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The Use of Arbitrarily Primed PCR (AP-PCR) Fingerprinting to Detect Exposure to Genotoxic Chemicals

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Abstract

Exposure of an organism to a genotoxic chemical may result in the formation of covalently bound adducts between the chemical (or its metabolites) and the DNA; faulty repair of these adducts often results in mutations and, sometimes, cytogenetic changes. The primary effects of such exposure (i.e. adduct formation) and the subsequent effects on the DNA (mutation, cytogenetic damage) may be monitored using a number of assays of varying sensitivity and specificity. Recent developments in molecular biology offer new possibilities for detecting DNA damage. In this laboratory DNA fingerprinting by arbitrarily primed polymerase chain reaction (AP-PCR) was investigated in order to establish whether it can reveal differences in the DNA fingerprints of animals exposed to benzo[a]pyrene in the laboratory and of animals from control and from polluted areas. The results indicate that differences between control and exposed animals were detectable; these results, together with those from other laboratories, indicate that DNA fingerprinting by AP-PCR offers a useful alternative biomarker assay for the detection of the genotoxic effects of environmental pollutants. This paper reviews the application of PCR based DNA fingerprinting procedures in mutation detection and discusses their application to ecotoxicological studies.

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References

  • Abshire, M.K., Buzard, G.S., Shiraishi, N. and Waalkes, M.P. (1996). Induction of c-myc and c-jun proto-oncogene expression in rat L6 myoblasts by cadmiun is inhibited by zinc preinduction of the metallothionein gene. J. Toxicol. Environ. Health 48, 359-77.

    Google Scholar 

  • Ames, B.N., McCann, J. and Yamasaki, E. (1975). Method for detecting carcinogens and mutagens with the Salmonellar mammalian microsomes mutagenicity test. Mutat. Res. 31, 347-64.

    Google Scholar 

  • Arbeit, R.D., Maslow, J.N. and Mulligan, M.E. (1994). Polymerase chain reaction-mediated genotyping in microbial epidemiology. Clin. Infect. Dis. 18, 1018-9.

    Google Scholar 

  • Atienzar, F., Child, P., Evenden, A., Jha, A., Savva, D., Walker, C.H. and Depledge, M.H. (1998). Application of the arbitrarily primed polymerase chain reaction for the detection of DNA damage. Mar. Environ. Res. 45, 331-5.

    Google Scholar 

  • Atienzar, F.A., Conradi, M., Evenden, A.J., Jha, A.N. and Depledge, M.H. (1999). Qualitative assessment of genotoxicity using random amplified polymorphic DNA: Comparison of genomic template stability with key fitness parameters in Daphnia magna exposed to benzo[a]pyrene. Environ. Toxicol. Chem. 18, 2275-82.

    Google Scholar 

  • Atienzar, F., Evenden, A., Jha, A., Savva, D. and Depledge, M.H. (2000). Optimised RAPD analysis generates high-quality genomic DNA profiles at high annealing temperature. Biotechniques 28, 52-4.

    Google Scholar 

  • Becerril, C., Ferrero, M., Sanz, F. and Castano, A. (1999). Detection of mitomycin C-induced genetic damage in fish cells by use of RAPD. Mutagenesis 14, 449-56.

    Google Scholar 

  • Bickham, J.W., Mazet, J.A., Blake, J., Smolen, M.J., Lou, Y.G. and Ballachey, B.E. (1998). Flow cytometric determination of genotoxic effects of exposure to petroleum in mink and sea otters. Ecotoxicology 7, 191-9.

    Google Scholar 

  • Botstein, D., White, R.L., Skolnick, M. and Davis, R.W. (1980). Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am. J. Hum. Genet. 32, 314-31.

    Google Scholar 

  • Carrano, A.V., Thompson, L.H., Lindli, P.A. and Minkler, J.L. (1978). Sister chromatid exchange as an indicator of mutagenesis. Nature 271, 551-3.

