Biomarker discovery and transcriptomic responses in Daphnia magna exposed to munitions constituents

Tissue-specific toxic effects of nano-copper on zebrafish

Understanding the behavior and potential toxicity of copper nanoparticles (nano-Cu) in the aquatic environment is a primary way to assess their environmental risks. In this study, RNA-seq was performed on three different tissues (gills, intestines, and muscles) of zebrafish exposed to nano-Cu, to explore the potential toxic mechanism of nano-Cu on zebrafish. The results indicated that the toxic mechanism of nano-Cu on zebrafish was tissue-specific. Nano-Cu enables the CB1 receptor of the presynaptic membrane of gill cells to affect short-term synaptic plasticity or long-term synaptic changes (ECB-LTD) through DSI and DSE, causing dysfunction of intercellular signal transmission. Imbalance of de novo synthesis of UMP in intestinal cells and its transformation to UDP, UTP, uridine, and uracil, resulted in many functions involved in the pyrimidine metabolic pathway being blocked. Meanwhile, the toxicity of nano-Cu caused abnormal expression of RAD51 gene in muscle cells, which affects the repair of damaged DNA through Fanconi anemia and homologous recombination pathway, thus causing cell cycle disorder. These results provide insights for us to better understand the differences in toxicity of nano-Cu on zebrafish tissues and are helpful for a comprehensive assessment of nano-Cu's effects on aquatic organisms.

Daphnia as a model organism to probe biological responses to nanomaterials-from individual to population effects via adverse outcome pathways

The importance of the cladoceran Daphnia as a model organism for ecotoxicity testing has been well-established since the 1980s. Daphnia have been increasingly used in standardised testing of chemicals as they are well characterised and show sensitivity to pollutants, making them an essential indicator species for environmental stress. The mapping of the genomes of D. pulex in 2012 and D. magna in 2017 further consolidated their utility for ecotoxicity testing, including demonstrating the responsiveness of the Daphnia genome to environmental stressors. The short lifecycle and parthenogenetic reproduction make Daphnia useful for assessment of developmental toxicity and adaption to stress. The emergence of nanomaterials (NMs) and their safety assessment has introduced some challenges to the use of standard toxicity tests which were developed for soluble chemicals. NMs have enormous reactive surface areas resulting in dynamic interactions with dissolved organic carbon, proteins and other biomolecules in their surroundings leading to a myriad of physical, chemical, biological, and macromolecular transformations of the NMs and thus changes in their bioavailability to, and impacts on, daphnids. However, NM safety assessments are also driving innovations in our approaches to toxicity testing, for both chemicals and other emerging contaminants such as microplastics (MPs). These advances include establishing more realistic environmental exposures via medium composition tuning including pre-conditioning by the organisms to provide relevant biomolecules as background, development of microfluidics approaches to mimic environmental flow conditions typical in streams, utilisation of field daphnids cultured in the lab to assess adaption and impacts of pre-exposure to pollution gradients, and of course development of mechanistic insights to connect the first encounter with NMs or MPs to an adverse outcome, via the key events in an adverse outcome pathway. Insights into these developments are presented below to inspire further advances and utilisation of these important organisms as part of an overall environmental risk assessment of NMs and MPs impacts, including in mixture exposure scenarios.

Machine Learning Models for Identification and Prediction of Toxic Organic Compounds Using Daphnia magna Transcriptomic Profiles

A wide range of environmental factors heavily impact aquatic ecosystems, in turn, affecting human health. Toxic organic compounds resulting from anthropogenic activity are a source of pollution in aquatic ecosystems. To evaluate these contaminants, current approaches mainly rely on acute and chronic toxicity tests, but cannot provide explicit insights into the causes of toxicity. As an alternative, genome-wide gene expression systems allow the identification of contaminants causing toxicity by monitoring the organisms' response to toxic substances. In this study, we selected 22 toxic organic compounds, classified as pesticides, herbicides, or industrial chemicals, that induce environmental problems in aquatic ecosystems and affect human-health. To identify toxic organic compounds using gene expression data from Daphnia magna, we evaluated the performance of three machine learning based feature-ranking algorithms (Learning Vector Quantization, Random Forest, and Support Vector Machines with a Linear kernel), and nine classifiers (Linear Discriminant Analysis, Classification And Regression Trees, K-nearest neighbors, Support Vector Machines with a Linear kernel, Random Forest, Boosted C5.0, Gradient Boosting Machine, eXtreme Gradient Boosting with tree, and eXtreme Gradient Boosting with DART booster). Our analysis revealed that a combination of feature selection based on feature-ranking and a random forest classification algorithm had the best model performance, with an accuracy of 95.7%. This is a preliminary study to establish a model for the monitoring of aquatic toxic substances by machine learning. This model could be an effective tool to manage contaminants and toxic organic compounds in aquatic systems.

Machine learning-based biomarkers identification from toxicogenomics - Bridging to regulatory relevant phenotypic endpoints

One of the major challenges in realization and implementations of the Tox21 vision is the urgent need to establish quantitative link between in-vitro assay molecular endpoint and in-vivo regulatory-relevant phenotypic toxicity endpoint. Current toxicomics approach still mostly rely on large number of redundant markers without pre-selection or ranking, therefore, selection of relevant biomarkers with minimal redundancy would reduce the number of markers to be monitored and reduce the cost, time, and complexity of the toxicity screening and risk monitoring. Here, we demonstrated that, using time series toxicomics in-vitro assay along with machine learning-based feature selection (maximum relevance and minimum redundancy (MRMR)) and classification method (support vector machine (SVM)), an "optimal" number of biomarkers with minimum redundancy can be identified for prediction of phenotypic toxicity endpoints with good accuracy. We included two case studies for in-vivo carcinogenicity and Ames genotoxicity prediction, using 20 selected chemicals including model genotoxic chemicals and negative controls, respectively. The results suggested that, employing the adverse outcome pathway (AOP) concept, molecular endpoints based on a relatively small number of properly selected biomarker-ensemble involved in the conserved DNA-damage and repair pathways among eukaryotes, were able to predict both Ames genotoxicity endpoints and in-vivo carcinogenicity in rats. A prediction accuracy of 76% with AUC = 0.81 was achieved while predicting in-vivo carcinogenicity with the top-ranked five biomarkers. For Ames genotoxicity prediction, the top-ranked five biomarkers were able to achieve prediction accuracy of 70% with AUC = 0.75. However, the specific biomarkers identified as the top-ranked five biomarkers are different for the two different phenotypic genotoxicity assays. The top-ranked biomarkers for the in-vivo carcinogenicity prediction mainly focused on double strand break repair and DNA recombination, whereas the selected top-ranked biomarkers for Ames genotoxicity prediction are associated with base- and nucleotide-excision repair The method developed in this study will help to fill in the knowledge gap in phenotypic anchoring and predictive toxicology, and contribute to the progress in the implementation of tox 21 vision for environmental and health applications.

