Identification of robust hypoxia biomarker candidates from fin of medaka (Oryzias latipes)

Altschul, 1997, Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res., 25, 3389, 10.1093/nar/25.17.3389 Bairoch, 1994, The SWISS-PROT protein sequence data bank: current status, Nucleic Acids Res., 22, 3578 Boeckmann, 2003, The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003, Nucleic Acids Res., 31, 365, 10.1093/nar/gkg095 Boswell, 2009, Comparison of gene expression responses to hypoxia in viviparous (Xiphophorus) and oviparous (Oryzias) fishes using a medaka microarray, Comp. Biochem. Physiol. C, 149, 258 Diaz, 2001, Overview of hypoxia around the world, J. Environ. Qual., 30, 275, 10.2134/jeq2001.302275x Diaz, 1995, Marine benthic hypoxia: a review of its ecological effects and the behavioral responses of benthic macrofauna, Oceanogr. Mar. Biol., 33, 245 Domenici, 1997, The kinematics and performance of fish fast-start swimming, J. Exp. Biol., 200, 1165, 10.1242/jeb.200.8.1165 Eisen, 1998, Cluster analysis and display of genome-wide expression patterns, Proc. Natl. Acad. Sci. U S A., 95, 14863, 10.1073/pnas.95.25.14863 Fraser, 2006, Hypoxia-inducible myoglobin expression in nonmuscle tissues, Proc. Natl. Acad. Sci. U. S. A, 103, 2977, 10.1073/pnas.0508270103 Fuchshofer, 2009, Hypoxia/reoxygenation induces CTGF and PAI-1 in cultured human retinal pigment epithelium cells, Exp. Eye Res., 88, 889, 10.1016/j.exer.2008.11.036 Gao, 2004, Induction of the glucose-6-phosphate dehydrogenase gene expression by chronic hypoxia in PC12 cells, FEBS Lett., 569, 256, 10.1016/j.febslet.2004.06.004 Gotz, 2008, High-throughput functional annotation and data mining with the Blast2GO suite, Nucleic Acids Res., 36, 3420, 10.1093/nar/gkn176 Gracey, 2001, Hypoxia-induced gene expression profiling in the euryoxic fish Gillichthys mirabilis, Proc. Natl. Acad. Sci. U. S. A, 98, 1993, 10.1073/pnas.98.4.1993 Hall, 2004, Sequence and expression of a constitutive, facilitated glucose transporter (GLUT1) in Atlantic cod Gadus morhua, J. Exp. Biol., 207, 4697, 10.1242/jeb.01346 Held, 2004, Microarrays in ecological research: a case study of a cDNA microarray for plant–herbivore interactions, BMC Ecol., 4, 13, 10.1186/1472-6785-4-13 Holeton, 1971, Respiratory and circulatory responses of rainbow trout larvae to carbon monoxide and to hypoxia, J. Exp. Biol., 55, 683, 10.1242/jeb.55.3.683 Howland, 1974, Optimal strategies for predator avoidance: the relative importance of speed and manoeuvrability, J. Theor. Biol., 47, 333, 10.1016/0022-5193(74)90202-1 Iuchi, 1985, Cellular and molecular basis of the larval-adult shift of hemoglobins in fish, Zool. Sci., 2, 1 Ju, 2007, DNA microarray technology in toxicogenomics of aquatic models: methods and applications, Comp. Biochem. Physiol. C, 145, 5 Ju, 2007, Multiple tissue gene expression analyses in Japanese medaka (Oryzias latipes) exposed to hypoxia, Comp. Biochem. Physiol. C, 145, 134 Law, 2006, Cloning and expression analysis of two distinct HIF-alpha isoforms–gcHIF-1alpha and gcHIF-4alpha—from the hypoxia-tolerant grass carp. Ctenopharyngodon idellus, BMC Mol. Biol., 7, 15, 10.1186/1471-2199-7-15 Lefrancois, 2005, The effect of hypoxia on locomotor performance and behaviour during escape in Liza aurata, J. Fish Biol., 67, 1711, 10.1111/j.1095-8649.2005.00884.x Li, 2007, Hypoxia-inducible factor, gsHIF, of the grass shrimp Palaemonetes pugio: molecular characterization and response to hypoxia, Comp. Biochem. Physiol. B, 147, 11, 10.1016/j.cbpb.2006.12.018 Li, 2009, Bioinformatic analysis of expressed sequence tags from grass shrimp Palaemonetes pugio exposed to environmental stressors, Comp. Biochem. Physiol. D, 4, 187 Li, 2009, Gene expression profile of grass shrimp Palaemonetes pugio exposed to chronic hypoxia, Comp. Biochem. Physiol. D, 4, 196 Lushchak, 2006, Temperature increase results in oxidative stress in goldfish tissues. 2. Antioxidant and associated enzymes, Comp. Biochem. Physiol. C, 143, 36 Luther, 1995, Muscle ultrastructure in the teleost fish, Micron, 26, 431, 10.1016/0968-4328(95)00015-1 Lutz, 1989, Interaction between hypometabolism and acid–base balance, Can. J. Zool., 67, 3018, 10.1139/z89-424 Maglott, 2007, Entrez Gene: gene-centered information at NCBI, Nucleic Acids Res., 35, D26, 10.1093/nar/gkl993 Marques, 2008, Transcriptome analysis of the response to chronic constant hypoxia in zebrafish hearts, J. Comp. Physiol. B, 178, 77, 10.1007/s00360-007-0201-4 Maruyama, K., Yasumasu, S., Iuchi, I., 2002. Characterization and expression of embryonic and adult globins of the teleost Oryzias latipes (medaka). J. Biochem. 