Systems toxicology: using the systems biology approach to assess chemical pollutants in the environment

Advances in Experimental Biology

Volumn 2, Issue , 2008, Pages 249-281

  Handy, Richard D ^a  

^a UNIVERSITY OF PLYMOUTH   (United Kingdom)

Author keywords

bioinformatics; cellular automata; chemicals; control system; data modelling; ecotoxicology; environmental protection; input; interactomes; modules; networks; output; Petri nets; pollution; risk assessment; software; systems biology; systems toxicology; toxicogenomics

Indexed keywords

EID: 45249108875     PISSN: 18722423     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S1872-2423(08)00007-0     Document Type: Review

References (53)

1. Aderem A., and Smith K.D. A system approach to dissecting immunity and inflammation. Semin. Immunol. 16 (2004) 55-67
2. Alves R., Antunes F., and Salvador A. Tools for kinetic modeling of biochemical networks. Nat. Biotechnol. 24 (2006) 667-672
3. Ashauer R., Boxall A., and Brown C. Predicting effects on aquatic organisms from fluctuating or pulsed exposure to pesticides. Environ. Toxicol. Chem. 25 (2006) 1899-1912
4. Baken K.A., Vandebriel R.J., Pennings J.L.A., Kleinjans J.C., and van Loveren H. Toxicogenomics in the assessment of immunotoxicity. Methods 41 (2007) 132-141
5. Barrett C.L., Kim T.Y., Kim H.U., Palsson B.O., and Lee S.Y. Systems biology as a foundation for genome-scale synthetic biology. Curr. Opin. Biotechnol. 17 (2006) 488-492
6. Brain R.A., Sanderson H., Sibley P.K., and Solomon K.R. Probabilistic ecological hazard assessment: Evaluating pharmaceutical effects on acquatic higher plants as an example. Ecotoxicology and Environmental Safety 64 (2006) 128-135
7. Craig A., Sidaway J., Holmes E., Orton T., Jackson D., Rowlinson R., Nickson J., Tonge R., Wilson I., and Nicholson J. Systems toxicology: Integrated genomic, proteomic and metabonomic analysis of methapyrilene induced hepatotoxicity in the rat. J. Proteome Res. 5 (2006) 1586-1601
8. Cusick M.E., Klitgord N., Vidal M., and Hill D.E. Interactome: Gateway into systems biology. Hum.Mol. Genet. 14 (2005) R171-R181
9. Dalzell D.J.B., Alte S., Aspichueta E., de la Sota A., Etxebarria J., Gutierrez M., Hoffmann C.C., Sales D., Obst U., and Christofi N. A comparison of five rapid direct toxicity assessment methods to determine toxicity of pollutants to activated sludge. Chemosphere 47 (2002) 535-545
10. Doull J., Borzelleca J.F., Becker R., Daston G., DeSesso J., Fan A., Fenner-Crisp P., Holsapple M., Holson J., Llewellyn G.C., MacGregor J., Seed J., Walls I., Woo Y.T., and Olin S. Framework for use of toxicity screening tools in context-based decision-making. Food Chem. Toxicol. 45 (2007) 759-796
11. Galloway T., and Handy R. Immunotoxicity of organophosphorus pesticides. Ecotoxicology 12 (2003) 345-363
12. Handy R.D. Intermittent exposure to aquatic pollutants-assessment, toxicity and sub-lethal responses in fish and invertebrates. Comp. Biochem. Physiol. C 107C (1994) 171-184
13. Handy R.D., Galloway T.S., and Depledge M.H. A proposal for the use of biomarkers for the assessment of chronic pollution and in regulatory toxicology. Ecotoxicology 12 (2003) 331-343
14. Handy R.D., Jha A.N., and Depledge M.H. Biomarker approaches for ecotoxicological biomonitoring at different levels of biological organisation. In: Burden F., McKelvie I., Förstner U., and Guenther A. (Eds). Handbook of Environmental Monitoring (2002), McGraw-Hill, New York 9.1-9.32
15. Heijne W.H.M., Kienhuis A.S., van Ommen B., Stierum R.H., and Groten J.P. Systems toxicology: Applications of toxicogenomics, transcriptomics, proteomics and metabolomics in toxicology. Expert Rev. Proteomics 2 (2005) 767-780
