Toxicogenomics in regulatory ecotoxicology

Derivation of Transcriptomics-Based Points of Departure for 20 Per- or Polyfluoroalkyl Substances Using a Larval Fathead Minnow (Pimephales promelas) Reduced Transcriptome Assay

Traditional toxicity testing has been unable to keep pace with the introduction of new chemicals into commerce. Consequently, there are limited or no toxicity data for many chemicals to which fish and wildlife may be exposed. Per- and polyfluoroalkyl substances (PFAS) are emblematic of this issue in that ecological hazards of most PFAS remain uncharacterized. The present study employed a high-throughput assay to identify the concentration at which 20 PFAS, with diverse properties, elicited a concerted gene expression response (termed a transcriptomics-based point of departure [tPOD]) in larval fathead minnows (Pimephales promelas; 5-6 days postfertilization) exposed for 24 h. Based on a reduced transcriptome approach that measured whole-body expression of 1832 genes, the median tPOD for the 20 PFAS tested was 10 µM. Longer-chain carboxylic acids (12-13 C-F); an eight-C-F dialcohol, N-alkyl sulfonamide; and telomer sulfonic acid were among the most potent PFAS, eliciting gene expression responses at concentrations <1 µM. With a few exceptions, larval fathead minnow tPODs were concordant with those based on whole-transcriptome response in human cell lines. However, larval fathead minnow tPODs were often greater than those for Daphnia magna exposed to the same PFAS. The tPODs overlapped concentrations at which other sublethal effects have been reported in fish (available for 10 PFAS). Nonetheless, fathead minnow tPODs were orders of magnitude higher than aqueous PFAS concentrations detected in tributaries of the North American Great Lakes, suggesting a substantial margin of safety. Overall, results broadly support the use of a fathead minnow larval transcriptomics assay to derive screening-level potency estimates for use in ecological risk-based prioritization. Environ Toxicol Chem 2024;00:1-16. © 2024 SETAC. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.

Gene network analyses of Sepia esculenta larvae exposed to copper and cadmium: A comprehensive investigation of oxidative stress, immune response, and toxicological mechanisms

Copper (Cu) and Cadmium (Cd), prevalent heavy metals in marine environments, have known implications in oxidative stress, immune response, and toxicity in marine organisms. Sepia esculenta, a cephalopod of significant economic value along China's eastern coastline, experiences alterations in growth, mobility, and reproduction when subjected to these heavy metals. However, the specific mechanisms resulting from heavy metal exposure in S. esculenta remain largely uncharted. In this study, we utilized transcriptome and four oxidative, immunity, and toxicity indicators to assess the toxicological mechanism in S. esculenta larvae exposed to Cu and Cd. The measurements of Superoxide Dismutase (SOD), Malondialdehyde (MDA), Glutathione S-Transferase (GST), and Metallothioneins (MTs) revealed that Cu and Cd trigger substantial oxidative stress, immune response, and metal toxicity. Further, we performed an analysis on the transcriptome data through Weighted Gene Co-expression Network Analysis (WGCNA) and Protein-Protein Interaction (PPI) network analysis. Our findings indicate that exposure methods and duration influence the type and the extent of toxicity and oxidative stress within the S. esculenta larvae. We took an innovative approach in this research by integrating WGCNA and PPI network analysis with four significant physiological indicators to closely examine the toxicity and oxidative stress profiles of S. esculenta upon exposure to Cu and Cd. This investigation is vital in decoding the toxicological, immunological, and oxidative stress mechanisms within S. esculenta when subjected to heavy metals. It provides foundational insights capable of advancing invertebrate environmental toxicology and informs S. esculenta artificial breeding practices.

Preliminary study on toxicological mechanism of golden cuttlefish (Sepia esculenta) larvae exposed to cd

BACKGROUND

Cadmium (Cd) flows into the ocean with industrial and agricultural pollution and significantly affects the growth and development of economic cephalopods such as Sepia esculenta, Amphioctopus fangsiao, and Loligo japonica. As of now, the reasons why Cd affects the growth and development of S. esculenta are not yet clear.

RESULTS

In this study, transcriptome and four oxidation and toxicity indicators are used to analyze the toxicological mechanism of Cd-exposed S. esculenta larvae. Indicator results indicate that Cd induces oxidative stress and metal toxicity. Functional enrichment analysis results suggest that larval ion transport, cell adhesion, and some digestion and absorption processes are inhibited, and the cell function is damaged. Comprehensive analysis of protein-protein interaction network and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis was used to explore S. esculenta larval toxicological mechanisms, and we find that among the 20 identified key genes, 14 genes are associated with neurotoxicity. Most of them are down-regulated and enriched to the neuroactive ligand-receptor interaction signaling pathway, suggesting that larval nervous system might be destroyed, and the growth, development, and movement process are significantly affected after Cd exposure.

CONCLUSIONS

S. esculenta larvae suffered severe oxidative damage after Cd exposure, which may inhibit digestion and absorption functions, and disrupt the stability of the nervous system. Our results lay a function for understanding larval toxicological mechanisms exposed to heavy metals, promoting the development of invertebrate environmental toxicology, and providing theoretical support for S. esculenta artificial culture.

An innovative index to incorporate transcriptomic data into weight of evidence approaches for environmental risk assessment

The sharp decrease in the cost of RNA-sequencing and the rapid improvement in computational analysis of eco-toxicogenomic data have brought new insights into the adverse effects of chemicals on aquatic organisms. Yet, transcriptomics is generally applied qualitatively in environmental risk assessments, hampering more effective exploitation of this evidence through multidisciplinary studies. In view of this limitation, a methodology is here presented to quantitatively elaborate transcriptional data in support to environmental risk assessment. The proposed methodology makes use of results from the application of Gene Set Enrichment Analysis to recent studies investigating the response of Mytilus galloprovincialis and Ruditapes philippinarum exposed to contaminants of emerging concern. The degree of changes in gene sets and the relevance of physiological reactions are integrated in the calculation of a hazard index. The outcome is then classified according to five hazard classes (from absent to severe), providing an evaluation of whole-transcriptome effects of chemical exposure. The application to experimental and simulated datasets proved that the method can effectively discriminate different levels of altered transcriptomic responses when compared to expert judgement (Spearman correlation coefficient of 0.96). A further application to data collected in two independent studies of Salmo trutta and Xenopus tropicalis exposed to contaminants confirmed the potential extension of the methodology to other aquatic species. This methodology can serve as a proof of concept for the integration of "genomic tools" in environmental risk assessment based on multidisciplinary investigations. To this end, the proposed transcriptomic hazard index can now be incorporated into quantitative Weight of Evidence approaches and weighed, with results from other types of analysis, to elucidate the role of chemicals in adverse ecological effects.

Comparison between droplet digital PCR and reverse transcription-quantitative PCR methods to measure ecotoxicology biomarkers

Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) is currently the gold-standard technique for detecting and quantifying messenger RNA. However, without proper validation, the method may produce artefactual and non-reproducible cycle threshold values generating poor-quality data. The newer droplet digital PCR (ddPCR) method allows for the absolute quantification of targeted nucleic acids providing more sensitive and accurate measurements without requiring external standards. This study compared these two PCR-based methods to measure the expression of well-documented genes used in ecotoxicology studies. We exposed Mediterranean mussels (Mytilus galloprovincialis) to copper and analyzed gene expression in gills and digestive glands using RT-qPCR and ddPCR assays. A step-by-step methodology to optimize and compare the two technologies is described. After ten-fold serial complementary DNA dilution, both RT-qPCR and ddPCR exhibited comparable linearity and efficiency and produced statistically similar results. We conclude that ddPCR is a suitable method to assess gene expression in an ecotoxicological context. However, RT-qPCR has a shorter processing time and remains more cost-effective.

