A new approach to toxicity testing in Daphnia magna: Application of high throughput FT-ICR mass spectrometry metabolomics

Metabolomics

Volumn 5, Issue 1, 2009, Pages 44-58

  Taylor, Nadine S ^a   Weber, Ralf J M ^a   Southam, Andrew D ^a   Payne, Tristan G ^a   Hrydziuszko, Olga ^a   Arvanitis, Theodoros N ^a   Viant, Mark R ^a  

^a UNIVERSITY OF BIRMINGHAM   (United Kingdom)

Author keywords

Environmental metabolomics; Metabonomics; Risk assessment; SIM stitching; Tiered testing; Water flea

Indexed keywords

CLADOCERA; DAPHNIA; DAPHNIA MAGNA; DAPHNIIDAE; SIPHONAPTERA (FLEAS);

EID: 61849120270     PISSN: 15733882     EISSN: 15733890     Source Type: Journal    
DOI: 10.1007/s11306-008-0133-3     Document Type: Article

References (64)

1. Ankley, G. T., Miracle, A., Perkins, E. J., & Daston, G. P. (2008). Genomics in regulatory ecotoxicology: Applications and challenges. Boca Raton, London: CRC Press.
2. Arambasic, M. B., Bjelic, S., & Subakov, G. (1995). Acute toxicity of heavy metals (copper, lead and zinc), phenol and sodium on Allium cepa L., Lepidium sativum L. and Daphnia magna ST-comparative investigations and the practical applications. Water Research, 29, 497-503. doi: 10.1016/0043-1354(94)00178-A.
3. Baldovin, A., Wu, W., Centner, V., et al. (1996). Feature selection for the discrimination between pollution types with partial least squares modelling. Analyst (London), 121, 1603-1608. doi: 10.1039/an9962101603.
4. Barata, C., Navarro, J. C., Varo, I., et al. (2005). Changes in antioxidant enzyme activities, fatty acid composition and lipid peroxidation in Daphnia magna during the aging process. Comparative Biochemistry and Physiology B: Comparative Biochemistry, 140, 81-90. doi: 10.1016/j.cbpc.2004.09.025.
5. Benjamini, Y., & Hochberg, Y. (1995). Controlling the false discovery rate - A practical and powerful approach to multiple testing. Journal of the Royal Statistical Society: Series B, 57, 289-300.
6. Benson, W. H., Gallagher, K., & McClintock, J. T. (2007). U.S. Environmental Protection Agency's activities to prepare for regulatory and risk assessment applications of genomics information. Environmental and Molecular Mutagenesis, 48, 359-362. doi: 10.1002/em.20302.
7. Berlett, B. S., & Stadtman, E. R. (1997). Protein oxidation in aging, disease, and oxidative stress. The Journal of Biological Chemistry, 272, 20313-20316. doi: 10.1074/jbc.272.33.20313.
8. Bligh, E. G., & Dyer, W. J. (1959). A rapid method of total lipid extraction and purification. Canadian Journal of Biochemistry and Physiology, 37, 911-917.
9. Bopp, S. K., Abicht, H. K., & Knauer, K. (2008). Copper-induced oxidative stress in rainbow trout gill cells. Aquatic Toxicology (Amsterdam, Netherlands), 86, 197-204. doi: 10.1016/ j.aquatox.2007.10.014.
10. Breitling, R., Pitt, A. R., & Barrett, M. P. (2006). Precision mapping of the metabolome. Trends in Biotechnology, 24, 543-548. doi: 10.1016/j.tibtech.2006.10.006.
11. Breitling, R., Vitkup, D., & Barrett, M. P. (2008). New surveyor tools for charting microbial metabolic maps. Nature Reviews. Microbiology, 6, 156-161. doi: 10.1038/nrmicro1797.
12. Brown, S. C., Kruppa, G., & Dasseux, J. L. (2005). Metabolomics applications of FT-ICR mass spectrometry. Mass Spectrometry Reviews, 24, 223-231. doi: 10.1002/mas.20011.
13. Casero, R. A., & Pegg, A. E. (1993). Spermidine spermine N1-acetyltransferase - the turning-point in polyamine metabolism. The FASEB Journal, 7, 653-661.
14. Coen, M., Holmes, E., Lindon, J. C., & Nicholson, J. K. (2008). NMR-based metabolic profiling and metabonomic approaches to problems in molecular toxicology. Chemical Research in Toxicology, 21, 9-27. doi: 10.1021/tx700335d.
