Ecotoxicogenomic Approaches for Understanding Molecular Mechanisms of Environmental Chemical Toxicity Using Aquatic Invertebrate, Daphnia Model Organism

Due to the rapid advent in genomics technologies and attention to ecological risk assessment, the term “ecotoxicogenomics” has recently emerged to describe integration of omics studies (i.e., transcriptomics, proteomics, metabolomics, and epigenomics) into ecotoxicological fields. Ecotoxicogenomics is defined as study of an entire set of genes or proteins expression in ecological organisms to provide insight on environmental toxicity, offering benefit in ecological risk assessment. Indeed, Daphnia is a model species to study aquatic environmental toxicity designated in the Organization for Economic Co-operation and Development’s toxicity test guideline and to investigate expression patterns using ecotoxicology-oriented genomics tools. Our main purpose is to demonstrate the potential utility of gene expression profiling in ecotoxicology by identifying novel biomarkers and relevant modes of toxicity in Daphnia magna. These approaches enable us to address adverse phenotypic outcomes linked to particular gene function(s) and mechanistic understanding of aquatic ecotoxicology as well as exploration of useful biomarkers. Furthermore, key challenges that currently face aquatic ecotoxicology (e.g., predicting toxicant responses among a broad spectrum of phytogenetic groups, predicting impact of temporal exposure on toxicant responses) necessitate the parallel use of other model organisms, both aquatic and terrestrial. By investigating gene expression profiling in an environmentally important organism, this provides viable support for the utility of ecotoxicogenomics.

[1]  Min-Kyeong Yeo,et al.  The effect of metal-doped TiO2 nanoparticles on zebrafish embryogenesis , 2014, Molecular & Cellular Toxicology.

[2]  J. Kwon,et al.  Recent toxicological investigations of metal or metal oxide nanoparticles in mammalian models in vitro and in vivo: DNA damaging potential, and relevant physicochemical characteristics , 2014, Molecular & Cellular Toxicology.

[3]  S. Son,et al.  Gene expression analysis reveals a functional role for the Ag-NPs-induced Egr-1 transcriptional factor in human keratinocytes , 2014, Molecular & Cellular Toxicology.

[4]  David Sheehan,et al.  Proteomic evaluation of citrate-coated silver nanoparticles toxicity in Daphnia magna. , 2014, The Analyst.

[5]  Gun-Dong Kim,et al.  Microarray analysis of gene expression in 3-methylcholanthrene-treated human endothelial cells , 2014, Molecular & Cellular Toxicology.

[6]  Mi Young Lee,et al.  Nanoparticles for gene delivery: therapeutic and toxic effects , 2014, Molecular & Cellular Toxicology.

[7]  Xiaofei Wang,et al.  Bisphenol A impairs mitochondrial function in spleens of mice via oxidative stress , 2013, Molecular & Cellular Toxicology.

[8]  Min-Kyeong Yeo,et al.  Effects of TiO2 nanoparticles and nanotubes on zebrafish caudal fin regeneration , 2013, Molecular & Cellular Toxicology.

[9]  Yang-Hoon Kim,et al.  Proteomic analysis in Daphnia magna exposed to As(III), As(V) and Cd heavy metals and their binary mixtures for screening potential biomarkers. , 2013, Chemosphere.

[10]  S. Klaine,et al.  Silver nanoparticle toxicity to Daphnia magna is a function of dissolved silver concentration , 2013, Environmental toxicology and chemistry.

[11]  M. Simpson,et al.  (1)H NMR-based metabolomics investigation of Daphnia magna responses to sub-lethal exposure to arsenic, copper and lithium. , 2013, Chemosphere.

[12]  Kyungho Choi,et al.  Toxicity and endocrine disruption in zebrafish (Danio rerio) and two freshwater invertebrates (Daphnia magna and Moina macrocopa) after chronic exposure to mefenamic acid. , 2013, Ecotoxicology and environmental safety.

[13]  Seok Won Jeong,et al.  Genomic expression responses toward bisphenol-A toxicity in Daphnia magna in terms of reproductive activity , 2013, Molecular & Cellular Toxicology.