A GABA Receptor Modulator and Semiochemical Compounds Evidenced Using Volatolomics as Candidate Markers of Chronic Exposure to Fipronil in Apis mellifera

Among the various "omics" approaches that can be used in toxicology, volatolomics is in full development. A volatolomic study was carried out on soil bacteria to validate the proof of concept, and this approach was implemented in a new model organism: the honeybee Apis mellifera. Emerging bees raised in the laboratory in pain-type cages were used. Volatolomics analysis was performed on cuticles, fat bodies, and adhering tissues (abdomens without the digestive tract), after 14 and 21 days of chronic exposure to 0.5 and 1 µg/L of fipronil, corresponding to sublethal doses. The VOCs analysis was processed using an HS-SPME/GC-MS method. A total of 281 features were extracted and tentatively identified. No significant effect of fipronil on the volatolome could be observed after 14 days of chronic exposure. Mainly after 21 days of exposure, a volatolome deviation appeared. The study of this deviation highlighted 11 VOCs whose signal abundances evolved during the experiment. Interestingly, the volatolomics approach revealed a VOC (2,6-dimethylcyclohexanol) that could act on GABA receptor activity (the fipronil target) and VOCs associated with semiochemical activities (pheromones, repellent agents, and compounds related to the Nasonov gland) leading to a potential impact on bee behavior.

Comparative plasma and urine metabolomics analysis of juvenile and adult canines

Background and aims

The metabolomic profile of a biofluid can be affected by age, and thus provides detailed information about the metabolic alterations in biological processes and reflects the in trinsic rule regulating the growth and developmental processes.

Methods

To systemically investigate the characteristics of multiple metabolic profiles associated with canine growth, we analyzed the metabolomics in the plasma and urine samples from 15 young and 15 adult beagle dogs via UHPLC-Q-TOFMS-based metabolomics. Blood routine and serum biochemical analyses were also performed on fasting blood samples.

Results

The metabolomics results showed remarkable differences in metabolite fingerprints both in plasma and urine between the young and adult groups. The most obvious age-related metabolite alterations include decreased serumlevels of oxoglutaric acid and essential amino acids and derivatives but increased levels of urine levels of O-acetylserine. These changes primarily involved in amino acid metabolism and bile secretion pathways. We also found that the levels of glutamine were consistently higher in both serum and urine of adults, while N-acetylhistamine and uracil concentrations were much lower in the adult group compared to younger ones.

Conclusion

Our study provides a whole metabolic profile of serum and urine characteristics of young and adult canines, identifying several metabolites that were significantly associated with age change, which provides theoretical support for the nutrition-related research and age-related homeostasis maintenance in dogs.

Pilot testing and optimization of a larval fathead minnow high throughput transcriptomics assay

Concentrations at which global gene expression profiles in cells or animals exposed to a test substance start to differ significantly from those of controls have been proposed as an alternative point of departure for use in screening level hazard assessment. The present study describes pilot testing of a high throughput compatible transcriptomics assay with larval fathead minnows. One day post hatch fathead minnows were exposed to eleven different concentrations of three metals, three selective serotonin reuptake inhibitors, and four neonicotinoid-like compounds for 24 h and concentration response modeling was applied to whole body gene expression data. Transcriptomics-based points of departure (tPODs) were consistently lower than effect concentrations reported in apical endpoint studies in fish. However, larval fathead minnow-based tPODs were not always lower than concentrations reported to elicit apical toxicity in other aquatic organisms like crustaceans or insects. Random in silico subsampling of data from the pilot assays was used to evaluate various assay design and acceptance considerations such as transcriptome coverage, number of replicate individuals to sequence per treatment, and minimum number of differentially expressed genes to produce a reliable tPOD estimate. Results showed a strong association between the total number of genes for which a concentration response relationship could be derived and the overall variability in the resulting tPOD estimates. We conclude that, for our current assay design and analysis pipeline, tPODs based on fewer than 15 differentially expressed genes are likely to be unreliable for screening and that interindividual variability in gene expression profiles appears to be a more significant driver of tPOD variability than sample size alone. Results represent initial steps toward developing high throughput transcriptomics assays for use in ecological hazard screening.

Effects of Metformin and its Metabolite Guanylurea on Fathead Minnow (Pimephales promelas) Reproduction

Metformin, along with its biotransformation product guanylurea, is commonly observed in municipal wastewaters and subsequent surface waters. Previous studies in fish have identified metformin as a potential endocrine-active compound, but there are inconsistencies with regard to its effects. To further investigate the potential reproductive toxicity of metformin and guanylurea to fish, a series of experiments was performed with adult fathead minnows (Pimephales promelas). First, explants of fathead minnow ovary tissue were exposed to 0.001-100 µM metformin or guanylurea to investigate whether the compounds could directly perturb steroidogenesis. Second, spawning pairs of fathead minnows were exposed to metformin (0.41, 4.1, and 41 µg/L) or guanylurea (1.0, 10, and 100 µg/L) for 23 days to assess impacts on reproduction. Lastly, male fathead minnows were exposed to 41 µg/L metformin, 100 µg/L guanylurea, or a mixture of both compounds, with samples collected over a 96-h time course to investigate potential impacts to the hepatic transcriptome or metabolome. Neither metformin nor guanylurea affected steroid production by ovary tissue exposed ex vivo. In the 23 days of exposure, neither compound significantly impacted transcription of endocrine-related genes in male liver or gonad, circulating steroid concentrations in either sex, or fecundity of spawning pairs. In the 96-h time course, 100 µg guanylurea/L elicited more differentially expressed genes than 41 µg metformin/L and showed the greatest impacts at 96 h. Hepatic transcriptome and metabolome changes were chemical- and time-dependent, with the largest impact on the metabolome observed at 23 days of exposure to 100 µg guanylurea/L. Overall, metformin and guanylurea did not elicit effects consistent with reproductive toxicity in adult fathead minnows at environmentally relevant concentrations. Environ Toxicol Chem 2022;41:2708-2720. © 2022 SETAC. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.

Bioaccumulation of total mercury, copper, cadmium, silver, and selenium in green turtles (Chelonia mydas) stranded along the Potiguar Basin, northeastern Brazil

Sea turtles face several threats and pollution has become a major concern for their conservation worldwide. We analyzed samples of the liver, muscles, and kidneys of 38 Chelonia mydas stranded along the Potiguar Basin, northeastern Brazil, between 2015 and 2018 to determine the total Hg concentration (THg), as well as the concentrations of Cu, Cd, Ag, and Se. The relation between turtle size and element concentrations revealed a negative correlation for THg and Se (liver, muscles, and kidneys), Cu and Cd (liver and kidneys) and a positive correlation for Ag in the three organs analyzed. Concentrations of THg, Cu, Ag, and Se were high in the liver, highlighting the Cu concentration (median = 25.1150 μg g^-1 w.w.), while the kidneys had the highest Cd levels (median = 12.2200 μg g^-1 w.w.). There was significant difference between element concentrations and the three organs analyzed, except for Ag and Se concentrations in the muscle and kidney samples. Our study showed that green turtles found in Potiguar Basin, northeastern Brasil, have bioaccumulated inorganic elements which indicate the need of further investigations on the environmental quality of the region.

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.

Multi-omic approach to evaluate the response of gilt-head sea bream (Sparus aurata) exposed to the UV filter sulisobenzone

Sulisobenzone (BP-4) is one of the benzophenone type UV filters most frequently detected in aquatic ecosystems. As a suspected endocrine disrupting compound, scarce information is available yet about other molecular effects and its mechanism of action. Here, we used an integrated transcriptomic and metabolomic approach to improve the current understanding on the toxicity of BP-4 towards aquatic species. Gilt-head sea bream individuals were exposed at environmentally relevant concentrations (10 μg L^-1) for 22 days. Transcriptomic analysis revealed 371 differentially expressed genes in liver while metabolomic analysis identified 123 differentially modulated features in plasma and 118 in liver. Integration of transcriptomic and metabolomic data showed disruption of the energy metabolism (>10 pathways related to the metabolism of amino acids and carbohydrates were impacted) and lipid metabolism (5 glycerophospholipids and the expression of 3 enzymes were affected), suggesting oxidative stress. We also observed, for the first time in vivo and at environmental relevant concentrations, the disruption of several enzymes involved in the steroid and thyroid hormones biosynthesis. DNA and RNA synthesis was also impacted by changes in the purine and pyrimidine metabolisms. Overall, the multiomic workflow presented here increases the evidence on suspected effects of BP-4 exposure and identifies additional modes of action of the compounds that could have been overlooked by using single omic approaches.

