Towards a system level understanding of non-model organisms sampled from the environment: A network biology approach

PLoS Computational Biology

Volumn 7, Issue 8, 2011, Pages

  Williams, Tim D ^a   Turan, Nil ^a   Diab, Amer M ^b   Wu, Huifeng ^a,c   Mackenzie, Carolynn ^b   Bartie, Katie L ^b   Hrydziuszko, Olga ^a   Lyons, Brett P ^d   Stentiford, Grant D ^d   Herbert, John M ^a   Abraham, Joseph K ^e,f   Katsiadaki, Ioanna ^d   Leaver, Michael J ^b   Taggart, John B ^b   George, Stephen G ^b   Viant, Mark R ^a   Chipman, Kevin J ^a   Falciani, Francesco ^a  

^a UNIVERSITY OF BIRMINGHAM   (United Kingdom)

^b UNIVERSITY OF STIRLING   (United Kingdom)

^c YANTAI INSTITUTE OF COASTAL ZONE RESEARCH   (China)

^d CENTRE FOR ENVIRONMENT   (United Kingdom)

^e CASE WESTERN RESERVE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^f IOWA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOTECHNOLOGY;

'OMICS'; FIELD POPULATIONS; LIVING ORGANISMS; MODEL ORGANISMS; MODEL SPECIES; MULTILEVELS; NETWORK BIOLOGY; SYSTEM LEVELS; SYSTEMS BIOLOGY; WILD POPULATIONS;

BIOLOGY;

ANIMAL TISSUE; ARTICLE; BIOLOGICAL MONITORING; CONTROLLED STUDY; ENVIRONMENTAL EXPOSURE; EUROPE; EVOLUTIONARY ADAPTATION; FLOUNDER; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; LIVER TOXICITY; MALE; METABOLOMICS; MOLECULAR DYNAMICS; MORPHOMETRICS; NONHUMAN; PHENOTYPIC VARIATION; PREDICTION; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY; TRANSCRIPTION REGULATION; TRANSCRIPTOMICS; WILD SPECIES; ANALYSIS OF VARIANCE; ANIMAL; BIOLOGICAL MODEL; CLUSTER ANALYSIS; DRUG EFFECT; ECOSYSTEM; HUMAN; LIVER; METABOLISM; METHODOLOGY; SEDIMENT;

PLATICHTHYS FLESUS;

TRANSCRIPTOME;

ANALYSIS OF VARIANCE; ANIMALS; CLUSTER ANALYSIS; ECOSYSTEM; ENVIRONMENTAL EXPOSURE; FLOUNDER; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORKS; GEOLOGIC SEDIMENTS; HUMANS; LIVER; METABOLIC NETWORKS AND PATHWAYS; METABOLOMICS; MODELS, BIOLOGICAL; SYSTEMS BIOLOGY; TRANSCRIPTOME;

EID: 80052324168     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1002126     Document Type: Article

References (67)