16. Hollis L., McGeer J.C., McDonald D.G., and Wood C.M. Effects of long term sublethal Cd exposure in rainbow trout during soft water exposure: Implications for biotic ligand modelling. Aquat. Toxicol. 51 (2000) 93-105
17. Hoyle I., and Handy R.D. Dose-dependent inorganic mercury absorption by isolated perfused intestine of rainbow trout, Oncorhynchus mykiss, involves both amiloride-sensitive and energy-dependent pathways. Aquat. Toxicol. 72 (2005) 147-159
18. Hutchings M., Johnson I., Hayes E., Girling A.E., Thain J., Thomas K., Benstead R., Whale G., Wordon J., Maddox R., and Chown P. Toxicity reduction evaluation, toxicity identification evaluation and toxicity tracking in direct toxicity assessment. Ecotoxicology 13 (2004) 475-484
19. Ivakhno S. From functional genomics to systems biology - meeting report based on the presentations at the 3rd EMBL Biennial Symposium 2006 (Heidelberg, Germany). FEBS J. 274 (2007) 2439-2448
20. Kammenga J.E., Herman M.A., Ouborg N.J., Johnson L., and Breitling R. Microarray challenges in ecology. Trends Ecol. Evol. 22 (2007) 273-279
21. Kim S.J., Kweon O., Jones R.C., Freeman J.P., Edmondson R.D., and Cerniglia C.E. Complete and integrated pyrene degradation pathway in Mycobacterium vanbaalenii PYR-1 based on systems biology. J. Bacteriol. 189 (2007) 464-472
22. Kitano H. Systems biology: A brief overview. Science 295 (2002) 1662-1664
23. Klingmuller U., Bauer A., Bohl S., Nickel P.J., Breitkopf K., Dooley S., Zellmer S., Kern C., Merfort I., Sparna T., Donauer J., Walz G., Geyer M., Kreutz C., Hermes M., Gotschel F., Hecht A., Walter D., Egger L., Neubert K., Borner C., Brulport M., Schormann W., Sauer C., Baumann F., Preiss R., MacNelly S., Godoy P., Wiercinska E., Ciuclan L., Edelmann J., Zeilinger K., Heinrich M., Zanger U.M., Gebhardt R., Maiwald T., Heinrich R., Timmer J., von Weizsacker F., and Hengstler J.G. Primary mouse hepatocytes for systems biology approaches: A standardized in vitro system for modelling of signal transduction pathways. IEE Proc. Syst. Biol. 153 (2006) 433-447
24. Kremling A., and Saez-Rodriguez J. Systems biology - an engineering perspective. J. Biotechnol. 129 (2007) 329-351
25. Laaksonen R., Katajamaa M., Päivä H., Sysi-Aho M., Saarinen L., Päivi J., Lütjohann D., Smet J., Van Coster R., Seppänen-Laakso T., Lehtimäki T., Soini J., and Orešič M. A systems biology strategy reveals biological pathways and plasma biomarker candidates for potentially toxic statin-induced changes in muscle. PLoS ONE 1 1 (2006) e97 doi: 10.1371/journal.pone.0000097
26. Linden R., Sartori S., Kellermann E., and Souto A.A. Substance identification in systematic toxicological analysis using a computer system for chromatographic parameter calculation and database retrieval. Quim. Nova 30 (2007) 468-475
27. Mansury Y., Kimura M., Lobo J., and Deisboeck T.S. Emerging patterns in tumor systems: Simulating the dynamics of multicellular clusters with an agent-based spatial agglomeration model. J. Theor. Biol. 219 (2002) 343-370
28. Martelli A., Rousselet E., Dycke C., Bouron A., and Moulis J.M. Cadmium toxicity in animal cells by interference with essential metals. Biochimie 88 (2006) 1807-1814
29. Martelli C., Giansanti A., Arisi I., and Rosato V. Asymptotic states and topological structure of an activation-deactivation chemical network. J. Theor. Biol. 245 (2007) 423-432
30. Materi W., and Wishart D.S. Computational systems biology in drug discovery and development: Methods and applications. Drug Discov. Today 12 (2007) 295-303
31. Mazzatorta P., Tran L.A., Schilter B., and Grigorov M. Integration of structure-activity relationship and artificial intelligence systems to improve in silico prediction of Ames test mutagenicity. J. Chem. Inf. Model. 47 (2007) 34-38
32. McCarty L.S., and Borgert C.J. Review of the toxicity of chemical mixtures: Theory, policy, and regulatory practice. Regul. Toxicol. Pharmacol. 45 (2006) 119-143
