메뉴 건너뛰기




Volumn 1, Issue 1, 2013, Pages

Shotgun proteomics as a viable approach for biological discovery in the Pacific oyster

Author keywords

Crassostrea gigas; Pacific oyster; Proteomics; Tandem mass spectrometry

Indexed keywords


EID: 84983489043     PISSN: None     EISSN: 20511434     Source Type: Journal    
DOI: 10.1093/conphys/cot009     Document Type: Article
Times cited : (11)

References (42)
  • 1
    • 84859479170 scopus 로고    scopus 로고
    • The proteomes of Sydney rock oysters vary spatially according to exposure to acid sulfate runoff
    • Amaral V, Thompson EL, Bishop MJ, Raftos DA (2012) The proteomes of Sydney rock oysters vary spatially according to exposure to acid sulfate runoff. Mar Freshw Res 63: 361-369.
    • (2012) Mar Freshw Res , vol.63 , pp. 361-369
    • Amaral, V.1    Thompson, E.L.2    Bishop, M.J.3    Raftos, D.A.4
  • 2
    • 49949089949 scopus 로고    scopus 로고
    • Low-coverage massively parallel pyrosequencing of cDNAs enables proteomics in non-model species: comparison of a species-specific database generated by pyrosequencing with databases from related species for proteome analysis of pea chloroplast envelopes
    • Bräutigam A, Shrestha RP, Whitten D, Wilkerson CG, Carr KM, Froehlich JE, Weber APM (2008) Low-coverage massively parallel pyrosequencing of cDNAs enables proteomics in non-model species: comparison of a species-specific database generated by pyrosequencing with databases from related species for proteome analysis of pea chloroplast envelopes. J Biotechnol 136: 44-53.
    • (2008) J Biotechnol , vol.136 , pp. 44-53
    • Bräutigam, A.1    Shrestha, R.P.2    Whitten, D.3    Wilkerson, C.G.4    Carr, K.M.5    Froehlich, J.E.6    Weber, A.P.M.7
  • 4
    • 27644587818 scopus 로고    scopus 로고
    • Response of the Pacific oyster Crassostrea gigas to hypoxia exposure under experimental conditions
    • David E, Tanguy A, Pichavant K, Moraga D (2005) Response of the Pacific oyster Crassostrea gigas to hypoxia exposure under experimental conditions. FEBS J 272: 5635-5652.
    • (2005) FEBS J , vol.272 , pp. 5635-5652
    • David, E.1    Tanguy, A.2    Pichavant, K.3    Moraga, D.4
  • 5
    • 34547925595 scopus 로고    scopus 로고
    • Peroxiredoxin 6 gene: a new physiological and genetic indicator of multiple environmental stress response in Pacific oyster Crassostrea gigas
    • David E, Tanguy A, Moraga D (2007) Peroxiredoxin 6 gene: a new physiological and genetic indicator of multiple environmental stress response in Pacific oyster Crassostrea gigas. Aquat Toxicol 84: 389-398.
    • (2007) Aquat Toxicol , vol.84 , pp. 389-398
    • David, E.1    Tanguy, A.2    Moraga, D.3
  • 6
    • 80053346979 scopus 로고    scopus 로고
    • Development of a Pacific oyster (Crassostrea gigas) 31, 918-feature microarray: identification of reference genes and tissue-enriched expression patterns
    • Dheilly NM, Lelong C, Huvet A, Favrel P (2011) Development of a Pacific oyster (Crassostrea gigas) 31, 918-feature microarray: identification of reference genes and tissue-enriched expression patterns. BMC Genomics 12: 468.
    • (2011) BMC Genomics , vol.12 , pp. 468
    • Dheilly, N.M.1    Lelong, C.2    Huvet, A.3    Favrel, P.4
  • 7
    • 84862128699 scopus 로고    scopus 로고
    • Time course proteomic profiling of cellular repsonses to immunological challenge in the sea urchin, Heliocidaris erythrogramma
    • Dheilly NM, Haynes PA, Raftos DA, Nair SV (2012) Time course proteomic profiling of cellular repsonses to immunological challenge in the sea urchin, Heliocidaris erythrogramma. Dev Comp Immunol 37: 243-256.