Trends in the Application of "Omics" to Ecotoxicology and Stress Ecology

Our ability to predict and assess how environmental changes such as pollution and climate change affect components of the Earth's biome is of paramount importance. This need positioned the fields of ecotoxicology and stress ecology at the center of environmental monitoring efforts. Advances in these interdisciplinary fields depend not only on conceptual leaps but also on technological advances and data integration. High-throughput "omics" technologies enabled the measurement of molecular changes at virtually all levels of an organism's biological organization and thus continue to influence how the impacts of stressors are understood. This bibliometric review describes literature trends (2000-2020) that indicate that more different stressors than species are studied each year but that only a few stressors have been studied in more than two phyla. At the same time, the molecular responses of a diverse set of non-model species have been investigated, but cross-species comparisons are still rare. While transcriptomics studies dominated until 2016, a shift towards proteomics and multiomics studies is apparent. There is now a wealth of data at functional omics levels from many phylogenetically diverse species. This review, therefore, addresses the question of how to integrate omics information across species.

Characterization of sediment toxicity in Shanghai Harbor using toxicity tests and digital gene expression analysis based on clams Ruditapes phillipinarum

In the present study, chemical analysis of contaminants (three classes of organic pollutants and seven metals) and elutriate toxicity test were adopted to evaluate the potential environmental hazards of dredged sediment samples from five sites (SS1-5) along Huangpu River Channel (Shanghai Harbor, China). The metal Pb, Cu, Cr, Zn and the organic pollutants including total hexachlorocyclohexane (HCHs) and total dichlorodiphenyltrichloroethane (DDTs) in the five samples exceeded the threshold for effects level (TEL) to varying degrees. The probable effect concentration quotients (Q_PECm) of contaminants from the five dredged samples were all above 0.25, which means potential toxicity risks. Elutriate toxicity tests using medaka fish (Oryzias melastigma) and manila clam (Ruditapes philippinarum) showed that SS2 caused mortality to both species and SS1 caused mortality to fish. To explore the molecular biomarkers that may reflect the toxic effects, differential expressed genes were identified by RNA-Seq-based transcriptome profiling from the survived clams exposed to the two polluted elutriates (SS1, SS2). In clams exposed to SS1 and SS2 elutriate, 368 and 860 differential expressed genes (DEGs) were up-regulated, 199 and 1304 genes were down-regulated, respectively. Fourteen DEGs were selected from the enriched pathways that reflect cytotoxicity and responses to xenobiotics for the following quantitative real time PCR analysis. The transcriptomic profiling and the selected gene's expression patterns from clams exposed to SS1 and SS2 showed significant differences with the non-contaminated and control groups. Using the expression data of the selected gene battery in Factor Analysis allowed the discrimination between contaminated and non-contaminated sites and may reflect an influence gradient of sites. The development of the assay of these molecular biomarkers may provide a rapid and high-throughput tool for the quality assessment of the dredging sediments.

Drivers of and Obstacles to the Adoption of Toxicogenomics for Chemical Risk Assessment: Insights from Social Science Perspectives

BACKGROUND

Some 20 y ago, scientific and regulatory communities identified the potential of omics sciences (genomics, transcriptomics, proteomics, metabolomics) to improve chemical risk assessment through development of toxicogenomics. Recognizing that regulators adopt new scientific methods cautiously given accountability to diverse stakeholders, the scope and pace of adoption of toxicogenomics tools and data have nonetheless not met the ambitious, early expectations of omics proponents.

OBJECTIVE

Our objective was, therefore, to inventory, investigate, and derive insights into drivers of and obstacles to adoption of toxicogenomics in chemical risk assessment. By invoking established social science frameworks conceptualizing innovation adoption, we also aimed to develop recommendations for proponents of toxicogenomics and other new approach methodologies (NAMs).

METHODS

We report findings from an analysis of 56 scientific and regulatory publications from 1998 through 2017 that address the adoption of toxicogenomics for chemical risk assessment. From this purposeful sample of toxicogenomics discourse, we identified major categories of drivers of and obstacles to adoption of toxicogenomics tools and data sets. We then mapped these categories onto social science frameworks for conceptualizing innovation adoption to generate actionable insights for proponents of toxicogenomics.

DISCUSSION

We identify the most salient drivers and obstacles. From 1998 through 2017, adoption of toxicogenomics was understood to be helped by drivers such as those we labeled Superior scientific understanding, New applications, and Reduced cost & increased efficiency but hindered by obstacles such as those we labeled Insufficient validation, Complexity of interpretation, and Lack of standardization. Leveraging social science frameworks, we find that arguments for adoption that draw on the most salient drivers, which emphasize superior and novel functionality of omics as rationales, overlook potential adopters' key concerns: simplicity of use and compatibility with existing practices. We also identify two perspectives-innovation-centric and adopter-centric-on omics adoption and explain how overreliance on the former may be undermining efforts to promote toxicogenomics. https://doi.org/10.1289/EHP6500.

The use of non-targeted metabolomics to assess the toxicity of bifenthrin to juvenile Chinook salmon (Oncorhynchus tshawytscha)

An increase in urban and agricultural application of pyrethroid insecticides in the San Francisco Bay Estuary and Sacramento San Joaquin Delta has raised concern for the populations of several salmonids, including Chinook salmon (Oncorhynchus tshawytscha). Bifenthrin, a type I pyrethroid, is among the most frequently detected pyrethroids in the Bay-Delta watershed, with surface water concentrations often exceeding chronic toxicity thresholds for several invertebrate and fish species. To better understand the mechanisms of bifenthrin-induced neurotoxicity, juvenile Chinook salmon were exposed to concentrations of bifenthrin previously measured in the Delta. Non-targeted metabolomic profiles were used to identify transcriptomic changes in the brains of bifenthrin-exposed fish. Pathway analysis software predicted increased apoptotic, inflammatory, and reactive oxygen species (ROS) responses in Chinook following exposure to 0.15 and 1.50 μg/L bifenthrin for 96 h. These responses were largely driven by reduced levels of inosine, hypoxanthine, and guanosine. Subsequently, in the brain, the expression of caspase 3, a predominant effector for apoptosis, was significantly upregulated following exposure to 1.50 μg/L bifenthrin. This data suggests that metabolites involved in inflammatory and apoptotic responses, as well as those involved in maintaining proper neuronal function may be disrupted following sublethal exposure to bifenthrin and further suggests that additional population studies should focus on behavioral responses associated with impaired brain function.

Factors Affecting the Perception of New Approach Methodologies (NAMs) in the Ecotoxicology Community

Given current legislative mandates to assess the safety of thousands of chemicals and the slow pace at which conventional testing proceeds, there is a need to accelerate chemical risk assessment. Governments and businesses are increasingly interested in new approach methodologies (NAMs) that promise to reduce costs and delays. We explore 5 sociological factors within the ecotoxicology community that can influence the perception of NAMs: 1) professional profile (educational cohort, employer), 2) internal science communication within professional forums, 3) concern for "error cost," 4) collaboration across stakeholders, and 5) fundamental beliefs regarding toxicology. We conducted an online survey (n = 171; 2018) asking participants about their experiences and perspectives at events of the Society of Environmental Toxicology and Chemistry (SETAC) to assess 1) how NAMs are discussed compared to conventional testing and 2) how respondents perceive their viability. We developed ordered logistic regression (OLR) models to understand the influence of exploratory variables (cohort, core views on toxicology, frequency of collaboration) on respondents' evaluation of the viability of different NAMs. Our results showed that 1) NAMs were more likely than conventional methods to be challenged in forum discussions, which may be fueled by concerns for error costs in regulatory decision making; 2) perceptions of the viability of NAMs tended to follow a "pattern of familiarity," whereby respondents that were more knowledgeable about a test method tended to find it more viable; 3) respondents who agreed with the Paracelsus maxim had a greater likelihood of finding conventional testing viable; and 4) the more a respondent reported collaborating with industry on alternative testing strategies, the more likely she or he was to report that NAMs were less viable. These results suggest that there are professional and organizational barriers to greater acceptance of NAMs that can be addressed through a social learning process within the professional community. Integr Environ Assess Manag 2020;16:269-281. © 2020 SETAC.

Metabolome response to anthropogenic contamination on microalgae: a review

BACKGROUND

Microalgae play a key role in ecosystems and are widely used in ecological status assessment. Research focusing on such organisms is then well developed and essential. Anyway, approaches for a better comprehension of their metabolome's response towards anthropogenic stressors are only emerging.