Induction of carbonyl reductase 1 (CR1) gene expression in Daphnia magna by TNT, but not its key metabolites 2-ADNT and 4-ADNT

2,4,6-trinitrotoluene (TNT) is a known source of reactive oxygen species (ROS), which cause oxidative stress in aquatic ecosystems. Carbonyl reductases (CRs) are one of several possible defense mechanisms induced against ROS products, especially those that result in the 'so-called' carbonyl stress. Daphnia magna, a freshwater organism living in stagnant freshwater bodies, expresses four copies of the CR gene (Dma_CR1, Dma_CR2, Dma_CR3 and Dma_CR4). In this study, induction of all four copies of Dma_CR by 2-amino-4,6-dinitrotoluene (2-ADNT) and 4-amino-2,6-dinitrotoluene (4-ADNT), was investigated. Reverse transcription polymerase chain reaction (RT-PCR) analysis of treated daphnids revealed up-regulation of Dma_CR1 alone in response to TNT, but not 2-ADNT and 4-ADNT (which are key metabolites of TNT). This concentration- and time-dependent up-regulation in mRNA-expression was observed both in the presence and absence of light, in the same magnitude. Moreover, significant change in mRNA-expression could be observed 8 h after treatment with TNT. In the presence of TNT, the antioxidant N-acetylcysteine (NAc) could not reverse TNT-induced up-regulation of Dma_CR1 mRNA-expression. On the other hand, withdrawal of TNT from the culture medium caused a significant reduction in the TNT-induced mRNA-expression of Dma_CR1 within 24 h. These findings highlight the potential of Dma_CR1 as a biomarker for biomonitoring of TNT levels in freshwater bodies.

Production of genome-edited Daphnia for heavy metal detection by fluorescence

Aquatic heavy metal pollution is a growing concern. To facilitate heavy metal monitoring in water, we developed transgenic Daphnia that are highly sensitive to heavy metals and respond to them rapidly. Metallothionein A, which was a metal response gene, and its promoter region was obtained from Daphnia magna. A chimeric gene fusing the promoter region with a green fluorescent protein (GFP) gene was integrated into D. magna using the TALEN technique and transgenic Daphnia named D. magna MetalloG were produced. When D. magna MetalloG was exposed to heavy metal solutions for 1 h, GFP expression was induced only in their midgut and hepatopancreas. The lowest concentrations of heavy metals that activated GFP expression were 1.2 µM Zn²⁺, 130 nM Cu²⁺, and 70 nM Cd²⁺. Heavy metal exposure for 24 h could lower the thresholds even further. D. magna MetalloG facilitates aqueous heavy metal detection and might enhance water quality monitoring.

Biokinetics and subcellular distribution of metals in Daphnia magna following Zn exposure: Implication for metal regulation

Although many studies have addressed the effects of various physicochemical and biological factors on metal bioaccumulation in aquatic organisms, the influences of metal exposure history have drawn much less attention. In the present study, we investigated the effects of different Zn exposure regimes (concentration: 1-200 μg/L, duration: 1-7 d) on the subsequent biokinetics, metallothionien-like protein (MTLP) induction and subcellular distribution of Cd and Zn in Daphnia magna. Zn body burden increased significantly with elevated exposure concentrations, but was kept within a narrow range regardless of the 200-fold variation of Zn concentrations. Significant induction (7-14 folds) of MTLP by Zn exposure was evident, but was decoupled from the Zn body accumulation. Under different regimes of Zn exposure, Zn was evenly distributed in insoluble (cellular debris, intracellular organelles and metal-rich granules) and soluble fractions (heat sensitive protein and MTLP). However, >60% of Cd was bound with MTLP regardless of the exposure concentration and duration. The biokinetic processes including uptake from the dissolved phase, food assimilation and excretion of Cd and Zn were quantified with radioactive tracers. The uptake rate constants of Cd and Zn from the dissolved phase either remained comparable or increased following Zn pre-exposure, and the efflux of Zn increased by nearly two-fold to counteract the increased uptake from water. The dietary assimilation of Zn also decreased significantly in response to Zn exposure. However, Cd assimilation efficiency was kept relatively constant in each Zn pre-exposure regime. Our results showed that Zn exposure had significant influences on the biokinetics and physiology of daphnids. Daphnids attempted to maintain the Zn body burden within a narrow range by modification of biokinetic processes instead of subcellular distribution.

Towards early-warning gene signature of Chlamydomonas reinhardtii exposed to Hg-containing complex media

The potential of using gene expression signature as a biomarker of toxicants exposure was explored in the microalga Chlamydomonas reinhardtii exposed 2 h to mercury (Hg) as inorganic mercury (IHg) and methyl mercury (MeHg) in presence of copper (Cu) and Suwannee River Humic Acid (SRHA). Total cellular Hg (THg = IHg + MeHg) decreased in presence of SRHA for 0.7 nM IHg and 0.4 nM MeHg, but increased for 70 nM IHg exposure. In mixtures of IHg + MeHg and (IHg or MeHg) + Cu, SRHA decreased THg uptake, except for 0.7 nM IHg + 0.4 nM MeHg which was unchanged (p-value>0.05). In the absence of SRHA, 0.5 μM Cu strongly decreased intracellular THg concentration for 70 nM IHg, while it had no effect for 0.7 nM IHg and 0.4 nM MeHg. The expression of single transcripts was not correlated with measured THg uptake, but a subset of 60 transcripts showed signatures specific to the exposed metal(s) and was congruent with exposure concentration. Notably, the range of fold change values of this subset correlated with THg bioaccumulation with a two-slope pattern in line with [THg]_intra/[THg]_med ratios. Gene expression signature seems a promising approach to complement chemical analyses to assess bioavailability of toxicants in presence of other metals and organic matter.

