Proceedings of the Third World Fisheries Congress: Feeding the World with Fish in the Next Millenium—The Balance between Production and Environment
Biochip Technology and Its Prospective Applications to Aquaculture
On 26 June 2000, the ambitious Human Genome Project, endowed by the governments of six countries (United States, United Kingdom, Germany, France, Japan, and China), declared that 97% (3,000 million base pairs [Mbp]) of the human genome sequence had been determined. It seemed probable that the complete Homo sapiens genome would be sequenced and the entire DNA sequence information gained by 2001. In 2000, the complete genomic sequence of 17 organisms, including bacteria Haemophilus influenzae (1.7 Mbp), Mycoplasma genitalium (0.6 Mbp), Escherichia coli (4.7 Mbp), Bacillus subtilis (4.2 Mbp), and Synechococcis spp. (3.6 Mbp); archaebacterium Methanococcus jannaschii (1.8 Mbp); eukaryote Saccharomyces cerevisiae; and fruit fly Drosophila melanogaster (100–150 Mbp) are already available (Goffeau 1997; Jordan 1998). At the same time, the genomic DNA of the worm Caenorhabditis elegans (–100 Mbp), the plant Arabidopsis thaliana (100–150 Mbp; Jordan 1998), rice, wheat, maize, mosquito, small mouse, pig, dog, cattle, chicken, and puffer fishes Fugu spp. and zebrafish Danio rero are being sequenced, and complete genome sequences will be obtained soon.
The genome age will change biology forever, providing blueprints for bacteria, fungi, plants, and animals. Whole genome sequences—the Holy Grail of structural genomics—will pave the way for functional genomics in the “postgenome” era. How to sufficiently use the unprecedented amount of DNA sequence information to study the function of genes and determine their worth has been the most important issue of this era.
Studies of functional genomics focus on uncovering the functions of each gene and understanding the mechanisms of how these genes shape organisms. The major goal of the Human Genome Project is to identify, sequence, characterize, and assign specific functions to all the genes spread throughout 3,000 Mbp of haploid DNA. The great challenge is to discern the underlying order and draw out the Biological Periodic Table of a biological system with 100,000 genes (Lander 1999). The Biological Periodic Table is not two-dimensional; it reflects similarities at many levels:
• primary DNA sequence in coding and regulatory regions;
• polymorphic variation within a species or subgroup;
• time and place of expression of RNAs during development, physiological response, and disease; and
• subcellular localization and intermolecular interaction of protein products.
However, the traditional gene-by-gene approach will not suffice to meet the sheer magnitude of the problem. It is necessary to take global views of biological process: simultaneous readouts of all components. Biochips offer the first great hope for such global views by providing a systematic way to survey DNA and RNA variation (Lander 1999).
A biochip is a silicon or glass microarray the size of a nail with of tens of thousands of different snippets of DNA or protein molecules that serve as probes for detecting the existence and quantity of fluorescence-labeled target molecules by specific molecular identification and binding, which can be determined by laser scanning and recorded by computers with a charge-coupled device (Figure 1). The main biochip is DNA chip, also called a DNA array, oligonucleotide microchip, or gene chip.