15. Coffino, P., & Poznanski, A. (1991). Killer polyamines. Journal of Cellular Biochemistry, 45, 54-58. doi: 10.1002/jcb.240450112.
16. Colbourne, J. K., Singan, V. R., & Gilbert, D. G. (2005). wFleaBase: The Daphnia genomics information system. http://wfleabase.org/.
17. Connon, R., Hooper, H. L., Sibly, R. M., et al. (2008). Linking molecular and population stress responses in Daphnia magna exposed to cadmium. Environmental Science and Technology, 42, 2181-2188. doi: 10.1021/es702469b.
18. De Coen, W. M., & Janssen, C. R. (2003). A multivariate biomarker-based model predicting population-level responses of Daphnia magna. Environmental Toxicology and Chemistry, 22, 2195-2201. doi: 10.1897/02-223.
19. Deleebeeck, N. M., De Schamphelaere, K. A., Heijerick, D. G., Bossuyt, B. T., & Janssen, C. R. (2008). The acute toxicity of nickel to Daphnia magna: Predictive capacity of bioavailability models in artificial and natural waters. Ecotoxicology and Environmental Safety, 70, 67-78. doi: 10.1016/j.ecoenv.2007.05.002.
20. De Meester, L., & Vanoverbeke, J. (1999). An uncoupling of male and sexual egg production leads to reduced inbreeding in the cyclical parthenogen Daphnia. Proceedings of the Biological Sciences, 266, 2471-2477. doi: 10.1098/rspb.1999.0948.
21. De Schamphelaere, K. A. C., & Janssen, C. R. (2004). Effects of dissolved organic carbon concentration and source, pH, and water hardness on chronic toxicity of copper to Daphnia magna. Environmental Toxicology and Chemistry, 23, 1115-1122. doi: 10.1897/02-593.
22. Dieterle, F., Ross, A., Schlotterbeck, G., & Senn, H. (2006). Probabilistic quotient normalization as robust method to account for dilution of complex biological mixtures. Application in 1H NMR metabonomics. Analytical Chemistry, 78, 4281-4290. doi: 10.1021/ ac051632c.
23. Dunn, W. B. (2008). Current trends and future requirements for the mass spectrometric investigation of microbial, mammalian and plant metabolomes. Physical Biology, 5, 11001. doi: 10.1088/1478-3975/5/1/ 011001.
24. Ekman, D. R., Teng, Q., Villeneuve, D. L., et al. (2008). Investigating compensation and recovery of fathead minnow (Pimephales promelas) exposed to 17 alpha-ethynylestradiol with metabolite profiling. Environmental Science and Technology, 42, 4188-4194. doi: 10.1021/ es8000618.
25. Gaetke, L. M., & Chow, C. K. (2003). Copper toxicity, oxidative stress, and antioxidant nutrients. Toxicology, 189, 147-163. doi: 10.1016/S0300-483X(03)00159-8.
26. Han, J., Danell, R. M., Patel, J. R., et al. (2008). Towards high-throughput metabolomics using ultrahigh-field Fourier transform ion cyclotron resonance mass spectrometry. Metabolomics, 4, 128-140. doi: 10.1007/s11306-008-0104-8.
27. Heckmann, L.-R., Sibly, R. M., Connon, R., et al. (2008). Systems biology meets stress ecology: Linking molecular and organismal stress responses in Daphnia magna. Genome Biology, 9, R40. doi: 10.1186/ gb-2008-9-2-r40.
28. Heijerick, D. G., Janssen, C. R., & De Coen, W. M. (2003). The combined effects of hardness, pH, and dissolved organic carbon on the chronic toxicity of Zn to D. magna: Development of a surface response model. Archives of Environmental Contamination and Toxicology, 44, 210-217. doi: 10.1007/s00244-002-2010-9.
29. Ikenaka, Y., Eun, H., Ishizaka, M., & Miyabara, Y. (2006). Metabolism of pyrene by aquatic crustacean, Daphnia magna. Aquatic Toxicology (Amsterdam, Netherlands), 80, 158-165. doi: 10.1016/ j.aquatox.2006.08.005.
30. Kanehisa, M., Goto, S., Hattori, M., et al. (2006). From genomics to chemical genomics: New developments in KEGG. Nucleic Acids Research, 34, D354-D357. doi: 10.1093/nar/gkj102.
31. Kind, T., & Fiehn, O. (2007). Seven Golden Rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry. BMC Bioinformatics, 8, 105. doi: 10.1186/1471-2105-8-105.
