De Novo Assembly of the Nearly Complete Fathead Minnow Reference Genome Reveals a Repetitive but Compact Genome.

The fathead minnow is a widely used model organism in environmental toxicology. The lack of a high-quality fathead minnow reference genome, however, has severely hampered its uses in toxicogenomics. We present the de novo assembly and annotation of the fathead minnow genome using long PacBio reads, Bionano and Hi-C scaffolding data, and large RNA-sequencing data sets from different tissues and life stages.

Development of omics biomarkers for estrogen exposure using mRNA, miRNA and piRNAs.

The number of chemicals requiring risk evaluation exceeds our capacity to provide the underlying data using traditional methodology. This has led to an increased focus on the development of novel approach methodologies. This work aimed to expand the panel of gene expression-based biomarkers to include responses to estrogens, to identify training strategies that maximize the range of applicable concentrations, and to evaluate the potential for two classes of small non-coding RNAs (sncRNAs), microRNA (miRNA) and piwi-interacting RNA (piRNA), as biomarkers.

Multigene Biomarkers of Pyrethroid Exposure: Exploratory Experiments.

We describe initial development of microarray-based assays for detecting 4 pyrethroid pesticides (bifenthrin, cypermethrin, esfenvalerate, and permethrin) in water. To facilitate comparison of transcriptional responses with gross apical responses, we estimated concentration-mortality curves for these pyrethroids using flow-through exposures of newly hatched Daphnia magna, Pimephales promelas adults, and 24 h posthatch P. promelas.

A statistical framework for applying RNA profiling to chemical hazard detection.

Use of 'omics technologies in environmental science is expanding. However, application is mostly restricted to characterizing molecular steps leading from toxicant interaction with molecular receptors to apical endpoints in laboratory species. Use in environmental decision-making is limited, due to difficulty in elucidating mechanisms in sufficient detail to make quantitative outcome predictions in any single species or in extending predictions to aquatic communities.

Aquatic concentrations of chemical analytes compared to ecotoxicity estimates.

We describe screening level estimates of potential aquatic toxicity posed by 227 chemical analytes that were measured in 25 ambient water samples collected as part of a joint USGS/USEPA drinking water plant study. Measured concentrations were compared to biological effect concentration (EC) estimates, including USEPA aquatic life criteria, effective plasma concentrations of pharmaceuticals, published toxicity data summarized in the USEPA ECOTOX database, and chemical structure-based predictions. Potential dietary exposures were estimated using a generic 3-tiered food web accumulation scenario.

Nationwide reconnaissance of contaminants of emerging concern in source and treated drinking waters of the United States.

When chemical or microbial contaminants are assessed for potential effect or possible regulation in ambient and drinking waters, a critical first step is determining if the contaminants occur and if they are at concentrations that may cause human or ecological health concerns. To this end, source and treated drinking water samples from 29 drinking water treatment plants (DWTPs) were analyzed as part of a two-phase study to determine whether chemical and microbial constituents, many of which are considered contaminants of emerging concern, were detectable in the waters. Of the 84 chemicals monitored in the 9 Phase I DWTPs, 27 were detected at least once in the source water, and 21 were detected at least once in treated drinking water.

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.

Evaluating the extent of pharmaceuticals in surface waters of the United States using a National-scale Rivers and Streams Assessment survey.

To assess the potential exposure of aquatic ecosystems to active pharmaceutical ingredients, the authors conducted a national-scale, probability-based statistical survey of the occurrence of these compounds in surface waters of the United States. The survey included 182 sampling sites and targeted rivers with close proximity to urban areas. The 46 analytes reported represent many classes of active pharmaceutical ingredients (APIs), including antibiotics, diuretics, antihypertensives, anticonvulsants, and antidepressants.

Concentrations of prioritized pharmaceuticals in effluents from 50 large wastewater treatment plants in the US and implications for risk estimation.

We measured concentrations of 56 active pharmaceutical ingredients (APIs) in effluent samples from 50 large wastewater treatment plants across the US. Hydrochlorothiazide was found in every sample. Metoprolol, atenolol, and carbamazepine were found in over 90% of the samples.

Predicting variability of aquatic concentrations of human pharmaceuticals.

Potential exposure to active pharmaceutical ingredients (APIs) in the aquatic environment is a subject of ongoing concern. We recently published maximum likely exposure rates for several hundred human prescription pharmaceuticals commonly used in the US. These rates were estimated from nationally aggregated marketing data and wastewater production rates.

Risks to aquatic organisms posed by human pharmaceutical use.

In order to help prioritize future research efforts within the US, risks associated with exposure to human prescription pharmaceutical residues in wastewater were estimated from marketing and pharmacological data. Masses of 371 active pharmaceutical ingredients (APIs) dispensed in the US in 2004 were estimated from marketing data, and then divided by therapeutic dose rate to normalize for potency. Metabolic inactivation of the 50 most dispensed APIs was estimated from published data, and active metabolites were tabulated.