AIM OF REVIEW

This review presents the biochemical responses of various microalgae species towards several contaminants including metals and chemicals as pesticides or industrial compounds. We aim to provide a comprehensive and up-to-date overview of analytical approaches deciphering anthropogenic contaminants impact on microalgae metabolome dynamics, in order to bring out relevant biochemical markers that could be used for risk assessment.

KEY SCIENTIFIC CONCEPTS OF REVIEW

Studies to date on ecotoxicological metabolomics on microalgae are highly heterogeneous in both analytical techniques and resulting metabolite identification. There is a real need for studies using complementary approaches to determine biomarkers usable for ecological risk assessment.

Identification and expression profile of Delta-GST in black tiger shrimp (Penaeus monodon) exposed to aflatoxin B1 (AFB1)

Delta GST is an insect-specific class and a prominent class of the glutathione S-transferases family that is involved in xenobiotic detoxification and antioxidant defense. The full-length complementary DNA of delta-class GST from Penaeus monodon (PmDeltaGST; 839 bp long with a 657 bp coding region) was cloned. The encoded polypeptide of 218 amino acids had a predicted molecular mass of 24.30 kDa. Sequence homology and phylogenetic analysis showed that PmDeltaGST was significant similarity to GST genes in crustaceans and insects. Tissue expression profile analysis by quantitative real-time reverse-transcription polymerase chain showed that PmDeltaGST was constitutively expressed in all the examined tissues, with the highest expression in hepatopancreas and intestine and the weakest expression in ovary. PmDeltaGST messenger RNA expression and protein levels in hepatopancreas was significantly increased at 14 days postexposure of aflatoxin B1 (AFB1), keeping on the high level at 28 days, but decreased at 56 days. The results suggested that PmDeltaGST was involved in the response to AFB1 exposure.

Using lipidomic methodology to characterize coral response to herbicide contamination and develop an early biomonitoring model

The use of omics technologies to profile an organism's systemic response to environmental changes can improve the effectiveness of biomonitoring. In cell physiology, the dynamic characteristics of membranes can be used to identify lipid profiles that detect environmental threats and assess the health problems associated with them. The efficacy of this approach was demonstrated by profiling glycerophosphocholines (GPCs, a major membrane lipid class) in the coral Seriatopora caliendrum after exposure to Irgarol 1051. A quantitative biomonitoring model for this photosystem II herbicide was developed by correlating variations in coral lipid profile with herbicide exposure levels and degree of photoinhibition. After 4 days of exposure, the predominant changes correlated with photoinhibition were an increase in lyso-GPCs and saturated GPCs and a decrease in phosphatidylcholines with unsaturated C18 chains or a polyunsaturated C22 chain. A time-course experiment showed that most of these lipid changes occurred opposite to the initial response and that the persistent changes can be attributed to photosynthetic shortages and the membrane accommodation of photoinhibition-induced oxidative conditions. These changes can help predict risk factors leading to coral bleaching. In this study, the application of a lipidomic methodology to characterize the adaptation of coral to ambient contamination serves as a basis for advancing environmental monitoring and assessment.

Volatolomics in Bacterial Ecotoxicology, A Novel Method for Detecting Signatures of Pesticide Exposure?

Volatile organic compounds (VOC) produced by microorganisms in response to chemical stressor showed recently increasing attention, because of possible environmental applications. In this work, we aimed to bring the first proof of concept that volatolomic (i.e., VOCs analysis) can be used to determine candidate VOC markers of two soil bacteria strains (Pseudomonas fluorescens SG-1 and Bacillus megaterium Mes11) exposure to pesticides. VOC determination was based on solid-phase microextraction (SPME) coupled with gas chromatography-mass spectrometry (GC-MS). Accordingly, we highlighted a set of bacterial VOCs modulated in each strains according to the nature of the pesticide used. Three out these VOCs were specifically modulated in P. fluorescens SG-1 when exposed with two pyrethroid pesticides (deltamethrine and cypermethrine): 2-hexanone; 1,3-ditertbutylbenzene and malonic acid, hexyl 3-methylbutyl ester. Our results thus suggest the possible existence of generic VOC markers of pyrethroids in this strain. Of particular interest, two out of these three VOCs, the 1,3-ditertbutylbenzene and the malonic acid, hexyl 3-methylbutyl ester were found also in B. megaterium Mes11 when exposed with cypermethrine. This result highlighted the possible existence of interspecific VOC markers of pyrethroid in these two bacteria. Altogether, our work underlined the relevance of volatolomic to detect signatures of pesticides exposure in microorganisms and more generally to microbial ecotoxicology. Based on these first results, considerations of volatolomics for the chemical risk assessment in environment such as soils can be indirectly explored in longer terms.

Differences among Unique Nanoparticle Protein Corona Constructs: A Case Study Using Data Analytics and Multi-Variant Visualization to Describe Physicochemical Characteristics

Gold nanoparticles (AuNPs) used in pharmaceutical treatments have been shown to effectively deliver a payload, such as an active pharmaceutical ingredient or image contrast agent, to targeted tissues in need of therapy or diagnostics while minimizing exposure, availability, and accumulation to surrounding biological compartments. Data sets collected in this field of study include some toxico- and pharmacodynamic properties (e.g., distribution and metabolism) but many studies lack information about adsorption of biological molecules or absorption into cells. When nanoparticles are suspended in blood serum, a protein corona cloud forms around its surface. The extent of the applications and implications of this formed cloud are unknown. Some researchers have speculated that the successful use of nanoparticles in pharmaceutical treatments relies on a comprehensive understanding of the protein corona composition. The work presented in this paper uses a suite of data analytics and multi-variant visualization techniques to elucidate particle-to-protein interactions at the molecular level. Through mass spectrometry analyses, corona proteins were identified through large and complex datasets. With such high-output analyses, complex datasets pose a challenge when visualizing and communicating nanoparticle-protein interactions. Thus, the creation of a streamlined visualization method is necessary. A series of user-friendly data informatics techniques were used to demonstrate the data flow of protein corona characteristics. Multi-variant heat maps, pie charts, tables, and three-dimensional regression analyses were used to improve results interpretation, facilitate an iterative data transfer process, and emphasize features of the nanoparticle-protein corona system that might be controllable. Data informatics successfully highlights the differences between protein corona compositions and how they relate to nanoparticle surface charge.

Multiple environmental stressors induce complex transcriptomic responses indicative of phenotypic outcomes in Western fence lizard

BACKGROUND

The health and resilience of species in natural environments is increasingly challenged by complex anthropogenic stressor combinations including climate change, habitat encroachment, and chemical contamination. To better understand impacts of these stressors we examined the individual- and combined-stressor impacts of malaria infection, food limitation, and 2,4,6-trinitrotoluene (TNT) exposures on gene expression in livers of Western fence lizards (WFL, Sceloporus occidentalis) using custom WFL transcriptome-based microarrays.

RESULTS

Computational analysis including annotation enrichment and correlation analysis identified putative functional mechanisms linking transcript expression and toxicological phenotypes. TNT exposure increased transcript expression for genes involved in erythropoiesis, potentially in response to TNT-induced anemia and/or methemoglobinemia and caused dose-specific effects on genes involved in lipid and overall energy metabolism consistent with a hormesis response of growth stimulation at low doses and adverse decreases in lizard growth at high doses. Functional enrichment results were indicative of inhibited potential for lipid mobilization and catabolism in TNT exposures which corresponded with increased inguinal fat weights and was suggestive of a decreased overall energy budget. Malaria infection elicited enriched expression of multiple immune-related functions likely corresponding to increased white blood cell (WBC) counts. Food limitation alone enriched functions related to cellular energy production and decreased expression of immune responses consistent with a decrease in WBC levels.

CONCLUSIONS

Despite these findings, the lizards demonstrated immune resilience to malaria infection under food limitation with transcriptional results indicating a fully competent immune response to malaria, even under bio-energetic constraints. Interestingly, both TNT and malaria individually increased transcriptional expression of immune-related genes and increased overall WBC concentrations in blood; responses that were retained in the TNT x malaria combined exposure. The results demonstrate complex and sometimes unexpected responses to multiple stressors where the lizards displayed remarkable resiliency to the stressor combinations investigated.

