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See detailRetrospective non-target analysis to support regulatory water monitoring: from masses of interest to recommendations via in silico workflows
Lai, Adelene UL; Singh, Randolph UL; Kovalova, Lubomira et al

in Environmental Sciences Europe (2021), 33(1), 43

Abstract Background Applying non-target analysis (NTA) in regulatory environmental monitoring remains challenging—instead of having exploratory questions, regulators usually already have specific ... [more ▼]

Abstract Background Applying non-target analysis (NTA) in regulatory environmental monitoring remains challenging—instead of having exploratory questions, regulators usually already have specific questions related to environmental protection aims. Additionally, data analysis can seem overwhelming because of the large data volumes and many steps required. This work aimed to establish an open in silico workflow to identify environmental chemical unknowns via retrospective NTA within the scope of a pre-existing Swiss environmental monitoring campaign focusing on industrial chemicals. The research question addressed immediate regulatory priorities: identify pollutants with industrial point sources occurring at the highest intensities over two time points. Samples from 22 wastewater treatment plants obtained in 2018 and measured using liquid chromatography–high resolution mass spectrometry were retrospectively analysed by (i) performing peak-picking to identify masses of interest; (ii) prescreening and quality-controlling spectra, and (iii) tentatively identifying priority “known unknown” pollutants by leveraging environmentally relevant chemical information provided by Swiss, Swedish, EU-wide, and American regulators. This regulator-supplied information was incorporated into MetFrag, an in silico identification tool replete with “post-relaunch” features used here. This study’s unique regulatory context posed challenges in data quality and volume that were directly addressed with the prescreening, quality control, and identification workflow developed. Results One confirmed and 21 tentative identifications were achieved, suggesting the presence of compounds as diverse as manufacturing reagents, adhesives, pesticides, and pharmaceuticals in the samples. More importantly, an in-depth interpretation of the results in the context of environmental regulation and actionable next steps are discussed. The prescreening and quality control workflow is openly accessible within the R package Shinyscreen, and adaptable to any (retrospective) analysis requiring automated quality control of mass spectra and non-target identification, with potential applications in environmental and metabolomics analyses. Conclusions NTA in regulatory monitoring is critical for environmental protection, but bottlenecks in data analysis and results interpretation remain. The prescreening and quality control workflow, and interpretation work performed here are crucial steps towards scaling up NTA for environmental monitoring. [less ▲]

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See detailOccurrence and Distribution of Pharmaceuticals and Their Transformation Products in Luxembourgish Surface Waters
Singh, Randolph UL; Lai, Adelene UL; Krier, Jessy UL et al

in ACS Environmental Au (2021)

Pharmaceuticals and their transformation products (TPs) are continuously released into the aquatic environment via anthropogenic activity. To expand knowledge on the presence of pharmaceuticals and their ... [more ▼]

Pharmaceuticals and their transformation products (TPs) are continuously released into the aquatic environment via anthropogenic activity. To expand knowledge on the presence of pharmaceuticals and their known TPs in Luxembourgish rivers, 92 samples collected during routine monitoring events between 2019 and 2020 were investigated using nontarget analysis. Water samples were concentrated using solid-phase extraction and then analyzed using liquid chromatography coupled to a high-resolution mass spectrometer. Suspect screening was performed using several open source computational tools and resources including Shinyscreen (https://git-r3lab.uni.lu/eci/shinyscreen/), MetFrag (https://msbi.ipb-halle.de/MetFrag/), PubChemLite (https://zenodo.org/record/4432124), and MassBank (https://massbank.eu/MassBank/). A total of 94 pharmaceuticals, 88 confirmed at a level 1 confidence (86 of which could be quantified, two compounds too low to be quantified) and six identified at level 2a, were found to be present in Luxembourg rivers. Pharmaceutical TPs (12) were also found at a level 2a confidence. The pharmaceuticals were present at median concentrations up to 214 ng/L, with caffeine having a median concentration of 1424 ng/L. Antihypertensive drugs (15), psychoactive drugs (15), and antimicrobials (eight) were the most detected groups of pharmaceuticals. A spatiotemporal analysis of the data revealed areas with higher concentrations of the pharmaceuticals, as well as differences in pharmaceutical concentrations between 2019 and 2020. The results of this work will help guide activities for improving water management in the country and set baseline data for continuous monitoring and screening efforts, as well as for further open data and software developments. [less ▲]