1. Van Aggelen G, Ankley GT, Baldwin WS, Bearden DW, Benson WH, et al. (2010) Integrating omic technologies into aquatic ecological risk assessment and environmental monitoring: hurdles, achievements, and future outlook. Environ Health Perspect 118: 1-5.
2. Roling JA, Bain LJ, Gardea-Torresdey J, Key PB, Baldwin WS, (2007) Using mummichog (Fundulus heteroclitus) arrays to monitor the effectiveness of remediation at a superfund site in Charleston, South Carolina, U.S.A. Environ Toxicol Chem 26: 1205-1213.
3. Baker ME, Ruggeri B, Sprague LJ, Eckhardt-Ludka C, Lapira J, et al. (2009) Analysis of endocrine disruption in Southern California coastal fish using an aquatic multispecies microarray. Environ Health Perspect 117: 223-230.
4. Moran PW, Aluru N, Black RW, Vijayan MM, (2007) Tissue contaminants and associated transcriptional response in trout liver from high elevation lakes of Washington. Environ Sci Technol 41: 6591-6597.
5. Fisher MA, Oleksiak MF, (2007) Convergence and divergence in gene expression among natural populations exposed to pollution. BMC Genomics 8: 108.
6. Larsen PF, Nielsen EE, Williams TD, Hemmer-Hansen J, Chipman JK, et al. (2007) Adaptive differences in gene expression in European flounder (Platichthys flesus). Mol Ecol 16: 4674-4683.
7. Larsen PF, Nielsen EE, Williams TD, Loeschcke V, (2008) Intraspecific variation in expression of candidate genes for osmoregulation, heme biosynthesis and stress resistance suggests local adaptation in European flounder (Platichthys flesus). Heredity 101: 247-259.
8. Williams TD, Diab A, Ortega F, Sabine VS, Godfrey RE, et al. (2008) Transcriptomic responses of European flounder (Platichthys flesus) to model toxicants. Aquat Toxicol 90: 83-91.
9. Falciani F, Diab AM, Sabine V, Williams TD, Ortega F, et al. (2008) Hepatic transcriptomic profiles of European flounder (Platichthys flesus) from field sites and computational approaches to predict site from stress gene responses following exposure to model toxicants. Aquat Toxicol 90: 92-101.
10. Koehler A, (2004) The gender-specific risk to liver toxicity and cancer of flounder (Platichthys flesus (L.)) at the German Wadden Sea coast. Aquat Toxicol 70: 257-276.
11. Stentiford GD, Longshaw M, Lyons BP, Jones G, Green M, et al. (2003) Histopathological biomarkers in estuarine fish species for the assessment of biological effects of contaminants. Mar Environ Res 55: 137-159.
12. Lyons BP, Stentiford GD, Green M, Bignell J, Bateman K, et al. (2004) DNA adduct analysis and histopathological biomarkers in European flounder (Platichthys flesus) sampled from UK estuaries. Mutat Res 552: 177-186.
13. Basso K, Margolin AA, Stolovitzky G, Klein U, Dalla-Favera R, et al. (2005) Reverse engineering of regulatory networks in human B cells. Nat Genet 37: 382-390.
14. Lyons BP, Thain JE, Stentiford GD, Hylland K, Davies IM, et al. (2010) Using biological effects tools to define Good Environmental Status under the European Union Marine Strategy Framework Directive. Mar Pollut Bull 60: 1647-1651.
15. Davis AP, Murphy CG, Saraceni-Richards CA, Rosenstein MC, Wiegers TC, et al. (2009) Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical-gene-disease networks. Nucleic Acids Res 37: D786-792.
16. Pistocchi A, Loos R, (2009) A map of European emissions and concentrations of PFOS and PFOA. Environ Sci Technol 43: 9237-9244.
17. Kiersch K, Jandl G, Meissner R, Leinweber P, (2010) Small scale variability of chlorinated POPs in the river Elbe floodplain soils (Germany). Chemosphere 79: 745-753.
18. Blumberg PM, (1988) Protein kinase C as the receptor for the phorbol ester tumor promoters: sixth Rhoads memorial award lecture. Cancer Res 48: 1-8.
19. Hook SE, Lampi MA, Febbo EJ, Ward JA, Parkerton TF, (2010) Temporal patterns in the transcriptomic response of rainbow trout, Oncorhynchus mykiss, to crude oil. Aquat Toxicol 99: 320-329.
20. Leaver MJ, Diab A, Boukouvala E, Williams TD, Chipman JK, et al. (2010) Hepatic gene expression in flounder chronically exposed to multiply polluted estuarine sediment: Absence of classical exposure 'biomarker' signals and induction of inflammatory, innate immune and apoptotic pathways. Aquat Toxicol 96: 234-245.