Real-time PCR array to study the effects of chemicals on the growth hormone/insulin-like growth factors (GH/IGFs) axis of zebrafish embryos/larvae

Growth hormone/insulin-like growth factors (GH/IGFs) axis PCR array of zebrafish (Danio rerio) larvae was developed based on the quantification of mRNA expressions of 19 genes that were confirmed to play vital roles in the regulation of fish growth. Zebrafish embryos were exposed to each of four concentrations of the six representative chemicals, bisphenol A (BPA), perfluorooctane sulfonates (PFOS), tris (1,3-dichloroisopropyl) phosphate (TDCIPP), cadmium chloride (CdCl₂), mercury (II) chloride (HgCl₂) and lead (II) acetate (PbAc) from 2 h post fertilization (hpf) to 96 hpf. Developmental endpoints and transcriptional profiles of the genes involved in GH/IGFs axis of zebrafish larvae were examined at 96 hpf. Body length of zebrfish larvae was found to be a more susceptible endpoint in zebrafish embryo toxicity test than other endpoints, including survival rate, hatching rate, malformation incidence and heart rate after exposure to each of those representative chemicals selected. Perturbation of mRNA expressions of GH/IGF axis genes accompanied by decreased body length indicated that indicated that the growth inhibition observed might be attributed to the dysregulation of GH/IGFs axis. Therefore, GH/IGF axis PCR array of zebrafish larvae could be used to evaluate the effects of chemicals on GH/IGF endocrine system.

Reduced Zebrafish Transcriptome Atlas toward Understanding Environmental Neurotoxicants

Transcriptomic approaches monitoring gene responses at genome-scale are increasingly used in toxicological research and help to clarify the molecular mechanisms of adverse effects caused by environmental toxicants. However, their applications for chemical assessment are hampered due to high expenses required and more importantly the lack of in-depth data mining and mechanistic perspectives. Here, we described a reduced transcriptome atlas (RTA) approach which integrates transcriptomic data sets and a comprehensive panel of genes generated to represent neurogenesis and the early neuronal development of zebrafish, to determine the potential neurodevelopmental toxicities of environmental chemicals. Transcriptomic data sets of 74 chemicals and 736 related gene expression profiles were integrated resulting in 135 exposure signatures. Chemical prioritization demonstrated four sets of hits to be neurotoxic: neuro-active chemicals (representatively, Valproic acid, VPA and Carbamazepine, CAR), xenoestrogens (Bisphenol A, BPA; Genistein, GEN; 17-α ethinylestradiol, EE2), microcystins (cyanopeptolin, CP1020; microcystin-LR, MCLR) and heavy metals (AgNO₃, AgNPs). The enriched biological pathways and processes were distinct among the four sets, while the overlapping functional enrichments were observed within each set, for example, over 25% differentially expressed genes and four of top five KEGG pathways were shared between VPA and CAR. Furthermore, gene expression index (GEI) analysis demonstrated that a gene panel with 300 genes was sufficient to effectively characterize and cluster chemicals and therefore offer an efficient and cost-effective tool for the prioritization of neurotoxicants. Thus, the RTA approach provides novel insights into the understanding of the in-depth molecular mechanisms of environmental neurotoxicants and can be used as an indication for potential adverse outcomes.

Effects of cadmium on oxidative stress activities in plasma of freshwater turtle Chinemys reevesii

Cadmium (Cd) has been recently found in high concentrations in the aquatic environment. This study was designed to examine the effects of Cd on the oxidative stress activities in plasma of freshwater turtle Chinemys reevesii. Experimental turtles were exposed to Cd at the concentration of 15 mg/kg by intraperitoneal injection, and redox status was investigated. Compared to the controls, superoxide dismutase (SOD) and catalase activities in plasma of the treated animals significantly decreased in week 1, week 2, and week 4. However, SOD activities gradually increased from week 4 to week 8. The treated animals had higher content of MDA and lower content of GSH in plasma over the observation period. In conclusion, our results showed that Cd decreased the antioxidant capacity and increased the level of oxidative damage product in plasma, which suggest that Cd causes oxidative stress and damage in the animal under the experimental conditions.

Systemic Homeostasis in Metabolome, Ionome, and Microbiome of Wild Yellowfin Goby in Estuarine Ecosystem

Data-driven approaches were applied to investigate the temporal and spatial changes of 1,022 individuals of wild yellowfin goby and its potential interaction with the estuarine environment in Japan. Nuclear magnetic resonance (NMR)-based metabolomics revealed that growth stage is a primary factor affecting muscle metabolism. Then, the metabolic, elemental and microbial profiles of the pooled samples generated according to either the same habitat or sampling season as well as the river water and sediment samples from their habitats were measured using NMR spectra, inductively coupled plasma optical emission spectrometry and next-generation 16 S rRNA gene sequencing. Hidden interactions in the integrated datasets such as the potential role of intestinal bacteria in the control of spawning migration, essential amino acids and fatty acids synthesis in wild yellowfin goby were further extracted using correlation clustering and market basket analysis-generated networks. Importantly, our systematic analysis of both the seasonal and latitudinal variations in metabolome, ionome and microbiome of wild yellowfin goby pointed out that the environmental factors such as the temperature play important roles in regulating the body homeostasis of wild fish.

Quantitative Shotgun Proteomics Associates Molecular-Level Cadmium Toxicity Responses with Compromised Growth and Reproduction in a Marine Copepod under Multigenerational Exposure

In this study, the copepod Tigriopus japonicus was exposed to different cadmium (Cd) treatments (0, 2.5, 5, 10, and 50 μg/L in seawater) for five generations (F0-F4), followed by a two-generation (F5-F6) recovery period in clean seawater. Six life-history traits (survival, developmental time of nauplius phase, developmental time to maturation, number of clutches, number of nauplii/clutch, and fecundity) were examined for each generation. Metal accumulation was also analyzed for generations F0-F6. Additionally, proteome profiling was performed for the control and 50 μg/L Cd-treated F4 copepods. In F0-F4 copepods, Cd accumulated in a concentration-dependent manner, prolonging the development of the nauplius phase and maturation and reducing the number of nauplii/clutch and fecundity. However, during F5-F6, Cd accumulation decreased rapidly, and significant but subtle effects on growth and reproduction were observed only for the highest metal treatment at F5. Proteomic analysis revealed that Cd treatment had several toxic effects including depressed nutrient absorption, dysfunction in cellular redox homeostasis and metabolism, and oxidative stress, resulting in growth retardation and reproduction limitation in this copepod species. Taken together, our results demonstrate the relationship between molecular toxicity responses and population-level adverse outcomes in T. japonicus under multigenerational Cd exposure.

Multiple-endpoints gene alteration-based (MEGA) assay: A toxicogenomics approach for water quality assessment of wastewater effluents

Wastewater effluents contain a significant number of toxic contaminants, which, even at low concentrations, display a wide variety of toxic actions. In this study, we developed a multiple-endpoints gene alteration-based (MEGA) assay, a real-time PCR-based transcriptomic analysis, to assess the water quality of wastewater effluents for human health risk assessment and management. Twenty-one genes from the human hepatoblastoma cell line (HepG2), covering the basic health-relevant stress responses such as response to xenobiotics, genotoxicity, and cytotoxicity, were selected and incorporated into the MEGA assay. The genes related to the p53-mediated DNA damage response and cytochrome P450 were selected as markers for genotoxicity and response to xenobiotics, respectively. Additionally, the genes that were dose-dependently regulated by exposure to the wastewater effluents were chosen as markers for cytotoxicity. The alterations in the expression of an individual gene, induced by exposure to the wastewater effluents, were evaluated by real-time PCR and the results were validated by genotoxicity (e.g., comet assay) and cell-based cytotoxicity tests. In summary, the MEGA assay is a real-time PCR-based assay that targets cellular responses to contaminants present in wastewater effluents at the transcriptional level; it is rapid, cost-effective, and high-throughput and can thus complement any chemical analysis for water quality assessment and management.