[14]  J. Park,et al.  Copper induces the accumulation of amyloid-beta in the brain , 2013, Molecular & Cellular Toxicology.

[15]  Hyun Cheol Bae,et al.  Effect of the size and surface charge of silica nanoparticles on cutaneous toxicity , 2013, Molecular & Cellular Toxicology.

[16]  H. Tenhu,et al.  Toxicity of two types of silver nanoparticles to aquatic crustaceans Daphnia magna and Thamnocephalus platyurus , 2013, Environmental Science and Pollution Research.

[17]  Sang Hyup Lee,et al.  Acute toxicity of Ag and CuO nanoparticle suspensions against Daphnia magna: the importance of their dissolved fraction varying with preparation methods. , 2012, Journal of hazardous materials.

[18]  Kim Rogers,et al.  Toxicogenomic responses of nanotoxicity in Daphnia magna exposed to silver nitrate and coated silver nanoparticles. , 2012, Environmental science & technology.

[19]  Chun-Mei Zhao,et al.  Importance of surface coatings and soluble silver in silver nanoparticles toxicity to Daphnia magna , 2012, Nanotoxicology.

[20]  Jeanne Garric,et al.  Effects of aged TiO2 nanomaterial from sunscreen on Daphnia magna exposed by dietary route. , 2012, Environmental pollution.

[21]  E. Jurado,et al.  Acute Toxicity of Alkylpolyglucosides to Vibrio fischeri, Daphnia magna and Microalgae: A Comparative Study , 2012, Bulletin of Environmental Contamination and Toxicology.

[22]  M. Cristescu,et al.  An integrated multi-disciplinary approach for studying multiple stressors in freshwater ecosystems: Daphnia as a model organism. , 2011, Integrative and comparative biology.

[23]  Colin R. Janssen,et al.  Epigenetics and its implications for ecotoxicology , 2011, Ecotoxicology.

[24]  Mark R Viant,et al.  Metabolomics of microliter hemolymph samples enables an improved understanding of the combined metabolic and transcriptional responses of Daphnia magna to cadmium. , 2011, Environmental science & technology.

[25]  Yasuhiko Kato,et al.  Environmental Sex Determination in the Branchiopod Crustacean Daphnia magna: Deep Conservation of a Doublesex Gene in the Sex-Determining Pathway , 2011, PLoS genetics.

[26]  D. Tautz Not just another genome , 2011, BMC Biology.

[27]  M. E. Hahn,et al.  Role of DNA methylation of AHR1 and AHR2 promoters in differential sensitivity to PCBs in Atlantic Killifish, Fundulus heteroclitus. , 2011, Aquatic toxicology.

[28]  Ralf J M Weber,et al.  Discriminating between different acute chemical toxicities via changes in the daphnid metabolome. , 2010, Toxicological sciences : an official journal of the Society of Toxicology.

[29]  S. Hardy,et al.  Reverse genetics in eukaryotes , 2010, Biology of the cell.

[30]  M. Vandegehuchte,et al.  Gene transcription and higher-level effects of multigenerational Zn exposure in Daphnia magna. , 2010, Chemosphere.

[31]  M. Vandegehuchte,et al.  Can metal stress induce transferable changes in gene transcription in Daphnia magna? , 2010, Aquatic toxicology.

[32]  Colin R. Janssen,et al.  Direct and transgenerational impact on Daphnia magna of chemicals with a known effect on DNA methylation. , 2010, Comparative biochemistry and physiology. Toxicology & pharmacology : CBP.

[33]  W. Burggren,et al.  Epigenetics and transgenerational transfer: a physiological perspective , 2010, Journal of Experimental Biology.

[34]  Y. Ishikawa,et al.  Gene up-regulation in response to predator kairomones in the water flea, Daphnia pulex , 2010, BMC Developmental Biology.

[35]  C. Martyniuk,et al.  Fish endocrinology meets functional genomics: what exactly is the message? , 2009, General and comparative endocrinology.

[36]  E. Rankin,et al.  Regulation of the Histone Demethylase JMJD1A by Hypoxia-Inducible Factor 1α Enhances Hypoxic Gene Expression and Tumor Growth , 2009, Molecular and Cellular Biology.

