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MOLECULAR BIOLOGY IN MARINE SCIENCE: SCIENTIFIC QUESTIONS, TECHNOLOGICAL APPROACHES, AND PRACTICAL IMPLICATIONS
bacterial DNA polymerase and specially constructed oligonucleotide primers to replicate specific DNA sequences in vitro. From as little as a single molecule of a target DNA sequence, enough material for standard analytical procedures such as RFLP analysis, gene mapping, DNA hybridization, DNA fingerprinting, or even DNA sequencing can be produced in about three hours. Advantages that can be gained by the use of PCR include (1) rapid detection and identification of microorganisms that occur at very low frequency (e.g., one or a few cells in a liter of water), symbiotic microorganisms, and minute individual fish and invertebrate larvae; (2) rapid analysis of individual genomes for population studies; (3) detection and analysis of “rare events” (e.g., gene rearrangements) that occur in a small fraction of cells in a tissue sample or field collection; and (4) estimation of water quality by detection of pathogenic viruses, bacteria, and/or parasites. Another advantage of PCR is that it eliminates the need to culture what are often found to be nonculturable microbial species and strains of ecological or biogeochemical importance. PCR currently is being used for biosystematics, population biology, conservation biology, ecology, developmental biology, and genetics (see reviews by Arnheim et al., 1990; Powers et al., 1990; Powers, 1993).
DNA Fingerprinting: Repetitive regions of DNA, called minisatellites, are dispersed throughout the genomes of a number of organisms. Jeffreys et al. (1985) showed that a subset of human minisatellites shared a common 10 to 15 base pair core that had hypervariable regions. Later they demonstrated that a nucleic acid hybridization probe could detect highly polymorphic minisatellites that could be used as DNA fingerprints specific to an individual. DNA fingerprinting is now commonplace in biomedical research and is routinely employed in a variety of legal situations. Moreover, the method is being used to address many scientific questions about terrestrial and aquatic organisms (reviewed by Ryland and Tyler, 1989; Burke et al., 1991; Powers, 1993).
Whales and other cetaceans have been studied more frequently than other marine species (e.g., Hoelzel et al., 1991; Schloetterer et al., 1991). However, DNA fingerprinting has also been applied to freshwater and marine fishes, invertebrates, and aquatic plants (reviewed by Ryland and Tyler, 1989; Powers, 1993). For example, Whitmore et al. (1990) used DNA fingerprinting to study sibling largemouth bass (M. salmoides.) They showed that DNA hydridization patterns were different for each individual but that siblings were more similar to each other than to fish from wild stocks. Wirgin et al. (1991) developed striped bass-specific DNA probes, 10 to 20 base pairs in length, which they used to study bass population structure. One of the probes allowed them to distinguish between Gulf of
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