Cadmium induces histopathological injuries and ultrastructural changes in the liver of freshwater turtle (Chinemys reevesii)

The study investigated the histopathological and ultrastructural lesions of liver of freshwater turtle Chinemys reevesii exposed to Cadmium (Cd). The animals were exposed to 0 mg kg^-1 (0.85% normal saline (NS)), 7.5 mg kg^-1, 15 mg kg^-1, 30 mg kg^-1 Cd chloride separately by intraperitoneal injection. Liver samples were collected for examination of lesions under light and electronic microscopes. Results showed that liver tissues from Cd -treated animals presented various degrees of histopathological lesions. Liver cells showed swollen, degeneration and necrosis with dose-dependent manner. Under electronic microscope, nucleus, mitochondria and rough endoplasmic reticulum presented various degrees of lesions with dose-dependent manner. In conclusion, Cd has significant toxicity on liver tissue of the freshwater turtle, which occurs in a dose-dependent manner.

Natural variability of biochemical biomarkers in the macro-zoobenthos: Dependence on life stage and environmental factors

Biomarkers are widely used in ecotoxicology as indicators of exposure to toxicants. However, their ability to provide ecologically relevant information remains controversial. One of the major problems is understanding whether the measured responses are determined by stress factors or lie within the natural variability range. In a previous work, the natural variability of enzymatic levels in invertebrates sampled in pristine rivers was proven to be relevant across both space and time. In the present study, the experimental design was improved by considering different life stages of the selected taxa and by measuring more environmental parameters. The experimental design considered sampling sites in 2 different rivers, 8 sampling dates covering the whole seasonal cycle, 4 species from 3 different taxonomic groups (Plecoptera, Perla grandis; Ephemeroptera, Baetis alpinus and Epeorus alpicula; Tricoptera, Hydropsyche pellucidula), different life stages for each species, and 4 enzymes (acetylcholinesterase, glutathione S-transferase, alkaline phosphatase, and catalase). Biomarker levels were related to environmental (physicochemical) parameters to verify any kind of dependence. Data were statistically elaborated using hierarchical multilevel Bayesian models. Natural variability was found to be relevant across both space and time. The results of the present study proved that care should be paid when interpreting biomarker results. Further research is needed to better understand the dependence of the natural variability on environmental parameters. Environ Toxicol Chem 2017;36:3158-3167. © 2017 SETAC.

Metabolomics Approach to Investigate Estrogen Receptor-Dependent and Independent Effects of o,p'-DDT in the Uterus and Brain of Immature Mice

Previous studies have demonstrated the endocrine disruption of o,p'-DDT. In this study, we used a ¹H NMR based metabolomics approach to investigate the estrogenic effects of o,p'-DDT (300 mg/kg) on the uterus and brain after 3 days of oral gavage administration, and ethynylestradiol (EE, 100 μg/kg) was used as a positive control. A supervised statistical analysis (PLS-DA) indicated that o,p'-DDT exerted both estrogenic receptor-(ER)-dependent and independent effects on the uterus but mainly ER-independent effects on the brain at metabolome levels, which was verified by coexposing with the antiestrogenic ICI 182,780. Four changed metabolites-glycine, choline, fumarate, and phenylalanine-were identified as ER-independent alterations in the uterus, while more metabolites, including γ-aminobutyrate, N-acetyl aspartate, and some amino acids, were disturbed based on the ER-independent mechanism in the brain. Together with biological end points, metabolomics is a promising approach to study potential estrogenic chemicals.

The response of Isidorella newcombi to copper exposure: Using an integrated biological framework to interpret transcriptomic responses from RNA-seq analysis

This study describes the transcriptomic response of the Australian endemic freshwater gastropod Isidorella newcombi exposed to 80±1μg/L of copper for 3days. Analysis of copper tissue concentration, lysosomal membrane destabilisation and RNA-seq were conducted. Copper tissue concentrations confirmed that copper was bioaccumulated by the snails. Increased lysosomal membrane destabilisation in the copper-exposed snails indicated that the snails were stressed as a result of the exposure. Both copper tissue concentrations and lysosomal destabilisation were significantly greater in snails exposed to copper. In order to interpret the RNA-seq data from an ecotoxicological perspective an integrated biological response model was developed that grouped transcriptomic responses into those associated with copper transport and storage, survival mechanisms and cell death. A conceptual model of expected transcriptomic changes resulting from the copper exposure was developed as a basis to assess transcriptomic responses. Transcriptomic changes were evident at all the three levels of the integrated biological response model. Despite lacking statistical significance, increased expression of the gene encoding copper transporting ATPase provided an indication of increased internal transport of copper. Increased expression of genes associated with endocytosis are associated with increased transport of copper to the lysosome for storage in a detoxified form. Survival mechanisms included metabolic depression and processes associated with cellular repair and recycling. There was transcriptomic evidence of increased cell death by apoptosis in the copper-exposed organisms. Increased apoptosis is supported by the increase in lysosomal membrane destabilisation in the copper-exposed snails. Transcriptomic changes relating to apoptosis, phagocytosis, protein degradation and the lysosome were evident and these processes can be linked to the degradation of post-apoptotic debris. The study identified contaminant specific transcriptomic markers as well as markers of general stress. From an ecotoxicological perspective, the use of a framework to group transcriptomic responses into those associated with copper transport, survival and cell death assisted with the complex process of interpretation of RNA-seq data. The broad adoption of such a framework in ecotoxicology studies would assist in comparison between studies and the identification of reliable transcriptomic markers of contaminant exposure and response.

Natural variability of enzymatic biomarkers in freshwater invertebrates

Biomarkers have been widely employed in ecotoxicology as early warning indicators of exposure to toxicants. Very often, they are used to compare reference and polluted sites, or to analyse time trends. However, very few studies focus on the natural variability range of biomarkers in the environment, which is pivotal to understand if the detected differences are actually determined by any adverse effects due to pollution. This work assesses the natural spatio-temporal variability of some enzymatic levels, frequently used as biomarkers, in freshwater benthic invertebrates. The influence of some environmental parameters on the enzymatic levels was also evaluated. Three families of insect larvae (Perlidae, Baetidae, and Heptageniidae) were sampled in three pristine streams and in eight different dates. Four enzymes (acetylcholinesterase, glutathione-S-transferase, alkaline phosphatase, and catalase) were measured. The natural variability of enzymatic levels was often significant in all considered species across both space and time. The observed pattern was poorly explained by the monitored environmental parameters. The results of this work show that great care should be paid when interpreting monitoring data in which biomarker levels are measured and compared among sites or dates. Presuming that measured differences are due to anthropogenic factors can be misleading, when other potentially influencing factors have not been accounted for.

The pros and cons of ecological risk assessment based on data from different levels of biological organization

Ecological risk assessment (ERA) is the process used to evaluate the safety of manufactured chemicals to the environment. Here we review the pros and cons of ERA across levels of biological organization, including suborganismal (e.g., biomarkers), individual, population, community, ecosystem and landscapes levels. Our review revealed that level of biological organization is often related negatively with ease at assessing cause-effect relationships, ease of high-throughput screening of large numbers of chemicals (it is especially easier for suborganismal endpoints), and uncertainty of the ERA because low levels of biological organization tend to have a large distance between their measurement (what is quantified) and assessment endpoints (what is to be protected). In contrast, level of biological organization is often related positively with sensitivity to important negative and positive feedbacks and context dependencies within biological systems, and ease at capturing recovery from adverse contaminant effects. Some endpoints did not show obvious trends across levels of biological organization, such as the use of vertebrate animals in chemical testing and ease at screening large numbers of species, and other factors lacked sufficient data across levels of biological organization, such as repeatability, variability, cost per study and cost per species of effects assessment, the latter of which might be a more defensible way to compare costs of ERAs than cost per study. To compensate for weaknesses of ERA at any particular level of biological organization, we also review mathematical modeling approaches commonly used to extrapolate effects across levels of organization. Finally, we provide recommendations for next generation ERA, submitting that if there is an ideal level of biological organization to conduct ERA, it will only emerge if ERA is approached simultaneously from the bottom of biological organization up as well as from the top down, all while employing mathematical modeling approaches where possible to enhance ERA. Because top-down ERA is unconventional, we also offer some suggestions for how it might be implemented efficaciously. We hope this review helps researchers in the field of ERA fill key information gaps and helps risk assessors identify the best levels of biological organization to conduct ERAs with differing goals.

