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Wittner R, Holub P, Mascia C, Frexia F, Müller H, Plass M, Allocca C, Betsou F, Burdett T, Cancio I, Chapman A, Chapman M, Courtot M, Curcin V, Eder J, Elliot M, Exter K, Goble C, Golebiewski M, Kisler B, Kremer A, Leo S, Lin‐Gibson S, Marsano A, Mattavelli M, Moore J, Nakae H, Perseil I, Salman A, Sluka J, Soiland‐Reyes S, Strambio‐De‐Castillia C, Sussman M, Swedlow JR, Zatloukal K, Geiger J. Toward a common standard for data and specimen provenance in life sciences. Learn Health Syst 2024; 8:e10365. [PMID: 38249839 PMCID: PMC10797572 DOI: 10.1002/lrh2.10365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 03/17/2023] [Accepted: 03/24/2023] [Indexed: 01/23/2024] Open
Abstract
Open and practical exchange, dissemination, and reuse of specimens and data have become a fundamental requirement for life sciences research. The quality of the data obtained and thus the findings and knowledge derived is thus significantly influenced by the quality of the samples, the experimental methods, and the data analysis. Therefore, a comprehensive and precise documentation of the pre-analytical conditions, the analytical procedures, and the data processing are essential to be able to assess the validity of the research results. With the increasing importance of the exchange, reuse, and sharing of data and samples, procedures are required that enable cross-organizational documentation, traceability, and non-repudiation. At present, this information on the provenance of samples and data is mostly either sparse, incomplete, or incoherent. Since there is no uniform framework, this information is usually only provided within the organization and not interoperably. At the same time, the collection and sharing of biological and environmental specimens increasingly require definition and documentation of benefit sharing and compliance to regulatory requirements rather than consideration of pure scientific needs. In this publication, we present an ongoing standardization effort to provide trustworthy machine-actionable documentation of the data lineage and specimens. We would like to invite experts from the biotechnology and biomedical fields to further contribute to the standard.
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Affiliation(s)
- Rudolf Wittner
- BBMRI‐ERICGrazAustria
- Institute of Computer Science & Faculty of InformaticsMasaryk UniversityBrnoCzechia
| | - Petr Holub
- BBMRI‐ERICGrazAustria
- Institute of Computer Science & Faculty of InformaticsMasaryk UniversityBrnoCzechia
| | - Cecilia Mascia
- CRS4—Center for Advanced StudiesResearch and Development in SardiniaPulaItaly
| | - Francesca Frexia
- CRS4—Center for Advanced StudiesResearch and Development in SardiniaPulaItaly
| | | | | | - Clare Allocca
- National Institute of Standards and TechnologyGaithersburgMarylandUSA
| | - Fay Betsou
- Biological Resource Center of Institut Pasteur (CRBIP)ParisFrance
| | - Tony Burdett
- EMBL's European Bioinformatics Institute (EMBL‐EBI)CambridgeUK
| | - Ibon Cancio
- Plentzia Marine Station (PiE‐UPV/EHU)University of the Basque Country, EMBRC‐SpainBilbaoSpain
| | | | | | | | | | | | - Mark Elliot
- Department of Social Statistics, School of Social SciencesUniversity of ManchesterManchesterUK
| | - Katrina Exter
- Flanders Marine Institute (VLIZ), EMBRC‐BelgiumOstendBelgium
| | - Carole Goble
- Department of Computer ScienceUniversity of ManchesterManchesterUK
| | - Martin Golebiewski
- Heidelberg Institute for Theoretical Studies (HITS gGmbH)HeidelbergGermany
| | | | | | - Simone Leo
- CRS4—Center for Advanced StudiesResearch and Development in SardiniaPulaItaly
| | | | - Anna Marsano
- Department of BiomedicineUniversity of BaselBaselSwitzerland
| | - Marco Mattavelli
- SCI‐STI‐MMÉcole Politechnique Fédérale de LausanneLausanneSwitzerland
| | - Josh Moore
- Centre for Gene Regulation and Expression and Division of Computational Biology, School of Life SciencesUniversity of DundeeDundeeUK
- German BioImaging–Gesellschaft für Mikroskopie und Bildanalyse e.V.KonstanzGermany
| | - Hiroki Nakae
- Japan bio‐Measurement and Analysis ConsortiumTokyoJapan
| | - Isabelle Perseil
- INSERM–Institut National de la Sante et de la Recherche MedicaleParisFrance
| | - Ayat Salman
- Standards Council of CanadaOttawaOntarioCanada
- Canadian Primary Care Sentinel Surveillance Network (CPCSSN) Department of Family MedicineQueen's UniversityKingstonOntarioCanada
| | - James Sluka
- Biocomplexity InstituteIndiana UniversityBloomingtonIndianaUSA
| | - Stian Soiland‐Reyes
- Department of Computer ScienceUniversity of ManchesterManchesterUK
- Informatics InstituteUniversity of AmsterdamAmsterdamThe Netherlands
| | | | - Michael Sussman
- US Department of AgricultureWashingtonDistrict of ColumbiaUSA
| | - Jason R. Swedlow
- Centre for Gene Regulation and Expression and Division of Computational Biology, School of Life SciencesUniversity of DundeeDundeeUK
| | | | - Jörg Geiger
- Interdisciplinary Bank of Biomaterials and Data Würzburg (ibdw)WürzburgGermany
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2
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Deans JR, Deol P, Titova N, Radi SH, Vuong LM, Evans JR, Pan S, Fahrmann J, Yang J, Hammock BD, Fiehn O, Fekry B, Eckel-Mahan K, Sladek FM. HNF4α isoforms regulate the circadian balance between carbohydrate and lipid metabolism in the liver. Front Endocrinol (Lausanne) 2023; 14:1266527. [PMID: 38111711 PMCID: PMC10726135 DOI: 10.3389/fendo.2023.1266527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 11/06/2023] [Indexed: 12/20/2023] Open
Abstract
Hepatocyte Nuclear Factor 4α (HNF4α), a master regulator of hepatocyte differentiation, is regulated by two promoters (P1 and P2) which drive the expression of different isoforms. P1-HNF4α is the major isoform in the adult liver while P2-HNF4α is thought to be expressed only in fetal liver and liver cancer. Here, we show that P2-HNF4α is indeed expressed in the normal adult liver at Zeitgeber time (ZT)9 and ZT21. Using exon swap mice that express only P2-HNF4α we show that this isoform orchestrates a distinct transcriptome and metabolome via unique chromatin and protein-protein interactions, including with different clock proteins at different times of the day leading to subtle differences in circadian gene regulation. Furthermore, deletion of the Clock gene alters the circadian oscillation of P2- (but not P1-)HNF4α RNA, revealing a complex feedback loop between the HNF4α isoforms and the hepatic clock. Finally, we demonstrate that while P1-HNF4α drives gluconeogenesis, P2-HNF4α drives ketogenesis and is required for elevated levels of ketone bodies in female mice. Taken together, we propose that the highly conserved two-promoter structure of the Hnf4a gene is an evolutionarily conserved mechanism to maintain the balance between gluconeogenesis and ketogenesis in the liver in a circadian fashion.
