Next-generation proteomics: Toward customized biomarkers for environmental biomonitoring

Environmental Science and Technology

Volumn 48, Issue 23, 2014, Pages 13560-13572

  Trapp, Judith ^a,b   Armengaud, Jean ^b   Salvador, Arnaud ^c   Chaumot, Arnaud ^a   Geffard, Olivier ^a  

^a UR MALY   (France)

^b DIF   (France)

^c UNIVERSITÉ LYON 1   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMALS; ECOSYSTEMS; PROTEINS; PROTEOMICS;

BIO-MARKER DISCOVERY; ECOTOXICOLOGICAL ASSESSMENT; ECOTOXICOLOGICAL TESTS; ENVIRONMENTAL BIOMONITORING; ENVIRONMENTAL ORGANISMS; IDENTIFICATION OF PROTEINS; PHYSIOLOGICAL FUNCTIONS; TARGETED PROTEOMICS;

BIOMARKERS;

ACETYLCHOLINESTERASE; ACTIN; ALDEHYDE DEHYDROGENASE; ARGININE KINASE; BIOLOGICAL MARKER; CARBOXYLESTERASE; CATALASE; ENOLASE; ETHOXYRESORUFIN DEETHYLASE; GLUCOSE 6 PHOSPHATE DEHYDROGENASE; GLUTATHIONE; GLUTATHIONE DISULFIDE; GLUTATHIONE PEROXIDASE; GLUTATHIONE TRANSFERASE; HEAT SHOCK PROTEIN 70; HYDROXYACYLGLUTATHIONE HYDROLASE; METALLOTHIONEIN; MYOSIN; PROTEIN; PROTON TRANSPORTING ADENOSINE TRIPHOSPHATE SYNTHASE; TUBULIN; UBIQUITINATED PROTEIN; XENOBIOTIC AGENT; YOLK PROTEIN;

BIOMARKER; BIOMONITORING; DATABASE; ECOTOXICOLOGY; PROTEIN; PROTEOMICS;

AMINO ACID SEQUENCE; AMPHIPODA; ANTIGEN ANTIBODY REACTION; ARTICLE; BIOLOGICAL MONITORING; DEFENSE MECHANISM; ECOTOXICOLOGY; ENVIRONMENTAL MONITORING; ENZYME LINKED IMMUNOSORBENT ASSAY; GAMMARUS; GENOMICS; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; LIPID PEROXIDATION; MASS SPECTROMETRY; NONHUMAN; PHYSIOLOGY; POLYACRYLAMIDE GEL ELECTROPHORESIS; PROCAMBARUS CLARKII; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN TARGETING; PROTEOMICS; SENSITIVITY AND SPECIFICITY; ANIMAL; AQUATIC SPECIES; ECOLOGY; ECOSYSTEM; GENETICS; INVERTEBRATE; METABOLISM; PROCEDURES;

INVERTEBRATA; VERTEBRATA;

ANIMALS; AQUATIC ORGANISMS; BIOLOGICAL MARKERS; ECOLOGY; ECOSYSTEM; ECOTOXICOLOGY; ENVIRONMENTAL MONITORING; INVERTEBRATES; MASS SPECTROMETRY; PROTEINS; PROTEOMICS;

EID: 84918799920     PISSN: 0013936X     EISSN: 15205851     Source Type: Journal    
DOI: 10.1021/es501673s     Document Type: Article

References (125)