    Google Scholar 

  • Castellani, S., Casini, S., Savva, D. and Mattei, N. (1995). Comparative analysis of alkaline unwinding and DNA fingerprinting tests in the validation of genetic damage in Zosterisessor ophiocephalus from Venice lagoon. Societa Italiana di Ecologia-ATTI 16, 611-3.

    Google Scholar 

  • Castellani, S., Mattei, N., Renzoni, A., Walker, C.H. and Savva, D. (1993). Preliminary studies on the use of PCR and DNA fingerprints to detect the genotoxic effects of environmental chemicals. First SETAC World Congress on Ecotoxicology and Environmental Chemistry, Lisbon, Portugal, Abstract Book, 246-7.

  • Castellani, S., Savva, D., Renzoni, A. and Mattei, N. (1996). Biomarkers of genotoxicity in two species of bivalve molluscs from coastal ecosystems of north Adriatic Sea. Societa Italiana di Ecologia-ATTI 17, 399-402.

    Google Scholar 

  • Catalan, J., Moreno, C. and Arruga, M.V. (1994). Distribution and sources of variability of sister chromatid exchange frequencies in cattle. Genet. Sel. Evol. 26, 3-14.

    Google Scholar 

  • Chipman, J.K. and Marsh, J.W. (1991). Bio-techniques for the detection of genetic toxicity in the aquatic environment. J. Biotechnol. 17, 199-208.

    Google Scholar 

  • Clark, A.G. and Lanigan, C.M.S. (1993). Prospect for estimating nucleotide divergence with RAPDs. Mol. Biol. Evol. 10, 1096-111.

    Google Scholar 

  • Conti, C., Mutti, I., Puglisi, P., Ferrarini, A., Regina, G., Maestri, E. and Marmiroli, N. (1998). DNA fingerprinting analysis by a PCR based method for monitoring the genotoxic effects of heavy metals pollution. Chemosphere 37, 2739-49.

    Google Scholar 

  • Counts, J.L. and Goodman, J.I. (1995). Hypomethylation of DNA: a possible epigenetic mechanism involved in tumor promotion. Prog. Clin. Biol. Res. 391, 81-101.

    Google Scholar 

  • Custer, T.W., Bickham, J.W., Lyne, T.B., Lewis, T. Ruedas, L.A., Custer, C.M. and Melancon, M.J. (1994). Flow-cytometry for monitoring contaminant exposure in black-crowned night-herons. Arch. Environ. Con. Tox. 27, 176-9.

    Google Scholar 

  • Custer, T.W., Hines, R.K., Melancon, M.J., Hoffman, D.J., Wickliffe, J.K., Bickham, J.W., Martin, J.W. and Henshel, D.S. (1997). Contaminant concentrations and biomarker response in great blue heron eggs from 10 colonies in the upper Mississippi River, USA. Environ. Toxicol. Chem. 16, 260-71.

    Google Scholar 

  • Devereaux, T.R., White, C.M., Sills, R.C., Bucher, J.R., Maronpot, R.R. and Anderson, M.W. (1994). Low frequency of H-ras mutations in hepatocellular adenomas and carcinomas and in hepatoblastomas from B6C3F1 mice exposed to oxazepam in the diet. Carcinogenesis 15, 1083-7.

    Google Scholar 

  • Dunn, B.P. (1991). Carcinogen adducts as an indicator for the public health risks of consuming carcinogen-exposed fish and shellfish. Environ. Health Persp. 90, 111-6.

    Google Scholar 

  • Everaarts, J.M., DenBesten, P.J., Hillebrand, M.T.J., Halbrook, R.S. and Shugart, L.R. (1998). DNA strand breaks, cytochrome P-450-dependent monooxygenase system activity and levels of chlorinated biphenyl congeners in the pyloric caeca of the seastar Asterias rubens from the North Sea. Ecotoxicology 7, 69-79.