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Affiliation(s)
- Jonathan R. Deans
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, Riverside, CA, United States
- Genetics, Genomics and Bioinformatics Graduate Program, University of California, Riverside, Riverside, CA, United States
| | - Poonamjot Deol
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, Riverside, CA, United States
| | - Nina Titova
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, Riverside, CA, United States
| | - Sarah H. Radi
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, Riverside, CA, United States
- Biochemistry and Molecular Biology Graduate Program, University of California, Riverside, Riverside, CA, United States
| | - Linh M. Vuong
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, Riverside, CA, United States
| | - Jane R. Evans
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, Riverside, CA, United States
| | - Songqin Pan
- Proteomics Core, Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, United States
| | - Johannes Fahrmann
- National Institutes of Health West Coast Metabolomics Center, University of California, Davis, Davis, CA, United States
| | - Jun Yang
- Department of Entomology and Nematology & UCD Comprehensive Cancer Center, University of California, Davis, Davis, CA, United States
| | - Bruce D. Hammock
- Department of Entomology and Nematology & UCD Comprehensive Cancer Center, University of California, Davis, Davis, CA, United States
| | - Oliver Fiehn
- National Institutes of Health West Coast Metabolomics Center, University of California, Davis, Davis, CA, United States
| | - Baharan Fekry
- Department of Biochemistry and Molecular Biology, McGovern Medical School at the University of Texas Health Science Center (UT Health), Houston, TX, United States
| | - Kristin Eckel-Mahan
- Department of Biochemistry and Molecular Biology, McGovern Medical School at the University of Texas Health Science Center (UT Health), Houston, TX, United States
- Institute of Molecular Medicine, McGovern Medical School at the University of Texas Health Science Center (UT Health), Houston, TX, United States
| | - Frances M. Sladek
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, Riverside, CA, United States
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Yao X, Saikawa E, Warner S, D’Souza PE, Ryan PB, Barr DB. Phytoremediation of Lead-Contaminated Soil in the Westside of Atlanta, GA. Geohealth 2023; 7:e2022GH000752. [PMID: 37637997 PMCID: PMC10450253 DOI: 10.1029/2022gh000752] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 06/13/2023] [Accepted: 07/19/2023] [Indexed: 08/29/2023]
Abstract
Phytoremediation has been explored as a cost-effective method to remediate soil Pb contamination. A greenhouse study was conducted to evaluate the efficacy of Vigna unguiculata, Brassica pekinensis, Gomphrena globose, and Helianthus annuus for removing and immobilizing Pb in soil collected from the Westside Lead Superfund site in Atlanta. Plants were cultivated in sampled soil with a Pb concentration of 515 ± 10 mg/kg for 60 days. Soils growing H. annuus were additionally treated with ethylenediaminetetraacetic acid (EDTA) (0.1 g/kg) or compost (20% soil blend) to assess their capabilities for enhancing phytoremediation. Mean post-phytoremediation Pb concentrations in the four plant species were 23.5, 25.7, 50.0, and 58.1 mg/kg dry weight (DW), respectively, and were substantially higher than 1.55 mg/kg DW in respective plant species grown in control soils with no Pb contamination. The highest Pb concentration, translocation factor, and biomass were found in V. unguiculate among four species without soil amendments. H. annuus treated with EDTA and compost resulted in a significant increase in the total Pb uptake and larger biomass compared to non-treated plants, respectively. Although this study found that V. unguiculata was the best candidate for Pb accumulation and immobilization among four species, soil remediation was limited to 54 mg/kg in a growing season. We find that it is critically important to perform phytostabilization in a secure manner, since Pb bioavailability of edible plant parts implies the potential risk associated with their unintentional consumption. Efficiently and effectively remediating Pb-contaminated soils in a low-cost manner needs to be further studied.
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Affiliation(s)
- X. Yao
- Department of Environmental SciencesEmory UniversityAtlantaGAUSA
| | - E. Saikawa
- Department of Environmental SciencesEmory UniversityAtlantaGAUSA
- Gangarosa Department of Environmental HealthEmory UniversityAtlantaGAUSA
| | - S. Warner
- Department of Environmental SciencesEmory UniversityAtlantaGAUSA
| | - P. E. D’Souza
- Gangarosa Department of Environmental HealthEmory UniversityAtlantaGAUSA
| | - P. B. Ryan
- Gangarosa Department of Environmental HealthEmory UniversityAtlantaGAUSA
| | - D. B. Barr
- Gangarosa Department of Environmental HealthEmory UniversityAtlantaGAUSA
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McClure RS, Rericha Y, Waters KM, Tanguay RL. 3' RNA-seq is superior to standard RNA-seq in cases of sparse data but inferior at identifying toxicity pathways in a model organism. Front Bioinform 2023; 3:1234218. [PMID: 37576716 PMCID: PMC10414111 DOI: 10.3389/fbinf.2023.1234218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 07/12/2023] [Indexed: 08/15/2023] Open
Abstract
Introduction: The application of RNA-sequencing has led to numerous breakthroughs related to investigating gene expression levels in complex biological systems. Among these are knowledge of how organisms, such as the vertebrate model organism zebrafish (Danio rerio), respond to toxicant exposure. Recently, the development of 3' RNA-seq has allowed for the determination of gene expression levels with a fraction of the required reads compared to standard RNA-seq. While 3' RNA-seq has many advantages, a comparison to standard RNA-seq has not been performed in the context of whole organism toxicity and sparse data. Methods and results: Here, we examined samples from zebrafish exposed to perfluorobutane sulfonamide (FBSA) with either 3' or standard RNA-seq to determine the advantages of each with regards to the identification of functionally enriched pathways. We found that 3' and standard RNA-seq showed specific advantages when focusing on annotated or unannotated regions of the genome. We also found that standard RNA-seq identified more differentially expressed genes (DEGs), but that this advantage disappeared under conditions of sparse data. We also found that standard RNA-seq had a significant advantage in identifying functionally enriched pathways via analysis of DEG lists but that this advantage was minimal when identifying pathways via gene set enrichment analysis of all genes. Conclusions: These results show that each approach has experimental conditions where they may be advantageous. Our observations can help guide others in the choice of 3' RNA-seq vs standard RNA sequencing to query gene expression levels in a range of biological systems.
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Affiliation(s)
- Ryan S. McClure
- Biological Sciences Division, Pacific Northwest Laboratory, Richland, WA, United States
| | - Yvonne Rericha
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, United States
| | - Katrina M. Waters
- Biological Sciences Division, Pacific Northwest Laboratory, Richland, WA, United States
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, United States
| | - Robyn L. Tanguay
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, United States
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Soriano MA, Warren JL, Clark CJ, Johnson NP, Siegel HG, Deziel NC, Saiers JE. Social Vulnerability and Groundwater Vulnerability to Contamination From Unconventional Hydrocarbon Extraction in the Appalachian Basin. Geohealth 2023; 7:e2022GH000758. [PMID: 37064218 PMCID: PMC10100439 DOI: 10.1029/2022gh000758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/20/2023] [Accepted: 03/07/2023] [Indexed: 06/19/2023]
Abstract
Unconventional oil and gas (UOG) development, made possible by horizontal drilling and high-volume hydraulic fracturing, has been fraught with controversy since the industry's rapid expansion in the early 2000's. Concerns about environmental contamination and public health risks persist in many rural communities that depend on groundwater resources for drinking and other daily needs. Spatial disparities in UOG risks can pose distributive environmental injustice if such risks are disproportionately borne by marginalized communities. In this paper, we analyzed groundwater vulnerability to contamination from UOG as a physically based measure of risk in conjunction with census tract level sociodemographic characteristics describing social vulnerability in the northern Appalachian Basin. We found significant associations between elevated groundwater vulnerability and lower population density, consistent with UOG development occurring in less densely populated rural areas. We also found associations between elevated groundwater vulnerability and lower income, higher proportions of elderly populations, and higher proportion of mobile homes, suggesting a disproportionate risk burden on these socially vulnerable groups. We did not find a statistically significant association between elevated groundwater vulnerability and populations of racial/ethnic minorities in our study region. Household surveys provided empirical support for a relationship between sociodemographic characteristics and capacity to assess and mitigate exposures to potentially contaminated water. Further research is needed to probe if the observed disparities translate to differences in chemical exposure and adverse health outcomes.