1. Kolkwitz, R.; Marsson, M. Ökologie der tierischen Saprobien Int. Rev. Ges. Hydrobiol. Hydrograph 1909, 2, 126-152
2. Attrill, M. J.; Depledge, M. H. Community and population indicators of ecosystem health: Targeting links between levels of biological organisation Aquat. Toxicol. 1997, 38 (1-3) 183-197
3. Clements, W. H. Integrating effects of contaminants across levels of biological organization: An overview J. Aquat. Ecosyst. Stress Recovery 2000, 7 (2) 113-116
4. Power, M. Recovery in aquatic ecosystems: an overview of knowledge and needs J. Aquat. Ecosyst. Stress Recovery 1998, 6 (3) 253-257
5. Depledge, M. H.; Fossi, M. C. The role of biomarkers in environmental assessment (2). Invertebrates Ecotoxicology 1994, 3 (3) 161-72
6. Forbes, V. E.; Palmqvist, A.; Bach, L. The use and misuse of biomarkers in ecotoxicology Environ. Toxicol. Chem. 2006, 25 (1) 272-280
7. Graves, P. R.; Haystead, T. A. Molecular biologist's guide to proteomics Microbiol. Mol. Biol. Rev. 2002, 66 (1) 39-63 table of contents.
8. Barnes, D. Invertebrate Zoology, 2 nd ed.; Saunders: Philadelphia, 1968.
9. Bedulina, D. S.; Timofeyev, M. A.; Zimmer, M.; Zwirnmann, E.; Menzel, R.; Steinberg, C. E. Different natural organic matter isolates cause similar stress response patterns in the freshwater amphipod, Gammarus pulex Environ. Sci. Pollut. Res. Int. 2010, 17 (2) 261-9
10. Bedulina, D. S.; Zimmer, M.; Timofeyev, M. A. Sub-littoral and supra-littoral amphipods respond differently to acute thermal stress Comp. Biochem. Physiol., Part B: Biochem Mol. Biol. 2010, 155 (4) 413-8
11. +)-ATPase in a series of hyper-regulating gammarid amphipods: enzyme characterisation and the effects of salinity acclimation Comp. Biochem. Physiol., A: Mol. Integr. Physiol. 2006, 144 (1) 24-32
12. Charron, L.; Geffard, O.; Chaumot, A.; Coulaud, R.; Queau, H.; Geffard, A.; Dedourge-Geffard, O. Effect of water quality and confounding factors on digestive enzyme activities in Gammarus fossarum Environ. Sci. Pollut. Res. Int. 2013, 20 (12) 9044-56
13. Correia, A. D.; Costa, F. O.; Neuparth, T.; Diniz, M. E.; Costa, M. H. Sub-lethal effects of copper-spiked sediments on the marine amphipod Gammarus locusta: Evidence of hormesis? Ecotoxicol. Environ. Res. 2001, 2) 32-38
14. Dedourge-Geffard, O.; Charron, L.; Hofbauer, C.; Gaillet, V.; Palais, F.; Lacaze, E.; Geffard, A.; Geffard, O. Temporal patterns of digestive enzyme activities and feeding rate in gammarids (Gammarus fossarum) exposed to inland polluted waters Ecotoxicol. Environ. Saf 2013, 97, 139-46
15. Dedourge-Geffard, O.; Palais, F.; Biagianti-Risbourg, S.; Geffard, O.; Geffard, A. Effects of metals on feeding rate and digestive enzymes in Gammarus fossarum: An in situ experiment Chemosphere 2009, 77 (11) 1569-76
16. Felten, V.; Charmantier, G.; Mons, R.; Geffard, A.; Rousselle, P.; Coquery, M.; Garric, J.; Geffard, O. Physiological and behavioural responses of Gammarus pulex (Crustacea: Amphipoda) exposed to cadmium Aquat. Toxicol. 2008, 86 (3) 413-25
17. Frank, S. N.; Godehardt, S.; Nachev, M.; Trubiroha, A.; Kloas, W.; Sures, B. Influence of the cestode Ligula intestinalis and the acanthocephalan Polymorphus minutus on levels of heat shock proteins (HSP70) and metallothioneins in their fish and crustacean intermediate hosts Environ. Pollut. 2013, 180, 173-9
18. Gismondi, E.; Rigaud, T.; Beisel, J. N.; Cossu-Leguille, C. Microsporidia parasites disrupt the responses to cadmium exposure in a gammarid Environ. Pollut. 2012, 160 (1) 17-23
19. Issartel, J.; Boulo, V.; Wallon, S.; Geffard, O.; Charmantier, G. Cellular and molecular osmoregulatory responses to cadmium exposure in Gammarus fossarum (Crustacea, Amphipoda) Chemosphere 2010, 81 (6) 701-10
20. Jubeaux, G.; Simon, R.; Salvador, A.; Lopes, C.; Lacaze, E.; Queau, H.; Chaumot, A.; Geffard, O. Vitellogenin-like protein measurement in caged Gammarus fossarum males as a biomarker of endocrine disruptor exposure: Inconclusive experience Aquat. Toxicol. 2012, 122-123, 9-18
