At the crossroads of genomics and ecology: The promise of a canary on a chip

BioScience

Volumn 54, Issue 5, 2004, Pages 403-412

  Klaper, Rebecca ^a,b   Thomas, Michael A ^c  

^a UNIVERSITY OF WISCONSIN MILWAUKEE   (United States)

^b AAAS   (United States)

^c Nucl Eng Idaho State University   (United States)

Author keywords

Ecology; Environmental monitoring; Environmental risk assessment; Genomics; Toxicogenomics

Indexed keywords

EID: 2442432526     PISSN: 00063568     EISSN: None     Source Type: Journal    
DOI: 10.1641/0006-3568(2004)054[0403:ATCOGA]2.0.CO;2     Document Type: Review

References (47)

1. Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, Miller W, Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Research 25: 3389-3402.
2. Anderson NL, Anderson NG. 2002. The human plasma proteome: History, character, and diagnostic prospects. Molecular and Cellular Proteomics 1: 845-867.
3. Andrew AS, Warren AJ, Barchowsky A, Temple KA, Klei L, Soucy NV, O'Hara KA, Hamilton JW. 2003. Genomic and proteomic profiling of responses to toxic metals in human lung cells. Environmental Health Perspectives 111: 825-838.
4. Bartosiewicz MJ, Jenkins D, Penn S, Emery J, Buckpitt A. 2001. Unique gene expression patterns in liver and kidney associated with exposure to chemical toxicants. Journal of Pharmacology and Experimental Therapeutics 297: 895-905.
5. Brazma A, et al. 2001. Minimum information about a microarray experiment (MIAME) - toward standards for microarray data. Nature Genetics 29: 365-371.
6. Clark A, Shamaan N, Sinclair M, Dauterman W. 1986. Insecticide metabolism by multiple glutathione S-transferase in two strains of the house fly Musca domestica (L.). Pesticide Biochemistry and Physiology 25: 169-175.
7. Crawford DL. 2001. Functional genomics does not have to be limited to a few select organisms. Genome Biology 2: 1001.1-1101.2. (26 March 2004; http://genomebiology.com/2001/2/1/interactions/1001)
8. [EPA] US Environmental Protection Agency. 2003. Draft Report on the Environment. Washington (DC): Office of Research and Development, EPA. Report no. EPA/600/R-03/050.
9. Fields S. 2001. Proteomics in genomeland. Science 291: 1221-1224.
10. Gibson G. 2002. Microarrays in ecology and evolution: A preview. Molecular Ecology 11: 17-24.
11. Hamadeh H, et al. 2002a. Gene expression analysis reveals chemical-specific profiles. Toxicological Sciences 67: 219-231.
12. _. 2002b. Prediction of compound signature using high density gene expression profiling. Toxicological Sciences 67: 232-240.
13. Haslett JN, Sanoudou D, Kho AT, Bennett RR, Greenberg SA, Kohane IS, Beggs AH, Kunkel LM. 2002. Gene expression comparison of biopsies from Duchenne muscular dystrophy (DMD) and normal skeletal muscle. Proceedings of the National Academy of Sciences 99: 15000-15005.
14. [Heinz Center] H. John Heinz III Center for Science, Economics, and the Environment. 2002. The State of the Nation's Ecosystems: Measuring the Lands, Waters, and Living Resources of the United States. Cambridge (United Kingdom): Cambridge University Press.
15. Helbing CC, Werry K, Crump D, Domanski D, Veldhoen N, Bailey CM. 2003. Expression profiles of novel thyroid hormone-responsive genes and proteins in the tail of Xenopus laevis tadpoles undergoing precocious metamorphosis. Molecular Endocrinology 17: 1395-1409.
16. Hood L. 2001. Opening remarks. Paper presented at the Symposium on Gene Expression and Proteomics in Environmental Health Research; 3-4 December 2001, Bethesda, MD.
17. Jelaso AM, Lehigh-Hirey E, Predenkiewicz A, Means J, Ide CF. 2002. Aroclor 1254 alters morphology, survival, and gene expression levels in Xenopus laevis tadpoles. Environmental and Molecular Mutagenesis 40: 24-35.
18. Jelaso AM, Lehigh-Shirey E, Means J, Ide CF. 2003. Gene expression patterns predict exposure to PCBs in developing Xenopus laevis tadpoles. Environmental and Molecular Mutagenesis 42: 1-10.
19. Knudsen S. 2002. A Biologist's Guide to Analysis of DNA Microarray Data. New York: Wiley.
20. Kreps JA, Wu Y, Chang HS, Zhu T, Wang X, Harper JF. 2002. Transcriptome changes for Arabidopsis in response to salt, osmotic, and cold stress. Plant Physiology 130: 2129-2141.
21. Kuska B. 1998. Molecular diagnostics takes one small step forward. Journal of the National Cancer Institute 90: 564-565.