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Affiliation(s)
- Mario A. Soriano
- School of the EnvironmentYale UniversityNew HavenCTUSA
- Integrated GroundWater Modeling CenterHigh Meadows Environmental InstitutePrinceton UniversityPrincetonNJUSA
| | - Joshua L. Warren
- Department of BiostatisticsSchool of Public HealthYale UniversityNew HavenCTUSA
| | - Cassandra J. Clark
- Department of Environmental Health SciencesSchool of Public HealthYale UniversityNew HavenCTUSA
| | - Nicholaus P. Johnson
- Department of Environmental Health SciencesSchool of Public HealthYale UniversityNew HavenCTUSA
| | | | - Nicole C. Deziel
- Department of Environmental Health SciencesSchool of Public HealthYale UniversityNew HavenCTUSA
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Rosofsky AS, Vorhees DJ. Bringing Multisectoral and Multidisciplinary Stakeholders Together to Optimize Environmental Health Research. Geohealth 2023; 7:e2022GH000746. [PMID: 36825115 PMCID: PMC9941472 DOI: 10.1029/2022gh000746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 01/26/2023] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Incorporating multisectoral and multidisciplinary stakeholder perspectives into environmental health research planning and implementation can help increase the utility of the research. It can also enhance the likelihood of stakeholders using the research to inform decisions. Health Effects Institute (HEI) Energy, a funding and research organization, undertook a multiyear research planning process to build its stakeholder network and integrate their perspectives, knowledge, and priorities into research on potential exposures and health effects associated with unconventional oil and gas development. This commentary describes that process, lessons learned, and how stakeholder involvement shaped HEI Energy's inaugural program of research and associated stakeholder engagement.
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Shams M, Mansukhani N, Hersam MC, Bouchard D, Chowdhury I. Environmentally sustainable implementations of two-dimensional nanomaterials. Front Chem 2023; 11:1132233. [PMID: 36936535 PMCID: PMC10020365 DOI: 10.3389/fchem.2023.1132233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 02/14/2023] [Indexed: 03/06/2023] Open
Abstract
Rapid advancement in nanotechnology has led to the development of a myriad of useful nanomaterials that have novel characteristics resulting from their small size and engineered properties. In particular, two-dimensional (2D) materials have become a major focus in material science and chemistry research worldwide with substantial efforts centered on their synthesis, property characterization, and technological, and environmental applications. Environmental applications of these nanomaterials include but are not limited to adsorbents for wastewater and drinking water treatment, membranes for desalination, and coating materials for filtration. However, it is also important to address the environmental interactions and implications of these nanomaterials in order to develop strategies that minimize their environmental and public health risks. Towards this end, this review covers the most recent literature on the environmental implementations of emerging 2D nanomaterials, thereby providing insights into the future of this fast-evolving field including strategies for ensuring sustainable development of 2D nanomaterials.
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Affiliation(s)
- Mehnaz Shams
- Civil and Environmental Engineering, Washington State University, Pullman, WA, United States
| | - Nikhita Mansukhani
- Departments of Materials Science and Engineering, Chemistry and Medicine, Northwestern University, Evanston, IL, United States
| | - Mark C. Hersam
- Departments of Materials Science and Engineering, Chemistry and Medicine, Northwestern University, Evanston, IL, United States
| | - Dermont Bouchard
- National Exposure Research Laboratory, United States Environmental Protection Agency, Athens, GA, United States
| | - Indranil Chowdhury
- Civil and Environmental Engineering, Washington State University, Pullman, WA, United States
- *Correspondence: Indranil Chowdhury,
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Jensen MA, Blatz DJ, LaLone CA. Defining the Biologically Plausible Taxonomic Domain of Applicability of an Adverse Outcome Pathway: A Case Study Linking Nicotinic Acetylcholine Receptor Activation to Colony Death. Environ Toxicol Chem 2023; 42:71-87. [PMID: 36263952 PMCID: PMC10100214 DOI: 10.1002/etc.5501] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/30/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
For the majority of developed adverse outcome pathways (AOPs), the taxonomic domain of applicability (tDOA) is typically narrowly defined with a single or a handful of species. Defining the tDOA of an AOP is critical for use in regulatory decision-making, particularly when considering protection of untested species. Structural and functional conservation are two elements that can be considered when defining the tDOA. Publicly accessible bioinformatics approaches, such as the Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) tool, take advantage of existing and growing databases of protein sequence and structural information to provide lines of evidence toward structural conservation of key events (KEs) and KE relationships (KERs) of an AOP. It is anticipated that SeqAPASS results could readily be combined with data derived from empirical toxicity studies to provide evidence of both structural and functional conservation, to define the tDOA for KEs, KERs, and AOPs. Such data could be incorporated in the AOP-Wiki as lines of evidence toward biological plausibility for the tDOA. We present a case study describing the process of using bioinformatics to define the tDOA of an AOP using an AOP linking the activation of the nicotinic acetylcholine receptor to colony death/failure in Apis mellifera. Although the AOP was developed to gain a particular biological understanding relative to A. mellifera health, applicability to other Apis bees, as well as non-Apis bees, has yet to be defined. The present study demonstrates how bioinformatics can be utilized to rapidly take advantage of existing protein sequence and structural knowledge to enhance and inform the tDOA of KEs, KERs, and AOPs, focusing on providing evidence of structural conservation across species. Environ Toxicol Chem 2023;42:71-87. © 2022 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.
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Affiliation(s)
- Marissa A. Jensen
- Department of Biology, Swenson College of Science and EngineeringUniversity of Minnesota DuluthDuluthMinnesotaUSA
- US Environmental Protection Agency, Center for Computational Toxicology and ExposureGreat Lakes Toxicology and Ecology DivisionDuluthMinnesotaUSA
| | | | - Carlie A. LaLone
- US Environmental Protection Agency, Center for Computational Toxicology and ExposureGreat Lakes Toxicology and Ecology DivisionDuluthMinnesotaUSA
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Savoie AM, Moody A, Gilbert M, Dillon KS, Howden SD, Shiller AM, Hayes CT. Impact of local rivers on coastal acidification. Limnol Oceanogr 2022; 67:2779-2795. [PMID: 37501934 PMCID: PMC10369924 DOI: 10.1002/lno.12237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 03/01/2022] [Accepted: 08/28/2022] [Indexed: 07/29/2023]
Abstract
Coastal ecosystems are highly dynamic areas for carbon cycling and are likely to be negatively impacted by increasing ocean acidification. This research focused on dissolved inorganic carbon (DIC) and total alkalinity (TA) in the Mississippi Sound to understand the influence of local rivers on coastal acidification. This area receives large fluxes of freshwater from local rivers, in addition to episodic inputs from the Mississippi River through a human-built diversion, the Bonnet Carré Spillway. Sites in the Sound were sampled monthly from August 2018 to November 2019 and weekly from June to August 2019 in response to an extended spillway opening. Prior to the 2019 spillway opening, the contribution of the local, lower alkalinity rivers to the Sound may have left the study area more susceptible to coastal acidification during winter months, with aragonite saturation states (Ωar) < 2. After the spillway opened, despite a large increase in TA throughout the Sound, aragonite saturation states remained low, likely due to hypoxia and increased CO2 concentrations in subsurface waters. Increased Mississippi River input could represent a new normal in the Sound's hydrography during spring and summer months. The spillway has been utilized more frequently over the last two decades due to increasing precipitation in the Mississippi River watershed, which is primarily associated with climate change. Future increases in freshwater discharge and the associated declines in salinity, dissolved oxygen, and Ωar in the Sound will likely be detrimental to oyster stocks and the resilience of similar ecosystems to coastal acidification.
