Inside this Issue

• Bioinformatics
• Next Generation Tsunami Modeling
• Space Weather Forecasting
• Navigating Information Space
• Imagining Without Constraints
• Internal Tides of the Ocean
• High-Flying at Mach 8

Story by Jenn Wagaman

DNA is often described as the building block of life. It is the structure that determines anything from the color of your eyes to the diseases that you might pass on to your children. Although there is a high degree of commonality between related species at the DNA level, each individual has a unique collection of molecules that make them who they are.
The biotechnology industry was given its start through Nobel Laureates James Watson and Francis Crick’s discovery of the unique double helix structure of the DNA molecule and how genetic information is passed on to generations through this structure. Watson and Crick showed that information is stored in a macromolecule that naturally works by its ability to seek out and form associations with similar molecules in cells, using a basic physical process called base pairing. The double helix, and base pairing, explained gene replication and that DNA is the primary genetic substance.
Many human diseases are related not only to a human’s genetically pre-disposed risk resulting from inheritance, but also to mutations that occur at different frequencies in the molecules that store underlying genetic information. Since these diseases can seriously affect the human condition, our economy, and our quality of life, governments invest significant funds in research in this area.

In turn, researchers such as those at the University of Alaska Fairbanks’ (UAF) Institute of Arctic Biology (IAB) and the Arctic Region Supercomputing Center (ARSC) seek to understand how organisms deal with the demands of their natural environment—as shown by the discovery of many remarkable adaptations that organisms have acquired living in the extremes of Alaska. Many of these adaptations have significant biomedical relevance in areas such as stroke, cardiovascular disease, and physiological stress. Somehow, our wild counterparts have adapted to severe environmental demands over long periods of time. Simultaneous to this research, scientists are also investigating the molecular changes that can be observed in humans as a result of their environment, such as through smoking or exposure to contaminants.

This push in research has resulted in the integration with life science research of approaches from many fields, including engineering, physics, mathematics, and computer science. One of the most well-known results of this is the Human Genome Project. Through this project, researchers were able to design instruments capable of performing many different types of molecular measurements so that statistically significant and large-scale sampling of these molecules could be achieved. Now, biomedical research is producing data that show researchers that things are not always where they expected them to be, while at the same time researchers are at a rapidly expanding phase of discovery and analysis of large, highly repeatable measurements of complex molecular systems.

One of the more important and generally applicable tools that has emerged from this type of research is called DNA microarrays, or DNA chip technology. This technology uses the fundamentals of Watson and Crick base-pairing along with hybridization to customize applications of DNA microarrays to simultaneously interrogate a large number of genetic loci (those locations on the DNA molecules that have differing biological roles). The result of this type of analysis is that experiments that once took ten years in thousands of laboratories can now be accomplished with a small number of experiments in just one laboratory.

As microarray technology continues to improve and diversify, it requires many measurements and significant experimental design to address different problems. The involvement of statisticians is helping guide these experiments and is making the application of these technologies more fruitful. This has made it even more important for research to begin focusing on the analysis of the DNA samples themselves being interrogated on the DNA chips. Computer science algorithms have also provided some very important findings in this area, and can be of significant help because DNA is so rich in data. DNA is made up of four base types: cytosine (C), thymine (T), adenine (A), and guanine (G). But despite DNA’s alphabet being only four letters, the full text of human DNA is three billion characters long.