22. Larkin P, Folmar LC, Hemmer MJ, Poston AJ, Lee HS, Denslow ND. 2002. Array technology as a tool to monitor exposure of fish to xenoestrogens. Marine Environmental Research 54: 395-399.
23. Lattier DL, Gordon DA, Burks DJ, Toth GP. 2001. Vitellogenin gene transcription: A relative quantitative exposure indicator of environmental estrogens. Environmental Toxicology and Chemistry 20: 1979-1985.
24. LeBlanc GA, Bain LJ. 1997. Chronic toxicity of environmental contaminants: Sentinels and biomarkers. Environmental Health Perspectives 105 (suppl.1): 65-80.
25. Li XM, Gu WK, Mohan S, Baylink AJ. 2002. DNA microarrays: Their use and misuse. Microcirculation 9: 13-22.
26. Matthews J, Celius T, Halgren R, Zacharewski T. 2000. Differential estrogen receptor binding of estrogenic substances: A species comparison. Journal of Steroid Biochemistry and Molecular Biology 74: 223-234.
27. Mattingly CJ, Colby GT, Forrest JN, Boyer JL. 2003. The Comparative Toxicogenomics Database (CTD). Environmental Health Perspectives 111: 793-795.
28. Mitchell-Olds T. 2001. Arabidopsis thaliana and its wild relatives: A model system for ecology and evolution. Trends in Ecology and Evolution 16: 693-700.
29. Neumann NF, Galvez F. 2002. DNA microarrays and toxicology: Applications for ecotoxicology? Biotechnology Advances 20: 391-419.
30. Normile D. 2001. Comparative genomics: Gene expression differs in human and chimp brains. Science 292: 44-45.
31. [NRC] Committee on Developmental Toxicology, Board on Environmental Studies and Toxicology, Commission on Life Sciences, National Research Council. 2000. Scientific Frontiers in Developmental Toxicology and Risk Assessment. Washington (DC): National Academies Press.
32. Oleksiak MF, Churchill GA, Crawford DL. 2002. Variation in gene expression within and among natural populations. Nature Genetics 32: 261-266.
33. Pennie WD. 2000. Use of cDNA microarrays to probe and understand the toxicological consequences of altered gene expression. Toxicological Letters 112: 473-477.
34. Quackenbush J. 2003. Microarrays - guilt by association. Science 302: 240-241.
35. Ramarathnam R, Subramaniam S. 2000. A novel microarray strategy for detecting genes and pathways in microbes with unsequenced genomes. Microbial Comparative Genomics 5: 153-161.
36. Sevenet N, Cussenot O. 2003. DNA microarrays in clinical practice: Past, present, and future. Clinical and Experimental Medicine 3: 1-3.
37. Shockcor JP, Holmes E. 2002. Metabonomic applications in toxicity screening and disease diagnosis. Current Topics in Medicinal Chemistry 2: 35-51.
38. Stearns SC, Magwene P. 2003. The naturalist in a world of genomics. The American Naturalist 161: 171-180.
39. Stegeman JJ, Brouwer M, DiGiulio RT, Förlin L, Fowler BA, Sanders BM, Van Veld PA. 1992. Molecular responses to environmental contamination: Enzyme and protein systems as indicators of chemical exposure and effect. Pages 235-335 in Huggett RJ, Kimerle RA, Mehrle PM Jr, Bergman HL, eds. Biomarkers: Biochemical, Physiological, and Histological Markers of Anthropogenic Stress. Boca Raton (FL): Lewis.
40. Suter GW, Barnthouse LW. 1993. Ecological Risk Assessment. Boca Raton (FL): Lewis.
41. [USGS] US Geological Survey. 2001. National Water Quality Assessment Program. USGS feet sheet 071-01. (27 March 2004; http://water.usgs.gov/pubs/fs/ fs-071-01/)
42. Vasseur P, Cossu-Leguille C. 2003. Biomarkers and community indices as complementary tools for environmental safety. Environment International 28: 711-717.
43. Viant MR, Rosenblum ES, Tjeerdema RS. 2003. NMR-based metanolomics: A powerful approach for characterizing the effects of environmental stressors on organism health. Environmental Science and Technology 37: 4982-4989.
44. Wan J, Shi J, Hui L, Wu D, Jin X, Zhao N, Huang W, Xia Z, Gengxi H. 2002. Association of genetic polymorphisms in CYP2E1, MPO, NQO1, GSTM1, and GSTT1 genes with benzene poisoning. Environmental Health Perspectives 110: 1213-1218.
45. Waring JF, Ciurlionis R, Joly RA, Heindel M, Ulrich RG. 2001. Microarray analysis of hepatotoxins in vitro reveals a correlation between gene expression profiles and mechanisms of toxicity. Toxicology Letters 120: 359-368.
46. Waters M, et al. 2003. Systems toxicology and the Chemical Effects in Biological Systems (CEBS) knowledge base. Environmental Health Perspectives 111: 811-824.
47. Wooster R, Weber BL. 2003. Breast and ovarian cancer. New England Journal of Medicine 348: 2339-2347.