[37]  Colin R. Janssen,et al.  Quantitative DNA-methylation in Daphnia magna and effects of multigeneration Zn exposure. , 2009, Comparative biochemistry and physiology. Toxicology & pharmacology : CBP.

[38]  A. Lennartsson,et al.  Histone modification patterns and epigenetic codes. , 2009, Biochimica et biophysica acta.

[39]  J. Bidwell,et al.  Toxicity of copper, lead, and zinc mixtures to Ceriodaphnia dubia and Daphnia carinata. , 2009, Ecotoxicology and environmental safety.

[40]  Colin R. Janssen,et al.  Occurrence of DNA methylation in Daphnia magna and influence of multigeneration Cd exposure. , 2009, Environment international.

[41]  Rebecca Klaper,et al.  Toxicity biomarker expression in daphnids exposed to manufactured nanoparticles: changes in toxicity with functionalization. , 2009, Environmental pollution.

[42]  E. Sontheimer,et al.  Origins and Mechanisms of miRNAs and siRNAs , 2009, Cell.

[43]  Theodoros N. Arvanitis,et al.  A new approach to toxicity testing in Daphnia magna: application of high throughput FT-ICR mass spectrometry metabolomics , 2009, Metabolomics.

[44]  N. Youngson,et al.  Transgenerational epigenetic effects. , 2008, Annual review of genomics and human genetics.

[45]  J. Borlak,et al.  The next innovation cycle in toxicogenomics: environmental epigenetics. , 2008, Mutation research.

[46]  Jiri Adamec,et al.  Development of GCxGC/TOF-MS metabolomics for use in ecotoxicological studies with invertebrates. , 2008, Aquatic toxicology.

[47]  Li Liu,et al.  Construction of a robust microarray from a non‐model species largemouth bass, Micropterus salmoides (Lacèpede), using pyrosequencing technology , 2008 .

[48]  G. Ankley,et al.  Altered gene expression in the brain and liver of female fathead minnows Pimephales promelas Rafinesque exposed to fadrozole , 2008 .

[49]  Anne Kahru,et al.  Toxicity of nanosized and bulk ZnO, CuO and TiO2 to bacteria Vibrio fischeri and crustaceans Daphnia magna and Thamnocephalus platyurus. , 2008, Chemosphere.

[50]  Rong-Lin Wang,et al.  DNA Microarray‐based ecotoxicological biomarker discovery in a small fish model species , 2008, Environmental toxicology and chemistry.

[51]  Taisen Iguchi,et al.  Linking molecular and population stress responses in Daphnia magna exposed to cadmium. , 2008, Environmental science & technology.

[52]  J. Colbourne,et al.  Ecological genomics in Daphnia: stress responses and environmental sex determination , 2008, Heredity.

[53]  Li Liu,et al.  Construction of a robust microarray from a non-model species (largemouth bass) using pyrosequencing technology. , 2008, Journal of fish biology.

[54]  Thomas H Hutchinson,et al.  Systems biology meets stress ecology: linking molecular and organismal stress responses in Daphnia magna , 2008, Genome Biology.

[55]  Justen Andrews,et al.  Profiling sex-biased gene expression during parthenogenetic reproduction in Daphnia pulex , 2007, BMC Genomics.

[56]  R. Crozier,et al.  From transcriptome to biological function: environmental stress in an ectothermic vertebrate, the coral reef fish Pomacentrus moluccensis , 2007, BMC Genomics.

[57]  P. Lam,et al.  Differential expression of chicken hepatic genes responsive to PFOA and PFOS. , 2007, Toxicology.

[58]  R. Blust,et al.  Molecular responses during cadmium-induced stress in Daphnia magna: integration of differential gene expression with higher-level effects. , 2007, Aquatic toxicology.

[59]  Li Liu,et al.  Development and validation of a 2,000‐gene microarray for the fathead minnow (Pimephales promelas) , 2007, Environmental toxicology and chemistry.

[60]  K. V. Van Look,et al.  Gonadal transcriptome responses and physiological consequences of exposure to oestrogen in breeding zebrafish (Danio rerio). , 2007, Aquatic toxicology.

[61]  P. Kille,et al.  Metabolic profile biomarkers of metal contamination in a sentinel terrestrial species are applicable across multiple sites. , 2007, Environmental science & technology.