Initial development of a multigene 'omics-based exposure biomarker for pyrethroid pesticides

Omics technologies have long since promised to address a number of long standing issues related to environmental regulation. Despite considerable resource investment, there are few examples where these tools have been adopted by the regulatory community, which is in part due to a focus of most studies on discovery rather than assay development. The current work describes the initial development of an omics based assay using 48h Pimephales promelas (FHM) larvae for identifying aquatic exposures to pyrethroid pesticides. Larval FHM were exposed to seven concentrations of each of four pyrethroids (permethrin, cypermethrin, esfenvalerate and bifenthrin) in order to establish dose response curves. Then, in three separate identical experiments, FHM were exposed to a single equitoxic concentration of each pyrethroid, corresponding to 33% of the calculated LC50. All exposures were separated by weeks and all materials were either cleaned or replaced between runs in an attempt to maintain independence among exposure experiments. Gene expression classifiers were developed using the random forest algorithm for each exposure and evaluated first by cross-validation using hold out organisms from the same exposure experiment and then against test sets of each pyrethroid from separate exposure experiments. Bifenthrin exposed organisms generated the highest quality classifier, demonstrating an empirical Area Under the Curve (eAUC) of 0.97 when tested against bifenthrin exposed organisms from other exposure experiments and 0.91 against organisms exposed to any of the pyrethroids. An eAUC of 1.0 represents perfect classification with no false positives or negatives. Additionally, the bifenthrin classifier was able to successfully classify organisms from all other pyrethroid exposures at multiple concentrations, suggesting a potential utility for detecting cumulative exposures. Considerable run-to-run variability was observed both in exposure concentrations and molecular responses of exposed fish across exposure experiments. The application of a calibration step in analysis successfully corrected this, resulting in a significantly improved classifier. Classifier evaluation suggested the importance of considering a number of aspects of experimental design when developing an expression based tool for general use in ecological monitoring and risk assessment, such as the inclusion of multiple experimental runs and high replicate numbers.

Combined Transcriptomic and Proteomic Approach to Identify Toxicity Pathways in Early Life Stages of Japanese Medaka (Oryzias latipes) Exposed to 1,2,5,6-Tetrabromocyclooctane (TBCO)

Currently, the novel brominated flame retardant 1,2,5,6-tetrabromocyclooctane (TBCO) is considered a potential replacement for hexabromocyclododecane (HBCD). Therefore, use of TBCO could increase in the near future. To assess potential toxicological risks to aquatic organisms, embryos of Japanese medaka (Oryzias latipes) were exposed to 10, 100, or 1000 μg/L TBCO from 2 h postfertilization until 1 day post-hatch. TBCO accumulated in embryos in the order of 0.43-1.3 × 10(4)-fold, and the rate constant of accumulation was 1.7-1.8 per day. The number of days to hatch and the hatching success of embryos exposed to the medium and the greatest concentrations of TBCO were impaired. Responses of the transcriptome (RNA-seq) and proteome were characterized in embryos exposed to 100 μg/L TBCO because this was the least concentration of TBCO that caused an effect on hatching. Consistent with effects on hatching, proteins whose abundances were reduced by exposure to TBCO were enriched in embryo development and hatching pathways. Also, on the basis of the responses of transcriptome and proteome, it was predicted that TBCO might impair vision and contraction of cardiac muscle, respectively, and these effects were confirmed by targeted bioassays. This study provided a comprehensive understanding of effects of TBCO on medaka at early life stages and illustrated the power of "omics" to explain and predict phenotypic responses to chemicals.

Linking the response of endocrine regulated genes to adverse effects on sex differentiation improves comprehension of aromatase inhibition in a Fish Sexual Development Test

The Fish Sexual Development Test (FSDT) is a non-reproductive test to assess adverse effects of endocrine disrupting chemicals. With the present study it was intended to evaluate whether gene expression endpoints would serve as predictive markers of endocrine disruption in a FSDT. For proof-of-concept, a FSDT according to the OECD TG 234 was conducted with the non-steroidal aromatase inhibitor fadrozole (test concentrations: 10μg/L, 32μg/L, 100μg/L) using zebrafish (Danio rerio). Gene expression analyses using quantitative RT-PCR were included at 48h, 96h, 28days and 63days post fertilization (hpf, dpf). The selection of genes aimed at finding molecular endpoints which could be directly linked to the adverse apical effects of aromatase inhibition. The most prominent effects of fadrozole exposure on the sexual development of zebrafish were a complete sex ratio shift towards males and an acceleration of gonad maturation already at low fadrozole concentrations (10μg/L). Due to the specific inhibition of the aromatase enzyme (Cyp19) by fadrozole and thus, the conversion of C19-androgens to C18-estrogens, the steroid hormone balance controlling the sex ratio of zebrafish was altered. The resulting key event is the regulation of directly estrogen-responsive genes. Subsequently, gene expression of vitellogenin 1 (vtg1) and of the aromatase cyp19a1b isoform (cyp19a1b), were down-regulated upon fadrozole treatment compared to controls. For example, mRNA levels of vtg1 were down-regulated compared to the controls as early as 48 hpf and 96 hpf. Further regulated genes cumulated in pathways suggested to be controlled by endocrine mechanisms, like the steroid and terpenoid synthesis pathway (e.g. mevalonate (diphospho) decarboxylase (mvd), lanosterol synthase (2,3-oxidosqualene-lanosterol cyclase; lss), methylsterol monooxygenase 1 (sc4mol)) and in lipid transport/metabolic processes (steroidogenic acute regulatory protein (star), apolipoprotein Eb (apoEb)). Taken together, this study demonstrated that the existing Adverse Outcome Pathway (AOP) for aromatase inhibition in fish can be translated to the life-stage of sexual differentiation. We were further able to identify MoA-specific marker gene expression which can be instrumental in defining new measurable key events (KE) of existing or new AOPs related to endocrine disruption.

Assessment of DNA damage and molecular responses in Labeo rohita (Hamilton, 1822) following short-term exposure to silver nanoparticles

The increasing application of silver nanoparticles (Ag-NPs) both in industries and in agricultural fields has led to its accumulation in the aquatic ecosystem through water run-off. In the present study, the effects of Ag-NPs in the liver of Labeo rohita, were investigated at genomic and cellular level for seven days at the concentrations of 100, 200, 400 and 800 μg l(-1) by using 18 and 29 nm sizes of Ag-NPs. The Ag-NPs sizes of 18 and 29 nm were synthesized by a chemical method using atomic force microscopy with the zeta potential of -55 mV and-31.4 mV respectively. They were found to be spherical with smooth surfaces. Assessment of genotoxic effects of the particles in the fish using single-cell gel electrophoresis showed DNA damage on exposure to concentrations of 400 and 800 μg l(-1). Histopathological examination of the liver revealed vacuolar degeneration, hepatocytes have undergone total degeneration and high accumulation of Ag-NPs that depicted both time and dose-dependent relationships. Furthermore, the expression study of stress-related genes showed down-regulation, due to the production of free radicals and reactive oxygen species. Ag-NPs can cause both DNA damage and affect the cellular responses of L. rohita.

Responses of the zebrafish hypothalamic-pituitary-gonadal-liver axis PCR array to prochloraz are dependent on timing of sampling

A PCR array, based on expression of genes along the hypothalamic-pituitary-gonadal-liver (HPGL) axis of fish, has been suggested as a useful method for screening of endocrine-disrupting chemicals (EDCs). However, effects of circadian rhythm on responses of the HPGL axis to exposure to chemicals were unknown. In this study, profiles of expression of genes along the HPGL axis and concentrations of 17β-estradiol (E2) in blood plasma of female zebrafish were compared at two sampling times of day (8:00 AM and 7:00 PM). Prochloraz (PCZ) was selected as a model chemical to evaluate differences in responses of the HPGL axis at these two times of day. Profiles of responses of concentrations of E2 in plasma and expressions of genes along the HPGL axis genes were different between the two times of sampling. Concentrations of E2 were less, and abundances of mRNA for several genes along the HPGL axis were significantly greater or lesser when samples were collected at 7:00 PM than they were when samples were collected at 8:00 AM. Exposure to three concentrations of PCZ (3, 30 or 300μg/L) for 48h resulted in significantly lesser concentrations of plasma E2 and caused compensatory up-regulation of genes included in hypothalamus, pituitary and ovary. Expressions of genes along the HPGL were more responsive to PCZ at 8:00 AM than they were when samples were collected at 7:00 PM. Correlations among parameters in samples collected at the two times indicated the effects might be due to different concentrations of E2 in plasma due to exposure to PCZ.