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See detailDiscovering Pesticides and their Transformation Products in Luxembourg Waters using Open Cheminformatics Approaches
Krier, Jessy UL; Singh, Randolph UL; Kondic, Todor UL et al

E-print/Working paper (2021)

Abstract The diversity of hundreds of thousands of potential organic pollutants and the lack of (publicly available) information about many of them is a huge challenge for environmental sciences ... [more ▼]

Abstract The diversity of hundreds of thousands of potential organic pollutants and the lack of (publicly available) information about many of them is a huge challenge for environmental sciences, engineering, and regulation. Suspect screening based on high-resolution liquid chromatography-mass spectrometry (LC-HRMS) has enormous potential to help characterize the presence of these chemicals in our environment, enabling the detection of known and newly emerging pollutants, as well as their potential transformation products (TPs). Here, suspect list creation (focusing on pesticides relevant for Luxembourg, incorporating data sources in 4 languages) was coupled to an automated retrieval of related TPs from PubChem based on high confidence suspect hits, to screen for pesticides and their TPs in Luxembourgish river samples. A computational workflow was established to combine LC-HRMS analysis and pre-screening of the suspects (including automated quality control steps), with spectral annotation to determine which pesticides and, in a second step, their related TPs may be present in the samples. The data analysis with Shinyscreen (https://git-r3lab.uni.lu/eci/shinyscreen/), an open source software developed in house, coupled with custom-made scripts, revealed the presence of 162 potential pesticide masses and 135 potential TP masses in the samples. Further identification of these mass matches was performed using the open source MetFrag (https://msbi.ipb-halle.de/MetFrag/). Eventual target analysis of 36 suspects resulted in 31 pesticides and TPs confirmed at Level-1 (highest confidence), and five pesticides and TPs not confirmed due to different retention times. Spatio-temporal analysis of the results showed that TPs and pesticides followed similar trends, with a maximum number of potential detections in July. The highest detections were in the rivers Alzette and Mess and the lowest in the Sûre and Eisch. This study (a) added pesticides, classification information and related TPs into the open domain, (b) developed automated open source retrieval methods - both enhancing FAIRness (Findability, Accessibility, Interoperability and Reusability) of the data and methods; and (c) will directly support “L’Administration de la Gestion de l’Eau” on further monitoring steps in Luxembourg. [less ▲]

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See detailOccurrence and Distribution of Pharmaceuticals and their Transformation Products in Luxembourgish Surface Waters
Singh, Randolph UL; Lai, Adelene UL; Krier, Jessy UL et al

E-print/Working paper (2021)

This pre-print describes the analysis of pharmaceuticals and their transformation products in surface water samples collected in Luxembourg from 2019 to 2020. Details of the experimental and computational ... [more ▼]

This pre-print describes the analysis of pharmaceuticals and their transformation products in surface water samples collected in Luxembourg from 2019 to 2020. Details of the experimental and computational tools and workflows used are fully described in the manuscript. Links to the suspect lists, codes used, and data files are also provided. [less ▲]

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See detailExpanded coverage of non-targeted LC-HRMS using atmospheric pressure chemical ionization: a case study with ENTACT mixtures.
Singh, Randolph UL; Chao, Alex; Phillips, Katherine A. et al

in Analytical and Bioanalytical Chemistry (2020)

Non-targeted analysis (NTA) is a rapidly evolving analytical technique with numerous opportunities to improve and expand instrumental and data analysis methods. In this work, NTA was performed on eight ... [more ▼]

Non-targeted analysis (NTA) is a rapidly evolving analytical technique with numerous opportunities to improve and expand instrumental and data analysis methods. In this work, NTA was performed on eight synthetic mixtures containing 1264 unique chemical substances from the U.S. Environmental Protection Agency’s Non-Targeted Analysis Collaborative Trial (ENTACT). These mixtures were analyzed by atmospheric pressure chemical ionization (APCI) and electrospray ionization (ESI) using both positive and negative polarities for a total of four modes. Out of the 1264 ENTACT chemical substances, 1116 were detected in at least one ionization mode, 185 chemicals were detected using all four ionization modes, whereas 148 were not detected. Forty-four chemicals were detected only by APCI, and 181 were detected only by ESI. Molecular descriptors and physicochemical properties were used to assess which ionization type was preferred for a given compound. One ToxPrint substructure (naphthalene group) was found to be enriched in compounds only detected using APCI, and eight ToxPrints (e.g., several alcohol moieties) were enriched in compounds only detected using ESI. Examination of physicochemical parameters for ENTACT chemicals suggests that those with higher aqueous solubility preferentially ionized by ESI−. While ESI typically detects a larger number of compounds, APCI offers chromatograms with less background, fewer co-elutions, and additional chemical space coverage, suggesting both should be considered for broader coverage in future NTA research. [less ▲]