21. Jubeaux, G.; Simon, R.; Salvador, A.; Queau, H.; Chaumot, A.; Geffard, O. Vitellogenin-like proteins in the freshwater amphipod Gammarus fossarum (Koch, 1835): functional characterization throughout reproductive process, potential for use as an indicator of oocyte quality and endocrine disruption biomarker in males Aquat. Toxicol. 2012, 112-113 (0) 72-82
22. Karaouzas, I.; Cotou, E.; Albanis, T. A.; Kamarianos, A.; Skoulikidis, N. T.; Giannakou, U. Bioassays and biochemical biomarkers for assessing olive mill and citrus processing wastewater toxicity Environ. Toxicol. 2011, 26 (6) 669-76
23. Lebrun, J. D.; Perret, M.; Geffard, A.; Gourlay-France, C. Modelling copper bioaccumulation in Gammarus pulex and alterations of digestive metabolism Ecotoxicology 2012, 21 (7) 2022-30
24. Maltby, L.; Hills, L. Spray drift of pesticides and stream macroinvertebrates: experimental evidence of impacts and effectiveness of mitigation measures Environ. Pollut. 2008, 156 (3) 1112-20
25. McLoughlin, N.; Yin, D. Q.; Maltby, L.; Wood, R. M.; Yu, H. X. Evaluation of sensitivity and specificity of two crustacean biochemical biomarkers Environ. Toxicol. Chem. 2000, 19 (8) 2085-2092
26. Neuparth, T.; Correia, A. D.; Costa, F. O.; Lima, G.; Costa, M. H. Multi-level assessment of chronic toxicity of estuarine sediments with the amphipod Gammarus locusta: I. Biochemical endpoints Mar. Environ. Res. 2005, 60 (1) 69-91
27. Scheil, V.; Triebskorn, R.; Kohler, H. R. Cellular and stress protein responses to the UV filter 3-benzylidene camphor in the amphipod crustacean Gammarus fossarum (Koch 1835) Arch. Environ. Contam. Toxicol. 2008, 54 (4) 684-9
28. Schill, R. O.; Gorlitz, H.; Kohler, H. R. Laboratory simulation of a mining accident: acute toxicity, hsc/hsp70 response, and recovery from stress in Gammarus fossarum (Crustacea, Amphipoda) exposed to a pulse of cadmium BioMetals 2003, 16 (3) 391-401
29. Schirling, M.; Jungmann, D.; Ladewig, V.; Ludwichowski, K. U.; Nagel, R.; Kohler, H. R.; Triebskorn, R. Bisphenol A in artificial indoor streams: II. Stress response and gonad histology in Gammarus fossarum (Amphipoda) Ecotoxicology 2006, 15 (2) 143-56
30. Schirling, M.; Jungmann, D.; Ladewig, V.; Nagel, R.; Triebskorn, R.; Kohler, H. R. Endocrine effects in Gammarus fossarum (Amphipoda): influence of wastewater effluents, temporal variability, and spatial aspects on natural populations Arch. Environ. Contam. Toxicol. 2005, 49 (1) 53-61
31. Simon, R.; Jubeaux, G.; Chaumot, A.; Lemoine, J.; Geffard, O.; Salvador, A. Mass spectrometry assay as an alternative to the enzyme-linked immunosorbent assay test for biomarker quantitation in ecotoxicology: application to vitellogenin in Crustacea (Gammarus fossarum) J. Chromatogr., A 2010, 1217 (31) 5109-15
32. Sroda, S.; Cossu-Leguille, C. Effects of sublethal copper exposure on two gammarid species: which is the best competitor? Ecotoxicology 2011, 20 (1) 264-73
33. Timofeyev, M. A.; Shatilina, Z. M.; Protopopova, M. V.; Bedulina, D. S.; Pavlichenko, V. V.; Kolesnichenko, A. V.; Steinberg, C. E. W. Thermal stress defense in freshwater amphipods from contrasting habitats with emphasis on small heat shock proteins (sHSPs) J. Therm. Biol. 2009, 34 (6) 281-285
34. Triebskorn, R.; Adam, S.; Casper, H.; Honnen, W.; Pawert, M.; Schramm, M.; Schwaiger, J.; Kohler, H. R. Biomarkers as diagnostic tools for evaluating effects of unknown past water quality conditions on stream organisms Ecotoxicology 2002, 11 (6) 451-465
35. Turja, R.; Guimaraes, L.; Nevala, A.; Kankaanpaa, H.; Korpinen, S.; Lehtonen, K. K. Cumulative effects of exposure to cyanobacteria bloom extracts and benzo[ a ]pyrene on antioxidant defence biomarkers in Gammarus oceanicus (Crustacea: Amphipoda) Toxicon 2014, 78, 68-77
36. Xuereb, B.; Noury, P.; Felten, V.; Garric, J.; Geffard, O. Cholinesterase activity in Gammarus pulex (Crustacea Amphipoda): characterization and effects of chlorpyrifos Toxicology 2007, 236 (3) 178-89