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Affiliation(s)
- Allison M. Savoie
- Department of OceanographyTexas A&M UniversityCollege StationTexas
- School of Ocean Science and EngineeringUniversity of Southern MississippiStennis Space CenterMississippi
| | - Amy Moody
- School of Ocean Science and EngineeringUniversity of Southern MississippiStennis Space CenterMississippi
| | - Melissa Gilbert
- School of Ocean Science and EngineeringUniversity of Southern MississippiStennis Space CenterMississippi
| | - Kevin S. Dillon
- School of Ocean Science and EngineeringUniversity of Southern MississippiOcean SpringsMississippi
| | - Stephan D. Howden
- School of Ocean Science and EngineeringUniversity of Southern MississippiStennis Space CenterMississippi
| | - Alan M. Shiller
- School of Ocean Science and EngineeringUniversity of Southern MississippiStennis Space CenterMississippi
| | - Christopher T. Hayes
- School of Ocean Science and EngineeringUniversity of Southern MississippiStennis Space CenterMississippi
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10
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Holder AL, Halliday HS, Virtaranta L. Impact of do-it-yourself air cleaner design on the reduction of simulated wildfire smoke in a controlled chamber environment. Indoor Air 2022; 32:e13163. [PMID: 36437679 PMCID: PMC9828579 DOI: 10.1111/ina.13163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/21/2022] [Accepted: 10/22/2022] [Indexed: 06/16/2023]
Abstract
During wildfire smoke events public health agencies release advisories to stay indoors, close doors and windows, and operate a portable air cleaner (PAC). The do-it-yourself (DIY) air cleaner consisting of a box fan and a furnace filter is a widely used low-cost alternative to commercial PACs because of its increased accessibility. In this study, we evaluate the clean air delivery rate (CADR) of different DIY air cleaner designs for reducing simulated wildfire smoke and identify operating parameters that may impact their performance and use. The simplest formulation of a DIY air cleaner (box fan with taped on minimum effectiveness reporting value - [MERV] 13 furnace filter) had a CADR of 111.2 ± 1.3 ft3 /min (CFM). Increasing the fan flow by changing the fan type, increasing the fan setting, or reducing the pressure drop across the filtering surface increased the CADR. Large increases in CADR could be obtained by using a shroud (40%), using a 4″ thick filter (123%) using two filters in a wedge shape (137%), or using four filters in a Corsi-Rosenthal (CR) box design (261%). The CADR was greatly reduced with filters heavily loaded with smoke, pointing to the need for frequent filter changes during smoke events.
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Affiliation(s)
- Amara L. Holder
- Office of Research and DevelopmentU.S. Environmental Protection AgencyResearch Triangle ParkNorth CarolinaUSA
| | - Hannah S. Halliday
- Office of Research and DevelopmentU.S. Environmental Protection AgencyResearch Triangle ParkNorth CarolinaUSA
| | - Larry Virtaranta
- Jacobs Technology InternationalResearch Triangle ParkNorth CarolinaUSA
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11
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Lemagie EP, Giddings SN, MacCready P, Seaton C, Wu X. Measuring Estuarine Total Exchange Flow From Discrete Observations. J Geophys Res Oceans 2022; 127:e2022JC018960. [PMID: 36582261 PMCID: PMC9787582 DOI: 10.1029/2022jc018960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 09/13/2022] [Accepted: 10/04/2022] [Indexed: 06/17/2023]
Abstract
The exchange between estuaries and the coastal ocean is a key dynamical driver impacting nutrient and phytoplankton concentrations and regulating estuarine residence time, hypoxia, and acidification. Estuarine exchange flows can be particularly challenging to monitor because many systems have strong vertical and lateral velocity shear and sharp gradients in water properties that vary over space and time, requiring high-resolution measurements in order to accurately constrain the flux. The total exchange flow (TEF) method provides detailed information about the salinity structure of the exchange, but requires observations (or model resolution) that resolve the time and spatial co-variability of salinity and currents. The goal of this analysis is to provide recommendations for measuring TEF with the most efficient spatial sampling resolution. Results from three realistic hydrodynamic models were investigated. These model domains included three estuary types: a bay (San Diego Bay), a salt-wedge (Columbia River), and a fjord (Salish Sea). Model fields were sampled using three different mooring strategies, varying the number of mooring locations (lateral resolution) and sample depths (vertical resolution) with each method. The exchange volume transport was more sensitive than salinity to the sampling resolution. Most (>90%) of the exchange flow magnitude was captured by three to four moorings evenly distributed across the estuarine channel with a minimum threshold of 1-5 sample depths, which varied depending on the vertical stratification. These results can improve our ability to observe and monitor the exchange and transport of water masses efficiently with limited resources.
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Affiliation(s)
- E. P. Lemagie
- Pacific Marine Environmental LaboratoryNOAASeattleWAUSA
| | | | | | - C. Seaton
- Columbia River Inter‐Tribal Fish CommissionPortlandORUSA
| | - X. Wu
- Shanghai Jiao Tong UniversityShanghaiChina
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12
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Pierro JD, Ahir BK, Baker NC, Kleinstreuer NC, Xia M, Knudsen TB. Computational model for fetal skeletal defects potentially linked to disruption of retinoic acid signaling. Front Pharmacol 2022; 13:971296. [PMID: 36172177 PMCID: PMC9511990 DOI: 10.3389/fphar.2022.971296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 07/21/2022] [Indexed: 11/13/2022] Open
Abstract
All-trans retinoic acid (ATRA) gradients determine skeletal patterning morphogenesis and can be disrupted by diverse genetic or environmental factors during pregnancy, leading to fetal skeleton defects. Adverse Outcome Pathway (AOP) frameworks for ATRA metabolism, signaling, and homeostasis allow for the development of new approach methods (NAMs) for predictive toxicology with less reliance on animal testing. Here, a data-driven model was constructed to identify chemicals associated with both ATRA pathway bioactivity and prenatal skeletal defects. The phenotype data was culled from ToxRefDB prenatal developmental toxicity studies and produced a list of 363 ToxRefDB chemicals with altered skeletal observations. Defects were classified regionally as cranial, post-cranial axial, appendicular, and other (unspecified) features based on ToxRefDB descriptors. To build a multivariate statistical model, high-throughput screening bioactivity data from >8,070 chemicals in ToxCast/Tox21 across 10 in vitro assays relevant to the retinoid signaling system were evaluated and compared to literature-based candidate reference chemicals in the dataset. There were 48 chemicals identified for effects on both in vivo skeletal defects and in vitro ATRA pathway targets for computational modeling. The list included 28 chemicals with prior evidence of skeletal defects linked to retinoid toxicity and 20 chemicals without prior evidence. The combination of thoracic cage defects and DR5 (direct repeats of 5 nucleotides for RAR/RXR transactivation) disruption was the most frequently occurring phenotypic and target disturbance, respectively. This data model provides valuable AOP elucidation and validates current mechanistic understanding. These findings also shed light on potential avenues for new mechanistic discoveries related to ATRA pathway disruption and associated skeletal dysmorphogenesis due to environmental exposures.