Molecular Effects, Speciation, and Competition of Inorganic and Methyl Mercury in the Aquatic Plant Elodea nuttallii

Mercury (Hg) remains hazardous in aquatic environments because of its biomagnification in food webs. Nonetheless, Hg uptake and impact in primary producers is still poorly understood. Here, we compared the cellular toxicity of inorganic and methyl Hg (IHg and MeHg, respectively) in the aquatic plant Elodea nuttallii. IHg and MeHg regulated contigs involved in similar categories (e.g., energy metabolism, development, transport, secondary metabolism), but MeHg regulated more contigs, supporting a higher molecular impact than IHg. At the organism level, MeHg induced antioxidants, while IHg decreased chlorophyll content. The uptake of Hg and expression of a subset of contigs was subsequently studied in complex media. Measured uptake pointed to a contrasted impact of cell walls and copper (Cu) on IHg and MeHg. Using a speciation modeling, differences in uptake were attributed to the differences in affinities of IHg and MeHg to organic matter in relation to Cu speciation. We also identified a distinct gene expression signature for IHg, MeHg, and Cu, further supporting different molecular toxicity of these trace elements. Our data provided fundamental knowledge on IHg and MeHg uptake in a key aquatic primary producer and confirmed the potential of transcriptomics to assess Hg exposure in environmentally realistic systems.

Molecular Toxicity of Metal Oxide Nanoparticles in Danio rerio

Metal oxide nanoparticles can exert adverse effects on humans and aquatic organisms; however, their toxic mechanisms are still unclear. We investigated the toxic effects and mechanisms of copper oxide, zinc oxide, and nickel oxide nanoparticles in Danio rerio using microarray analysis and the comet assay. Copper oxide nanoparticles were more lethal than the other metal oxide nanoparticles. Gene ontology analysis of genes that were differentially expressed following exposure to all three metal oxide nanoparticles showed that the nanoparticles mainly affected nucleic acid metabolism in the nucleus via alterations in nucleic acid binding. KEGG analysis classified the differentially expressed genes to the genotoxicity-related pathways "cell cycle", "Fanconi anemia", "DNA replication", and "homologous recombination". The toxicity of metal oxide nanoparticles may be related to impairments in DNA synthesis and repair, as well as to increased production of reactive oxygen species.

Toxic Effects and Molecular Mechanism of Different Types of Silver Nanoparticles to the Aquatic Crustacean Daphnia magna

Silver nanoparticles (AgNPs) have been assessed to have a high exposure risk for humans and aquatic organisms. Toxicity varies considerably between different types of AgNPs. This study aimed to investigate the toxic effects of AgNPs with different particle sizes (40 and 110 nm) and different surface coatings (sodium citrate and polyvinylpyrrolidone, PVP) on Daphnia magna and their mechanisms of action. The results revealed that the citrate-coated AgNPs were more toxic than PVP-coated AgNPs and that the 40 nm AgNPs were more toxic than the 110 nm AgNPs. Transcriptome analysis further revealed that the toxic effects of AgNPs on D. magna were related to the mechanisms of ion binding and several metabolic pathways, such as the "RNA polymerase" pathway and the "protein digestion and absorption" pathway. Moreover, the principal component analysis (PAC) results found that surface coating was the major factor that determines the toxicities compared to particle size. These results could help us better understand the possible mechanism of AgNP toxicity in aquatic invertebrates at the transcriptome level and establish an important foundation for revealing the broad impacts of nanoparticles on aquatic environments.

Multigenerational effects evaluation of the flame retardant tris(2-butoxyethyl) phosphate (TBOEP) using Daphnia magna

Tris(2-butoxyethyl) phosphate (TBOEP) is an organophosphate ester used as substitute following the phase-out of brominated flamed retardants. Because of its high production volume and its use in a broad range of applications, this chemical is now frequently detected in the environment and biota. However, limited information is available on the long-term effects of TBOEP in aquatic organisms. In this study, Daphnia magna were exposed over three 21d generations to an environmentally relevant concentration of TBOEP (10μg/L) and effects were evaluated at the gene transcription, protein, and life-history (i.e., survival, reproduction and growth) levels. Chronic exposure to TBEOP did not impact survival or reproduction of D. magna but affected the growth output. The mean number of molts was also found to be lower in daphnids exposed to the chemical compared to control for a given generation, however there were no significant differences over the three generations. Molecular responses indicated significant differences in the transcription of genes related to growth, molting, ecdysteroid and juvenile hormone signaling, proteolysis, oxidative stress, and oxygen transport within generations. Levels of mRNA were also found to be significantly different for genes known to be involved in endocrine-mediated mechanisms such as reproduction and growth between generations F0, F1, and F2, indicating effects of parental exposure on offspring. Transcription results were supported by protein analyses with the significant decreased in catalase (CAT) activity in F1 generation, following the decreased transcription of cat in the parental generation. Taken together, these multi-biological level results suggest long-term potential endocrine disruption effects of TBOEP in D. magna exposed to an environmentally relevant concentration. This study highlights the importance of using chronic and multigenerational biological evaluation to assess risks of emerging chemicals.

Metabolomic responses to sublethal contaminant exposure in neonate and adult Daphnia magna

The use of consumer products and pharmaceuticals that act as contaminants entering waterways through runoff and wastewater effluents alters aquatic ecosystem health. Traditional toxicological endpoints may underestimate the toxicity of contaminants, as lethal concentrations are often orders of magnitude higher than those found within freshwater ecosystems. While newer techniques examine the metabolic responses of sublethal contaminant exposure, there has been no direct comparison with ontogeny in Daphnia. It was hypothesized that Daphnia magna would have distinct metabolic changes after 3 different sublethal contaminant exposures, because of differences in the toxic mode of action and ontogeny. To test this hypothesis, the proton nuclear magnetic resonance metabolomic profiles were measured in D. magna aged day 0 and 18 after exposure to 28% of the lethal concentration of 50% of organisms tested (LC50) of atrazine, propranolol, and perfluorooctanesulfonic acid (PFOS) for 48 h. Principal component analysis revealed significant separation of contaminants from the control daphnids in both neonates and adults exposed to propranolol and PFOS. In contrast, atrazine exposure caused separation from the controls in only the adult D. magna. Minimal ontogenetic changes in the targeted metabolites were seen after exposure to propranolol. For both atrazine and PFOS exposures ontogeny exhibited unique changes in the targeted metabolites. These results indicate that, depending on the contaminant studied, neonates and adults respond uniquely to sublethal contaminant exposure. Environ Toxicol Chem 2017;36:938-946. © 2016 SETAC.

