Gene expression profile of grass shrimp Palaemonetes pugio exposed to chronic hypoxia

Comparative Biochemistry and Physiology - Part D: Genomics and Proteomics

Volumn 4, Issue 3, 2009, Pages 196-208

  Li, Tiandao ^a,b   Brouwer, Marius ^a  

^a UNIVERSITY OF SOUTHERN MISSISSIPPI   (United States)

^b UNIVERSITY OF ARIZONA   (United States)

Author keywords

Annotation; Crustacean; Gene expression; Grass shrimp; Hypoxia; Microarray; Palaemonetes pugio

Indexed keywords

CITRIC ACID; COMPLEMENTARY DNA; CYTOCHROME C OXIDASE; HEMOCYANIN; LECTIN; OXIDOREDUCTASE; PHOSPHOENOLPYRUVATE CARBOXYKINASE (GTP); PROTON TRANSPORTING ADENOSINE TRIPHOSPHATE SYNTHASE; VITELLOGENIN;

ARTICLE; CHRONIC DISEASE; CITRIC ACID CYCLE; CONTROLLED STUDY; DNA LIBRARY; DNA MICROARRAY; DNA SEQUENCE; DOWN REGULATION; ENVIRONMENTAL STRESS; EXPRESSED SEQUENCE TAG; GENE CLUSTER; GENE CONTROL; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HYPOXIA; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN DEGRADATION; SHRIMP; TRANSCRIPTION REGULATION; UPREGULATION;

CRUSTACEA; DECAPODA (CRUSTACEA); PALAEMONETES PUGIO;

EID: 67650158441     PISSN: 1744117X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cbd.2009.03.004     Document Type: Article

References (62)