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Affiliation(s)
- Jocylin D. Pierro
- Center for Computational Toxicology and Exposure (CCTE), Computational Toxicology and Bioinformatics Branch (CTBB), Office of Research and Development (ORD), U.S. Environmental Protection Agency (USEPA), Research Triangle Park, NC, United States
| | - Bhavesh K. Ahir
- Eurofins Medical Device Testing, Lancaster, PA, United States
| | - Nancy C. Baker
- Scientific Computing and Data Curation Division (SCDCD), Leidos Contractor, Center for Computational Toxicology and Exposure (CCTE), USEPA/ORD, Research Triangle Park, NC, United States
| | - Nicole C. Kleinstreuer
- Interagency Center for the Evaluation of Alternative Toxicological Methods (NICEATM), National Toxicology Program, National Institutes of Health, Research Triangle Park, NC, United States
| | - Menghang Xia
- Division for Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, United States
| | - Thomas B. Knudsen
- Center for Computational Toxicology and Exposure (CCTE), Computational Toxicology and Bioinformatics Branch (CTBB), Office of Research and Development (ORD), U.S. Environmental Protection Agency (USEPA), Research Triangle Park, NC, United States
- *Correspondence: Thomas B. Knudsen, , orcid.org/0000-0002-5036-596x
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13
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Jankowski MD, Fairbairn DJ, Baller JA, Westerhoff BM, Schoenfuss HL. Using the Daphnia magna Transcriptome to Distinguish Water Source: Wetland and Stormwater Case Studies. Environ Toxicol Chem 2022; 41:2107-2123. [PMID: 35622010 PMCID: PMC9545677 DOI: 10.1002/etc.5392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 02/15/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
A major challenge in ecotoxicology is accurately and sufficiently measuring chemical exposures and biological effects given the presence of complex and dynamic contaminant mixtures in surface waters. It is impractical to quantify all chemicals in such matrices over space and time, and even if it were practical, concomitant biological effects would not be elucidated. Our study examined the performance of the Daphnia magna transcriptome to detect distinct responses across three water sources in Minnesota: laboratory (well) waters, wetland waters, and storm waters. Pyriproxyfen was included as a gene expression and male neonate production positive control to examine whether gene expression resulting from exposure to this well-studied juvenoid hormone analog can be detected in complex matrices. Laboratory-reared (<24 h) D. magna were exposed to a water source and/or pyriproxyfen for 16 days to monitor phenotypic changes or 96 h to examine gene expression responses using Illumina HiSeq 2500 (10 million reads per library, 50-bp paired end [2 × 50]). The results indicated that a unique gene expression profile was produced for each water source. At 119 ng/L pyriproxyfen (~25% effect concentration) for male neonate production, as expected, the Doublesex1 gene was up-regulated. In descending order, gene expression patterns were most discernable with respect to pyriproxyfen exposure status, season of stormwater sample collection, and wetland quality, as indicated by the index of biological integrity. However, the biological implications of the affected genes were not broadly clear given limited genome resources for invertebrates. Our study provides support for the utility of short-term whole-organism transcriptomic testing in D. magna to discern sample type, but highlights the need for further work on invertebrate genomics. Environ Toxicol Chem 2022;41:2107-2123. © 2022 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.
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Affiliation(s)
- Mark D. Jankowski
- Minnesota Pollution Control AgencySt. PaulMinnesotaUSA
- Veterinary Population Medicine DepartmentUniversity of Minnesota—Twin CitiesSt. PaulMinnesotaUSA
- US Environmental Protection AgencySeattleWashingtonUSA
| | | | - Joshua A. Baller
- Minnesota Supercomputing InstituteUniversity of Minnesota—Twin CitiesMinneapolisMinnesotaUSA
| | | | - Heiko L. Schoenfuss
- Aquatic Toxicology LaboratorySt. Cloud State UniversitySt. CloudMinnesotaUSA
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14
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Abstract
Three dimensional, self-assembled organoids that recapitulate key developmental and organizational events during embryogenesis have proven transformative for the study of human central nervous system (CNS) development, evolution, and disease pathology. Brain organoids have predominated the field, but human pluripotent stem cell (hPSC)-derived models of the spinal cord are on the rise. This has required piecing together the complex interactions between rostrocaudal patterning, which specifies axial diversity, and dorsoventral patterning, which establishes locomotor and somatosensory phenotypes. Here, we review how recent insights into neurodevelopmental biology have driven advancements in spinal organoid research, generating experimental models that have the potential to deepen our understanding of neural circuit development, central pattern generation (CPG), and neurodegenerative disease along the body axis. In addition, we discuss the application of bioengineering strategies to drive spinal tissue morphogenesis in vitro, current limitations, and future perspectives on these emerging model systems.
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Affiliation(s)
- Nisha R. Iyer
- Department of Biomedical Engineering, Tufts University, Medford, MA, United States
- Wisconsin Institute for Discovery, University of Wisconsin—Madison, Madison, WI, United States
- Department of Biomedical Engineering, University of Wisconsin—Madison, Madison, WI, United States
| | - Randolph S. Ashton
- Wisconsin Institute for Discovery, University of Wisconsin—Madison, Madison, WI, United States
- Department of Biomedical Engineering, University of Wisconsin—Madison, Madison, WI, United States
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15
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Taslakyan L, Baker MC, Shrestha DS, Strawn DG, Möller G. CO 2 e footprint and eco-impact of ultralow phosphorus removal by hydrous ferric oxide reactive filtration: A municipal wastewater LCA case study. Water Environ Res 2022; 94:e10777. [PMID: 36004674 PMCID: PMC9540262 DOI: 10.1002/wer.10777] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/07/2022] [Accepted: 08/08/2022] [Indexed: 06/15/2023]
Abstract
Dual upflow reactive filtration by a slowly moving sand bed with continuously renewed, hydrous ferric oxide-coated sand is used for removing polluting substances and for meeting the ultralow 0.05 mg/l total phosphorus discharge permit limits at a 1.2 million liters per day (0.32 million gallons per day) water resource recovery facility in Plummer, Idaho, in the United States. A life cycle assessment (LCA) of this reactive filtration installation was carried out to assess the environmental hotspots in the system and analyze alternative system configurations with a focus on CO2 equivalent (CO2 e) global warming potential, freshwater and marine eutrophication, and mineral resource scarcity. "What if" scenarios with alternative inputs for the energy, metal salts, and air compressor optimization show trade-offs between the impact categories. Key results that show a comparative reduction of global warming potential include the use of Fe versus Al metal salts, the use of renewable energy, and the energy efficiency benefit of optimizing process inputs, such as compressor air pressure, to match operational demand. The LCA shows a 2 × 10-2 kg CO2 e footprint per cubic meter of water, with 47% from housing concrete, and an overall freshwater eutrophication impact reduced by 99% versus no treatment. The use of renewable hydropower energy at this site isolates construction concrete as a target for lowering the CO2 e footprint. PRACTITIONER POINTS: The main LCA eco-impact hotspots in this dual reactive filtration tertiary treatment are construction concrete and the ferric sulfate used. Iron salts show smaller impact in global warming, freshwater eutrophication, and mineral resource scarcity than "what if scenario" aluminum salts. The energy mix for this site is predominantly hydropower; other energy mix "what if" scenarios show larger impacts. Operational energy efficiency and thermodynamic analysis show that fine tuning the air compressor helps reduce carbon footprint and energy use. LCA shows a favorable 2 x 10-2 kg CO2e/m3 water impact with 99% reduction of freshwater eutrophication potential versus no treatment.
