIV virus is probably much older than we originally thought. A discovery at the University of Arizona by Dr. Michael Worobey backs the date that the virus jumped from chimps to humans sometime around 1900 - at least 30 years earlier than originally thought.

This should not be treated as some sort of background story. In fact, it is probably the most important, and under-reported, story of the week. If you take a look at the map from the CDC below, you can see that the AIDS pandemic is showing no signs of abating.

By understanding when the virus actually made the jump from chimps to humans, we can get a better grasp on its rate of evolution. One of the biggest obstacles to the development of effective HIV vaccines has been the rapid mutation rate of the virus. As a virus mutates, it evolves, or changes, its associated proteins. Vaccines frequently target the unique proteins on the surface of a virus. Without an understanding of how this virus is continuing to evolve, the development of a vaccine could actually create more harm than good, since vaccinated people may feel that they are "safe" and can return to unsafe sexual practices and other risky behaviors. Worobey's work should provide some important insight into how HIV evolves. We should be seeing some interesting developments in the near future stemming from this discovery.