37. Xuereb, B.; Lefevre, E.; Garric, J.; Geffard, O. Acetylcholinesterase activity in Gammarus fossarum (Crustacea Amphipoda): linking AChE inhibition and behavioural alteration Aquat. Toxicol. 2009, 94 (2) 114-22
38. Besse, J. P.; Coquery, M.; Lopes, C.; Chaumot, A.; Budzinski, H.; Labadie, P.; Geffard, O. Caged Gammarus fossarum (Crustacea) as a robust tool for the characterization of bioavailable contamination levels in continental waters: towards the determination of threshold values Water Res. 2013, 47 (2) 650-60
39. Lacaze, E.; Devaux, A.; Mons, R.; Bony, S.; Garric, J.; Geffard, A.; Geffard, O. DNA damage in caged Gammarus fossarum amphipods: a tool for freshwater genotoxicity assessment Environ. Pollut. 2011, 159 (6) 1682-91
40. Coulaud, R.; Geffard, O.; Xuereb, B.; Lacaze, E.; Queau, H.; Garric, J.; Charles, S.; Chaumot, A. In situ feeding assay with Gammarus fossarum (Crustacea): Modelling the influence of confounding factors to improve water quality biomonitoring Water Res. 2011, 45 (19) 6417-29
41. Maltby, L.; Clayton, S. A.; Wood, R. M.; McLoughlin, N. Evaluation of the Gammarus pulex in situ feeding assay as a biomonitor of water quality: Robustness, responsiveness, and relevance Environ. Toxicol. Chem. 2002, 21 (2) 361-368
42. Handy, R. D.; Galloway, T. S.; Depledge, M. H. A proposal for the use of biomarkers for the assessment of chronic pollution and in regulatory toxicology Ecotoxicology 2003, 12 (1-4) 331-343
43. Sanchez, W.; Porcher, J. M. Fish biomarkers for environmental monitoring within the Water Framework Directive of the European Union Trends Anal. Chem. 2009, 28 (2) 150-158
44. Goksøyr, A.; Förlin, L. The cytochrome P-450 system in fish, aquatic toxicology and environmental monitoring Aquat. Toxicol. 1992, 22 (4) 287-311
45. James, M. O.; Boyle, S. M. Cytochromes P450 in crustacea Comp. Biochem. Physiol., Part C: Pharmacol. Toxicol. Endocrinol. 1998, 121 (1-3) 157-72
46. Koenig, S.; Fernandez, P.; Sole, M. Differences in cytochrome P450 enzyme activities between fish and crustacea: relationship with the bioaccumulation patterns of polychlorobiphenyls (PCBs) Aquat. Toxicol. 2012, 108, 11-7
47. Depledge, M. H.; Galloway, T. S. Healthy animals, healthy ecosystems Front. Ecol. Environ. 2005, 3 (5) 251-258
48. Lemos, M. F. L.; Soares, A. M. V. M; Correia, A. C.; Esteves, A. C. Proteins in ecotoxicology-How, why and why not? Proteomics 2010, 10 (4) 873-887
49. Kime, D. E.; Nash, J. P.; Scott, A. P. Vitellogenesis as a biomarker of reproductive disruption by xenobiotics Aquaculture 1999, 177 (1-4) 345-352
50. Matozzo, V.; Gagne, F.; Marin, M. G.; Ricciardi, F.; Blaise, C. Vitellogenin as a biomarker of exposure to estrogenic compounds in aquatic invertebrates: A review Environ. Int. 2008, 34 (4) 531-45
51. LeBlanc, G. A. Crustacean endocrine toxicology: A review Ecotoxicology 2007, 16 (1) 61-81
52. Hayward, A.; Takahashi, T.; Bendena, W. G.; Tobe, S. S.; Hui, J. H. Comparative genomic and phylogenetic analysis of vitellogenin and other large lipid transfer proteins in metazoans FEBS Lett. 2010, 584 (6) 1273-8
53. Cheng, W.; Tsai, I. H.; Huang, C. J.; Chiang, P. C.; Cheng, C. H.; Yeh, M. S. Cloning and characterization of hemolymph clottable proteins of kuruma prawn (Marsupenaeus japonicus) and white shrimp (Litopenaeus vannamei) Dev. Comp. Immunol. 2008, 32 (3) 265-74
54. Short, S.; Yang, G.; Kille, P.; Ford, A. T. Vitellogenin is not an appropriate biomarker of feminisation in a crustacean Aquat. Toxicol. 2014, 153 (0) 89-97
55. Borowsky, R.; Guarna, M. M. Excess amylase in Gammarus palustris (Crustacea, Amphipoda)-its release into and possible roles in the environment Marine Biology 1989, 101 (4) 529-534
56. Correia, A. D.; Costa, M. H.; Luis, O. J.; Livingstone, D. R. Age-related changes in antioxidant enzyme activities, fatty acid composition and lipid peroxidation in whole body Gammarus locusta (Crustacea: Amphipoda) J. Exp. Mar. Biol. Ecol. 2003, 289 (1) 83-101
