Spatial patterns in markers of contaminant exposure, glucose and glycogen metabolism, and immunological response in juvenile winter flounder (Pseudoplueronectes americanus)

Anders, 2010, Differential expression analysis for sequence count data, Genome Biol., 11, R106, 10.1186/gb-2010-11-10-r106 Armitage, 2011, Hepcidin regulation by innate immune and infectious stimuli, Blood, 118, 4129, 10.1182/blood-2011-04-351957 Baker, 2009, Analysis of endocrine disruption in southern California coastal fish using an aquatic multispecies microarray, Environ. Health Perspect., 117, 223, 10.1289/ehp.11627 Baker, 2013, Molecular analysis of endocrine disruption in hornyhead turbot at wastewater outfalls in southern California using a second generation multi-species microarray, PLoS One, 8, e75553, 10.1371/journal.pone.0075553 Barker, 2012, Transcriptomic and proteomic analyses of the Aspergillus fumigatus hypoxia response using an oxygen-controlled fermenter, BMC Genet., 13, 62, 10.1186/1471-2164-13-62 Ba Sow, 2008, Role of hepcidin in the innate immune response to Mycobacterium tuberculosis, FASEB, 22, S556, 10.1096/fasebj.22.2_supplement.556 Black, 1988, The effect of inherited contamination on egg and larval winter flounder, Pseudoplueronectes americanus, Mar. Environ. Res., 25, 45, 10.1016/0141-1136(88)90360-1 Bols, 2001, Ecotoxicology and innate immunity in fish, Dev. Comp. Immunol., 25, 853, 10.1016/S0145-305X(01)00040-4 Byon, 2006, Comparative immune responses in Japanese flounder, Paralichthys olivaceus after vaccination with viral hemorrhagic septicemia virus (VHSV) recombinant glycoprotein and DNA vaccine using a microarray analysis, Vaccine, 24, 921, 10.1016/j.vaccine.2005.08.087 Chandra, 2012, Sustained high temperature increases the vitellogenin response to 17α-ethynylestradiol in mummichog (Fundulus heteroclitus), Aquat. Toxicol., 118, 130, 10.1016/j.aquatox.2012.04.004 Choi, 2007, Acute hypoxia–reperfusion triggers immunocompromise in Nile tilapia, J. Aquat. Anim. Health, 19, 128, 10.1577/H06-010.1 Cole, 1997, Isolation and characterization of pleurocidin, an antimicrobial peptide in the skin secretions of winter flounder, J. Biol. Chem., 272, 12008, 10.1074/jbc.272.18.12008 Crawley, 2012 CT DEP, 2011, A study of marine recreational fisheries in Connecticut Doherty, 2013 Douglas, 2001, Cloning and developmental expression of a family of pleurocidin-like antimicrobial peptides from winter flounder, Pleuronectes americanus (Walbaum), Dev. Comp. Immunol., 25, 137, 10.1016/S0145-305X(00)00052-5 Duffy, 2009, Variable susceptibility and response to estrogenic chemicals in Menidia menidia, Mar. Ecol. Prog. Ser., 380, 245, 10.3354/meps07928 Elskus, 2001, Toxicant resistance in wildlife: fish populations, 273 Encinas, 2010, Zebrafish fin immune responses during high mortality infections with viral haemorrhagic septicemia rhabdovirus. A proteomic and transcriptomic approach, BMC Genomics, 11, 518, 10.1186/1471-2164-11-518 Falciani, 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, 10.1016/j.aquatox.2008.07.020 Fast, 2008, Cortisol response and immune-related effects of Atlantic salmon (Salmo salar Linnaeus) subjected to short- and long-term stress, Fish Shellfish Immunol., 24, 194, 10.1016/j.fsi.2007.10.009 Ferguson, 2001, Distribution and fate of neutral alkylphenol ethoxylate metabolites in a sewage-impacted urban estuary, Environ. Sci. Technol., 35, 2428, 10.1021/es001871b Frazier, 2011, Hepcidin expression in human airway epithelial cells is regulated by interferon-γ, Respir. Res., 12, 100, 10.1186/1465-9921-12-100 Frisk, 2013, Restoring Long Island's winter flounder fishery: influence of natural and anthropogenic factors on health, fitness and recruitment success Gallagher, 2015, Factors influencing daily growth in young-of-the-year winter flounder along an urbangradient revealed using hierarchical linear models., Mar. Coast. Fish: Dyn. Manage. Ecosys. Sci., 10.1080/19425120.2015.1020175 Hemmer, 2002, Vitellogenin mRNA regulation and plasma clearance in male sheepshead minnow (Cyprinodon variegatus) after cessation of exposure to 17ß-estradiol and P-nonylphenol, Aquat. Toxicol., 58, 99, 10.1016/S0166-445X(01)00238-7 Heppell, 1995, Universal assay of vitellogenin as a biomarker for environmental estrogens, Environ. Health Perspect., 