    Google Scholar 

  • Fossi, M.C., Savelli, C., Casini, S., Franchi, E., Mattei, N. and Corsi, I. (1997). Multiresponse biomarker approach in the crab, Carcinus aestuarii, experimentally exposed to benzo(a)pyrene, PCBs and methyl mercury. Biomarkers 2, 311-9.

    Google Scholar 

  • Gordon, D.J., Milner, A.E., Vaughan, A.T. and Chipman, J.K. (1989). The use of flow cytometry in the detection of radiation-and chemically-induced nuclear damage in human mononuclear cells. Mutagenesis 4, 35-8.

    Google Scholar 

  • Grawe, J., Nusse, M. and Adler, I.D. (1997). Quantitative and qualitative studies of micronucleus induction in mouse erythrocytes using flow cytometry. I. Measurement of micronucleus induction in peripheral blood polychromatic erythrocytes by chemicals with known and suspected genotoxicity. Mutagenesis 12, 1-8.

    Google Scholar 

  • Gupta, R.C., Reddy, M.V. and Randerath, K. (1982). 32P-postlabelling analysis of non-radioactive aromatic carcinogen-DNA adducts. Carcinogenesis 3, 1081-92.

    Google Scholar 

  • Halbrook, R.S., Kilpatrick, R.L., Bevan, D.R. and Dunn, B.P. (1992). DNA adducts detected in muskrats by P-32 postlabelling analysis. Environ. Toxicol. Chem. 11, 1605-13.

    Google Scholar 

  • Harvey, R.G. (1982). Polycyclic hydrocarbons and cancer. Am. Sci. 70, 386-93.

    Google Scholar 

  • Ip, C. (1996). Mammary tumorigenesis and chemoprevention studies in carcinogen-treated rats. J. Mammary Gland Biol. Neopl. 1, 37-47.

    Google Scholar 

  • Jeffreys, A.J. (1987). Highly variable minisatellites and DNA fingerprints. Biochem. Soc. Trans. 15, 309-17.

    Google Scholar 

  • Jowett, T., Wajidi, M.F.F., Oxtoby, E. and Wolf, C.R. (1991). Mammalian genes expressed in Drosophila-Atransgenic model for the study of mechanisms of chemical mutagenesis and metabolism. EMBO J. 10, 1075-81.

    Google Scholar 

  • Kohlpoth, M., Rusche, B. and Nusse, M. (1999). Flow cytometric measurement of micronuclei induced in a permanent fish cell line as a possible screening test for the genotoxicity of industrial waste waters. Mutagenesis 14, 397-402.

    Google Scholar 

  • Krahn, M.M., Ylitalo, G.M., Buzitis, J., Chan, S.L. and Varanasi, U. (1993). Rapid high performance liquid chromatographic methods that screen for aromatic compounds in environmental samples. J. Chromatogr. 642, 15-32.

    Google Scholar 

  • Lamb, T., Bickham, J.W., Lyne, T.B. and Gibbons, J.W. (1995). The slider turtle as an environmental sentinel-multiple tissue-assays using flow cytometric analysis. Ecotoxicology 4, 5-13.

    Google Scholar 

  • Liang, P. and Pardee, A. (1992). Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction. Science 257, 967-70.

    Google Scholar 

  • Liu, S.F., Rappaport, S.M., Rasmussen, J. and Bodell, W.J. (1988). Detection of styrene oxide DNA adducts by 32P-postlabelling. Carcinogenesis 9, 1401-4.

    Google Scholar 

  • Lloyd-Jones, G. (1995). 32P-postlabelling: a valid biomarker for environmental assessment? TEN 2, 100-4.

    Google Scholar 

  • Lopez, A., Xamena, N., Cabre, O., Creus, A., Marcos, R. and Velasquez, A. (1999). Analysis of genomic damage in the mutagen-sensitive mus-201 mutant of Drosophila melanogaster by arbitrarily primed PCR AP-PCR fingerprinting. Mutat. Res. 435, 63-75.