Transcriptomic, cellular and life-history responses of Daphnia magna chronically exposed to benzotriazoles: Endocrine-disrupting potential and molting effects

Benzotriazoles (BZTs) are ubiquitous aquatic contaminants used in a wide range of industrial and domestic applications from aircraft deicers to dishwasher tablets. Acute toxicity has been reported in aquatic organisms for some of the BZTs but their mode of action remains unknown. The objectives of this study were to evaluate the transcriptomic response of D. magna exposed to sublethal doses of 1H-benzotriazole (BTR), 5-methyl-1H-benzotriazole (5MeBTR) and 5-chloro-1H-benzotriazole (5ClBTR) using RNA-sequencing and quantitative real-time PCR. Cellular and life-history endpoints (survival, number of neonates, growth) were also investigated. Significant effects on the molting frequency were observed after 21-d exposure to 5MeBTR and 5ClBTR. No effects on molting frequency were observed for BTR but RNA-seq results indicated that this BZT induced the up-regulation of genes coding for cuticular proteins, which could have compensated the molting disruption. Molting in cladocerans is actively controlled by ecdysteroid hormones. Complementary short-term temporal analysis (4- and 8-d exposure) of the transcription of genes related to molting and hormone-mediated processes indicated that the three compounds had specific modes of action. BTR induced the transcription of genes involved in 20-hydroxyecdysone synthesis, which suggests pro-ecdysteroid properties. 5ClBTR exposure induced protein activity and transcriptional levels of chitinase enzymes, associated with an impact on ecdysteroid signaling pathways, which could explain the decrease in molt frequency. Finally, 5MeBTR seemed to increase molt frequency through epigenetic processes. Overall, results suggested that molting effects observed at the physiological level could be linked to endocrine regulation impacts of BZTs at the molecular level.

Daphnia magna's sense of competition: intra-specific interactions (ISI) alter life history strategies and increase metals toxicity

This work investigates whether the scale-up to multi-animal exposures that is commonly applied in genomics studies provides equivalent toxicity outcomes to single-animal experiments of standard Daphnia magna toxicity assays. Specifically, we tested the null hypothesis that intraspecific interactions (ISI) among D. magna have neither effect on the life history strategies of this species, nor impact toxicological outcomes in exposure experiments with Cu and Pb. The results show that ISI significantly increased mortality of D. magna in both Cu and Pb exposure experiments, decreasing 14 day LC50 s and 95 % confidence intervals from 14.5 (10.9-148.3) to 8.4 (8.2-8.7) µg Cu/L and from 232 (156-4810) to 68 (63-73) µg Pb/L. Additionally, ISI potentiated Pb impacts on reproduction eliciting a nearly 10-fold decrease in the no-observed effect concentration (from 236 to 25 µg/L). As an indication of environmental relevance, the effects of ISI on both mortality and reproduction in Pb exposures were sustained at both high and low food rations. Furthermore, even with a single pair of Daphnia, ISI significantly increased (p < 0.05) neonate production in control conditions, demonstrating that ISI can affect life history strategy. Given these results we reject the null hypothesis and conclude that results from scale-up assays cannot be directly applied to observations from single-animal assessments in D. magna. We postulate that D. magna senses chemical signatures of conspecifics which elicits changes in life history strategies that ultimately increase susceptibility to metal toxicity.

Biomarker discovery and gene expression responses in Lycopersicon esculentum root exposed to lead

Gene expression analysis has shown particular promise for the identification of molecular biomarkers that can be used for further evaluation of potential toxicity of chemicals present in agricultural soil. In the study, we focused on the development of molecular markers to detect Pb toxicity in agricultural soil. Using the results obtained from microarray analysis, twelve Pb-responsive genes were selected and tested in different Pb concentrations to examine their concentration-response characteristics using real-time quantitative polymerase chain reaction (RT-qPCR). All the Pb treatments set in our study could generally induce the differential expression of the 12 genes, while the lowest observable adverse effect concentration (LOAEC) of Pb for seed germination, root elongation, biomass and structural modification derived from 1,297, 177, 177, and 1,297 mg Pb/kg soil, respectively, suggesting that the transcriptional approach was more sensitive than the traditional end points of death, growth, and morphology for the evaluation of Pb toxicity. The relative expression of glycoalkaloid metabolism 1 (P=-0.790), ethylene-responsive transcription factor ERF017 (P=-0.686) and CASP-like protein 4C2 (P=-0.652) demonstrates a dose-dependent response with Pb content in roots, implying that the three genes can be used as sensitive bioindicators of Pb stress in Lycopersicon esculentum.

Relating suborganismal processes to ecotoxicological and population level endpoints using a bioenergetic model

Ecological effects of environmental stressors are commonly evaluated using organismal or suborganismal data, such as standardized toxicity tests that characterize responses of individuals (e.g., mortality and reproduction) and a rapidly growing body of "omics" data. A key challenge for environmental risk assessment is relating such information to population dynamics. One approach uses dynamic energy budget (DEB) models that relate growth and reproduction of individuals to underlying flows of energy and elemental matter. We hypothesize that suborganismal information identifies DEB parameters that are most likely impacted by a particular stressor and that the DEB model can then project suborganismal effects on life history and population endpoints. We formulate and parameterize a model of growth and reproduction for the water flea Daphnia magna. Our model resembles previous generic bioenergetic models, but has explicit representation of discrete molts, an important feature of Daphnia life history. We test its ability to predict six endpoints commonly used in chronic toxicity studies in specified food environments. With just one adjustable parameter, the model successfully predicts growth and reproduction of individuals from a wide array of experiments performed in multiple laboratories using different clones of D. magna raised on different food sources. Fecundity is the most sensitive endpoint, and there is broad correlation between the sensitivities of fecundity and long-run growth rate, as is desirable for the default metric used in chronic toxicity tests. Under some assumptions, we can combine our DEB model with the Euler-Lotka equation to estimate longrun population growth rates at different food levels. A review of Daphnia gene-expression experiments on the effects of contaminant exposure reveals several connections to model parameters, in particular a general trend of increased transcript expression of genes involved in energy assimilation and utilization at concentrations affecting growth and reproduction. The sensitivity of fecundity to many model parameters was consistent with frequent generalized observations of decreased expression of genes involved in reproductive physiology, but interpretation of these observations requires further mechanistic modeling. We thus propose an approach based on generic DEB models incorporating few essential species-specific features for rapid extrapolation of ecotoxicogenomic assays for Daphnia-based population risk assessment.

Chronic toxicity evaluation of the flame retardant tris (2-butoxyethyl) phosphate (TBOEP) using Daphnia magna transcriptomic response

Tris (2-butoxyethyl) phosphate (TBOEP) is an organophosphorous-containing flame retardant (OPFR) of high production volume used in a broad range of applications. The use of TBOEP containing products has resulted in its release and ubiquitous occurrence in the aquatic environment. In this study, Daphnia magna transcriptomic response was measured by microarray to evaluate sublethal effects of TBOEP as part of a multi-level biological approach including specific gene transcription measured by qRT-PCR, enzyme activity, and life-history endpoints (i.e., survival, growth and reproduction). Chronic exposure (21 d) to a range of sublethal concentrations of TBOEP (14.7-1470μgL(-1)) did not impact growth, survival or reproduction, although the number of offspring decreased between the lowest and the highest dose. Gene transcription profiling by microarray analysis revealed that 101 genes were differentially transcribed in response to TBOEP (fold change treated/control ±1, p<0.05). Most of the responding genes were involved in protein metabolism (9), biosynthesis (4) and energy metabolism (6) indicating that TBOEP could have chronic toxic effects on aquatic organisms at sublethal doses by disrupting essential biological pathways. Nine genes were found to be commonly affected by more than one dose, including a gene coding for cathepsin D and multiple isoforms of genes coding for hemoglobin, suggesting potential biomarkers of interest. Microarray results were confirmed by qRT-PCR and measurements at the protein level as cathepsin D enzymatic activity increased significantly in the highest dose treatment. Results highlight the relevance of using the transcriptomic response of D. magna as a first line of evidence to unravel the mode of action of chemicals.