103, 9, 10.1289/ehp.95103s79 Hoffmann, 2008, Detecting genetic responses to environmental change, Nat. Rev. Genet., 9, 421, 10.1038/nrg2339 IEC, 2009 Kanehisa, 2014, Data, information, knowledge and principle: back to metabolism in KEGG, Nucleic Acids Res., 42, D199, 10.1093/nar/gkt1076 Kennedy, 2008, Immunological alterations in juvenile Pacific herring, Clupea pallasi, exposed to aqueous hydrocarbons derived from crude oil, Environ. Pollut., 153, 638, 10.1016/j.envpol.2007.09.003 Kibenge, 2012, Countermeasures against viral diseases of farmed fish, Antiviral Res., 95, 257, 10.1016/j.antiviral.2012.06.003 Klein-MacPhee, 2002, Righteye flounders, 3, 560 Kloepper-Sams, 1987, The temporal relationships between P450E-protein content, catalytic activity, and mRNA levels in the teleost Fundulus heteroclitus following treatment with ß-naphthoflavone, Arch. Biochem. Biophys., 268, 525, 10.1016/0003-9861(89)90319-6 Kobayashi, 2001, Hypoxia regulates glutamate metabolism and membrane transport in rat PC12 cells, J. Neurochem., 76, 1935, 10.1046/j.1471-4159.2001.00214.x Kurokawa, 1995, Structure of the exocrine pancreas of flounder (Paralichthys olivaceus): immunological localization of zymogen granules in the digestive tract using anti-trypsinogen antibody, J. Fish Biol., 46, 292, 10.1111/j.1095-8649.1995.tb05970.x Li, 2010, RNA-Seq gene expression estimation with read mapping uncertainty, Bioinformatics, 26, 493, 10.1093/bioinformatics/btp692 Livak, 2001, Analysis of relative gene expression data using real-time quantitative PCR and the 2 ΔΔCT method, Methods, 25, 402, 10.1006/meth.2001.1262 Long, 1995, Incidence of adverse biological effects within ranges of chemical concentrations in marine and estuarine sediments, Environ. Manag., 19, 81, 10.1007/BF02472006 MacDonald, 1975, The distribution of glutamate decarboxylase in rat tissues; isotopic vs fluorimetric assays, J. Neurochem., 24, 29 MacKenzie, 2008, Comparative analysis of the acute response of the trout, O. mykiss, head kidney to in vivo challenge with virulent and attenuated infectious hematopoietic necrosis virus and LPS-induced inflammation, BMC Genomics, 9, 141, 10.1186/1471-2164-9-141 Maes, 2013, Gene transcription reflects poor health status of resident European eel chronically exposed to environmental pollutants, Aquat. Toxicol., 126, 242, 10.1016/j.aquatox.2012.11.006 McElroy, 2006, Sediments from Jamaica Bay New York cause endocrine disruption in young-of-the-year winter flounder — nonylphenol implicated as causative agent, 06 Mena, 2006, Endocrine disruption in winter flounder (Pseudoplueronectes americanus) from an urban estuary, Jamaica Bay, NY USA, Mar. Environ. Res., 62, S223 Monosson, 1994, Induced cytochrome P4501A in winter flounder, Pleuronectes americanus, from offshore and coastal sites, Can. J. Fish. Aquat. Sci., 51, 933, 10.1139/f94-092 Nelson, 1991, Comparative reproductive success of winter flounder in Long Island Sound: a three-year study (biology, biochemistry, and chemistry), Estuaries, 14, 318, 10.2307/1351666 Nemeth, 2003, Hepcidin, a putative mediator of anemia of inflammation, is a type II acute-phase protein, Blood, 101, 2461-2463, 10.1182/blood-2002-10-3235 Nuttall, 2011, Identifying 120years of decline in ecosystem structure and maturity of Great South Bay, New York using the Ecopath modelling approach, Ecol. Model., 222, 3335, 10.1016/j.ecolmodel.2011.07.004 O'Leary, 2013, Severe inbreeding and small effective number of breeders in a formerly abundant marine fish, PLoS One, 8, e66126, 10.1371/journal.pone.0066126 Oleksiak, 2010, Genomic approaches with natural fish populations, J. Fish Biol., 76, 1067, 10.1111/j.1095-8649.2010.02563.x Patrzykat, 2003, Novel antimicrobial peptides derived from flatfish genes, Antimicrob. Agents Chemother., 47, 2464, 10.1128/AAC.47.8.2464-2470.2003 Perry, 1991, Sublethal abnormalities in embryos of winter flounder, Pseudoplueronectes americanus, from Long Island Sound, Estuaries, 14, 308, 10.2307/1351665 Peyssonnaux, 2007, Regulation of iron homeostasis by the hypoxia-inducible transcription factors (HIFs), J. Clin. Invest., 117, 1926, 10.1172/JCI31370 Pickering, 1989, Stress responses and disease resistance in salmonid fish: effects of chronic elevation of plasma cortisol, Fish Physiol. Biochem., 7, 253, 10.1007/BF00004714 