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See detailConnecting environmental exposure and neurodegeneration using cheminformatics and high resolution mass spectrometry: potential and challenges
Schymanski, Emma UL; Baker, Nancy C.; Williams, Antony J et al

in Environmental Science. Processes and Impacts (2019)

Connecting chemical exposures over a lifetime to complex chronic diseases with multifactorial causes such as neurodegenerative diseases is an immense challenge requiring a long-term, interdisciplinary ... [more ▼]

Connecting chemical exposures over a lifetime to complex chronic diseases with multifactorial causes such as neurodegenerative diseases is an immense challenge requiring a long-term, interdisciplinary approach. Rapid developments in analytical and data technologies, such as non-target high resolution mass spectrometry (NT-HR-MS), have opened up new possibilities to accomplish this, inconceivable 20 years ago. While NT-HR-MS is being applied to increasingly complex research questions, there are still many unidentified chemicals and uncertainties in linking exposures to human health outcomes and environmental impacts. In this perspective, we explore the possibilities and challenges involved in using cheminformatics and NT-HR-MS to answer complex questions that cross many scientific disciplines, taking the identification of potential (small molecule) neurotoxicants in environmental or biological matrices as a case study. We explore capturing literature knowledge and patient exposure information in a form amenable to high-throughput data mining, and the related cheminformatic challenges. We then briefly cover which sample matrices are available, which method(s) could potentially be used to detect these chemicals in various matrices and what remains beyond the reach of NT-HR-MS. We touch on the potential for biological validation systems to contribute to mechanistic understanding of observations and explore which sampling and data archiving strategies may be required to form an accurate, sustained picture of small molecule signatures on extensive cohorts of patients with chronic neurodegenerative disorders. Finally, we reflect on how NT-HR-MS can support unravelling the contribution of the environment to complex diseases. [less ▲]

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See detailTowards a harmonized method for the global reconnaissance of multi-class antimicrobials and other pharmaceuticals in wastewater and receiving surface waters
Singh, Randolph UL; Angeles, Luisa; Butryn, Deena et al

in Environment International (2019), 124

Antimicrobial resistance is a worldwide problem that is both pressing and challenging due to the rate at which it is spreading, and the lack of understanding of the mechanisms that link human, animal and ... [more ▼]

Antimicrobial resistance is a worldwide problem that is both pressing and challenging due to the rate at which it is spreading, and the lack of understanding of the mechanisms that link human, animal and environmental sources contributing to its proliferation. One knowledge gap that requires immediate attention is the significance of antimicrobial residues and other pharmaceuticals that are being discharged from wastewater treatment plants (WWTPs) on the dissemination of antimicrobial resistance in the environment. In this work we provide an approach to develop a harmonized analytical method for 8 classes of antimicrobials and other pharmaceuticals that can be used for global monitoring in wastewater and receiving waters. Analysis of these trace organic chemicals in the influent and effluent wastewater, and in the respective upstream and downstream receiving waters from different countries across the globe is not trivial. Here, we demonstrated that sample preparation using solid-phase extraction (SPE) not only provides a convenient and cost-effective shipping of samples, but also adds stability to the analytes during international shipping. It is important that SPE cartridges are maintained at cold temperature during shipment if the duration is longer than 7 days because a significant decrease in recoveries were observed after 7 days in the cartridges stored at room temperature, especially for sulfonamides and tetracyclines. To compensate for sample degradation during shipment, and matrix effects in liquid chromatography/mass spectrometry, the use of stable isotope labeled compounds should be employed when available and affordable. The importance of applying a defined tolerance for the ion ratios (Q/q) that have been optimized for wastewater and surface water is discussed. The tolerance range was set to be the mean Q/q of the analyte standard at various concentrations ±40% for the influent, and ±30% for the effluent, upstream, and downstream samples; for tetracyclines and quinolones, however, the tolerance range was ±80% in order to minimize false negative and false positive detection. The optimized procedures were employed to reveal differences in antimicrobial and pharmaceutical concentrations in influent, effluent, and surface water samples from Hong Kong, India, Philippines, Sweden, Switzerland, and United States. The antimicrobials with the highest concentrations in influent and effluent samples were ciprofloxacin (48,103 ng/L, Hong Kong WWTP 1) and clarithromycin (5178 ng/L, India WWTP 2), respectively. On the other hand, diclofenac (108,000 ng/L, Sweden WWTP 2), caffeine (67,000 ng/L, India WWTP 1), and acetaminophen (28,000 ng/L, India WWTP 1) were the highest detected pharmaceuticals in the receiving surface water samples. Hong Kong showed the highest total antimicrobial concentrations that included macrolides, quinolones, and sulfonamides with concentrations reaching 60,000 ng/L levels in the influent. Antidepressants were predominant in Sweden, Switzerland, and the United States. [less ▲]