Microarray-based analysis of gene expression in lycopersicon esculentum seedling roots in response to cadmium, chromium, mercury, and lead

The effects of heavy metals in agricultural soils have received special attention due to their potential for accumulation in crops, which can affect species at all trophic levels. Therefore, there is a critical need for reliable bioassays for assessing risk levels due to heavy metals in agricultural soil. In the present study, we used microarrays to investigate changes in gene expression of Lycopersicon esculentum in response to Cd-, Cr-, Hg-, or Pb-spiked soil. Exposure to (1)/10 median lethal concentrations (LC50) of Cd, Cr, Hg, or Pb for 7 days resulted in expression changes in 29 Cd-specific, 58 Cr-specific, 192 Hg-specific and 864 Pb-specific genes as determined by microarray analysis, whereas conventional morphological and physiological bioassays did not reveal any toxicant stresses. Hierarchical clustering analysis showed that the characteristic gene expression profiles induced by Cd, Cr, Hg, and Pb were distinct from not only the control but also one another. Furthermore, a total of three genes related to "ion transport" for Cd, 14 genes related to "external encapsulating structure organization", "reproductive developmental process", "lipid metabolic process" and "response to stimulus" for Cr, 11 genes related to "cellular metabolic process" and "cellular response to stimulus" for Hg, 78 genes related to 20 biological processes (e.g., DNA metabolic process, monosaccharide catabolic process, cell division) for Pb were identified and selected as their potential biomarkers. These findings demonstrated that microarray-based analysis of Lycopersicon esculentum was a sensitive tool for the early detection of potential toxicity of heavy metals in agricultural soil, as well as an effective tool for identifying the heavy metal-specific genes, which should be useful for assessing risk levels due to heavy metals in agricultural soil.

Endocrinology: advances through omics and related technologies

The rapid development of new omics technologies to measure changes at genetic, transcriptomic, proteomic, and metabolomics levels together with the evolution of methods to analyze and integrate the data at a systems level are revolutionizing the study of biological processes. Here we discuss how new approaches using omics technologies have expanded our knowledge especially in nontraditional models. Our increasing knowledge of these interactions and evolutionary pathway conservation facilitates the use of nontraditional species, both invertebrate and vertebrate, as new model species for biological and endocrinology research. The increasing availability of technology to create organisms overexpressing key genes in endocrine function allows manipulation of complex regulatory networks such as growth hormone (GH) in transgenic fish where disregulation of GH production to produce larger fish has also permitted exploration of the role that GH plays in testis development, suggesting that it does so through interactions with insulin-like growth factors. The availability of omics tools to monitor changes at nearly any level in any organism, manipulate gene expression and behavior, and integrate data across biological levels, provides novel opportunities to explore endocrine function across many species and understand the complex roles that key genes play in different aspects of the endocrine function.

Effect of deltamethrin (pyrethroid insecticide) on two clones of Daphnia magna (Crustacea, Cladocera): a proteomic investigation

Deltamethrin is a class II pyrethroid insecticide commonly used in agriculture. It is hazardous to freshwater ecosystems, especially for the cladoceran Daphnia magna (Straus 1820). The results of our previous studies based on acute and chronic ecotoxicity experiments revealed differences in the sensitivity between two different clones. In this work, to investigate deltamethrin toxicity mechanisms in two clones of D. magna, we used a proteomic approach in order to analyze changes in protein expression profiles after 48 h of exposure. We detected 1339 spots; then applying statistical criteria (ANOVA p<0.001 and minimum fold change 1.5), only 128 spots were significantly different in the normalized volume. Among the preselected proteins there were 88 up-regulated and 40 down-regulated proteins. Results showed differences in sensitivities after deltamethrin exposure between the clones. Moreover, using the 2-DIGE method, proteomic investigation for deltamethrin exposure proved to be a reliable and powerful approach to investigate effects of deltamethrin as part of research for new metabolic and cellular biomarkers. After identification by mass spectrometry, there were 39 proteins recognized and identified, in which 21 and 18 were up- and down-regulated, respectively, in deltamethrin-exposed clone A compared to three other conditions (controls of each clone and deltamethrin-exposed clone 2). Up- and down-regulated proteins belonged to 12 biological processes (i.e. metabolic processes, apoptosis and stimulus response) and 5 molecular functions (i.e. catalytic activity, binding, structural molecular activity, antioxidant and receptor activities). Identification of these deregulated proteins opens a new way in discovering new molecular targets and putative biomarkers in daphnids exposed to deltamethrin.

Assessing mechanisms of toxicant response in the amphipod Melita plumulosa through transcriptomic profiling

This study describes the function of transcripts with altered abundance in the epibenthic amphipod, Melita plumulosa, following whole-sediment exposure to a series of common environmental contaminants. M. plumulosa were exposed for 48 h to sediments spiked and equilibrated with the following contaminants at concentrations predicted to cause sublethal effects to reproduction: porewater ammonia 30 mg L(-1); bifenthrin at 100 μg kg(-1); fipronil at 50 μg kg(-1); 0.6% diesel; 0.3% crude oil; 250 mg Cu kg(-1); 400 mg Ni kg(-1); and 400 mg Zn kg(-1). RNA was extracted and hybridized against a custom Agilent microarray developed for this species. Although the microarray represented a partial transcriptome and not all features on the array could be annotated, unique transcriptomic profiles were generated for each of the contaminant exposures. Hierarchical clustering grouped the expression profiles together by contaminant class, with copper and zinc, the petroleum products and nickel, and the pesticides each forming a distinct cluster. Many of the transcriptional changes observed were consistent with patterns previously described in other crustaceans. The changes in the transcriptome demonstrated that contaminant exposure caused changes in digestive function, growth and moulting, and the cytoskeleton following metal exposure, whereas exposure to petroleum products caused changes in carbohydrate metabolism, xenobiotic metabolism and hormone cycling. Functional analysis of these gene expression profiles can provide a better understanding of modes of toxic action and permits the prediction of mixture effects within contaminated ecosystems.