    • (2012) Dev Comp Immunol , vol.37 , pp. 243-256
    • Dheilly, N.M.1    Haynes, P.A.2    Raftos, D.A.3    Nair, S.V.4
  • 8
    • 84875577762 scopus 로고    scopus 로고
    • Shotgun proteomics of coelomic fluid from the purple sea urchin, Strongylocentrotus purpuratus
    • Dheilly NM, Raftos DA, Haynes PA, Smith LC, Nair SV (2013) Shotgun proteomics of coelomic fluid from the purple sea urchin, Strongylocentrotus purpuratus. Dev Comp Immunol 40: 35-50.
    • (2013) Dev Comp Immunol , vol.40 , pp. 35-50
    • Dheilly, N.M.1    Raftos, D.A.2    Haynes, P.A.3    Smith, L.C.4    Nair, S.V.5
  • 10
    • 84881234326 scopus 로고    scopus 로고
    • Elevated CO2 alters larval proteome and its phosphorylation status in the commercial oyster, Crassostrea hongkongensis
    • In press
    • Dineshram R, Thiyagarajan V, Lane A, Ziniu Y, Xiao S, Leung PTY (2013) Elevated CO2 alters larval proteome and its phosphorylation status in the commercial oyster, Crassostrea hongkongensis. Mar Biol In press.
    • (2013) Mar Biol
    • Dineshram, R.1    Thiyagarajan, V.2    Lane, A.3    Ziniu, Y.4    Xiao, S.5    Leung, P.T.Y.6
  • 11
    • 0000857494 scopus 로고
    • An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database
    • Eng JK, McCormack AL, Yates JR (1994) An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J Am Soc Mass Spectrom 5: 976-989.
    • (1994) J Am Soc Mass Spectrom , vol.5 , pp. 976-989
    • Eng, J.K.1    McCormack, A.L.2    Yates, J.R.3
  • 12
    • 84857231830 scopus 로고    scopus 로고
    • Microarray analysis highlights immune response of Pacific oysters as a determinant of resistance to summer mortality
    • Fleury E, Huvet A (2012) Microarray analysis highlights immune response of Pacific oysters as a determinant of resistance to summer mortality. Mar Biotechnol 14: 203-217.
    • (2012) Mar Biotechnol , vol.14 , pp. 203-217
    • Fleury, E.1    Huvet, A.2
  • 14
    • 33744943777 scopus 로고    scopus 로고
    • Cathepsin B and glutathione peroxidase show differing transcriptional responses in the grass shrimp, Palaemonetes pugio following exposure to three xenobiotics
    • Griffitt RJ, Chandler GT, Greig TW, Quattro JM (2006) Cathepsin B and glutathione peroxidase show differing transcriptional responses in the grass shrimp, Palaemonetes pugio following exposure to three xenobiotics. Environ Sci Technol 40: 3640-3645.
    • (2006) Environ Sci Technol , vol.40 , pp. 3640-3645
    • Griffitt, R.J.1    Chandler, G.T.2    Greig, T.W.3    Quattro, J.M.4
  • 15
    • 0036897967 scopus 로고    scopus 로고
    • Application of genomics and proteomics for study of the integrated response to zinc exposure in a non-model fish species, the rainbow trout
    • Hogstrand C, Balesaria S, Glover CN (2002) Application of genomics and proteomics for study of the integrated response to zinc exposure in a non-model fish species, the rainbow trout. Comp Biochem Physiol B Biochem Mol Biol 133: 523-535.
    • (2002) Comp Biochem Physiol B Biochem Mol Biol , vol.133 , pp. 523-535
    • Hogstrand, C.1    Balesaria, S.2    Glover, C.N.3
  • 16
    • 84862675237 scopus 로고    scopus 로고
    • Identification of differentially expressed proteins involved in the early larval development of the Pacific oyster Crassostrea gigas
    • Huan P, Wang H, Dong B, Liu B (2012) Identification of differentially expressed proteins involved in the early larval development of the Pacific oyster Crassostrea gigas. J Proteomics 75: 3855-3865.
    • (2012) J Proteomics , vol.75 , pp. 3855-3865
    • Huan, P.1    Wang, H.2    Dong, B.3    Liu, B.4
  • 17
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID Bioinformatics Resources
    • Huang DW, Sherman BT, Lempicki RA (2009a) Systematic and integrative analysis of large gene lists using DAVID Bioinformatics Resources. Nat Protoc 4: 44-57.