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See detailBinding of iodinated contrast media (ICM) and their transformation products with hormone receptors: Are ICM the new EDCs?
Singh, Randolph UL; Rajnarayanan, Rajendram; Aga, Diana

in Science of the Total Environment (2019)

Iodinated contrast media (ICM) have been detected at high concentrations (as high as about 3 μg/L) in surface water systems, and recently in fish brains and gonad. The mismatch between the polarity of ICM ... [more ▼]

Iodinated contrast media (ICM) have been detected at high concentrations (as high as about 3 μg/L) in surface water systems, and recently in fish brains and gonad. The mismatch between the polarity of ICM and the high lipid content of brain raises questions on whether their bioaccumulation is receptor-mediated. Furthermore, the structural similarity of ICM to the natural thyroid hormones thyroxine and triiodothyronine suggest potential binding of ICM to nuclear receptors in the endocrine system. Therefore, an in silico approach based on Surflex-Dock module of SYBYL was used to investigate the molecular docking of selected ICM (diatrizoic acid, iohexol, iopamidol, and iopromide). These ICM showed interaction with nuclear receptors that play key roles in endocrine regulation, including the androgen and estrogen receptors. Furthermore, the results indicate peroxisome proliferator-activated receptor gamma (PPARg) as one of the viable targets in the endocrine disrupting potential of ICM with higher Cscores for the ICM and iopromide transformation products than the reference ligand for the receptor. The data obtained from in silico calculations showed stronger binding of iohexol to the transthyretin-binding pocket compared to the natural hormones, thyroxine and triiodothyronine, suggesting the potential of ICM to act as endocrine disrupting chemicals (EDCs) in the environment. [less ▲]

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See detailUsing prepared mixtures of ToxCast chemicals to evaluate non-targeted analysis (NTA) method performance
Sobus, Jon R.; Grossman, Jarod N.; Chao, Alex et al

in Analytical and bioanalytical chemistry (2019), 411(4), 835-851

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See detailMicrobiota alter metabolism and mediate neurodevelopmental toxicity of 17β-estradiol
Catron, Tara R.; Swank, Adam; Wehmas, Leah C. et al

in Scientific Reports (2019), 9(1), 7064

Estrogenic chemicals are widespread environmental contaminants associated with diverse health and ecological effects. During early vertebrate development, estrogen receptor signaling is critical for many ... [more ▼]

Estrogenic chemicals are widespread environmental contaminants associated with diverse health and ecological effects. During early vertebrate development, estrogen receptor signaling is critical for many different physiologic responses, including nervous system function. Recently, host-associated microbiota have been shown to influence neurodevelopment. Here, we hypothesized that microbiota may biotransform exogenous 17-βestradiol (E2) and modify E2 effects on swimming behavior. Colonized zebrafish were continuously exposed to non-teratogenic E2 concentrations from 1 to 10 days post-fertilization (dpf). Changes in microbial composition and predicted metagenomic function were evaluated. Locomotor activity was assessed in colonized and axenic (microbe-free) zebrafish exposed to E2 using a standard light/dark behavioral assay. Zebrafish tissue was collected for chemistry analyses. While E2 exposure did not alter microbial composition or putative function, colonized E2-exposed larvae showed reduced locomotor activity in the light, in contrast to axenic E2-exposed larvae, which exhibited normal behavior. Measured E2 concentrations were significantly higher in axenic relative to colonized zebrafish. Integrated peak area for putative sulfonated and glucuronidated E2 metabolites showed a similar trend. These data demonstrate that E2 locomotor effects in the light phase are dependent on the presence of microbiota and suggest that microbiota influence chemical E2 toxicokinetics. More broadly, this work supports the concept that microbial colonization status may influence chemical toxicity. [less ▲]

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