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Affiliation(s)
- Lusine Taslakyan
- Department of Soil and Water SystemsUniversity of IdahoMoscowIdahoUSA
- Water Resources ProgramUniversity of IdahoMoscowIdahoUSA
| | - Martin C. Baker
- Department of Soil and Water SystemsUniversity of IdahoMoscowIdahoUSA
| | - Dev S. Shrestha
- Department of Chemical and Biological EngineeringUniversity of IdahoMoscowIdahoUSA
| | - Daniel G. Strawn
- Department of Soil and Water SystemsUniversity of IdahoMoscowIdahoUSA
- Water Resources ProgramUniversity of IdahoMoscowIdahoUSA
| | - Gregory Möller
- Department of Soil and Water SystemsUniversity of IdahoMoscowIdahoUSA
- Department of Chemical and Biological EngineeringUniversity of IdahoMoscowIdahoUSA
- Water Resources ProgramUniversity of IdahoMoscowIdahoUSA
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16
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McAliley WA, Day‐Lewis FD, Rey D, Briggs MA, Shapiro AM, Werkema D. Application of Recursive Estimation to Heat Tracing for Groundwater/Surface-Water Exchange. Water Resour Res 2022; 58:1-18. [PMID: 35813986 PMCID: PMC9257602 DOI: 10.1029/2021wr030443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 05/13/2022] [Accepted: 05/21/2022] [Indexed: 06/15/2023]
Abstract
We present and demonstrate a recursive-estimation framework to infer groundwater/surface-water exchange based on temperature time series collected at different vertical depths below the sediment/water interface. We formulate the heat-transport problem as a state-space model (SSM), in which the spatial derivatives in the convection/conduction equation are approximated using finite differences. The SSM is calibrated to estimate time-varying specific discharge using the Extended Kalman Filter (EKF) and Extended Rauch-Tung-Striebel Smoother (ERTSS). Whereas the EKF is suited to real-time ("online") applications and uses only the past and current measurements for estimation (filtering), the ERTSS is intended for near-real time or batch-processing ("offline") applications and uses a window of data for batch estimation (smoothing). The two algorithms are demonstrated with synthetic and field-experimental data and are shown to be efficient and rapid for the estimation of time-varying flux over seasonal periods; further, the recursive approaches are effective in the presence of rapidly changing flux and (or) nonperiodic thermal boundary conditions, both of which are problematic for existing approaches to heat tracing of time-varying groundwater/surface-water exchange.
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Affiliation(s)
- W. Anderson McAliley
- Student Contractor to the U.S. Geological SurveyGoldenCOUSA
- Now at U.S. Geological SurveyWater Mission AreaGoldenCOUSA
| | - Frederick D. Day‐Lewis
- Pacific Northwest National LaboratoryEarth Systems Science DivisionEnvironmental Subsurface Science GroupRichlandWAUSA
| | - David Rey
- U.S. Geological SurveyWater Mission AreaDenver Federal CenterDenverCOUSA
| | | | | | - Dale Werkema
- Environmental Protection AgencyOffice of Research and DevelopmentCenter for Public Health and Environmental AssessmentPacific Ecological Systems DivisionPacific Coast Ecology BranchNewportORUSA
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17
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Schwantes RH, Lacey FG, Tilmes S, Emmons LK, Lauritzen PH, Walters S, Callaghan P, Zarzycki CM, Barth MC, Jo DS, Bacmeister JT, Neale RB, Vitt F, Kluzek E, Roozitalab B, Hall SR, Ullmann K, Warneke C, Peischl J, Pollack IB, Flocke F, Wolfe GM, Hanisco TF, Keutsch FN, Kaiser J, Bui TPV, Jimenez JL, Campuzano‐Jost P, Apel EC, Hornbrook RS, Hills AJ, Yuan B, Wisthaler A. Evaluating the Impact of Chemical Complexity and Horizontal Resolution on Tropospheric Ozone Over the Conterminous US With a Global Variable Resolution Chemistry Model. J Adv Model Earth Syst 2022; 14:e2021MS002889. [PMID: 35864945 PMCID: PMC9286600 DOI: 10.1029/2021ms002889] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 02/24/2022] [Accepted: 04/24/2022] [Indexed: 05/19/2023]
Abstract
A new configuration of the Community Earth System Model (CESM)/Community Atmosphere Model with full chemistry (CAM-chem) supporting the capability of horizontal mesh refinement through the use of the spectral element (SE) dynamical core is developed and called CESM/CAM-chem-SE. Horizontal mesh refinement in CESM/CAM-chem-SE is unique and novel in that pollutants such as ozone are accurately represented at human exposure relevant scales while also directly including global feedbacks. CESM/CAM-chem-SE with mesh refinement down to ∼14 km over the conterminous US (CONUS) is the beginning of the Multi-Scale Infrastructure for Chemistry and Aerosols (MUSICAv0). Here, MUSICAv0 is evaluated and used to better understand how horizontal resolution and chemical complexity impact ozone and ozone precursors over CONUS as compared to measurements from five aircraft campaigns, which occurred in 2013. This field campaign analysis demonstrates the importance of using finer horizontal resolution to accurately simulate ozone precursors such as nitrogen oxides and carbon monoxide. In general, the impact of using more complex chemistry on ozone and other oxidation products is more pronounced when using finer horizontal resolution where a larger number of chemical regimes are resolved. Large model biases for ozone near the surface remain in the Southeast US as compared to the aircraft observations even with updated chemistry and finer horizontal resolution. This suggests a need for adding the capability of replacing sections of global emission inventories with regional inventories, increasing the vertical resolution in the planetary boundary layer, and reducing model biases in meteorological variables such as temperature and clouds.
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18
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Belova A, Gould CA, Munson K, Howell M, Trevisan C, Obradovich N, Martinich J. Projecting the Suicide Burden of Climate Change in the United States. Geohealth 2022; 6:e2021GH000580. [PMID: 35582318 PMCID: PMC9089437 DOI: 10.1029/2021gh000580] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 04/01/2022] [Accepted: 04/06/2022] [Indexed: 06/15/2023]
Abstract
We quantify and monetize changes in suicide incidence across the conterminous United States (U.S.) in response to increasing levels of warming. We develop an integrated health impact assessment model using binned and linear specifications of temperature-suicide relationship estimates from Mullins and White (2019), in combination with monthly age- and sex-specific baseline suicide incidence rates, projections of six climate models, and population projections at the conterminous U.S. county scale. We evaluate the difference in the annual number of suicides in the U.S. corresponding to 1-6°C of warming compared to 1986-2005 average temperatures (mean U.S. temperatures) and compute 2015 population attributable fractions (PAFs). We use the U.S. Environmental Protection Agency's Value of a Statistical Life to estimate the economic value of avoiding these mortality impacts. Assuming the 2015 population size, warming of 1-6°C could result in an annual increase of 283-1,660 additional suicide cases, corresponding to a PAF of 0.7%-4.1%. The annual economic value of avoiding these impacts is $2 billion-$3 billion (2015 U.S. dollars, 3% discount rate, and 2015 income level). Estimates based on linear temperature-suicide relationship specifications are 7% larger than those based on binned temperature specifications. Accounting for displacement decreases estimates by 17%, while accounting for precipitation decreases estimates by 7%. Population growth between 2015 and the future warming degree arrival year increases estimates by 15%-38%. Further research is needed to quantify and monetize other climate-related mental health outcomes (e.g., anxiety and depression) and to characterize these risks in socially vulnerable populations.
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Affiliation(s)
| | - Caitlin A. Gould
- Climate Change DivisionU.S. Environmental Protection AgencyWashingtonDCUSA
| | | | | | | | - Nick Obradovich
- Center for Humans and MachinesMax Planck Institute for Human DevelopmentBerlinGermany
| | - Jeremy Martinich
- Climate Change DivisionU.S. Environmental Protection AgencyWashingtonDCUSA
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19
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Petroff RL, Padmanabhan V, Dolinoy DC, Watkins DJ, Ciarelli J, Haggerty D, Ruden DM, Goodrich JM. Prenatal Exposures to Common Phthalates and Prevalent Phthalate Alternatives and Infant DNA Methylation at Birth. Front Genet 2022; 13:793278. [PMID: 35432478 PMCID: PMC9010032 DOI: 10.3389/fgene.2022.793278] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 01/31/2022] [Indexed: 12/23/2022] Open
Abstract
Phthalates are a diverse group of chemicals used in consumer products. Because they are so widespread, exposure to these compounds is nearly unavoidable. Recently, growing scientific consensus has suggested that phthalates produce health effects in developing infants and children. These effects may be mediated through mechanisms related to the epigenome, the constellation of mitotically heritable chemical marks and small compounds that guide transcription and translation. The present study examined the relationship between prenatal, first-trimester exposure of seven phthalates and epigenetics in two pregnancy cohorts (n = 262) to investigate sex-specific alterations in infant blood DNA methylation at birth (cord blood or neonatal blood spots). Prenatal exposure to several phthalates was suggestive of association with altered DNA methylation at 4 loci in males (all related to ΣDEHP) and 4 loci in females (1 related to ΣDiNP; 2 related to BBzP; and 1 related to MCPP) at a cutoff of q < 0.2. Additionally, a subset of dyads (n = 79) was used to interrogate the relationships between two compounds increasingly used as substitutions for common phthalates (ΣDINCH and ΣDEHTP) and cord blood DNA methylation. ΣDINCH, but not ΣDEHTP, was suggestive of association with DNA methylation (q < 0.2). Together, these results demonstrate that prenatal exposure to both classically used phthalate metabolites and their newer alternatives is associated with sex-specific infant DNA methylation. Research and regulatory actions regarding this chemical class should consider the developmental health effects of these compounds and aim to avoid regrettable substitution scenarios in the present and future.