57. Hanson, N.; Forlin, L.; Larsson, A. Spatial and annual variation to define the normal range of biological endpoints: An example with biomarkers in perch Environ. Toxicol. Chem. 2010, 29 (11) 2616-24
58. Xuereb, B.; Chaumot, A.; Mons, R.; Garric, J.; Geffard, O. Acetylcholinesterase activity in Gammarus fossarum (Crustacea Amphipoda) intrinsic variability, reference levels, and a reliable tool for field surveys Aquat. Toxicol. 2009, 93 (4) 225-33
59. Lacaze, E.; Devaux, A.; Jubeaux, G.; Mons, R.; Gardette, M.; Bony, S.; Garric, J.; Geffard, O. DNA damage in Gammarus fossarum sperm as a biomarker of genotoxic pressure: intrinsic variability and reference level Sci. Total Environ. 2011, 409 (17) 3230-6
60. Gevaert, K.; Vandekerckhove, J. Protein identification methods in proteomics Electrophoresis 2000, 21 (6) 1145-1154
61. Vioque-Fernandez, A.; Alves de Almeida, E.; Lopez-Barea, J. Assessment of Donana National Park contamination in Procambarus clarkii: integration of conventional biomarkers and proteomic approaches Sci. Total Environ. 2009, 407 (5) 1784-97
62. Armengaud, J. Microbiology and proteomics, getting the best of both worlds! Environ. Microbiol. 2013, 15 (1) 12-23
63. Apraiz, I.; Mi, J.; Cristobal, S. Identification of proteomic signatures of exposure to marine pollutants in mussels (Mytilus edulis) Mol. Cell Proteomics 2006, 5 (7) 1274-85
64. Rodriguez-Ortega, M. J.; Grosvik, B. E.; Rodriguez-Ariza, A.; Goksoyr, A.; Lopez-Barea, J. Changes in protein expression profiles in bivalve molluscs (Chamaelea gallina) exposed to four model environmental pollutants Proteomics 2003, 3 (8) 1535-43
65. Amelina, H.; Apraiz, I.; Sun, W.; Cristobal, S. Proteomics-based method for the assessment of marine pollution using liquid chromatography coupled with two-dimensional electrophoresis J. Proteome Res. 2007, 6 (6) 2094-104
66. Liu, F. J.; Wang, W. X. Proteome pattern in oysters as a diagnostic tool for metal pollution J. Hazard Mater. 2012, 239 (0) 241-248
67. Binelli, A.; Marisa, I.; Fedorova, M.; Hoffmann, R.; Riva, C. First evidence of protein profile alteration due to the main cocaine metabolite (benzoylecgonine) in a freshwater biological model Aquat. Toxicol. 2013, 140-141, 268-78
68. Chora, S.; Starita-Geribaldi, M.; Guigonis, J. M.; Samson, M.; Romeo, M.; Bebianno, M. J. Effect of cadmium in the clam Ruditapes decussatus assessed by proteomic analysis Aquat. Toxicol. 2009, 94 (4) 300-8
69. Dondero, F.; Negri, A.; Boatti, L.; Marsano, F.; Mignone, F.; Viarengo, A. Transcriptomic and proteomic effects of a neonicotinoid insecticide mixture in the marine mussel (Mytilus galloprovincialis, Lam.) Sci. Total Environ. 2010, 408 (18) 3775-86
70. Ji, C.; Wu, H.; Wei, L.; Zhao, J.; Yu, J. Proteomic and metabolomic analysis reveal gender-specific responses of mussel Mytilus galloprovincialis to 2,2′,4,4′-tetrabromodiphenyl ether (BDE 47) Aquat. Toxicol. 2013, 140-141, 449-57
71. Leung, P. T.; Wang, Y.; Mak, S. S.; Ng, W. C.; Leung, K. M. Differential proteomic responses in hepatopancreas and adductor muscles of the green-lipped mussel Perna viridis to stresses induced by cadmium and hydrogen peroxide Aquat. Toxicol. 2011, 105 (1-2) 49-61
72. Liu, F.; Wang, D. Z.; Wang, W. X. Cadmium-induced changes in trace element bioaccumulation and proteomics perspective in four marine bivalves Environ. Toxicol. Chem. 2012, 31 (6) 1292-300
73. Manduzio, H.; Cosette, P.; Gricourt, L.; Jouenne, T.; Lenz, C.; Andersen, O. K.; Leboulenger, F.; Rocher, B. Proteome modifications of blue mussel (Mytilus edulis L.) gills as an effect of water pollution Proteomics 2005, 5 (18) 4958-63
74. Maria, V. L.; Gomes, T.; Barreira, L.; Bebianno, M. J. Impact of benzo(a)pyrene, Cu and their mixture on the proteomic response of Mytilus galloprovincialis Aquat. Toxicol. 2013, 144-145, 284-95
75. Riva, C.; Binelli, A. Analysis of the Dreissena polymorpha gill proteome following exposure to dioxin-like PCBs: Mechanism of action and the role of gender Comp. Biochem. Physiol., Part D: Genomics Proteomics 2014, 9 (1) 23-30