33. Moens L.N., Smolders R., van der Ven K., van Remortel P., Del-Favero J., and De Coen W.M. Effluent impact assessment using microarray-based analysis in common carp: A systems toxicology approach. Chemosphere 67 (2007) 2293-2304
34. Moore D.F., Gelderman M.P., Ferreira P.A., Fuhrmann S.R., Yi H.Q., Elkahloun A., Lix L.M., Brady R.O., Schiffmann R., and Goldin E. Genomic abnormalities of the murine model of Fabry disease after disease-related perturbation, a systems biology approach. Proc. Natl. Acad. Sci. USA 104 (2007) 8065-8070
35. Munter T., Cottrell L., Ghai R., Golding B.T., and Watson W.P. The metabolism and molecular toxicology of chloroprene. Chem. Biol. Interact. 166 (2007) 323-331
36. Noble D. The rise of computational biology. Nat. Rev. Mol. Cell. Biol. 3 (2002) 460-463
37. Noble D. Systems biology and the heart. Biosystems 83 (2006) 75-80
38. Pollino C.A., Woodberry O., Nicholson A., Korb K., and Hart B.T. Parameterisation and evaluation of a Bayesian network for use in an ecological risk assessment. Environ. Modell. Software 22 (2007) 1140-1152
39. Procaccini G., Olsen J.L., and Reusch T.B.H. Contribution of genetics and genomics to seagrass biology and conservation. J. Exp. Mar. Biol. Ecol. 350 (2007) 234-259
40. Randall D., Burggren W., and French K. Eckert's Animal Physiology. 5th Edition (2002), W. H. Freeman, New York
41. Robbens J., van der Ven K., Maras M., Blust R., and De Coen W. Ecotoxicological risk assessment using DNA chips and cellular reporters. Trends Biotechnol. 25 (2007) 460-466
42. Schäfer R.B., Caquet T., Siimes K., Mueller R., Lagadic L., and Liess M. Effects of pesticides on community structure and ecosystem functions in agricultural streams of three biogeographical regions in Europe. Sci. Total Environ. 382 (2007) 272-285
43. Simon-Hettich B., Rothfuss A., and Steger-Hartmann T. Use of computer-assisted prediction of toxic effects of chemical substances. Toxicology 224 (2006) 156-162
44. Slikker W., Paule M.G., Wright L.K.M., Patterson T.A., and Wang C. Systems biology approaches for toxicology. J. Appl. Toxicol. 27 (2007) 201-217
45. Sulkava M., Luyssaert S., Rautio P., Janssens I.A., and Hollmen J. Modelling the effects of varying data quality on trend detection in environmental monitoring. Ecol. Inform. 2 (2007) 167-176
46. Thomas M.A., and Klaper R. Genomics for the ecological toolbox. Trends Ecol. Evol. 19 (2004) 439-444
47. Waters M., Boorman G., Bushel P., Cunningham M., Irwin R., Merrick A., Olden K., Paules R., Selkirk J., Stasiewicz S., Weis B., Van Houten B., Walker N., and Tennant R. Systems toxicology and the chemical effects in biological systems (CEBS) knowledge base. Environ. Health Perspect. 111 (2003) 811-824
48. Waters M.D., and Fostel J.M. Toxicogenomics and systems toxicology: Aims and prospects. Nat. Rev. Genet. 5 (2004) 936-948
49. Waters M., and Yauk C. Consensus recommendations to promote and advance predictive systems toxicology and toxicogenomics. Environ. Mol. Mutagen. 48 (2007) 400-403
50. Wharfe J., Tinsley D., and Crane M. Managing complex mixtures of chemicals - a forward look from the regulators' perspective. Ecotoxicology 13 (2004) 485-492
51. Wolkenhauer O. Systems biology: The reincarnation of systems theory applied in biology?. Brief. Bioinform. 2 (2001) 258-270
52. Wolkenhauer O., and Hofmeyr J.H.S. An abstract cell model that describes the self-organization of cell function in living systems. J. Theor. Biol. 246 (2007) 461-476
53. Yang, E., Maguire, T., Yarmush, M. L., Berthiaume, F. and Androulakis, I. P. (2007). Bioinformatics analysis of the early inflammatory response in a rat thermal injury model. BMC Bioinformatics 8(10). Available at http://www.biomedcentral.com/1471-2105/8/10