1. Allison D.B., Cui X., Page G.P., and Sabripour M. Microarray data analysis: from disarray to consolidation and consensus. Nat. Rev. Genet. 7 (2005) 55-65
2. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., and Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25 (1997) 3389-3402
3. Ashburner M., Ball C.A., Blake J.A., Botstein D., Butler H., Cherry J.M., Davis A.P., Dolinski K., Dwight S.S., Eppig J.T., Harris M.A., Hill D.P., Issel-Tarver L., Kasarskis A., Lewis S., Matese J.C., Richardson J.E., Ringwald M., Rubin G.M., and Sherlock G. Gene Ontology: tool for the unification of biology. Nat. Genet. 25 (2000) 25-29
4. Benjamini Y., and Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Statist. Soc. B 57 (1995) 289-300
5. Brouwer M., Larkin P., Brown-Peterson N., King C., Manning S., and Denslow N. Effects of hypoxia on gene and protein expression in the blue crab, Callinectes sapidus. Mar. Environ. Res. 58 (2004) 787-792
6. Brouwer M., Brown-Peterson N., Larkin P., Manning S., Denslow N., and Rose K. Molecular and organismal indicators of chronic and intermittent hypoxia in marine crustacea. Estuar. Indic. (2005) 261-276
7. Brouwer M., Brown-Peterson N.J., Larkin P., Patel V., Denslow N., Manning S., and Brouwer T.H. Molecular and whole animal responses of grass shrimp, Palaemonetes pugio, exposed to chronic hypoxia. J. Exp. Mar. Biol. Ecol. 341 (2007) 16-31
8. Brown-Peterson N.J., Larkin P., Denslow N., King C., Manning S., and Brouwer M. Molecular indicators of hypoxia in the blue crab Callinectes sapidus. Mar. Ecol. Prog. Ser. 286 (2005) 203-215
9. Carter M.G., Sharov A.A., VanBuren V., Dudekula D.B., Carmack C.E., Nelson C., and Ko M.S. Transcript copy number estimation using a mouse whole-genome oligonucleotide microarray. Genome Biol. 6 (2005) R61
10. Coblentz F.E., Towle D.W., and Shafer T.H. Expressed sequence tags from normalized cDNA libraries prepared from gill and hypodermal tissues of the blue crab, Callinectes sapidus. Comp. Biochem. Physiol. Part D Genomics Proteomics 1 (2006) 200-208
11. Currie R.A., Bombail V., Oliver J.D., Moore D.J., Lim F.L., Gwilliam V., Kimber I., Chipman K., Moggs J.G., and Orphanides G. Gene Ontology mapping as an unbiased method for identifying molecular pathways and processes affected by toxicant exposure: application to acute effects caused by the rodent non-genotoxic carcinogen diethylhexylphthalate. Toxicol. Sci. 86 (2005) 453-469
12. Dahlquist K.D., Salomonis N., Vranizan K., Lawlor S.C., and Conklin B.R. GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways. Nat. Genet. 31 (2002) 19-20
13. Decker H., Schweikardt T., Nillius D., Salzbrunn U., Jaenicke E., and Tuczek F. Similar enzyme activation and catalysis in hemocyanins and tyrosinases. Gene 398 (2007) 183-191
14. Decuypere S., Vandesompele J., Yardley V., Doncker S.D., Laurent T., Rijal S., Llanos-Cuentas A., Chappuis F., Arevalo J., and Dujardin J.-C. Differential polyadenylation of ribosomal RNA during post-transcriptional processing in Leishmania. Parasitology 131 (2005) 321-329
15. deFur P.L., and Pease A.L. Metabolic and respiratory compensation during long term hypoxia in blue crab, Callinectus sapidus. Understanding the Estuary: Advances in Chesapeake Bay Research vol. 128 (1988) 608-616
16. Doniger S.W., Salomonis N., Dahlquist K.D., Vranizan K., Lawlor S.C., and Conklin B.R. MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data. Genome Biol. 4 (2003) R7
17. Gracey A.Y., Fraser E.J., Li W., Fang Y., Taylor R.R., Rogers J., Brass A., and Cossins A.R. Coping with cold: an integrative, multitissue analysis of the transcriptome of a poikilothermic vertebrate. Proc. Natl. Acad. Sci. U.S.A. 101 (2004) 10970-10975
18. Griffitt R.J., Chandler G.T., Greig T.W., and Quattro J.M. Cathepsin B and glutathione peroxidase show differing transcriptional responses in the grass shrimp, Palaemonetes pugio following exposure to three xenobiotics. Environ. Sci. Technol. 40 (2006) 3640-3645
19. Griffitt R.J., Greig T.W., Chandler G.T., and Quattro J.M. Serial analysis of gene expression reveals identifiable patterns in transcriptome profiles of Palaemonetes pugio exposed to three common environmental stressors. Environ. Toxicol. Chem. 26 (2007) 2413-2419