    Google Scholar 

  • Lynch, M. (1990). The similarity index and DNA fingerprinting. Mol. Biol. Evol. 7, 478-84.

    Google Scholar 

  • MacGregor, J.T., Tucker, J.D., Eastmond, D.A. and Wyrobek, A.J. (1995). Integration of cytogenetic assays with toxicology studies. Environ. Mol. Mutagen. 25, 328-37.

    Google Scholar 

  • Marcon, F., Zijno, A., Crebelli, R., Carere, A., Veidebaum, T., Peltonen, K., Parks, R., Schuler, M. and Eastmond, D.A. (1999). Chromosome damage and aneuploidy detected by multicolour FISH in benzene exposed shale oil workers. Mutat. Res. 445, 155-66.

    Google Scholar 

  • McKenzie, D. and Buchner, R. (1995). Use of RAP-PCR to identify differential gene transcripts present in mutagenised cell lines. Strategies 8, 61-2.

    Google Scholar 

  • Meyers-Schone, L., Shugart, L.R., Beauchamp, J.J. and Walton, B.T. (1993). Comparison of 2 fresh-water turtle species as monitors of radionuclide and chemical contamination-DNA-damage and residue analysis. Environ. Toxicol. Chem. 12, 1487-96.

    Google Scholar 

  • Michelmore, C.L. and Chipman, J.K. (1998). DNA strand breakage in aquatic organisms and the potential value of the comet assay in environmental monitoring. Mutat. Res. 399, 135-47.

    Google Scholar 

  • Murti, J.R., Schimenti, K.J. and Schimenti, J.C. (1994). A recombination-based transgenic mouse system for genotoxicity testing. Mutat. Res. 307, 583-95.

    Google Scholar 

  • Ostling, O. and Johanson, K.J. (1984). Microelectrophoretic study of radiation-induced DNA damages in individual mammalian cells. Biochem. Biophys. Res. Comm. 123, 291-8.

    Google Scholar 

  • Peakall, D.B. (1992). Animal Biomarkers as Pollution Indicators. London: Chapman and Hall.

    Google Scholar 

  • Peakall, D.B. (1994). Biomarkers : The way forward in environmental assessment. TEN 1, 55-60.

    Google Scholar 

  • Peakall, D.B. and Shugart, L.R. (eds) (1993). Biomarkers: Research and Application in the Assessment of Environmental Health. Berlin: Springer Verlag.

    Google Scholar 

  • Phillips, D.H., Hewer, A., Martin, C.N., Garner, R.C. and King, M.M. (1988). Correlation of DNA adduct levels in human lung with cigarette smoking. Nature 336, 790-2.

    Google Scholar 

  • Poirier, M.C. (1984). The use of carcinogen-DNA adduct antisera for quantitation and localization of genomic damage in animal models and the human population. Environ. Mutagen. 6, 879-87.

    Google Scholar 

  • Richardson, K.K., Richardson, F.C., Crosby, R.M., Swenberg, J.A. and Skopek, T.R. (1987). DNA base changes and alkylation following in vivo exposure of Escherichia coli to N-methyl-N-nitrosourea or N-ethyl-N-nitrosourea. Proc. Natl. Acad. Sci. USA 84, 344-78.

    Google Scholar 

  • Rossiello, M.R., Rao, P.M., Rajalakshami, S. and Sarma, D.S. (1994). Similar patterns of hypomethylation in the β-hydroxy-β-methylglutaryl coenzyme A reductase gene in hepatic nodules induced by different carcinogens. Mol. Carcinog. 10, 237-45.

    Google Scholar 

  • Roy, S., Lindstrom-Seppa, P. and Hanninen, O. (1996). Integrative approach to aquatic environment biomonitoring. In M. Richardson (ed) Environmental Xenobiotics, pp. 123-42. London: Taylor & Francis Ltd.