[62]  L. Moens,et al.  Effluent impact assessment using microarray-based analysis in common carp: a systems toxicology approach. , 2007, Chemosphere.

[63]  Hajime Watanabe,et al.  Development of a daphnia magna DNA microarray for evaluating the toxicity of environmental chemicals , 2007, Environmental toxicology and chemistry.

[64]  Elizabeth C. Theil,et al.  Daphnia magna ecotoxicogenomics provides mechanistic insights into metal toxicity. , 2007, Environmental science & technology.

[65]  L. Moens,et al.  Daphnia magna and ecotoxicogenomics: gene expression profiles of the anti-ecdysteroidal fungicide fenarimol using energy-, molting- and life stage-related cDNA libraries. , 2007, Chemosphere.

[66]  Daniel L Villeneuve,et al.  A graphical systems model to facilitate hypothesis-driven ecotoxicogenomics research on the teleost brain-pituitary-gonadal axis. , 2007, Environmental science & technology.

[67]  Z. Gong,et al.  Transcriptome kinetics of arsenic-induced adaptive response in zebrafish liver. , 2006, Physiological genomics.

[68]  M. Lynch,et al.  A microsatellite-based genetic linkage map of the waterflea, Daphnia pulex: On the prospect of crustacean genomics. , 2006, Genomics.

[69]  Jurgen Del-Favero,et al.  Expression profiling of endocrine-disrupting compounds using a customized Cyprinus carpio cDNA microarray. , 2006, Toxicological sciences : an official journal of the Society of Toxicology.

[70]  Ana Conesa,et al.  Development of the GENIPOL European flounder (Platichthys flesus) microarray and determination of temporal transcriptional responses to cadmium at low dose. , 2006, Environmental science & technology.

[71]  Jing Chen,et al.  Aryl Hydrocarbon Receptor Activation Produces Heart-Specific Transcriptional and Toxic Responses in Developing Zebrafish , 2006, Molecular Pharmacology.

[72]  Thomas H Hutchinson,et al.  Expression of target and reference genes in Daphnia magna exposed to ibuprofen , 2006, BMC Genomics.

[73]  D. Ray,et al.  A reassessment of the neurotoxicity of pyrethroid insecticides. , 2006, Pharmacology & therapeutics.

[74]  Hajime Watanabe,et al.  Using ecotoxicogenomics to evaluate the impact of chemicals on aquatic organisms , 2006 .

[75]  W. Norwood,et al.  Assessment of the toxicity of mixtures of copper, 9,10‐phenanthrenequinone, and phenanthrene to Daphnia magna: Evidence for a reactive oxygen mechanism , 2006, Environmental toxicology and chemistry.

[76]  S. Kullman,et al.  Dynamic gene expression changes precede dioxin-induced liver pathogenesis in medaka fish. , 2006, Toxicological sciences : an official journal of the Society of Toxicology.

[77]  B K Larsen,et al.  The Potential of Ecotoxicoproteomics in Environmental Monitoring: Biomarker Profiling in Mussel Plasma Using Proteinchip Array Technology , 2006, Journal of toxicology and environmental health. Part A.

[78]  Hajime Watanabe,et al.  Application of Ecotoxicogenomics for Studying Endocrine Disruption in Vertebrates and Invertebrates , 2005, Environmental health perspectives.

[79]  W. Lampert Daphnia: Model herbivore, predator and prey , 2006 .

[80]  Bart Naudts,et al.  Molecular impact of propiconazole on Daphnia magna using a reproduction-related cDNA array. , 2006, Comparative biochemistry and physiology. Toxicology & pharmacology : CBP.

[81]  François Fuks,et al.  DNA methylation and histone modifications: teaming up to silence genes. , 2005, Current opinion in genetics & development.

[82]  H. F. Carvalho,et al.  The prima donna of epigenetics: the regulation of gene expression by DNA methylation. , 2005, Brazilian journal of medical and biological research = Revista brasileira de pesquisas medicas e biologicas.

[83]  James R. Knight,et al.  Genome sequencing in microfabricated high-density picolitre reactors , 2005, Nature.