32. Knops, M., Altenburger, R., & Segner, H. (2001). Alterations of physiological energetics, growth and reproduction of Daphnia magna under toxicant stress. Aquatic Toxicology (Amsterdam, Netherlands), 53, 79-90. doi: 10.1016/S0166-445X(00)00170-3.
33. Linder, M. C., & Hazegh-Azam, M. (1996). Copper biochemistry and molecular biology. The American Journal of Clinical Nutrition, 63, 797S-811S.
34. Makarov, A., Denisov, E., Lange, O., & Horning, S. (2006). Dynamic range of mass accuracy in LTQ orbitrap hybrid mass spectrometer. Journal of the American Society for Mass Spectrometry, 17, 977-982. doi: 10.1016/ j.jasms.2006.03.006.
35. Martins, J., Oliva Teles, L., & Vasconcelos, V. (2007a). Assays with Daphnia magna and Danio rerio as alert systems in aquatic toxicology. Environment International, 33, 414-425. doi: 10.1016/ j.envint.2006.12.006.
36. Martins, J., Soares, M. L., Saker, M. L., Olivateles, L., & Vasconcelos, V. M. (2007b). Phototactic behavior in Daphnia magna Straus as an indicator of toxicants in the aquatic environment. Ecotoxicology and Environmental Safety, 67, 417-422. doi: 10.1016/j.ecoenv.2006.11.003.
37. Nicholson, J. K., Connelly, J., Lindon, J. C., & Holmes, E. (2002). Metabonomics: A platform for studying drug toxicity and gene function. Nature Reviews. Drug Discovery, 1, 153-161. doi: 10.1038/nrd728.
38. OECD. (1998). Guidelines for testing of chemicals, no. 211 - Daphnia magna reproduction test (p. 21). Organisation for Economic Cooperation and Development.
39. OECD. (2004). Guidelines for Testing of Chemicals, No. 202 - Daphnia sp.acute immobilisation test (p. 12). Organisation for Economic Cooperation and Development.
40. Olsen, J. V., de Godoy, L. M. F., Li, G., Macek, B., Mortensen, P., Pesch, R., et al. (2005). Parts per million mass accuracy on an Orbitrap mass spectrometer via lock mass injection into a C-trap. Molecular & Cellular Proteomics, 4, 2010-2021. doi: 10.1074/mcp.T500030-MCP200.
41. Parsons, H. M., Ludwig, C., Günther, U. L., & Viant, M. R. (2007). Improved classification accuracy in 1- and 2-dimensional NMR metabolomics data using the variance stabilising generalised logarithm transformation. BMC Bioinformatics, 8, 234. doi: 10.1186/1471-2105-8-234.
42. Poynton, H. C., Varshavsky, J. R., Chang, B., et al. (2007). Daphnia magna ecotoxicogenomics provides mechanistic insights into metal toxicity. Environmental Science and Technology, 41, 1044-1050. doi: 10.1021/es0615573.
43. REACH. (2006). Registration, evaluation, authorisation and restriction of chemicals REACH, regulation no. 1907/2006. The European Parliament and The Council of The European Union.
44. Robosky, L. C., Robertson, D. G., Baker, J. D., Rane, S., & Reily, M. D. (2002). In vivo toxicity screening programs using metabonomics. Combinatorial Chemistry & High Throughput Screening, 5, 651-662.
45. Sandbacka, M., Christianson, I., & Isomaa, B. (2000). The acute toxicity of surfactants on fish cells, Daphnia magna and fish-a comparative study. Toxicology In Vitro, 14, 61-68. doi: 10.1016/ S0887-2333(99)00083-1.
46. Sangster, T. P., Wingate, J. E., Burton, L., Teichert, F., & Wilson, I. D. (2007). Investigation of analytical variation in metabonomic analysis using liquid chromatography/mass spectrometry. Rapid Communications in Mass Spectrometry, 21, 2965-2970. doi: 10.1002/ rcm.3164.
47. Santojanni, A., Gorbi, G., & Sartore, F. (1998). Prediction of fecundity in chronic toxicity tests on Daphnia magna. Water Research, 32, 3146-3156. doi: 10.1016/S0043-1354(98)00052-9.
48. Smolders, R., Baillieul, M., & Blust, R. (2005). Relationship between the energy status of Daphnia magna and its sensitivity to environmental stress. Aquatic Toxicology (Amsterdam, Netherlands), 73, 155-170. doi: 10.1016/j.aquatox.2005.03.006.