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Affiliation(s)
- Rebekah L. Petroff
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, United States
| | - Vasantha Padmanabhan
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, United States
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, United States
- Department of Nutritional Sciences, University of Michigan, Ann Arbor, MI, United States
| | - Dana C. Dolinoy
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, United States
- Department of Nutritional Sciences, University of Michigan, Ann Arbor, MI, United States
| | - Deborah J. Watkins
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, United States
| | - Joseph Ciarelli
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, United States
| | - Diana Haggerty
- Scholarly Activities and Scientific Support, Spectrum Health West Michigan, Grand Rapids, MI, United States
| | - Douglas M. Ruden
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, United States
| | - Jaclyn M. Goodrich
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, United States
- *Correspondence: Jaclyn M. Goodrich,
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20
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Montagnino E, Lytle DA, Rose J, Cwiertny D, Whelton AJ. School and childcare center drinking water: Copper chemistry, health effects, occurrence, and remediation. AWWA Water Sci 2022; 4:e1270. [PMID: 35865674 PMCID: PMC9286453 DOI: 10.1002/aws2.1270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 01/12/2022] [Accepted: 01/18/2022] [Indexed: 06/15/2023]
Abstract
The study goal was to better understand the risks of elevated copper levels at US schools and childcare centers. Copper health effects, chemistry, occurrence, and remediation actions were reviewed. Of the more than 98,000 schools and 500,000 childcare centers, only 0.2% had copper water testing data in the federal Safe Drinking Water Information System database. Of the facilities designated public water systems, about 13% had reported an exceedance. Schools that were not designated a public water system (PWS) also had exceedances. Few studies document levels in schools and childcare centers. Widely different sampling and remedial actions were reported. Flushing contaminated water was the most evaluated remedial action but was unreliable because copper quickly rebounded when flushing stopped. Building water treatment systems have been used, but some were not capable of making the water safe. The health risk was difficult to determine due to the limited occurrence data and lack of best management practice studies. A national drinking water testing campaign and field studies are recommended.
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Affiliation(s)
| | | | - Joan Rose
- Michigan State UniversityEast LansingMichiganUSA
| | - David Cwiertny
- Department of Civil and Environmental EngineeringUniversity of IowaIowa CityIowaUSA
- Center for Health Effects of Environmental ContaminationUniversity of IowaIowa CityIowaUSA
- Public Policy CenterUniversity of IowaIowa CityIowaUSA
| | - Andrew J. Whelton
- Lyles School of Civil Engineering and Division of Environmental and Ecological EngineeringPurdue UniversityWest LafayetteIndianaUSA
- Center for Plumbing SafetyPurdue UniversityWest LafayetteIndianaUSA
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21
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DeMarini DM, Linak WP. Mutagenicity and carcinogenicity of combustion emissions are impacted more by combustor technology than by fuel composition: A brief review. Environ Mol Mutagen 2022; 63:135-150. [PMID: 35253926 PMCID: PMC9311424 DOI: 10.1002/em.22475] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/27/2022] [Accepted: 03/03/2022] [Indexed: 05/17/2023]
Abstract
Studies during the past 50 years have characterized the carcinogenicity and mutagenicity of extractable organic material (EOM) of particulate matter (PM) in ambient air and from combustion emissions. We have summarized conclusions from these studies and present data supporting those conclusions for 50 combustion emissions, including carcinogenic potencies on mouse skin (papillomas/mouse/mg EOM), mutagenic potencies (revertants/μg EOM) in the Salmonella (Ames) mutagenicity assay, and mutagenicity emission factors (revertants/kg fuel or revertants/MJthermal ) in Salmonella. Mutagenic potencies of EOM from PM in ambient air and combustion emissions span 1-2 orders of magnitude, respectively. In contrast, the revertants/m3 span >5 orders of magnitude due to variable PM concentrations in ambient air. Carcinogenic potencies of EOM from combustion emissions on mouse skin and EOM-associated human lung cancer risk from those emissions both span ~3 orders of magnitude and are highly associated. The ubiquitous presence of polycyclic aromatic hydrocarbons (PAHs), nitroarenes, and aromatic amines results in mutagenic and carcinogenic potencies of PM that span only 1-3 orders of magnitude; most PM induces primarily G to T mutations. Mutagenicity emission factors of combustion emissions span 3-5 orders of magnitude and correlate with PAH emission factors (r > 0.9). Mutagenicity emission factors were largely a function of how material was burned (highly efficient modern combustors versus open burning) rather than what materials were burned. Combustion systems that minimize kinetic and mass-transfer limitations and promote complete oxidation also minimize the mutagenicity of their emissions. This fundamental engineering principle can inform environmental and public health assessments of combustion emissions.
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Affiliation(s)
- David M. DeMarini
- Air Methods and Characterization Division, Center for Environmental Measurement and ModelingU.S. Environmental Protection AgencyResearch Triangle ParkNorth CarolinaUSA
| | - William P. Linak
- Air Methods and Characterization Division, Center for Environmental Measurement and ModelingU.S. Environmental Protection AgencyResearch Triangle ParkNorth CarolinaUSA
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22
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Mortensen HM, Martens M, Senn J, Levey T, Evelo CT, Willighagen EL, Exner T. The AOP-DB RDF: Applying FAIR Principles to the Semantic Integration of AOP Data Using the Research Description Framework. Front Toxicol 2022; 4:803983. [PMID: 35295213 PMCID: PMC8915825 DOI: 10.3389/ftox.2022.803983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 01/13/2022] [Indexed: 01/12/2023] Open
Abstract
Computational toxicology is central to the current transformation occurring in toxicology and chemical risk assessment. There is a need for more efficient use of existing data to characterize human toxicological response data for environmental chemicals in the US and Europe. The Adverse Outcome Pathway (AOP) framework helps to organize existing mechanistic information and contributes to what is currently being described as New Approach Methodologies (NAMs). AOP knowledge and data are currently submitted directly by users and stored in the AOP-Wiki (https://aopwiki.org/). Automatic and systematic parsing of AOP-Wiki data is challenging, so we have created the EPA Adverse Outcome Pathway Database. The AOP-DB, developed by the US EPA to assist in the biological and mechanistic characterization of AOP data, provides a broad, systems-level overview of the biological context of AOPs. Here we describe the recent semantic mapping efforts for the AOP-DB, and how this process facilitates the integration of AOP-DB data with other toxicologically relevant datasets through a use case example.