[84]  A. Oikari,et al.  Transcriptome responses to carbon tetrachloride and pyrene in the kidney and liver of juvenile rainbow trout (Oncorhynchus mykiss). , 2005, Aquatic toxicology.

[85]  Hajime Watanabe,et al.  Analysis of expressed sequence tags of the water flea Daphnia magna. , 2005, Genome.

[86]  T. Shimada,et al.  Identification of molting fluid carboxypeptidase A (MF-CPA) in Bombyx mori. , 2005, Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology.

[87]  Almut Gerhardt,et al.  Evidence for the Stepwise Stress Model: Gambusia holbrooki and Daphnia magna under acid mine drainage and acidified reference water stress. , 2005, Environmental science & technology.

[88]  T. Snell,et al.  Profiling differential gene expression of corals along a transect of waters adjacent to the Bermuda municipal dump. , 2005, Marine pollution bulletin.

[89]  G. Ankley,et al.  Ecotoxicogenomics: linkages between exposure and effects in assessing risks of aquatic contaminants to fish. , 2005, Reproductive toxicology.

[90]  C. Rexroad,et al.  Gene expression in the brain and kidney of rainbow trout in response to handling stress , 2005, BMC Genomics.

[91]  Barbara A. Wetmore,et al.  Toxicoproteomics: proteomics applied to toxicology and pathology. , 2004, Toxicologic pathology.

[92]  R. Martienssen,et al.  The role of RNA interference in heterochromatic silencing , 2004, Nature.

[93]  J. Kocerha,et al.  Gene expression fingerprints of largemouth bass (Micropterus salmoides) exposed to pulp and paper mill effluents. , 2004, Mutation research.

[94]  Yasuhiko Kato,et al.  A vitellogenin chain containing a superoxide dismutase-like domain is the major component of yolk proteins in cladoceran crustacean Daphnia magna. , 2004, Gene.

[95]  Thomas H Hutchinson,et al.  Ecotoxicogenomics: the challenge of integrating genomics into aquatic and terrestrial ecotoxicology. , 2004, Aquatic toxicology.

[96]  W. Lampert,et al.  Growth and reproduction of migrating and non-migrating Daphnia species under simulated food and temperature conditions of diurnal vertical migration , 1984, Oecologia.

[97]  Barbara A Wetmore,et al.  Toxicoproteomics: proteomics applied to toxicology and pathology. , 2004, Toxicologic pathology.

[98]  H. Merzendorfer,et al.  Chitin metabolism in insects: structure, function and regulation of chitin synthases and chitinases , 2003, Journal of Experimental Biology.

[99]  M. Greeley,et al.  Proteomics in Zebrafish Exposed to Endocrine Disrupting Chemicals , 2003, Ecotoxicology.

[100]  Hajime Watanabe,et al.  Juvenile hormone agonists affect the occurrence of male Daphnia. , 2003, Chemosphere.

[101]  M. Rodríguez-Ortega,et al.  Changes in protein expression profiles in bivalve molluscs (Chamaelea gallina) exposed to four model environmental pollutants , 2003, Proteomics.

[102]  C. Chow,et al.  Copper toxicity, oxidative stress, and antioxidant nutrients. , 2003, Toxicology.

[103]  A. Bird,et al.  Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals , 2003, Nature Genetics.

[104]  C. Hogstrand,et al.  Application of genomics and proteomics for study of the integrated response to zinc exposure in a non-model fish species, the rainbow trout. , 2002, Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology.

[105]  B. Brooks,et al.  Toxicity of Select Beta Adrenergic Receptor-Blocking Pharmaceuticals (B-Blockers) on Aquatic Organisms , 2002, Archives of environmental contamination and toxicology.

[106]  T. Iguchi,et al.  Styrene dimers and trimers affect reproduction of daphnid (Ceriodaphnia dubia). , 2002, Chemosphere.

[107]  S. Tanabe,et al.  Endocrine disruptor issues in Japan , 2002, Congenital anomalies.

[108]  Y. Wang,et al.  Oxidative stress and liver toxicity in rats and human hepatoma cell line induced by pentachlorophenol and its major metabolite tetrachlorohydroquinone. , 2001, Toxicology letters.