Poole, 1966, Growth and age of winter flounder in four bays of Long Island, N. Y. Fish Game J., 13, 206 Prasch, 2004, Interactions between 2, 3, 7, 8, tetrachlorodibenzo-p-dioxin (TCDD) and hypoxia signaling pathways in zebrafish: hypoxia decreases responses to TCDD in zebrafish embryos, Toxicol. Sci., 78, 68, 10.1093/toxsci/kfh053 Prieto-Álamo, 2009, Solea senegalensis genes responding to lipopolysaccharide and copper sulphate challenges: large-scale identification by suppression subtractive hybridization and absolute quantification of transcriptional profiles by real-time RT-PCR, Aquat. Toxicol., 91, 312, 10.1016/j.aquatox.2008.11.001 Pruzanski, 1991, Phospholipase A2 a mediator between proximal and distal effectors of inflammation, Immunol. Today, 12, 143 Rahman, 2012, Effects of hypoxia exposure on hepatic cytochrome P450 1A (CYP1A) expression in Atlantic croaker: molecular mechanisms of CYP1A down-regulation, PLoS One, 7, e40825, 10.1371/journal.pone.0040825 Roth, 2004, Modulation of glucokinase expression by hypoxia-inducible factor 1 and upstream stimulatory factor 2 in primary rat hepatocytes, J. Biol. Chem., 385, 239 Romany, 2015, Measures of immune system status in young-of-the-year winter flounder (Pseudoplueronectes americanus) from Long Island coastal bays, J. Fish Biol., 86, 148, 10.1111/jfb.12553 Sagarese, 2011, Diet composition and feeding habits of common fishes in Long Island Bays, New York. Northeast, Naturalist, 18, 291 Schlenk, 2008, Biomarkers, 683 Schlenk, 2008, Biotransformation in fishes, 153 Smith, 2013, RNA-seq analysis reveals extensive transcriptional plasticity to temperature stress in a freshwater fish species, BMC Genomics, 14, 375, 10.1186/1471-2164-14-375 Socrates, 2006 Stegeman, 1994, Biochemistry and molecular biology of monooxygenases: current perspectives on forms, functions, and regulation of cytochrome P450 in aquatic species, 87 Straub, 2004, Suppression subtractive hybridization cDNA libraries to identify differentially expressed genes from contrasting fish habitats, Mar. Biotechnol., 6, 386, 10.1007/s10126-004-3146-6 Swanson, 1992, Recreation vs. waste disposal: the use and management of Jamaica Bay, Long Island Hist J., 5, 21 Swanson, 2010, What history reveals about Forge River pollution on Long Island, New York's south shore, Mar. Pollut. Bull., 60, 804, 10.1016/j.marpolbul.2010.03.007 Thomas, 2009, Biomarkers of hypoxia exposure and reproductive function in Atlantic croaker: A review with some preliminary findings from the northern Gulf of Mexico hypoxic zone, J. Exp. Mar. Biol. Ecol., 381, S38, 10.1016/j.jembe.2009.07.008 Trapnell, 2009, TopHat: discovering splice junctions with RNA-Seq, Bioinformatics, 25, 1105, 10.1093/bioinformatics/btp120 Tyler, 1998, Endocrine disruption in wildlife: a critical review of the evidence, CRC Crit. Rev. Toxicol., 28, 319, 10.1080/10408449891344236 Velloso, 1994, Regulation of GAD expression in islets of Langerhans occurs both at the mRNA and protein level, Mol. Cell. Endocrinol., 102, 31, 10.1016/0303-7207(94)90094-9 Vidal-Dorsch, 2013, Genomic and phenotypic response of hornyhead turbot exposed to municipal wastewater effluents, Aquat. Toxicol., 140–141, 174, 10.1016/j.aquatox.2013.05.017 Vidal-Dorsch, 2014, Biological responses of marine flatfish exposed to municipal wastewater effluent, Environ. Toxicol. Chem., 33, 583, 10.1002/etc.2466 Weinstein, 2002, Inappropriate expression of hepcidin is associated with iron refractory anemia: implications for anemia of chronic disease, Blood, 100, 3776, 10.1182/blood-2002-04-1260 Wedemeyer, 1990, Stress and acclimation, Meth. Fish Biol., 451–489 Whyte, 2007, The innate immune response of fishes — a review of current knowledge, Fish Shellfish Immunol., 23, 1127, 10.1016/j.fsi.2007.06.005 Williams, 2008, Transcriptomic responses of European flounder (Platichthys flesus) to model toxicants, Aquat. Toxicol., 90, 83, 10.1016/j.aquatox.2008.07.019 Williams, 2011, Towards a system level understanding of non-model organisms sampled from the environment: a network biology approach, PLoS Comput. Biol., 7, e1002126, 10.1371/journal.pcbi.1002126 Yencho, 2015, Growth and mortality in coastal populations of winter flounder: implications for recovery of a depleted population, Mar. Coast. Fish., 10.1080/19425120.2015.1045960