Silver nanowire exposure results in internalization and toxicity to Daphnia magna

Nanowires (NWs), high-aspect-ratio nanomaterials, are increasingly used in technological materials and consumer products and may have toxicological characteristics distinct from nanoparticles. We carried out a comprehensive evaluation of the physicochemical stability of four silver nanowires (AgNWs) of two sizes and coatings and their toxicity to Daphnia magna . Inorganic aluminum-doped silica coatings were less effective than organic poly(vinyl pyrrolidone) coatings at preventing silver oxidation or Ag(+) release and underwent a significant morphological transformation within 1 h following addition to low ionic strength Daphnia growth media. All AgNWs were highly toxic to D. magna but less toxic than ionic silver. Toxicity varied as a function of AgNW dimension, coating, and solution chemistry. Ag(+) release in the media could not account for observed AgNW toxicity. Single-particle inductively coupled plasma mass spectrometry distinguished and quantified dissolved and nanoparticulate silver in microliter-scale volumes of Daphnia magna hemolymph with a limit of detection of approximately 10 ppb. The silver levels within the hemolymph of Daphnia exposed to both Ag(+) and AgNW met or exceeded the initial concentration in the growth medium, indicating effective accumulation during filter feeding. Silver-rich particles were the predominant form of silver in hemolymph following exposure to both AgNWs and Ag(+). Scanning electron microscopy imaging of dried hemolymph found both AgNWs and silver precipitates that were not present in the AgNW stock or the growth medium. Both organic and inorganic coatings on the AgNW were transformed during ingestion or absorption. Pathway, gene ontology, and clustering analyses of gene expression response indicated effects of AgNWs distinct from ionic silver on Daphnia magna .

Selection of reliable biomarkers from PCR array analyses using relative distance computational model: methodology and proof-of-concept study

It is increasingly evident about the difficulty to monitor chemical exposure through biomarkers as almost all the biomarkers so far proposed are not specific for any individual chemical. In this proof-of-concept study, adult male zebrafish (Danio rerio) were exposed to 5 or 25 µg/L 17β-estradiol (E2), 100 µg/L lindane, 5 nM 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) or 15 mg/L arsenic for 96 h, and the expression profiles of 59 genes involved in 7 pathways plus 2 well characterized biomarker genes, vtg1 (vitellogenin1) and cyp1a1 (cytochrome P450 1A1), were examined. Relative distance (RD) computational model was developed to screen favorable genes and generate appropriate gene sets for the differentiation of chemicals/concentrations selected. Our results demonstrated that the known biomarker genes were not always good candidates for the differentiation of pair of chemicals/concentrations, and other genes had higher potentials in some cases. Furthermore, the differentiation of 5 chemicals/concentrations examined were attainable using expression data of various gene sets, and the best combination was the set consisting of 50 genes; however, as few as two genes (e.g. vtg1 and hspa5 [heat shock protein 5]) were sufficient to differentiate the five chemical/concentration groups in the present test. These observations suggest that multi-parameter arrays should be more reliable for biomonitoring of chemical exposure than traditional biomarkers, and the RD computational model provides an effective tool for the selection of parameters and generation of parameter sets.

Molecular toxicity identification evaluation (mTIE) approach predicts chemical exposure in Daphnia magna

Daphnia magna is a bioindicator organism accepted by several international water quality regulatory agencies. Current approaches for assessment of water quality rely on acute and chronic toxicity that provide no insight into the cause of toxicity. Recently, molecular approaches, such as genome wide gene expression responses, are enabling an alternative mechanism based approach to toxicity assessment. While these genomic methods are providing important mechanistic insight into toxicity, statistically robust prediction systems that allow the identification of chemical contaminants from the molecular response to exposure are needed. Here we apply advanced machine learning approaches to develop predictive models of contaminant exposure using a D. magna gene expression data set for 36 chemical exposures. We demonstrate here that we can discriminate between chemicals belonging to different chemical classes including endocrine disruptors and inorganic and organic chemicals based on gene expression. We also show that predictive models based on indices of whole pathway transcriptional activity can achieve comparable results while facilitating biological interpretability.

How does exposure to nickel and cadmium affect the transcriptome of yellow perch (Perca flavescens)--results from a 1000 candidate-gene microarray

The molecular mechanisms underlying nickel (Ni) and cadmium (Cd) toxicity and their specific effects on fish are poorly understood. Documenting gene transcription profiles offers a powerful approach toward identifying the molecular mechanisms affected by these metals and to discover biomarkers of their toxicity. However, confounding environmental factors can complicate the interpretation of the results and the detection of biomarkers for fish captured in their natural environment. In the present study, a 1000 candidate-gene microarray, developed from a previous RNA-seq study on a subset of individual fish from contrasting level of metal contamination, was used to investigate the transcriptional response to metal (Ni and Cd) and non metal (temperature, oxygen, and diet) stressors in yellow perch (Perca flavescens). Specifically, we aimed at (1) identifying transcriptional signatures specific to Ni and Cd exposure, (2) investigating the mechanisms of their toxicity, and (3) developing a predictive tool to identify the sublethal effects of Ni and Cd contaminants in fish sampled from natural environments. A total of 475 genes displayed significantly different transcription levels when temperature varied while 287 and 176 genes were differentially transcribed at different concentrations of Ni and Cd, respectively. These metals were found to mainly affect the transcription level of genes involved in iron metabolism, transcriptional and translational processes, vitamin metabolism, blood coagulation, and calcium transport. In addition, a linear discriminant analysis (LDA) made using gene transcription levels yielded 94% correctly reassigned samples regarding their level of metal contamination, which indicates the potential of the microarray to detect perch response to Cd or Ni effects.

Identification of metabolic pathways in Daphnia magna explaining hormetic effects of selective serotonin reuptake inhibitors and 4-nonylphenol using transcriptomic and phenotypic responses

The molecular mechanisms explaining hormetic effects of selective serotonin reuptake inhibitors (SSRIs) and 4-nonylphenol in Daphnia magna reproduction were studied in juveniles and adults. Transcriptome analyses showed changes in mRNA levels for 1796 genes in juveniles and 1214 genes in adults (out of 15000 total probes) exposed to two SSRIs (fluoxetine and fluvoxamine) or to 4-nonylphenol. Functional annotation of affected genes was improved by assuming the annotations of putatively homologous Drosophila genes. Self-organizing map analysis and partial least-square regression coupled with selectivity ratio procedures analyses allowed to define groups of genes with specific responses to the different treatments. Differentially expressed genes were analyzed for functional enrichment using Gene Ontology and Kyoto Encyclopaedia of Genes and Genomes databases. Serotonin metabolism, neuronal developmental processes, and carbohydrates and lipid metabolism functional categories appeared as selectively affected by SSRI treatment, whereas 4-nonylphenol deregulated genes from the carbohydrate metabolism and the ecdysone regulatory pathway. These changes in functional and metabolic pathways are consistent with previously reported SSRIs and 4-nonylphenol hormetic effects in D. magna, including a decrease in reserve carbohydrates and an increase in respiratory metabolism.