132, 581–589. Mason, 1998, Regional tumor oxygen tension: fluorine echo planar imaging of hexafluorobenzene reveals heterogeneity of dynamics, Int. J. Radiat. Oncol. Biol Phys., 42, 747, 10.1016/S0360-3016(98)00306-X McLoughlin, 2000, Evaluation of sensitive and specificity of two crustacean biochemical biomarkers, Environ. Toxicol. Chem., 19, 2085, 10.1002/etc.5620190818 Nakatani, 2007, Cellular and molecular processes of regeneration, with special emphasis on fish fins, Dev. Growth Differ., 49, 145, 10.1111/j.1440-169X.2007.00917.x Ng, 2003, Molecular cloning and characterization of a hypoxia-responsive CITED3 cDNA from grass carp, Comp. Biochem. Physiol. B, 136, 163, 10.1016/S1096-4959(03)00224-0 Nikinmaa, 2005, Oxygen-dependent gene expression in fishes, Am. J. Physiol. Regul. Integr. Comp. Physiol., 288, R1079, 10.1152/ajpregu.00626.2004 Oehlers, 2007, Comp. Biochem. Physiol. C, 145, 120 Randall, 1982, The control of respiration and circulation in fish during exercise and hypoxia, J. Exp. Biol., 100, 275, 10.1242/jeb.100.1.275 Roesner, 2006, Hypoxia induces a complex response of globin expression in zebrafish (Danio rerio), J. Exp. Biol., 209, 2129, 10.1242/jeb.02243 Roesner, 2008, Globins and hypoxia adaptation in the goldfish. Carassius auratus, FEBS J., 275, 3633, 10.1111/j.1742-4658.2008.06508.x Rusinova, 2000, Seasonal changes in glucose-6-phosphate dehydrogenase activity in the tissues of Black Sea mussel, J. GidrobiologicheskII Zh., 36, 87 Ryba, 2008, Assessment of caudal fin clip as a non-lethal technique for predicting muscle tissue mercury concentrations in largemouth bass, Environ. Chem., 5, 200, 10.1071/EN08017 Schlenk, 1999, Necessity of defining biomarkers for use in ecological risk assessments, Mar. Pollut. Bull., 39, 48, 10.1016/S0025-326X(99)00015-6 Shang, 2004, Auquatic hypoxia is a teratogen and affects fish embryonic development, Environ. Sci. Technol., 38, 4763, 10.1021/es0496423 Shen, 2009, Differential expression of ubiquitin-conjugating enzyme E2r in the developing ovary and testis of penaeid shrimp Marsupenaeus japonicus, Mol. Biol. Rep., 36, 1149, 10.1007/s11033-008-9291-7 Terwilliger, 1998, Functional adaptations of oxygen-transport proteins, J. Exp. Biol., 201, 1085, 10.1242/jeb.201.8.1085 Thompson, 2005, A comparison of elastomer marks and fin clips as marking techniques for walleye, N. Am. J. Fish. Manage., 25, 308, 10.1577/M03-237.1 Ton, 2003, Gene expression profile of zebrafish exposed to hypoxia during development, Physiol. Genomics, 1282002 Van den Thillart, 1985, Teleosts in hypoxia: aspects of anaerobic metabolism, Mol. Physiol., 8, 393 van der Meer, 2005, 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, 1512, 10.1152/ajpregu.00089.2005 Wang, 2008, Inductive transcription and protective role of fish heme oxygenase-1 under hypoxic stress, J. Exp. Biol., 211, 2700, 10.1242/jeb.019141 Webb, 1976, Root growth in Acer saccharum Marsh. seedlings: effects of light intensity and photoperiod on root elongation rates, Bot. Gaz., 137, 211, 10.1086/336860 Wong, 2007, Characterization of a hypoxia-responsive leptin receptor (omLepRL) cDNA from the marine medaka (Oryzias melastigma), Mar. Pollut. Bull., 54, 797, 10.1016/j.marpolbul.2007.01.025 Wu, 2002, Hypoxia: from molecular responses to ecosystem responses, Mar. Pollut. Bull., 45, 35, 10.1016/S0025-326X(02)00061-9 Wu, 2003, Aquatic hypoxia is a disrupter and impairs fish reproduction, Environ. Sci. Technol., 37, 1137, 10.1021/es0258327 Yu, 2006, Hypoxia induces telomerase reverse transcriptase (TERT) gene expression in non-tumor fish tissues in vivo: the marine medaka (Oryzias melastigma) model, BMC Mol. Biol., 7, 27, 10.1186/1471-2199-7-27 Zhang, 2003, Isolation, characterization and expression analysis of a hypoxia-responsive glucose transporter gene from the grass carp, Ctenopharyngodon idellus, Eur. J. Biochem., 270, 3010, 10.1046/j.1432-1033.2003.03678.x Zhang, 2007, Ribosomal protein L24 is differentially expressed in ovary and testis of the marine shrimp Marsupenaeus japonicus, Comp. Biochem. Physiol. B, 147, 466, 10.1016/j.cbpb.2007.02.013 Zhang, 2009, Genomic approaches in the identification of hypoxia biomarkers in model fish species, J. Exp. Mar. Biol. Ecol., 381, S180, 10.1016/j.jembe.2009.07.021