Down to the Sea on (Gene) Chips

By Hahn, Mark E. | Oceanus, September 1, 2004 | Go to article overview

Down to the Sea on (Gene) Chips


Hahn, Mark E., Oceanus


The genomics revolution is transforming the way scientists can study life in the oceans

A half-century ago, James Watson and Francis Crick (aided by Rosalind Franklin and Maurice Wilkins) discovered the double-helical structure of deoxyribonucleic acid (DNA). Other scientists soon showed how DNA-through a triplet code of nucleotide bases on the DNA "spiral staircase" and through ribonucleic acid (RNA) intermediaries-instructs cells to assemble essential lifesustaining proteins. These discoveries opened the door to a new understanding of life by revealing the genetic "blue-prints" that underlie the ability of organisms to grow, survive, and reproduce.

A revolution in biotechnology ensued, giving scientists methods to isolate and identify genes, make millions of copies of them, and determine their sequences of nucleotide bases. Together, the accelerating pace of biotechnological advances and the exponential increase in DNA sequence information ignited an explosion in molecular biology and led to the emergence of a new field: genomics. These advances were initially applied in the biomedical arena, leading to new information on the genes responsible for heritable diseases, the molecular signatures of cancer cells, the biology of human pathogens, and genetic factors that influence an individual's sensitivity to drugs or toxicants.

Now, the genomics revolution has reached the oceans. New genomic techniques are being used to find previously unknown life forms in the oceans; to learn how species, and genes themselves, evolved over Earth's long history; to understand the genetic tools that allow species to adapt to diverse and often harsh environments; and to investigate species' responses to pollutants. Genomics gives marine scientists powerful new ways to address age-old questions about life in the oceans.

What is genomics?

Genomics is more than simply determining the sequence of nucleotides in an organism's genome (the entire set of genetic information contained within a cell's DNA). It is a new approach to questions in biology, distinguished from traditional approaches by its scale. Rather than studying genes one by one, genomic approaches involve the systematic gathering and analysis of information about multiple genes and their evolution, functions, and complex interactions within networks of genes and proteins.

Genomics has two branches. One is structural genomics-studies of how genes and genomes are organized and how that varies among individuals, populations, and species. It includes characterization of the sequences of DNA nucleotides that encode proteins, as well as the DNA found between and within genes that does not code for proteins.

Using structural genomics, we can compare DNA sequences among individuals of a species to reveal minor variations in the DNA nucleotide code at certain positions in the genome, called "single-nucleotide polymorphisms, " or SNPs (pronounced "snips"). These SNPs can be responsible for genetic diseases, or for hypersensitivity or resistance to drugs or toxicants.

By comparing DNA sequences among species (called "comparative genomics"), scientists can identify changes in genomes that have occurred as species evolved. They can also begin to determine the function of specific DNA sequences shared among different species.

The second branch is functional genomics-the study of the RNA and proteins produced by genes (referred to as "gene expression"), and how these molecules interact to carry out cellular processes.

Among the most elegant and widely used tools of functional genomics is the microarray, or "gene chip" (see figure), which became available less than a decade ago. By using microarrays to simultaneously measure the amounts of hundreds or thousands of specific RNAs contained in cells or tissues, biologists can "see" what cells are doing and how they are responding to particular environmental conditions.

Genes reveal marine biodiversity

Though the genomics revolution immediately swept into biomedical research, its entrance into oceanography and marine biology lagged. …

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