20. Hansen B.H., Altin D., Nordtug T., and Olsen A.J. Suppression subtractive hybridization library prepared from the copepod Calanus finmarchicus exposed to a sublethal mixture of environmental stressors. Comp. Biochem. Physiol. Part D Genomics Proteomics 2 (2007) 250-256
21. Heinloth A.N., Irwin R.D., Boorman G.A., Nettesheim P., Fannin R.D., Sieber S.O., Snell M.L., Tucker C.J., Li L., Travlos G.S., Vansant G., Blackshear P.E., Tennant R.W., Cunningham M.L., and Paules R.S. Gene expression profiling of rat livers reveals indicators of potential adverse effects. Toxicol. Sci. 80 (2004) 193-202
22. Hochachka P.W., Buck L.T., Doll C.J., and Land S.C. Unifying theory of hypoxia tolerance: molecular/metabolic defense and rescue mechanisms for surviving oxygen lack. Proc. Natl. Acad. Sci. U.S.A. 93 (1996) 9493-9498
23. Isaac D.D., and Andrew D.J. Tubulogenesis in Drosophila: a requirement for the trachealess gene product. Genes Dev. 10 (1996) 103-117
24. Johansson M., and Soderhall K. The prophenoloxidase activating system and associated proteins in invertebrates. Prog. Mol. Subcell. Biol. 15 (1996) 46-66
25. Ju Z., Dunham R.A., and Liu Z. Differentially expressed genes in the brain of channel catfish (Ictalurus punctatus) in response to cold acclimation. Mol. Genet. Genomics 268 (2002) 87-95
26. Ju Z., Wells M.C., Heater S.J., and Walter R.B. Multiple tissue gene expression analyses in Japanese medaka (Oryzias latipes) exposed to hypoxia. Comp. Biochem. Physiol. Part C Toxicol. Pharmacol. 145 (2007) 134-144
27. Ju Z., Wells M.C., and Walter R.B. DNA microarray technology in toxicogenomics of aquatic models: methods and applications. Comp. Biochem. Physiol. Part C Toxicol. Pharmacol. 145 (2007) 5-14
28. Kanehisa M., Goto S., Hattori M., Aoki-Kinoshita K.F., Itoh M., Kawashima S., Katayama T., Araki M., and Hirakawa M. From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res. 34 (2006) D354-D357 (Database Issue)
29. Kimura T., Jindo T., Narita T., Naruse K., Kobayashi D., Shin-I T., Kitagawa T., Sakaguchi T., Mitani H., Shima A., Kohara Y., and Takeda H. Large-scale isolation of ESTs from medaka embryos and its application to medaka developmental genetics. Mech. Dev. 121 (2004) 915-932
30. Krasnov A., Koskinen H., Pehkonen P., Rexroad C.E., Afanasyev S., and Molsa H. Gene expression in the brain and kidney of rainbow trout in response to handling stress. BMC Genomics 6 (2005) 3
31. Kronick M.N. Creation of the whole human genome microarray. Expert Rev. Proteomics 1 (2004) 19-28
32. Li T., and Brouwer M. Hypoxia inducible factor, gsHIF, of the grass shrimp Palaemonetes pugio: molecular characterization and response to hypoxia. Comp. Biochem. Physiol. Part B Biochem. Mol. Biol. 147 (2007) 11-19
33. Li T., and Brouwer M. Bioinformatic analysis of expressed sequence tags from grass shrimp Palaemonetes pugio exposed to environmental stressors. Comp. Biochem. Physiol. Part D Genomics Proteomics 4 (2009) 187-195
34. Mangum C.P. Adaptation of the oxygen transport system to hypoxia in the blue crab, Callinectes sapidus. Am. Zool. 37 (1997) 604-611
35. Manning C.S., Schesny A.L., Hawkins W.E., Barnes D.H., Barnes C.S., and Walker W.W. Exposure methodologies and systems for long-term chemical carcinogenicity studies with small fish species. Toxicol. Mechan. Methods 9 (1999) 201-217
36. Marchant G.E. Toxicogenomics and toxic torts. Trends Biotechnol. 20 (2002) 329-332
37. Martyniuk C.J., Xiong H., Crump K., Chiu S., Sardana R., Nadler A., Gerrie E.R., Xia X., and Trudeau V.L. Gene expression profiling in the neuroendocrine brain of male goldfish (Carassius auratus) exposed to 17alpha-ethinylestradiol. Physiol. Genomics 27 (2006) 328-336
38. Miracle A.L., Toth G.P., and Lattier D.L. The path from molecular indicators of exposure to describing dynamic biological systems in an aquatic organism: microarrays and the fathead minnow. Ecotoxicology 12 (2003) 457-462
39. Mitchell B., and Crews S.T. Expression of the Artemia trachealess gene in the salt gland and epipod. Evol. Dev. 4 (2002) 344-353
40. Moggs J.G., Tinwell H., Spurway T., Chang H.-S., Pate I., Lim F.L., Moore D.J., Soames A., Stuckey R., Currie R., Zhu T., Kimber I., Ashby J., and Orphanides G. Phenotypic anchoring of gene expression changes during estrogen-induced uterine growth. Environ. Health Perspect. 112 (2004) 1589-1606