    • (2009) Nat Protoc , vol.4 , pp. 44-57
    • Huang, D.W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 18
    • 58549112996 scopus 로고    scopus 로고
    • Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists
    • Huang DW, Sherman BT, Lempicki RA (2009b) Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 37: 1-13.
    • (2009) Nucleic Acids Res , vol.37 , pp. 1-13
    • Huang, D.W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 19
    • 0029781971 scopus 로고    scopus 로고
    • Differences in protein patterns of gill epithelial cells of the fish Gillichthys mirabilis after osmotic and thermal acclimation
    • Kültz D, Somero GN (1996) Differences in protein patterns of gill epithelial cells of the fish Gillichthys mirabilis after osmotic and thermal acclimation. J Comp Physiol B 166: 88-100.
    • (1996) J Comp Physiol B , vol.166 , pp. 88-100
    • Kültz, D.1    Somero, G.N.2
  • 20
    • 84867737662 scopus 로고    scopus 로고
    • Proteome pattern in oysters as a diagnostic tool for metal pollution
    • Liu F, Wang W (2012) Proteome pattern in oysters as a diagnostic tool for metal pollution. J Hazard Mater 239-240: 241-248.
    • (2012) J Hazard Mater , vol.239-240 , pp. 241-248
    • Liu, F.1    Wang, W.2
  • 21
    • 77957850989 scopus 로고    scopus 로고
    • Transcriptomic responses to heat stress in invasive and native blue mussels (genus Mytilus): molecular correlates of invasive success
    • Lockwood BL, Sanders JG, Somero GN (2010) Transcriptomic responses to heat stress in invasive and native blue mussels (genus Mytilus): molecular correlates of invasive success. J Exp Biol 213: 3548-3558.
    • (2010) J Exp Biol , vol.213 , pp. 3548-3558
    • Lockwood, B.L.1    Sanders, J.G.2    Somero, G.N.3
  • 22
    • 36749044848 scopus 로고    scopus 로고
    • Identification of differentially expressed genes of the Pacific oyster Crassostrea gigas exposed to prolonged thermal stress
    • Meistertzheim AL, Tanguy A, Moraga D, Thébault MT (2007) Identification of differentially expressed genes of the Pacific oyster Crassostrea gigas exposed to prolonged thermal stress. FEBS J 274: 6392-6402.
    • (2007) FEBS J , vol.274 , pp. 6392-6402
    • Meistertzheim, A.L.1    Tanguy, A.2    Moraga, D.3    Thébault, M.T.4
  • 23
    • 77951497989 scopus 로고    scopus 로고
    • Comparative metaproteomics reveals ocean-scale shifts in microbial nutrient utilization and energy transduction
    • Morris RM, Nunn BL, Frazer C, Goodlett DR, Ting YS, Rocap G (2010) Comparative metaproteomics reveals ocean-scale shifts in microbial nutrient utilization and energy transduction. ISME J 4: 673-685.
    • (2010) ISME J , vol.4 , pp. 673-685
    • Morris, R.M.1    Nunn, B.L.2    Frazer, C.3    Goodlett, D.R.4    Ting, Y.S.5    Rocap, G.6
  • 24
    • 84860337474 scopus 로고    scopus 로고
    • Quantitative proteomics of heavy metal stress responses in Sydney rock oysters
    • Muralidharan S, Thompson E, Raftos D, Birch G, Haynes PA (2012) Quantitative proteomics of heavy metal stress responses in Sydney rock oysters. Proteomics 12: 906-921.
    • (2012) Proteomics , vol.12 , pp. 906-921
    • Muralidharan, S.1    Thompson, E.2    Raftos, D.3    Birch, G.4    Haynes, P.A.5
  • 25
    • 0042338362 scopus 로고    scopus 로고
    • A statistical model for identifying proteins by tandem mass spectrometry
    • Nesvizhskii AI, Keller A, Kolker E, Aebersold R (2003) A statistical model for identifying proteins by tandem mass spectrometry. Anal Chem 75: 4646-4658.