Monitoring of deiodinase deficiency based on transcriptomic responses in SH-SY5Y cells

Iodothyronine deiodinase types I, II, and III (D1, D2, and D3, respectively), which constitute a family of selenoenzymes, activate and inactivate thyroid hormones through the removal of specific iodine moieties from thyroxine and its derivatives. These enzymes are important in the biological effects mediated by thyroid hormones. The expression of activating and inactivating deiodinases plays a critical role in a number of cell systems, including the neuronal system, during development as well as in adult vertebrates. To investigate deiodinase-disrupting chemicals based on transcriptomic responses, we examined differences in gene expression profiles between T3-treated and deiodinase-knockdown SH-SY5Y cells using microarray analysis and quantitative real-time RT-PCR. A total of 1,558 genes, consisting of 755 upregulated and 803 downregulated genes, were differentially expressed between the T3-treated and deiodinase-knockdown cells. The expression levels of 10 of these genes (ID2, ID3, CCL2, TBX3, TGOLN2, C1orf71, ZNF676, GULP1, KLF9, and ITGB5) were altered by deiodinase-disrupting chemicals (2,3,7,8-tetrachlorodibenzo-p-dioxin, polychlorinated biphenyls, propylthiouracil, iodoacetic acid, methylmercury, β-estradiol, methimazole, 3-methylcholanthrene, aminotriazole, amiodarone, cadmium chloride, dimethoate, fenvalerate, octylmethoxycinnamate, iopanoic acid, methoxychlor, and 4-methylbenzylidene-camphor). These genes are potential biomarkers for detecting deiodinase deficiency and predicting their effects on thyroid hormone production.

Differential gene expression in Iberian green frogs (Pelophylax perezi) inhabiting a deactivated uranium mine

Iberian green frogs (Pelophylax perezi) were found inhabiting a deactivated uranium mine, especially an effluent pond, seriously contaminated with metals and radionuclides. These animals were previously assessed for oxidative stress parameters and did not revealed significant alterations. In order to better understand which mechanisms may be involved in the ability to withstand permanent contamination gene expression analysis was performed in the liver, through suppression subtractive hybridization (SSH). The SSH outcome in the liver revealed the up-regulation of genes coding for the ribosomal protein L7a and for several proteins typical from blood plasma: fibrinogen, hemoglobin and albumin. Besides their normal function, some of these proteins can play an important role as protective agents against oxidative stress. This work provides new insights on possible basal protection mechanisms that may act in organisms exposed chronically to contamination.

Assessment of chemical mixtures and groundwater effects on Daphnia magna transcriptomics

Small organisms can be used as biomonitoring tools to assess chemicals in the environment. Chemical stressors are especially hard to assess and monitor when present as complex mixtures. Here, fifteen polymerase chain reaction assays targeting Daphnia magna genes were calibrated to responses elicited in D. magna exposed for 24 h to five different doses each of the munitions constituents 2,4,6-trinitrotoluene, 2,4-dinitrotoluene, 2,6-dinitrotoluene, trinitrobenzene, dinitrobenzene, or 1,3,5-trinitro-1,3,5-triazacyclohexane. A piecewise-linear model for log-fold expression changes in gene assays was used to predict response to munitions mixtures and contaminated groundwater under the assumption that chemical effects were additive. The correlations of model predictions with actual expression changes ranged from 0.12 to 0.78 with an average of 0.5. To better understand possible mixture effects, gene expression changes from all treatments were compared using high-density microarrays. Whereas mixtures and groundwater exposures had genes and gene functions in common with single chemical exposures, unique functions were also affected, which was consistent with the nonadditivity of chemical effects in these mixtures. These results suggest that, while gene behavior in response to chemical exposure can be partially predicted based on chemical exposure, estimation of the composition of mixtures from chemical responses is difficult without further understanding of gene behavior in mixtures. Future work will need to examine additive and nonadditive mixture effects using a much greater range of different chemical classes in order to clarify the behavior and predictability of complex mixtures.

An integrated multi-disciplinary approach for studying multiple stressors in freshwater ecosystems: Daphnia as a model organism

The increased overexploitation of freshwater ecosystems and their extended watersheds often generates a cascade of anthropogenic stressors (e.g., acidification, eutrophication, metal contamination, Ca decline, changes in the physical environment, introduction of invasive species, over-harvesting of resources). The combined effect of these stressors is particularly difficult to study, requiring a coordinated multi-disciplinary effort and insights from various sub-disciplines of biology, including ecology, evolution, toxicology, and genetics. It also would benefit from a well-developed and broadly accepted model systems. The freshwater crustacean Daphnia is an excellent model organism for studying multiple stressors because it has been a chosen focus of study in all four of these fields. Daphnia is a widespread keystone species in most freshwater ecosystems, where it is routinely exposed to a multitude of anthropogenic and natural stressors. It has a fully sequenced genome, a well-understood life history and ecology, and a huge library of responses to toxicity. To make the case for its value as a model species, we consider the joint and separate effects of natural and three anthropogenic stressors-climatic change, calcium decline, and metal contaminants on daphniids. We propose that integrative approaches marrying various subfields of biology can advance our understanding of the combined effects of stressors. Such approaches can involve the measuring of multiple responses at several levels of biological organization from molecules to natural populations. For example, novel interdisciplinary approaches such as transcriptome profiling and mutation accumulation experiments can offer insights into how multiple stressors influence gene transcription and mutation rates across genomes, and, thus, help determine the causal mechanism between environmental stressors and population/community effects as well as long-term evolutionary patterns.