21. Southam AD, Easton JM, Stentiford GD, Ludwig C, Arvanitis TN, et al. (2008) Metabolic changes in flatfish hepatic tumours revealed by NMR-based metabolomics and metabolic correlation networks. J Proteome Res 7: 5277-5285.
22. Small HJ, Williams TD, Sturve J, Chipman JK, Southam AD, et al. (2010) Gene expression analyses of hepatocellular adenoma and hepatocellular carcinoma from the marine flatfish Limanda limanda. Dis Aquat Organ 88: 127-141.
23. Fricke B, Heink S, Steffen J, Kloetzel PM, Kruger E, (2007) The proteasome maturation protein POMP facilitates major steps of 20S proteasome formation at the endoplasmic reticulum. EMBO Rep 8: 1170-1175.
24. Tijet N, Boutros PC, Moffat ID, Okey AB, Tuomisto J, et al. (2006) Aryl hydrocarbon receptor regulates distinct dioxin-dependent and dioxin-independent gene batteries. Mol Pharmacol 69: 140-153.
25. Wiseman SB, Vijayan MM, (2007) Aryl hydrocarbon receptor signaling in rainbow trout hepatocytes: role of hsp90 and the proteasome. Comp Biochem Physiol C Toxicol Pharmacol 146: 484-491.
26. Santiago-Josefat B, Pozo-Guisado E, Mulero-Navarro S, Fernandez-Salguero PM, (2001) Proteasome inhibition induces nuclear translocation and transcriptional activation of the dioxin receptor in mouse embryo primary fibroblasts in the absence of xenobiotics. Mol Cell Biol 21: 1700-1709.
27. Sun B, Karin M, (2008) NF-kappaB signaling, liver disease and hepatoprotective agents. Oncogene 27: 6228-6244.
28. Andoh T, (2007) Amino acids are more important insulinotropins than glucose in a teleost fish, barfin flounder (Verasper moseri). Gen Comp Endocrinol 151: 308-317.
29. Thangavel P, Sumathiral K, Karthikeyan S, Ramaswamy M, (2005) Endocrine response of the freshwater teleost, Sarotherodon mossambicus (Peters) to dimecron exposure. Chemosphere 61: 1083-1092.
30. Yamamoto Y, Moore R, Hess HA, Guo GL, Gonzalez FJ, et al. (2006) Estrogen receptor alpha mediates 17alpha-ethynylestradiol causing hepatotoxicity. J Biol Chem 281: 16625-16631.
31. Maass T, Thieringer FR, Mann A, Longerich T, Schirmacher P, et al. (2010) Liver specific overexpression of platelet-derived growth factor-B accelerates liver cancer development in chemically induced liver carcinogenesis. Int J Cancer 128: 1259-1268.
32. Bierie B, Moses HL, (2010) Transforming growth factor beta (TGF-beta) and inflammation in cancer. Cytokine Growth Factor Rev 21: 49-59.
33. Yazawa R, Hirono I, Ohira T, Aoki T, (2005) Functional analysis of tumor necrosis factor gene promoter from Japanese flounder, Paralichthys olivaceus, using fish cell lines. Dev Comp Immunol 29: 73-81.
34. Farazi PA, DePinho RA, (2006) Hepatocellular carcinoma pathogenesis: from genes to environment. Nat Rev Cancer 6: 674-687.
35. Fernandez M, Semela D, Bruix J, Colle I, Pinzani M, et al. (2009) Angiogenesis in liver disease. J Hepatol 50: 604-620.
36. Warner FJ, Lubel JS, McCaughan GW, Angus PW, (2007) Liver fibrosis: a balance of ACEs? Clin Sci (Lond) 113: 109-118.
37. Yoshiji H, Kuriyama S, Yoshii J, Ikenaka Y, Noguchi R, et al. (2001) Angiotensin-II type 1 receptor interaction is a major regulator for liver fibrosis development in rats. Hepatology 34: 745-750.
38. Jonsson JR, Clouston AD, Ando Y, Kelemen LI, Horn MJ, et al. (2001) Angiotensin-converting enzyme inhibition attenuates the progression of rat hepatic fibrosis. Gastroenterology 121: 148-155.
39. Stentiford G, Bignell JP, Lyons BP, Feist SW, (2009) Site-specific disease profiles in fish and their use in environmental monitoring. Marine Ecology Progress Series 381: 1-5.
40. Feist SW, Lang T, Stentiford GD, Kohler A, (2004) Biological effects of contaminants: use of liver pathology of the European flatfish dab (Limanda limanda L.) and flounder (Platichthys flesus L.) for monitoring. ICES Techniques in Marine Environmental Sciences 38: 42.
41. Kirby MF, Allen YT, Dyer RA, Feist SW, Katsiadaki I, et al. (2004) Surveys of plasma vitellogenin and intersex in male flounder (Platichthys flesus) as measures of endocrine disruption by estrogenic contamination in United Kingdom estuaries: temporal trends, 1996 to 2001. Environ Toxicol Chem 23: 748-758.