    • (2003) Anal Chem , vol.75 , pp. 4646-4658
    • Nesvizhskii, A.I.1    Keller, A.2    Kolker, E.3    Aebersold, R.4
  • 27
    • 84863724279 scopus 로고    scopus 로고
    • A proteomics approach reveals divergent molecular responses to salinity in populations of European whitefish (Coregonus lavaretus)
    • Papakostas S, Vasemagi A, Vaha JP, Himberg M, Peil L, Primmer CR (2012) A proteomics approach reveals divergent molecular responses to salinity in populations of European whitefish (Coregonus lavaretus). Mol Ecol 21: 3516-3530.
    • (2012) Mol Ecol , vol.21 , pp. 3516-3530
    • Papakostas, S.1    Vasemagi, A.2    Vaha, J.P.3    Himberg, M.4    Peil, L.5    Primmer, C.R.6
  • 29
    • 84555203214 scopus 로고    scopus 로고
    • Gene discovery in the threatened elkhorn coral: 454 sequencing of the Acropora palmata transcriptome
    • Polato NR, Vera JC, Baums IB (2011) Gene discovery in the threatened elkhorn coral: 454 sequencing of the Acropora palmata transcriptome. PLoS One 6: e28634.
    • (2011) PLoS One , vol.6
    • Polato, N.R.1    Vera, J.C.2    Baums, I.B.3
  • 30
    • 70149113077 scopus 로고    scopus 로고
    • R Foundation for Statistical Computing, Vienna, Austria
    • R Development Core Team (2009) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0. http://www.R-project.org.
    • (2009) R: A language and environment for statistical computing
  • 31
    • 70449533839 scopus 로고    scopus 로고
    • Proteomic clues to the identification of QX disease-resistance biomarkers in selectively bred Sydney rock oysters, Saccostrea glomerata
    • Simonian M, Nair SV, Neil JA, Raftos DA (2009) Proteomic clues to the identification of QX disease-resistance biomarkers in selectively bred Sydney rock oysters, Saccostrea glomerata. J Proteomics 73: 209-217.
    • (2009) J Proteomics , vol.73 , pp. 209-217
    • Simonian, M.1    Nair, S.V.2    Neil, J.A.3    Raftos, D.A.4
  • 32
    • 80052091031 scopus 로고    scopus 로고
    • CO2 induced seawater acidification impacts sea urchin larval development II: gene expression patterns in pluteus larvae
    • Stumpp M, Dupont S, Thorndyke MC, Melzner F (2011) CO2 induced seawater acidification impacts sea urchin larval development II: gene expression patterns in pluteus larvae. Comp Biochem Physiol A Mol Integr Physiol 160: 320-330.
    • (2011) Comp Biochem Physiol A Mol Integr Physiol , vol.160 , pp. 320-330
    • Stumpp, M.1    Dupont, S.2    Thorndyke, M.C.3    Melzner, F.4
  • 33
    • 79960610118 scopus 로고    scopus 로고
    • REVIGO summarizes and visualizes long lists of gene ontology terms
    • Supek F, Bošnjak M, Škunca N, Šmuc T (2011) REVIGO summarizes and visualizes long lists of gene ontology terms. PLoS One 6: e21800.
    • (2011) PLoS One , vol.6
    • Supek, F.1    Bošnjak, M.2    Škunca, N.3    Šmuc, T.4
  • 34
    • 12544253695 scopus 로고    scopus 로고
    • Molecular identification and expression study of differentially regulated genes in the Pacific oyster Crassostrea gigas in response to pesticide exposure
    • Tanguy A, Boutet I, Laroche J, Moraga D (2005) Molecular identification and expression study of differentially regulated genes in the Pacific oyster Crassostrea gigas in response to pesticide exposure. FEBS J 272: 390-403.
    • (2005) FEBS J , vol.272 , pp. 390-403
    • Tanguy, A.1    Boutet, I.2    Laroche, J.3    Moraga, D.4
  • 35
    • 79955658107 scopus 로고    scopus 로고
    • A proteomic analysis of the effects of metal contamination on Sydney Rock Oyster (Saccostrea glomerata) haemolymph
    • Thompson EL, Taylor DA, Nair SV, Birch G, Haynes PA, Raftos DA (2011) A proteomic analysis of the effects of metal contamination on Sydney Rock Oyster (Saccostrea glomerata) haemolymph. Aquat Toxicol 103: 241-249.