76. Riva, C.; Binelli, A.; Rusconi, F.; Colombo, G.; Pedriali, A.; Zippel, R.; Provini, A. A proteomic study using zebra mussels (D. polymorpha) exposed to benzo(α)pyrene: The role of gender and exposure concentrations Aquat. Toxicol. 2011, 104 (1-2) 14-22
77. Riva, C.; Cristoni, S.; Binelli, A. Effects of triclosan in the freshwater mussel Dreissena polymorpha: a proteomic investigation Aquat. Toxicol. 2012, 118-119 (0) 62-71
78. Romero-Ruiz, A.; Carrascal, M.; Alhama, J.; Gomez-Ariza, J. L.; Abian, J.; Lopez-Barea, J. Utility of proteomics to assess pollutant response of clams from the Donana bank of Guadalquivir Estuary (SW Spain) Proteomics 2006, 6 (Suppl 1) S245-55
79. Thompson, E. L.; Taylor, D. A.; Nair, S. V.; Birch, G.; Haynes, P. A.; Raftos, D. A. A proteomic analysis of the effects of metal contamination on Sydney Rock Oyster (Saccostrea glomerata) haemolymph Aquat. Toxicol. 2011, 103 (3-4) 241-9
80. Zhou, J.; Cai, Z. H.; Li, L.; Gao, Y. F.; Hutchinson, T. H. A proteomics based approach to assessing the toxicity of bisphenol A and diallyl phthalate to the abalone (Haliotis diversicolor supertexta) Chemosphere 2010, 79 (5) 595-604
81. Besse, J. P.; Geffard, O.; Coquery, M. Relevance and applicability of active biomonitoring in continental waters under the Water Framework Directive Trends Anal. Chem. 2012, 36 (0) 113-127
82. Leroy, D.; Haubruge, E.; De Pauw, E.; Thome, J. P.; Francis, F. Development of ecotoxicoproteomics on the freshwater amphipod Gammarus pulex: identification of PCB biomarkers in glycolysis and glutamate pathways Ecotoxicol. Environ. Saf 2010, 73 (3) 343-52
83. Ralston-Hooper, K. J.; Sanchez, B. C.; Adamec, J.; Sepulveda, M. S. Proteomics in aquatic amphipods: can it be used to determine mechanisms of toxicity and interspecies responses after exposure to atrazine? Environ. Toxicol. Chem. 2011, 30 (5) 1197-203
84. Silvestre, F.; Gillardin, V.; Dorts, J. Proteomics to assess the role of phenotypic plasticity in aquatic organisms exposed to pollution and global warming Integr. Comp. Biol. 2012, 52 (5) 681-94
85. Neave, M. J.; Streten-Joyce, C.; Nouwens, A. S.; Glasby, C. J.; McGuinness, K. A.; Parry, D. L.; Gibb, K. S. The transcriptome and proteome are altered in marine polychaetes (Annelida) exposed to elevated metal levels J. Proteomics 2012, 75 (9) 2721-35
86. Bradley, B. P.; Shrader, E. A.; Kimmel, D. G.; Meiller, J. C. Protein expression signatures: an application of proteomics Mar. Environ. Res. 2002, 54 (3-5) 373-7
87. Dircksen, H.; Neupert, S.; Predel, R.; Verleyen, P.; Huybrechts, J.; Strauss, J.; Hauser, F.; Stafflinger, E.; Schneider, M.; Pauwels, K.; Schoofs, L.; Grimmelikhuijzen, C. J. Genomics, transcriptomics, and peptidomics of Daphnia pulex neuropeptides and protein hormones J. Proteome Res. 2011, 10 (10) 4478-504
88. Fröhlich, T.; Arnold, G. J.; Fritsch, R.; Mayr, T.; Laforsch, C., LC-MS/MS-based proteome profiling in Daphnia pulex and Daphnia longicephala: The Daphnia pulex genome database as a key for high throughput proteomics in Daphnia. BMC Genomics 2009, 10.
89. Paik, Y. K.; Jeong, S. K.; Lee, E. Y.; Jeong, P. Y.; Shim, Y. H. C. elegans: An invaluable model organism for the proteomics studies of the cholesterol-mediated signaling pathway Expert Rev. Proteomics 2006, 3 (4) 439-53
90. Dowling, V. A.; Sheehan, D. Proteomics as a route to identification of toxicity targets in environmental toxicology Proteomics 2006, 6 (20) 5597-604
91. Monsinjon, T.; Knigge, T. Proteomic applications in ecotoxicology Proteomics 2007, 7 (16) 2997-3009
92. Carpentler, S. C.; Panis, B.; Vertommen, A.; Swennen, R.; Sergeant, K.; Renaut, J.; Laukens, K.; Witters, E.; Samyn, B.; Devreese, B. Proteome analysis of non-model plants: A challenging but powerful approach Mass Spectrom. Rev. 2008, 27 (4) 354-377
93. Martyniuk, C. J.; Alvarez, S.; Denslow, N. D. DIGE and iTRAQ as biomarker discovery tools in aquatic toxicology Ecotoxicol. Environ. Saf. 2012, 76 (2) 3-10