    Google Scholar 

  • Ryskova, M., Chroust, K., Trbusek, M., Benedik, J. and Jowett, T. (1997). Genotoxicity of N-nitroso-N-methylurea and acetone oxime in the transgenic Drosophila carrying the human gene encoding a subunit of glutathione-S-transferase. Folia Biol. 43, 19-24.

    Google Scholar 

  • Saiki, R.K., Gelfand, D.H., Stoffel, S., Scharf, S.J., Higuchi, R., Horn, G.T., Mullis, K.B. and Erlich, H.A. (1988). Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239, 487-91.

    Google Scholar 

  • Sambrook, J., Fritsch, E.F. and Maniatis, T. (1989). Molecular Cloning. Cold Spring Harbor: Cold Spring Harbor Laboratory Press.

    Google Scholar 

  • Sancar, A. and Sancar, G.B. (1988). DNA repair enzymes. Ann. Rev. Biochem. 57, 29-67.

    Google Scholar 

  • Santella, R.M. (1988). Application of new techniques for the detection of carcinogen adducts to human population monitoring. Mutat. Res. 205, 271-82.

    Google Scholar 

  • Savva, D. (1996). DNA fingerprinting as a biomarker in ecotoxicology. TEN 3, 110-4.

    Google Scholar 

  • Savva, D. (1998). Use of DNA fingerprinting to detect genotoxic effects. Ecotox. Environ. Safe. 41, 103-6.

    Google Scholar 

  • Savva, D., Castellani, S., Mattei, N., Renzoni, A. and Walker, C.H. (1994). The use of PCR and DNA fingerprints to detect the genotoxic effects of environmental chemicals. In S.P. Varnavas (ed) Environmental Contamination, pp 105-10. Edinburgh: CEP Consultants Ltd.

    Google Scholar 

  • Selden, J.R., Dolbeare, F., Clair, J.H., Miller, J.E., McGettigan, K., DiJohn, J.A., Dysart, G.R. and DeLuca, J.G. (1994). Validation of a flow cytometric in vitro DNA repair UDS assay in rat hepatocytes. Mutat. Res. 315, 147-67.

    Google Scholar 

  • Shugart, L.R. (1988). Quantitation of chemically induced damage to DNA by alkaline unwinding assay. Aquat. Toxicol. 13, 43-52.

    Google Scholar 

  • Southern, E.M. (1975). Detection of specific sequences among DNA fragments separated by gel electrophoresis. J. Mol. Biol. 98, 503-17.

    Google Scholar 

  • Sparagano, O., Sage, T., Fossi, M.C., Lari, L., Child, P., Savva, D., Depledge, M.H., Bamber, S. and Walker, C. (1999). Induction of a putative monooxygenase of crabs (Carcinus spp.) by polycyclic aromatic hydrocarbons. Biomarkers 4, 203-13.

    Google Scholar 

  • Stepanova, L.I., Glaser, V.M., Savinova, T.I., Kotelevtsev, S.V. and Savva, D. (1999). Accumulation of mutagenic xenobiotics in fresh water (Lake Baikal) and marine (Hornoya Island) ecosystems. Ecotoxicology 8, 83-96.

    Google Scholar 

  • Sukumar, S., Notario, V., Martin-Zanca, D. and Barbacid, M. (1983). Induction of mammary carcinomas in rats by nitrosomethylurea involves malignant activation of Ha-ras-1 locus by single point mutations. Nature 306, 658-61.

    Google Scholar 

  • Swaminathan, B. and Barrett, T.J. (1995). Amplification methods for epidemiologic investigations of infectious diseases. J. Microbil. Methods 23, 129-39.

    Google Scholar 

  • Tardiff, R.G., Lohman, P.H.M. and Wogan, G.N. (eds) (1994). Methods to Assess DNA Damage and Repair. Chichester: John Wiley & Sons.