42. George SG, Young P, (1986) The time course of effects of cadmium and 3-methylcholanthrene on activities of enzymes of xenobiotic metabolism and metallothionein levels in the plaice, Pleuronectes platessa. Comp Biochem Physiol C 83: 37-44.
43. Williams TD, Lee JS, Sheader DL, Chipman JK, (2000) The cytochrome P450 1A gene (CYP1A) from European flounder (Platichthys flesus), analysis of regulatory regions and development of a dual luciferase reporter gene system. Mar Environ Res 50: 1-6.
44. Leaver MJ, Wright J, George SG, (1997) Structure and expression of a cluster of glutathione S-transferase genes from a marine fish, the plaice (Pleuronectes platessa). Biochemical Journal 321: 405-412.
45. Leaver MJ, Boukouvala E, Antonopoulou E, Diez A, Favre-Krey L, et al. (2005) Three peroxisome proliferator-activated receptor isotypes from each of two species of marine fish. Endocrinology 146: 3150-3162.
46. Raymond M, Rousset F, (1995) GENEPOP(V. 1.2): A population genetics software for exact tests and ecumenicism. J Hered 86: 248-249.
47. Felsenstein J, (1989) PHYLIP- Phylogeny Inference Package (Version 3.2). Cladistics 5: 164-166.
48. Williams TD, Diab AM, George SG, Godfrey RE, Sabine V, et al. (2006) Development of the GENIPOL European flounder (Platichthys flesus) microarray and determination of temporal transcriptional responses to cadmium at low dose. Environ Sci Technol 40: 6479-6488.
49. Diab AM, Williams TD, Sabine VS, Chipman JK, George SG, (2008) The GENIPOL European flounder Platichthys flesus L. toxicogenomics microarray: application for investigation of the response to furunculosis vaccination. J Fish Biol 72: 2154-2169.
50. Wu H, Southam AD, Hines A, Viant MR, (2008) High-throughput tissue extraction protocol for NMR- and MS-based metabolomics. Anal Biochem 372: 204-212.
51. Huang X, Madan A, (1999) CAP3: A DNA sequence assembly program. Genome Res 9: 868-877.
52. Bligh EG, Dyer WJ, (1959) A rapid method of total lipid extraction and purification. Can J Biochem Physiol 37: 911-917.
53. Katsiadaki I, Williams TD, Ball JS, Bean TP, Sanders MB, et al. (2010) Hepatic transcriptomic and metabolomic responses in the Stickleback (Gasterosteus aculeatus) exposed to ethinyl-estradiol. Aquat Toxicol 97: 174-187.
54. Daub CO, Kloska S, Selbig J, (2003) MetaGeneAlyse: analysis of integrated transcriptional and metabolite data. Bioinformatics 19: 2332-2333.
55. Johnson WE, Li C, Rabinovic A, (2007) Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 8: 118-127.
56. Golotvin S, Williams A, (2000) Improved baseline recognition and modeling of FT NMR spectra. J Magn Reson 146: 122-125.
57. Benjamini Y, Hochberg Y, (1995) Controlling the false discovery rate: A practical and powerful approach to multiple testing. J R Statist Soc B 57: 289-300.
58. Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, et al. (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21: 3674-3676.
59. Gotz S, Garcia-Gomez JM, Terol J, Williams TD, Nagaraj SH, et al. (2008) High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res 36: 3420-3435.
60. Bluthgen N, Brand K, Cajavec B, Swat M, Herzel H, et al. (2005) Biological profiling of gene groups utilizing Gene Ontology. Genome Inform 16: 106-115.
61. Herbert JM, Buffa FM, Vorschmitt H, Egginton S, Bicknell R, (2009) A new procedure for determining the genetic basis of a physiological process in a non-model species, illustrated by cold induced angiogenesis in the carp. BMC Genomics 10: 490.
62. Saeed AI, Bhagabati NK, Braisted JC, Liang W, Sharov V, et al. (2006) TM4 microarray software suite. Methods Enzymol 411: 134-193.
63. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, et al. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13: 2498-2504.
64. Abraham K, Sameith K, Falciani F, Improving functional module detection; 2009; Ohio. pp. 110-115.
65. Trevino V, Falciani F, (2006) GALGO: an R package for multivariate variable selection using genetic algorithms. Bioinformatics 22: 1154-1156.
66. Dennis G Jr, Sherman BT, Hosack DA, Yang J, Gao W, et al. (2003) DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol 4: P3.
67. Huang da W, Sherman BT, Lempicki RA, (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4: 44-57.