41. Oleksiak M.F., Kolell K.J., and Crawford D.L. Utility of natural populations for microarray analyses: isolation of genes necessary for functional genomic studies. Mar. Biotechnol. 3 Supplement 1 (2001) S203-S211
42. Oshlack A., Emslie D., Corcoran L.M., and Smyth G.K. Normalization of boutique two-color microarrays with a high proportion of differentially expressed probes. Genome Biol. 8 (2007) R2
43. Proudfoot N., and O'Sullivan J. Polyadenylation: a tail of two complexes. Curr. Biol. 12 (2002) R855-R857
44. R Development Core Team. R: A Language and Environment for Statistical Computing (2008), R Foundation for Statistical Computing
45. Reichert K., and Menzel R. Expression profiling of five different xenobiotics using a Caenorhabditis elegans whole genome microarray. Chemosphere 61 (2005) 229-237
46. Rice P., Longden I., and Bleasby A. EMBOSS: The European Molecular Biology Open Software Suite. Trends Genet. 16 (2000) 276-277
47. Rise M.L., von Schalburg K.R., Brown G.D., Mawer M.A., Devlin R.H., Kuipers N., Busby M., Beetz-Sargent M., Alberto R., Gibbs A.R., Hunt P., Shukin R., Zeznik J.A., Nelson C., Jones S.R., Smailus D.E., Jones S.J., Schein J.E., Marra M.A., Butterfield Y.S., Stott J.M., Ng S.H., Davidson W.S., and Koop B.F. Development and application of a salmonid EST database and cDNA microarray: data mining and interspecific hybridization characteristics. Genome Res. 14 (2004) 478-490
48. Salomonis N., Hanspers K., Zambon A.C., Vranizan K., Lawlor S.C., Dahlquist K.D., Doniger S.W., Stuart J., Conklin B.R., and Pico A.R. GenMAPP 2: new features and resources for pathway analysis. BMC Bioinformatics 8 (2007) 217
49. Slomovic S., Laufer D., Geiger D., and Schuster G. Polyadenylation of ribosomal RNA in human cells. Nucleic Acids Res. 34 (2006) 2966-2975
50. Smyth G.K. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol. 3 (2004) Article 3
51. Smyth G.K., Michaud J., and Scott H.S. Use of within-array replicate spots for assessing differential expression in microarray experiments. Bioinformatics 21 (2005) 2067-2075
52. Soderhall K., and Cerenius L. Role of the prophenoloxidase-activating system in invertebrate immunity. Curr. Opin. Immunol. 10 (1998) 23-28
53. Stepanyan R., Day K., Urban J., Hardin D.L., Shetty R.S., Derby C.D., Ache B.W., and McClintock T.S. Gene expression and specificity in the mature zone of the lobster olfactory organ. Physiol. Genomics 25 (2006) 224-233
54. Sugumaran M. Unified mechanism for sclerotization of insect cuticle. Adv. Insect Physiol. 27 (1998) 229-334
55. Sussman A.S. The functions of tyrosinase in insects. Q. Rev. Biol. 24 (1949) 328-341
56. Teranishi K.S., and Stillman J.H. A cDNA microarray analysis of the response to heat stress in hepatopancreas tissue of the porcelain crab Petrolisthes cinctipes. Comp. Biochem. Physiol. Part D Genomics Proteomics 2 (2007) 53-62
57. Ton C., Stamatiou D., and Liew C.-C. Gene expression profile of zebrafish exposed to hypoxia during development. Physiol. Genomics 13 (2003) 97-106
58. van der Meer D.L.M., van den Thillart G.E.E.J.M., Witte F., de Bakker M.A.G., Besser J., Richardson M.K., Spaink H.P., Leito J.T.D., and Batowski C.P. Gene expression profiling of the long-term adaptive response to hypoxia in the gills of adult zebrafish. Am. J. Physiol., Regul. Integr. Comp. Physiol. 289 (2005) 1512-1519
59. van der Ven K., Wit M.D., Keil D., Moens L., Leemput K.V., Naudts B., and Coen W.D. Development and application of a brain-specific cDNA microarray for effect evaluation of neuro-active pharmaceuticals in zebrafish (Danio rerio). Comp. Biochem. Physiol. Part B Biochem. Mol. Biol. 141 (2005) 408-417
60. Watanabe H., Tatarazako N., Oda S., Nishide H., Uchiyama I., Morita M., and Iguchi T. Analysis of expressed sequence tags of the water flea Daphnia magna. Genome 48 (2005) 606-609
61. Waters M.D., Olden K., and Tennant R.W. Toxicogenomic approach for assessing toxicant-related disease. Mutat. Res. 544 (2003) 415-424
62. Williams T.D., Gensberg K., Minchin S.D., and Chipman J.K. A DNA expression array to detect toxic stress response in European flounder (Platichthys flesus). Aquat. Toxicol. 65 (2003) 141-157