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Donald C. Malins,¹ John J. Stegeman,² Jack W. Anderson,^3,* Paul M. Johnson,¹ Jordan Gold,⁴ and Katie M. Anderson¹

¹Biochemical Oncology Program, Pacific Northwest Research Institute, Seattle, Washington, USA; ²Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA; ³Columbia Analytical Services, Kelso, Washington, USA; ⁴Applied Marine Sciences, Inc., Livermore, California, USA

Abstract
Structural differences were identified in gill DNA from two groups of English sole collected from Puget Sound, Washington, in October 2000. One group was from the industrialized Duwamish River (DR) in Seattle and the other from relatively clean Quartermaster Harbor (QMH) . Chemical markers of sediment contamination [e.g., polynuclear aromatic hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs) ] established that the DR was substantially more contaminated than QMH. The levels of these chemicals in the sediments of both sites were consistent with levels of cytochrome P450 1A (CYP1A) expression in the gills of English sole from the same sites. Structural differences in gill DNA between the groups were evinced via statistical models of Fourier transform-infrared (FT-IR) spectra. Marked structural damage was found in the gill DNA of the DR fish as reflected in differences in base functional groups (e.g., C-O and NH₂) and conformational properties (e.g., arising from perturbations in vertical base stacking interactions) . These DNA differences were used to discriminate between the two fish groups through principal components analysis of mean FT-IR spectra. In addition, logistic regression analysis allowed for the development of a "DNA damage index" to assess the effects of contaminants on the gill. The evidence implies that environmental chemicals contribute to the DNA changes in the gill. The damaged DNA is a promising marker for identifying, through gill biopsies, contaminant effects on fish. Key words: contaminant effects, cytochrome P450 1A, DNA markers, DNA structure, fish gills, Fourier transform-infrared spectroscopy, Puget Sound. Environ Health Perspect 112:511-515 (2004) . doi:10.1289/ehp.6719 available via http://dx.doi.org/ [Online 18 December 2003]

Address correspondence to D.C. Malins, Biochemical Oncology Program, Pacific Northwest Research Institute, 720 Broadway, Seattle, WA 98122 USA. Telephone: (206) 726-1240. Fax: (206) 726-1235. E-mail: dmalins@pnri.org

*Current address: Battelle Marine Sciences Laboratory, Sequim, Washington, USA.

We thank K.-E. Hellström for helpful comments, R. Smolowitz for consulting on gill pathologies, M. Woodall and the Washington State Department of Ecology for the map of Puget Sound (to which we added labels) , and V.M. Green for editorial assistance. We also thank B.R. Woodin, B. Duer, N. Gilman, and A. Ray for technical assistance.

This publication was made possible by grant P42 ES04696 (D.C.M.) and 5-P42-ESO7381 (J.J.S.) from the National Institute of Environmental Health Sciences (NIEHS) , National Institutes of Health (NIH) . Its contents are solely the responsibility of the authors and do not necessarily represent the official views of the NIEHS or the NIH. Contribution number 10827 from the Woods Hole Oceanographic Institution.

The authors declare they have no competing financial interests.

Received 29 August 2003 ; accepted 15 December 2003.