94. Martyniuk, C. J.; Denslow, N. D. Towards functional genomics in fish using quantitative proteomics Gen. Comp. Endrocrinol. 2009, 164 (2-3) 135-41
95. Gorg, A.; Weiss, W.; Dunn, M. J. Current two-dimensional electrophoresis technology for proteomics Proteomics 2004, 4 (12) 3665-85
96. Tonge, R.; Shaw, J.; Middleton, B.; Rowlinson, R.; Rayner, S.; Young, J.; Pognan, F.; Hawkins, E.; Currie, I.; Davison, M. Validation and development of fluorescence two-dimensional differential gel electrophoresis proteomics technology Proteomics 2001, 1 (3) 377-96
97. Washburn, M. P.; Wolters, D.; Yates, J. R., 3rd. Large-scale analysis of the yeast proteome by multidimensional protein identification technology Nat. Biotechnol. 2001, 19 (3) 242-7
98. Perrot, M.; Sagliocco, F.; Mini, T.; Monribot, C.; Schneider, U.; Shevchenko, A.; Mann, M.; Jeno, P.; Boucherie, H. Two-dimensional gel protein database of Saccharomyces cerevisiae (update 1999) Electrophoresis 1999, 20 (11) 2280-98
99. Colbourne, J. K.; Pfrender, M. E.; Gilbert, D.; Thomas, W. K.; Tucker, A.; Oakley, T. H.; Tokishita, S.; Aerts, A.; Arnold, G. J.; Basu, M. K.; Bauer, D. J.; Caceres, C. E.; Carmel, L.; Casola, C.; Choi, J. H.; Detter, J. C.; Dong, Q.; Dusheyko, S.; Eads, B. D.; Frohlich, T.; Geiler-Samerotte, K. A.; Gerlach, D.; Hatcher, P.; Jogdeo, S.; Krijgsveld, J.; Kriventseva, E. V.; Kultz, D.; Laforsch, C.; Lindquist, E.; Lopez, J.; Manak, J. R.; Muller, J.; Pangilinan, J.; Patwardhan, R. P.; Pitluck, S.; Pritham, E. J.; Rechtsteiner, A.; Rho, M.; Rogozin, I. B.; Sakarya, O.; Salamov, A.; Schaack, S.; Shapiro, H.; Shiga, Y.; Skalitzky, C.; Smith, Z.; Souvorov, A.; Sung, W.; Tang, Z.; Tsuchiya, D.; Tu, H.; Vos, H.; Wang, M.; Wolf, Y. I.; Yamagata, H.; Yamada, T.; Ye, Y.; Shaw, J. R.; Andrews, J.; Crease, T. J.; Tang, H.; Lucas, S. M.; Robertson, H. M.; Bork, P.; Koonin, E. V.; Zdobnov, E. M.; Grigoriev, I. V.; Lynch, M.; Boore, J. L. The ecoresponsive genome of Daphnia pulex Science 2011, 331 (6017) 555-61
100. Carvalho, P. C.; Fischer, J. S.; Chen, E. I.; Yates, J. R., 3rd.; Barbosa, V. C. PatternLab for proteomics: A tool for differential shotgun proteomics BMC Bioinf. 2008, 9, 316
101. Peterson, K. J.; Lyons, J. B.; Nowak, K. S.; Takacs, C. M.; Wargo, M. J.; McPeek, M. A. Estimating metazoan divergence times with a molecular clock Proc. Natl. Acad. Sci. U.S.A. 2004, 101 (17) 6536-41
102. Studer, R. A.; Robinson-Rechavi, M. How confident can we be that orthologs are similar, but paralogs differ? Trends Genet. 2009, 25 (5) 210-6
103. Nikinmaa, M.; Rytkonen, K. T. Functional genomics in aquatic toxicology-do not forget the function Aquat. Toxicol. 2011, 105 (3-4 Suppl) 16-24
104. 13C-labeled peptide standards Proteomics 2004, 4 (4) 1175-1186
105. Muraoka, S.; Kume, H.; Watanabe, S.; Adachi, J.; Kuwano, M.; Sato, M.; Kawasaki, N.; Kodera, Y.; Ishitobi, M.; Inaji, H.; Miyamoto, Y.; Kato, K.; Tomonaga, T. Strategy for SRM-based verification of biomarker candidates discovered by iTRAQ method in limited breast cancer tissue samples J. Proteome Res. 2012, 11 (8) 4201-10
106. Gallien, S.; Duriez, E.; Domon, B. Selected reaction monitoring applied to proteomics J. Mass Spectrom. 2011, 46 (3) 298-312
107. Anderson, L.; Hunter, C. L. Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins Mol. Cell Proteomics 2006, 5 (4) 573-88
108. von der Ohe, P. C.; Liess, M. Relative sensitivity distribution of aquatic invertebrates to organic and metal compounds Environ. Toxicol. Chem. 2004, 23 (1) 150-6
109. Celander, M. C.; Goldstone, J. V.; Denslow, N. D.; Iguchi, T.; Kille, P.; Meyerhoff, R. D.; Smith, B. A.; Hutchinson, T. H.; Wheeler, J. R. Species extrapolation for the 21st century Environ. Toxicol. Chem. 2011, 30 (1) 52-63
110. Schrimpf, S. P.; Weiss, M.; Reiter, L.; Ahrens, C. H.; Jovanovic, M.; Malmstrom, J.; Brunner, E.; Mohanty, S.; Lercher, M. J.; Hunziker, P. E.; Aebersold, R.; von Mering, C.; Hengartner, M. O. Comparative functional analysis of the Caenorhabditis elegans and Drosophila melanogaster proteomes PLoS Biol. 2009, 7 (3) e48