    Google Scholar 

  • Theodorakis, C.W. and Shugart, L.R. (1997). Genetic ecotoxicology. 2. Population genetic structure in mosquito fish exposed to radionuclides. Ecotoxicology 6, 335-54.

    Google Scholar 

  • Theodorakis, C.W. and Shugart, L.R. (1998). Genetic ecotoxicology. III. The relationship between DNA strand breaks and genotype in mosquito fish exposed to radiation. Ecotoxicology 7, 227-36.

    Google Scholar 

  • Theodorakis, C.W., Dsurney, S.J. and Shugart, L.R. (1994). Detection of genotoxic insult as DNA strand breaks in fish blood cells by agarose gel electrophoresis. Environ. Toxicol. Chem. 13, 1023-31.

    Google Scholar 

  • Theodorakis, C.W., Elbl, T. and Shugart, L.R. (1999). Genetic ecotoxicology. IV. Survival and DNA strand breakage is dependent on genotype in radionuclide-exposed mosquito fish. Aquat. Toxicol. 45, 279-91.

    Google Scholar 

  • Timbrell, J.A., Draper, R. and Waterfield, C.J. (1994). Biomarkers in toxicology: New uses for some old molecules? TEN 1, 4-14.

    Google Scholar 

  • Upcroft, P., Mitchell, R. and Boreham, P.F.L. (1990). DNA fingerprinting of the intestinal parasite Giardia duodenalis with the M13 phage genome. Int. J. Parasitol. 20, 319-23.

    Google Scholar 

  • Varanasi, U., Reichert, W.L. and Stein, J.E. (1989). 32P-Postlabelling analysis of DNA adducts in liver of English sole (Parophys vetulus) and winter flounder (Pseudopleuronectes americanus). Cancer Res. 49, 1171-7.

    Google Scholar 

  • Walker, C.H. (1996). Biomarkers and risk assessment. Pestic. Outlook 7, 7-12.

    Google Scholar 

  • Walker, C.H. (1998). Biomarker strategies to evaluate the environmental effects of chemicals. Environ. Health Persp. 106, 613-22.

    Google Scholar 

  • Walker, C.H. and Savva, D. (2000). Biochemical responses of crabs Carcinus spp. to polycyclic aromatic hydrocarbons. In P. Garrigues, C.H. Walker and H. Barth (eds) Biomarkers in Marine Ecosystems: A Practical Approach. In press. Amsterdam: Elsevier.

    Google Scholar 

  • Walker, C.H., Hopkin, S.P., Sibly, R.M. and Peakall, D.B. (1996). Principles of Ecotoxicology. London: Taylor & Francis.

    Google Scholar 

  • Welsh, J. and McClelland, M. (1990). Fingerprinting genomes using PCR with arbitrary primers. Nucl. Acids Res. 22, 7213-8.

    Google Scholar 

  • Welsh, J., Perucho, M., Peinado, M., Ralph, D. and McClelland, M. (1995). Fingerprinting of DNA and RNA using arbitrarily primed PCR. In M.J. McPherson, B.D. Hames and G.R. Taylor (eds) PCR 2. A Practical Approach, pp. 197-218. Oxford: IRL Press.

    Google Scholar 

  • Williams, J.G.K., Kubelik, A.R., Livak, K.J., Rafalski, J.A. and Tingey, S.V. (1990). DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucl. Acids Res. 18, 6531-5.

    Google Scholar 

  • Zarbl, H., Sukumar, S., Arthur, A.V., Martin-Zanca, D. and Barbacid, M. (1985). Direct mutagenesis of Ha-ras-1 oncogenes by N-nitroso-N-methylurea during initiation of mammary carcinognesis in rats. Nature 315, 382-5.

    Google Scholar 

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Savva, D. The Use of Arbitrarily Primed PCR (AP-PCR) Fingerprinting to Detect Exposure to Genotoxic Chemicals. Ecotoxicology 9, 341–353 (2000). https://doi.org/10.1023/A:1026577326366

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