    • (2011) Aquat Toxicol , vol.103 , pp. 241-249
    • Thompson, E.L.1    Taylor, D.A.2    Nair, S.V.3    Birch, G.4    Haynes, P.A.5    Raftos, D.A.6
  • 36
    • 84863482561 scopus 로고    scopus 로고
    • Proteomic analysis of Sydney Rock oysters (Saccostrea glomerata) exposed to metal contamination in the field
    • Thompson EL, Taylor DA, Nair SV, Birch G, Hose GC, Raftos DA (2012a) Proteomic analysis of Sydney Rock oysters (Saccostrea glomerata) exposed to metal contamination in the field. Environ Pollut 170: 102-112.
    • (2012) Environ Pollut , vol.170 , pp. 102-112
    • Thompson, E.L.1    Taylor, D.A.2    Nair, S.V.3    Birch, G.4    Hose, G.C.5    Raftos, D.A.6
  • 37
    • 84856618679 scopus 로고    scopus 로고
    • Proteomic discovery of biomarkers of metal contamination in Sydney Rock oysters (Saccostrea glomerata)
    • Thompson EL, Taylor DA, Nair SV, Birch G, Haynes PA, Raftos DA (2012b) Proteomic discovery of biomarkers of metal contamination in Sydney Rock oysters (Saccostrea glomerata). Aquat Toxicol 109: 202-212.
    • (2012) Aquat Toxicol , vol.109 , pp. 202-212
    • Thompson, E.L.1    Taylor, D.A.2    Nair, S.V.3    Birch, G.4    Haynes, P.A.5    Raftos, D.A.6
  • 38
    • 68249114202 scopus 로고    scopus 로고
    • Transcriptomic response of sea urchin larvae Strongylocentrotus purpuratus to CO2-driven seawater acidification
    • Todgham AE, Hofmann GE (2009) Transcriptomic response of sea urchin larvae Strongylocentrotus purpuratus to CO2-driven seawater acidification. J Exp Biol 212: 2579-2594.
    • (2009) J Exp Biol , vol.212 , pp. 2579-2594
    • Todgham, A.E.1    Hofmann, G.E.2
  • 39
    • 79957487425 scopus 로고    scopus 로고
    • Proteomic response to elevated PCO2 level in eastern oysters, Crassostrea virginica: evidence for oxidative stress
    • Tomanek L, Zuzow MJ, Ivanina AV, Beniash E, Sokolova IM (2011) Proteomic response to elevated PCO2 level in eastern oysters, Crassostrea virginica: evidence for oxidative stress. J Exp Biol 214: 1836-1844.
    • (2011) J Exp Biol , vol.214 , pp. 1836-1844
    • Tomanek, L.1    Zuzow, M.J.2    Ivanina, A.V.3    Beniash, E.4    Sokolova, I.M.5
  • 40
    • 77957753494 scopus 로고    scopus 로고
    • Microarray analysis of gene expression in eastern oyster (Crassostrea virginica) reveals a novel combination of antimicrobial and oxidative stress host responses after dermo (Perkinsus marinus) challenge
    • Wang S, Peatman E, Liu H, Bushek D, Ford SE, Kucuktas H, Quilang J, Li P, Wallace R, Wang Y et al. (2010) Microarray analysis of gene expression in eastern oyster (Crassostrea virginica) reveals a novel combination of antimicrobial and oxidative stress host responses after dermo (Perkinsus marinus) challenge. Fish Shellfish Immunol 29: 921-929.
    • (2010) Fish Shellfish Immunol , vol.29 , pp. 921-929
    • Wang, S.1    Peatman, E.2    Liu, H.3    Bushek, D.4    Ford, S.E.5    Kucuktas, H.6    Quilang, J.7    Li, P.8    Wallace, R.9    Wang, Y.10
  • 41
    • 67651173106 scopus 로고    scopus 로고
    • Proteomics by mass spectrometry: approaches, advances, and applications
    • Yates JR, Ruse CI, Nakorchevsky A (2009) Proteomics by mass spectrometry: approaches, advances, and applications. Annu Rev Biomed Eng 11: 49-79.
    • (2009) Annu Rev Biomed Eng , vol.11 , pp. 49-79
    • Yates, J.R.1    Ruse, C.I.2    Nakorchevsky, A.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.