Alterations in gene expression levels provide early indicators of chemical stress during Xenopus laevis embryo development: A case study with perfluorooctane sulfonate (PFOS)

In the present study, Xenopus laevis embryos were exposed to a range of perfluorooctane sulfonate (PFOS) concentrations (0, 0.5, 6, 12, 24, 48 and 96mg/L) for 96h in laboratorial conditions to establish toxicity along with possible gene expression changes. Mortality and deformities were monitored daily and head-tail length was measured at the end of the assay as an indicator of growth. At 24 and 96h post-exposure (hpe), the mRNA expression levels of the genetic markers involved in general stress responses (hsp70, hsp47, crh-a and ucn1), oxidative stress (cat.2 and sod), lipid metabolism (ppard) and apoptosis (tp53 and bax) were analyzed by RT-qPCR. Malformations were significantly higher in the embryos exposed to the highest PFOS concentration (41.8% to 56.4%) compared to controls (5.5%) at 48, 72 and 96hpe. Growth inhibition was observed in the embryos exposed to PFOS concentrations≥48mg/L. At 24 hpe, a statistically significant up-regulation of genes hsp70, hsp47, ppard, tp53 and bax in relation to controls was found. Similar responses were found for genes hsp70, hsp47, crh-a, ucn1, sod and ppard at 96 hpe. Alterations in the mRNA expression levels indicated both a stress response to PFOS exposure during X. laevis embryo development, and alterations in the regulation of oxidative stress, apoptosis, and differentiation. These molecular alterations were detected at an earlier exposure time or at lower concentrations than those producing developmental toxicity. Therefore, these sensitive warning signals could be used together with other biomarkers to supplement alternative methods (i.e. the frog embryo test) for developmental toxicity safety evaluations, and as tools in amphibian risk assessments for PFOS and its potential substitutes.

Metabolomics reveals the physiological response of Pseudomonas putida KT2440 (UWC1) after pharmaceutical exposure

Human pharmaceuticals have been detected in wastewater treatment plants, rivers, and estuaries throughout Europe and the United States. It is widely acknowledged that there is insufficient information available to determine whether prolonged exposure to low levels of these substances is having an impact on the microbial ecology in such environments. In this study we attempt to measure the effects of exposing cultures of Pseudomonas putida KT2440 (UWC1) to six pharmaceuticals by looking at differences in metabolite levels. Initially, we used Fourier transform infrared (FT-IR) spectroscopy coupled with multivariate analysis to discriminate between cell cultures exposed to different pharmaceuticals. This suggested that on exposure to propranolol there were significant changes in the lipid complement of P. putida. Metabolic profiling with gas chromatography-mass spectrometry (GC-MS), coupled with univariate statistical analyses, was used to identify endogenous metabolites contributing to discrimination between cells exposed to the six drugs. This approach suggested that the energy reserves of exposed cells were being expended and was particularly evident on exposure to propranolol. Adenosine triphosphate (ATP) concentrations were raised in P. putida exposed to propranolol. Increased energy requirements may be due to energy dependent efflux pumps being used to remove propranolol from the cell.

Ecotoxicogenomics: Microarray interlaboratory comparability

Transcriptomic analysis can complement traditional ecotoxicology data by providing mechanistic insight, and by identifying sub-lethal organismal responses and contaminant classes underlying observed toxicity. Before transcriptomic information can be used in monitoring and risk assessment, it is necessary to determine its reproducibility and detect key steps impacting the reliable identification of differentially expressed genes. A custom 15K-probe microarray was used to conduct transcriptomics analyses across six laboratories with estuarine amphipods exposed to cyfluthrin-spiked or control sediments (10 days). Two sample types were generated, one consisted of total RNA extracts (Ex) from exposed and control samples (extracted by one laboratory) and the other consisted of exposed and control whole body amphipods (WB) from which each laboratory extracted RNA. Our findings indicate that gene expression microarray results are repeatable. Differentially expressed data had a higher degree of repeatability across all laboratories in samples with similar RNA quality (Ex) when compared to WB samples with more variable RNA quality. Despite such variability a subset of genes were consistently identified as differentially expressed across all laboratories and sample types. We found that the differences among the individual laboratory results can be attributed to several factors including RNA quality and technical expertise, but the overall results can be improved by following consistent protocols and with appropriate training.

Transcriptome assembly and expression profiling of molecular responses to cadmium toxicity in hepatopancreas of the freshwater crab Sinopotamon henanense

Cadmium (Cd) pollution is a serious global problem, which causes irreversible toxic effects on animals. Freshwater crab, Sinopotamon henanense, is a useful environmental indicator since it is widely distributed in benthic habitats whereby it tends to accumulate Cd and other toxicants. However, its molecular responses to Cd toxicity remain unclear. In this study, we performed transcriptome sequencing and gene expression analyses of its hepatopancreas with and without Cd treatments. A total of 7.78 G clean reads were obtained from the pooled samples, and 68,648 unigenes with an average size of 622 bp were assembled, in which 5,436 were metabolism-associated and 2,728 were stimulus response-associated that include 380 immunity-related unigenes. Expression profile analysis demonstrated that most genes involved in macromolecular metabolism, oxidative phosphorylation, detoxification and anti-oxidant defense were up-regulated by Cd exposure, whereas immunity-related genes were down-regulated, except the genes involved in phagocytosis were up-regulated. The current data indicate that Cd exposure alters gene expressions in a concentration-dependent manner. Therefore, our results provide the first comprehensive S.henanense transcriptome dataset, which is useful for biological and ecotoxicological studies on this crab and its related species at molecular level, and some key Cd-responsive genes may provide candidate biomarkers for monitoring aquatic pollution by heavy metals.

Predicting environmental risk: A road map for the future

Frameworks for environmental risk assessment (ERA) focus on comparing results from separate exposure and effect assessments. Exposure assessment generally relies on mechanistic fate models, whereas the effects assessment is anchored in standard test protocols and descriptive statistics. This discrepancy prevents a useful link between these two pillars of ERA, and jeopardizes the realism and efficacy of the entire process. Similar to exposure assessment, effects assessment requires a mechanistic approach to translate the output of fate models into predictions for impacts on populations and food webs. The aim of this study was to discuss (1) the central importance of the individual level, (2) different strategies of dealing with biological complexity, and (3) the role that toxicokinetic-toxicodynamic (TKTD) models, energy budgets, and molecular biology play in a mechanistic revision of the ERA framework. Consequently, an outline for a risk assessment paradigm was developed that incorporates a mechanistic effects assessment in a consistent manner, and a "roadmap for the future." Such a roadmap may play a critical role to eventually arrive at a more scientific and efficient ERA process, and needs to be used to shape our long-term research agendas.

Defining the role of omics in assessing ecosystem health: Perspectives from the Canadian environmental monitoring program

Scientific reviews and studies continue to describe omics technologies as the next generation of tools for environmental monitoring, while cautioning that there are limitations and obstacles to overcome. However, omics has not yet transitioned into national environmental monitoring programs designed to assess ecosystem health. Using the example of the Canadian Environmental Effects Monitoring (EEM) program, the authors describe the steps that would be required for omics technologies to be included in such an established program. These steps include baseline collection of omics endpoints across different species and sites to generate a range of what is biologically normal within a particular ecosystem. Natural individual variability in the omes is not adequately characterized and is often not measured in the field, but is a key component to an environmental monitoring program, to determine the critical effect size or action threshold for management. Omics endpoints must develop a level of standardization, consistency, and rigor that will allow interpretation of the relevance of changes across broader scales. To date, population-level consequences of routinely measured endpoints such as reduced gonad size or intersex in fish is not entirely clear, and the significance of genome-wide molecular, proteome, or metabolic changes on organism or population health is further removed from the levels of ecological change traditionally managed. The present review is not intended to dismiss the idea that omics will play a future role in large-scale environmental monitoring studies, but rather outlines the necessary actions for its inclusion in regulatory monitoring programs focused on assessing ecosystem health.