[109]  J. McLachlan,et al.  Environmental signaling: what embryos and evolution teach us about endocrine disrupting chemicals. , 2001, Endocrine reviews.

[110]  S. Penn,et al.  Applications of gene arrays in environmental toxicology: fingerprints of gene regulation associated with cadmium chloride, benzo(a)pyrene, and trichloroethylene. , 2000, Environmental health perspectives.

[111]  N. Lehman,et al.  Multi‐locus genetic evidence for rapid ecologically based speciation in Daphnia , 2000, Molecular ecology.

[112]  B. Olsson,et al.  Protein expression signatures identified in Mytilus edulis exposed to PCBs, copper and salinity stress. , 2000, Marine environmental research.

[113]  J. Trent,et al.  Microarrays and toxicology: The advent of toxicogenomics , 1999, Molecular carcinogenesis.

[114]  E. Shimizu,et al.  Transgenerational induction of defences in animals and plants , 1999 .

[115]  Sac-fry Stages,et al.  OECD GUIDELINE FOR TESTING OF CHEMICALS , 2002 .

[116]  M. Lynch,et al.  Allozyme and mtDNA variation in populations of the Daphnia pulex complex from both sides of the Rocky Mountains , 1997, Heredity.

[117]  E. Werner,et al.  MECHANISMS CREATING COMMUNITY STRUCTURE ACROSS A FRESHWATER HABITAT GRADIENT , 1996 .

[118]  C. Theodorakis,et al.  Genetic ecotoxicology: The genotypic diversity approach , 1996 .

[119]  D. Bagchi,et al.  Oxidative mechanisms in the toxicity of metal ions. , 1995, Free radical biology & medicine.

[120]  M. Depledge Genotypic toxicity: implications for individuals and populations. , 1994, Environmental health perspectives.

[121]  M. Comber,et al.  The effects of nonylphenol on Daphnia magna , 1993 .

[122]  R. Tollrian Neckteeth formation in Daphnia pulex as an example of continuous phenotypic plasticity: morphological effects of Chaoborus kairomone concentration and their quantification , 1993 .

[123]  B. Kurelec The genotoxic disease syndrome , 1993 .

[124]  Carsten J. Loose,et al.  Metabolic costs during predator‐induced dielvertical migration of Daphnia , 1992 .

[125]  Anders Hobæk,et al.  Sexual reproduction in Daphnia magna requires three stimuli , 1992 .

[126]  H. Schat,et al.  Genetic control of copper tolerance in Silene vulgaris , 1992, Heredity.

[127]  J. Thompson,et al.  Phenotypic plasticity as a component of evolutionary change. , 1991, Trends in Ecology & Evolution.

[128]  G. Fryer Functional morphology and the adaptive radiation of the Daphniidae (Branchiopoda: Anomopoda) , 1991 .

[129]  B. Bayne,et al.  The metabolic/physiological basis of genotype-dependent mortality during copper exposure in Mytilus edulis , 1989 .

[130]  D. Schindler Detecting Ecosystem Responses to Anthropogenic Stress , 1987 .

[131]  H. Hennig Metal-binding proteins as metal pollution indicators. , 1986, Environmental health perspectives.

[132]  P. Hebert,et al.  Clonal diversity in populations of Daphnia pulex reproducing by obligate parthenogenesis , 1983, Heredity.

[133]  T. Schultz,et al.  Uptake, depuration, and distribution of selenium inDaphnia and its effects on survival and ultrastructure , 1980, Archives of environmental contamination and toxicology.

[134]  P. Hebert THE POPULATION BILOGY OF DAPHNIA (CRUSTACEA, DAPHNIDAE) , 1978 .

[135]  J. Oakeshott Selection at the alcohol dehydrogenase locus in Drosophila melanogaster imposed by environmental ethanol. , 1975, Genetical research.

[136]  M. Cohn,et al.  On the mode of action of 2, 4-dinitrophenol in uncoupling oxidative phosphorylation. , 1958, The Journal of biological chemistry.

[137]  John William Lubbock,et al.  VI. An account of the two methods of reproduction in Daphnia, and of the structure of the Ephippium , 1857, Philosophical Transactions of the Royal Society of London.