49. Soetaert, A., Vandenbrouck, T., van der Ven, K., et al. (2007a). Molecular responses during cadmium-induced stress in Daphnia magna: Integration of differential gene expression with higher-level effects. Aquatic Toxicology (Amsterdam, Netherlands), 83, 212-222. doi: 10.1016/ j.aquatox.2007.04.010.
50. Soetaert, A., van der Ven, K., Moens, L. N., et al. (2007b). Daphnia magna and ecotoxicogenomics: Gene expression profiles of the anti-ecdysteroidal fungicide fenarimol using energy-, molting- and life stage-related cDNA libraries. Chemosphere, 67, 60-71. doi: 10.1016/ j.chemosphere.2006.09.076.
51. Soga, T., Baran, R., Suematsu, M., et al. (2006). Differential metabolomics reveals ophthalmic acid as an oxidative stress biomarker indicating hepatic glutathione consumption. The Journal of Biological Chemistry, 281, 16768-16776. doi: 10.1074/jbc.M601876200.
52. Southam, A. D., Payne, T. G., Cooper, H. J., Arvanitis, T. N., & Viant, M. R. (2007). Dynamic range and mass accuracy of wide-scan direct infusion nanoelectrospray Fourier transform ion cyclotron resonance mass spectrometry-based metabolomics increased by the spectral stitching method. Analytical Chemistry, 79, 4595-4602. doi: 10.1021/ac062446p.
53. Stohs, S. J., & Bagchi, D. (1995). Oxidative mechanisms in the toxicity of metal ions. Free Radical Biology and Medicine, 18, 321-336. doi: 10.1016/0891-5849(94)00159-H.
54. Sugimoto, H., Matsuzaki, S., Hamana, K., Yamada, S., & Kobayashi, S. (1991). Alpha-tocopherol and superoxide-dismutase suppress and diethyldithiocarbamate and phorone enhance the lipopolysaccharide-induced increase in N1-acetylspermidine concentrations in mouse-liver. Circulatory Shock, 33, 171-177.
55. Sumner, L. W., Amberg, A., Barrett, D., et al. (2007). Proposed minimum reporting standards for chemical analysis. Metabolomics, 3, 211-221. doi: 10.1007/s11306-007-0082-2.
56. Takahashi, H., Kai, K., Shinbo, Y., et al. (2008). Metabolomics approach for determining growth-specific metabolites based on Fourier transform ion cyclotron resonance mass spectrometry. Analytical and Bioanalytical Chemistry, 391, 2769-2782. doi: 10.1007/s00216-008-2195-5.
57. Tsui, M. T., & Wang, W. X. (2007). Biokinetics and tolerance development of toxic metals in Daphnia magna. Environmental Toxicology and Chemistry, 26, 1023-1032. doi: 10.1897/06-430R.1.
58. US-EPA. (2004). Potential implications of genomics for regulatory and risk assessment applications at EPA (p. 70). United States Environmental Protection Agency.
59. Viant, M. R., Bundy, J. G., Pincetich, C. A., de Ropp, J. S., & Tjeerdema, R. S. (2005). NMR-derived developmental metabolic trajectories: An approach for visualizing the toxic actions of trichloroethylene during embryogenesis. Metabolomics, 1, 149-158. doi: 10.1007/s11306-005-4429-2.
60. 1H NMR metabolomics. Aquatic Toxicology (Amsterdam, Netherlands), 77, 359-371. doi: 10.1016/j.aquatox.2006.01.009.
61. Watanabe, H., Takahashi, E., Nakamura, Y., et al. (2007). Development of a Daphnia magna DNA microarray for evaluating the toxicity of environmental chemicals. Environmental Toxicology and Chemistry, 26, 669-676. doi: 10.1897/06-075R.1.
62. Westerhuis, J. A., Hoefsloot, H. C. J., Smit, S., et al. (2008). Assessment of PLSDA cross validation. Metabolomics, 4, 81-89. doi: 10.1007/s11306-007-0099-6.
63. Wu, H., Southam, A. D., Hines, A., & Viant, M. R. (2008). High throughput tissue extraction protocol for NMR- and MS-based metabolomics. Analytical Biochemistry, 372, 204-212. doi: 10.1016/ j.ab.2007.10.002.
64. Zhang, L. K., Rempel, D., Pramanik, B. N., & Gross, M. L. (2005). Accurate mass measurements by Fourier transform mass spectrometry. Mass Spectrometry Reviews, 24, 286-309. doi: 10.1002/mas.20013.