111. Jubeaux, G.; Audouard-Combe, F.; Simon, R.; Tutundjian, R.; Salvador, A.; Geffard, O.; Chaumot, A. Vitellogenin-like proteins among invertebrate species diversity: Potential of proteomic mass spectrometry for biomarker development Environ. Sci. Technol. 2012, 46 (11) 6315-23
112. Armengaud, J.; Trapp, J.; Pible, O.; Geffard, O.; Chaumot, A.; Hartmann, E. M. Non-model organisms, a species endangered by proteogenomics J. Proteomics 2014, 105 (0) 5-18
113. Hook, S. E.; Twine, N. A.; Simpson, S. L.; Spadaro, D. A.; Moncuquet, P.; Wilkins, M. R. 454 pyrosequencing-based analysis of gene expression profiles in the amphipod Melita plumulosa: transcriptome assembly and toxicant induced changes Aquat. Toxicol. 2014, 153 (0) 73-88
114. Bouetard, A.; Noirot, C.; Besnard, A. L.; Bouchez, O.; Choisne, D.; Robe, E.; Klopp, C.; Lagadic, L.; Coutellec, M. A. Pyrosequencing-based transcriptomic resources in the pond snail Lymnaea stagnalis, with a focus on genes involved in molecular response to diquat-induced stress Ecotoxicology 2012, 21 (8) 2222-34
115. Marinković, M.; de Leeuw, W. C.; de Jong, M.; Kraak, M. H. S.; Admiraal, W.; Breit, T. M.; Jonker, M. J. Combining next-generation sequencing and microarray technology into a transcriptomics approach for the non-model organism Chironomus riparius. PLoS One 2012, 7, (10), 10.1371/journal.pone.0048096.
116. Jaffe, J. D.; Berg, H. C.; Church, G. M. Proteogenomic mapping as a complementary method to perform genome annotation Proteomics 2004, 4 (1) 59-77
117. Eisen, J. A. Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis Genome Res. 1998, 8 (3) 163-7
118. Avarre, J. C.; Lubzens, E.; Babin, P. J. Apolipocrustacein, formerly vitellogenin, is the major egg yolk precursor protein in decapod crustaceans and is homologous to insect apolipophorin II/I and vertebrate apolipoprotein B BMC Evol. Biol. 2007, 7, 3
119. Laurent, J. M.; Vogel, C.; Kwon, T.; Craig, S. A.; Boutz, D. R.; Huse, H. K.; Nozue, K.; Walia, H.; Whiteley, M.; Ronald, P. C.; Marcotte, E. M. Protein abundances are more conserved than mRNA abundances across diverse taxa Proteomics 2010, 10 (23) 4209-4212
120. Chen, J. E.; Li, J. Y.; You, Z. Y.; Liu, L. L.; Liang, J. S.; Ma, Y. Y.; Chen, M.; Zhang, H. R.; Jiang, Z. D.; Zhong, B. X. Proteome analysis of silkworm, Bombyx mori, larval gonads: Characterization of proteins involved in sexual dimorphism and gametogenesis J. Proteome Res. 2013, 12 (6) 2422-38
121. Ventura, T.; Manor, R.; Aflalo, E. D.; Weil, S.; Raviv, S.; Glazer, L.; Sagi, A. Temporal silencing of an androgenic gland-specific insulin-like gene affecting phenotypical gender differences and spermatogenesis Endocrinology 2009, 150 (3) 1278-86
122. Ventura, T.; Manor, R.; Aflalo, E. D.; Chalifa-Caspi, V.; Weil, S.; Sharabi, O.; Sagi, A. Post-embryonic transcriptomes of the prawn Macrobrachium rosenbergii: Multigenic succession through metamorphosis PLoS One 2013, 8 (1) e55322
123. Geffard, O.; Xuereb, B.; Chaumot, A.; Geffard, A.; Biagianti, S.; Noel, C.; Abbaci, K.; Garric, J.; Charmantier, G.; Charmantier-Daures, M. Ovarian cycle and embryonic development in Gammarus fossarum: Application for reproductive toxicity assessment Environ. Toxicol. Chem. 2010, 29 (10) 2249-59
124. Trapp, J.; Geffard, O.; Imbert, G.; Gaillard, J. C.; Davin, A. H.; Chaumot, A.; Armengaud, J. Proteogenomics of Gammarus fossarum to document the reproductive system of amphipods Mol. Cell Proteomics 2014, pii: mcp.M114.038851
125. Ankley, G. T.; Bennett, R. S.; Erickson, R. J.; Hoff, D. J.; Hornung, M. W.; Johnson, R. D.; Mount, D. R.; Nichols, J. W.; Russom, C. L.; Schmieder, P. K.; Serrrano, J. A.; Tietge, J. E.; Villeneuve, D. L. Adverse outcome pathways: a conceptual framework to support ecotoxicology research and risk assessment Environ. Toxicol. Chem. 2010, 29 (3) 730-41