Genomic investigation of year-long and multigenerational exposures of fathead minnow to the munitions compound RDX

We assessed the impacts of exposure to an environmentally representative concentration (0.83 mg/L) of the explosive cyclotrimethylenetrinitramine (RDX) on fathead minnows (Pimephales promelas) in one-year and multigenerational bioassays. In the one-year bioassay, impacts were assessed by statistical comparisons of females from breeding groups reared in control or RDX-exposure conditions. The RDX had no significant effect on gonadosomatic index or condition factor assayed at 1 d and at one, three, six, nine, and 12 months. The liver-somatic index was significantly increased versus controls only at the 12-month timepoint. RDX had no significant effect on live-prey capture rates, egg production, or fertilization. RDX caused minimal differential-transcript expression with no consistent discernable effect on gene-functional categories for either brain or liver tissues in the one-year exposure. In the multigenerational assay, the effects of acute (96 h) exposure to RDX were compared in fish reared to the F(2) generation in either control or RDX-exposure conditions. Enrichment of gene functions including neuroexcitatory glutamate metabolism, sensory signaling, and neurological development were observed comparing control-reared and RDX-reared fish. Our results indicated that exposure to RDX at a concentration representing the highest levels observed in the environment (0.83 mg/L) had limited impacts on genomic, individual, and population-level endpoints in fathead minnows in a one-year exposure. However, multigenerational exposures altered transcript expression related to neural development and function. Environ.

Systems biology: leading the revolution in ecotoxicology

The rapid development of new technologies such as transcriptomics, proteomics, and metabolomics (Omics) are changing the way ecotoxicology is practiced. The data deluge has begun with genomes of over 65 different aquatic species that are currently being sequenced, and many times that number with at least some level of transcriptome sequencing. Integrating these top-down methodologies is an essential task in the field of systems biology. Systems biology is a biology-based interdisciplinary field that focuses on complex interactions in biological systems, with the intent to model and discover emergent properties of the system. Recent studies demonstrate that Omics technologies provide valuable insight into ecotoxicity, both in laboratory exposures with model organisms and with animals exposed in the field. However, these approaches require a context of the whole animal and population to be relevant. Powerful approaches using reverse engineering to determine interacting networks of genes, proteins, or biochemical reactions are uncovering unique responses to toxicants. Modeling efforts in aquatic animals are evolving to interrelate the interacting networks of a system and the flow of information linking these elements. Just as is happening in medicine, systems biology approaches that allow the integration of many different scales of interaction and information are already driving a revolution in understanding the impacts of pollutants on aquatic systems.

Differential gene expression in Daphnia magna suggests distinct modes of action and bioavailability for ZnO nanoparticles and Zn ions

Zinc oxide nanoparticles (ZnO NPs) are being rapidly developed for use in consumer products, wastewater treatment, and chemotherapy providing several possible routes for ZnO NP exposure to humans and aquatic organisms. Recent studies have shown that ZnO NPs undergo rapid dissolution to Zn(2+), but the relative contribution of Zn(2+) to ZnO NP bioavailability and toxicity is not clear. We show that a fraction of the ZnO NPs in suspension dissolves, and this fraction cannot account for the toxicity of the ZnO NP suspensions to Daphnia magna. Gene expression profiling of D. magna exposed to ZnO NPs or ZnSO(4) at sublethal concentrations revealed distinct modes of toxicity. There was also little overlap in gene expression between ZnO NPs and SiO(x) NPs, suggesting specificity for the ZnO NP expression profile. ZnO NPs effected expression of genes involved in cytoskeletal transport, cellular respiration, and reproduction. A specific pattern of differential expression of three biomarker genes including a multicystatin, ferritin, and C1q containing gene were confirmed for ZnO NP exposure and provide a suite of biomarkers for identifying environmental exposure to ZnO NPs and differentiating between NP and ionic exposure.

A new approach to construct pathway connected networks and its application in dose responsive gene expression profiles of rat liver regulated by 2,4DNT

Abstract

Background

Military and industrial activities have lead to reported release of 2,4-dinitrotoluene (2,4DNT) into soil, groundwater or surface water. It has been reported that 2,4DNT can induce toxic effects on humans and other organisms. However the mechanism of 2,4DNT induced toxicity is still unclear. Although a series of methods for gene network construction have been developed, few instances of applying such technology to generate pathway connected networks have been reported.

Results

Microarray analyses were conducted using liver tissue of rats collected 24h after exposure to a single oral gavage with one of five concentrations of 2,4DNT. We observed a strong dose response of differentially expressed genes after 2,4DNT treatment. The most affected pathways included: long term depression, breast cancer regulation by stathmin1, WNT Signaling; and PI3K signaling pathways. In addition, we propose a new approach to construct pathway connected networks regulated by 2,4DNT. We also observed clear dose response pathway networks regulated by 2,4DNT.

Conclusions

We developed a new method for constructing pathway connected networks. This new method was successfully applied to microarray data from liver tissue of 2,4DNT exposed animals and resulted in the identification of unique dose responsive biomarkers in regards to affected pathways.

Gene transcription profiles, global DNA methylation and potential transgenerational epigenetic effects related to Zn exposure history in Daphnia magna

A reduced level of DNA methylation has recently been described in both Zn-exposed and non-exposed offspring of Daphnia magna exposed to Zn. The hypothesis examined in this study is that DNA hypomethylation has an effect on gene transcription. A second hypothesis is that accumulative epigenetic effects can affect gene transcription in non-exposed offspring from parents with an exposure history of more than one generation. Transcriptional gene regulation was studied with a cDNA microarray. In the exposed and non-exposed hypomethylated daphnids, a large proportion of common genes were similarly up- or down-regulated, indicating a possible effect of the DNA hypomethylation. Two of these genes can be mechanistically involved in DNA methylation reduction. The similar transcriptional regulation of two and three genes in the F0 and F1 exposed daphnids on one hand and their non-exposed offspring on the other hand, could be the result of a one-generation temporary transgenerational epigenetic effect, which was not accumulative.

Gene transcription and higher-level effects of multigenerational Zn exposure in Daphnia magna

Zn exposure of Daphnia magna during one generation has been shown to modulate gene transcription differently in Zn exposed organisms compared to their non-exposed offspring. Here we studied the transcriptional gene regulation with a cDNA microarray in D.magna exposed to Zn for three generations (F0-F2). For the first time molecular effects of multigeneration toxicant exposure in D. magna are described. Out of 73 differentially transcribed genes in the F1Zn exposed generation (compared to the F1 control), only seven genes were also differentially transcribed in the same direction in the F0Zn exposed daphnids (up or down, compared to the F0 control). The majority of the differentially transcribed unigenes in F1Zn exposed daphnids (78%) were not differentially transcribed in the F0Zn exposed organisms. This indicates that Zn exposure affected other molecular pathways in the second exposed generation, although a reduced reproduction and a reduction in juvenile growth were observed in both Zn exposed generations, compared to the respective controls. In the third Zn exposed generation (F2), no reduction in growth or reproduction compared to the control was observed. This acclimation was reflected in a significantly lower number of differentially transcribed genes, compared to the Zn exposed F0 and F1 generations.