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Affiliation(s)
- Holly M. Mortensen
- United States Environmental Protection Agency, Office of Research and Development, Center for Public Health and Environmental Assessment, Research Triangle Park, Durham, NC, United States
- *Correspondence: Holly M. Mortensen,
| | - Marvin Martens
- Department of Bioinformatics (BiGCaT), Maastricht University, Maastricht, Netherlands
| | - Jonathan Senn
- Oak Ridge Associated Universities, Oak Ridge, TN, United States
| | - Trevor Levey
- Oak Ridge Associated Universities, Oak Ridge, TN, United States
- SAS Institute, Cary, NC, United States
| | - Chris T. Evelo
- Department of Bioinformatics (BiGCaT), Maastricht University, Maastricht, Netherlands
- Maastricht Centre for Systems Biology, Maastricht University, Maastricht, Netherlands
| | - Egon L. Willighagen
- Department of Bioinformatics (BiGCaT), Maastricht University, Maastricht, Netherlands
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Abstract
Human brain is undoubtedly the most complex organ in the body. Thus, it is difficult to develop adequate and at the same time human relevant test systems and models to cover the aspects of brain homeostasis and even more challenging to address brain development. Animal tests for Developmental Neurotoxicity (DNT) have been devised, but because of complex underlying mechanisms of neural development, and interspecies differences, there are many limitations of animal-based approaches. The high costs, high number of animals used per test and technical difficulties of these tests are prohibitive for routine DNT chemical screening. Therefore, many potential DNT chemicals remain unidentified. New approach methodologies (NAMs) are needed to change this. Experts in the field have recommended the use of a battery of human in vitro tests to be used for the initial prioritization of high-risk environmental chemicals for DNT testing. Microphysiological systems (MPS) of the brain mimic the in vivo counterpart in terms of cellular composition, recapitulation of regional architecture and functionality. These systems amendable to use in a DNT test battery with promising features such as (i) complexity, (ii) closer recapitulation of in vivo response and (iii) possibility to multiplex many assays in one test system, which can increase throughput and predictivity for human health. The resent progress in 3D brain MPS research, advantages, limitations and future perspectives are discussed in this review.
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LaLone CA, Basu N, Browne P, Edwards SW, Embry M, Sewell F, Hodges G. International Consortium to Advance Cross-Species Extrapolation of the Effects of Chemicals in Regulatory Toxicology. Environ Toxicol Chem 2021; 40:3226-3233. [PMID: 34551147 PMCID: PMC9161440 DOI: 10.1002/etc.5214] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 08/30/2021] [Accepted: 09/14/2021] [Indexed: 05/04/2023]
Affiliation(s)
- Carlie A. LaLone
- Great Lakes Toxicology and Ecology Division, Center for Computational Toxicology and Exposure, Office of Research and DevelopmentUS Environmental Protection AgencyDuluthMinnesotaUSA
| | - Niladri Basu
- Faculty of Agricultural and Environmental SciencesMcGill UniversityMontrealQuebecCanada
| | - Patience Browne
- Environment DirectorateOrganisation for Economic Co‐operation and DevelopmentParisFrance
| | - Stephen W. Edwards
- GenOmics, Bioinformatics, and Translational Research CenterRTI InternationalResearch Triangle ParkNorth CarolinaUSA
| | - Michelle Embry
- Health and Environmental Sciences InstituteWashingtonDistrict of ColumbiaUSA
| | - Fiona Sewell
- National Centre for the Replacement, Refinement, and Reduction of Animals in ResearchLondonUK
| | - Geoff Hodges
- Safety and Environmental Assurance Centre, Unilever, Sharnbrook, BedfordshireUK
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Murray A, Hall A, Weaver J, Kremer F. Methods for Estimating Locations of Housing Units Served by Private Domestic Wells in the United States Applied to 2010. J Am Water Resour Assoc 2021; 57:1-16. [PMID: 34987281 PMCID: PMC8722366 DOI: 10.1111/1752-1688.12937] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
UNLABELLED In 1990, the last time the decennial census included a question on domestic drinking water source, it was estimated that private domestic water wells (PDWs) supplied household water to about 15.1 million housing units (15% of the population) in the United States (U.S.). PDWs are not regulated by the Safe Drinking Water Act, and with few exceptions, are not subject to the water quality testing required of public water suppliers. We expanded two methods in estimating housing units reliant on PDWs from an Oklahoma pilot study (Weaver et al. 2017), nationally. Both use 1990 census data on drinking water sources as a baseline. The first method uses housing unit change and private well drilling logs for 20 states. This allows for the rate of well use to change between 1990 and 2010 in these states. The second, based solely on housing unit change, assumes a constant rate of well use. Ordinary least squares regression demonstrated (R 2 = 0.78) that the methods yield similar estimates for nationwide well use. Using the housing unit change method, it is estimated that in 2010, 23 million housing units were reliant on PDWs (17% of the population). We provide these estimates at the census block group and census block resolution. This dataset will assist in a better understanding of the reliance on PDWs in the U.S., and position local, tribal, state, and national groups to better protect this water resource from contaminant sources. RESEARCH IMPACT STATEMENT The work provides improved estimates of the spatial distribution of housing units reliant on private domestic wells in the United States and a foundation to protect this water supply at all levels of government.
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Affiliation(s)
| | - Alexander Hall
- Office of Research and DevelopmentUnited States Environmental Protection AgencyCincinnatiOhioUSA
| | - James Weaver
- Office of Research and DevelopmentUnited States Environmental Protection AgencyCincinnatiOhioUSA
| | - Fran Kremer
- Office of Research and DevelopmentUnited States Environmental Protection AgencyCincinnatiOhioUSA
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26
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Mebane CA, Ivey CD, Wang N, Steevens JA, Cleveland D, Elias MC, Justice JR, Gallagher K, Brent RN. Direct and Delayed Mortality of Ceriodaphnia dubia and Rainbow Trout Following Time-Varying Acute Exposures to Zinc. Environ Toxicol Chem 2021; 40:2484-2498. [PMID: 34288068 PMCID: PMC8457064 DOI: 10.1002/etc.5131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/27/2021] [Accepted: 05/26/2021] [Indexed: 06/13/2023]
Abstract
The potential for delayed mortality following short-term episodic pollution events was evaluated by exposing cladocerans (Ceriodaphnia dubia) and rainbow trout (Oncorhynchus mykiss) to zinc (Zn) in various 1- to 48-h and 1- to 96-h exposures, respectively, followed by transferring the exposed organisms to clean water for up to 47 h for C. dubia and up to 95 h for trout for additional observation. For C. dubia, 1-h exposures of up to 3790 µg Zn/L never resulted in mortality during the actual Zn exposures, but by 48 h, a 1-h exposure to 114 µg/L, a concentration similar to the present US national water quality acute criterion for the test water conditions, ultimately killed 70% of C. dubia. With C. dubia, the speed of action of Zn toxicity was faster for intermediate concentrations than for the highest concentrations tested. For rainbow trout, pronounced delayed mortalities by 96 h only occurred following ≥8-h exposures. For both species, ultimate mortalities from Zn exposures ≤8 h mostly presented as delayed mortalities, whereas for exposures ≥24 h, almost all ultimate mortalities presented during the actual exposure periods. With Zn, risks of delayed mortality following exposures to all concentrations tested were much greater for the more sensitive, small-bodied invertebrate (C. dubia) than for the less sensitive, larger-bodied fish (rainbow trout). These results, along with previous studies, show that delayed mortality is an important consideration in evaluating risks to aquatic organisms from brief, episodic exposures to some substances. Environ Toxicol Chem 2021;40:2484-2498. © 2021 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC. This article has been contributed to by US Government employees and their work is in the public domain in the USA.
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Affiliation(s)
| | | | - Ning Wang
- Columbia Environmental Research CenterUS Geological SurveyColumbiaMissouri
| | | | - Danielle Cleveland
- Columbia Environmental Research CenterUS Geological SurveyColumbiaMissouri
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Scavia D, Bertani I, Testa JM, Bever AJ, Blomquist JD, Friedrichs MAM, Linker LC, Michael BD, Murphy RR, Shenk GW. Advancing estuarine ecological forecasts: seasonal hypoxia in Chesapeake Bay. Ecol Appl 2021; 31:e02384. [PMID: 34128283 PMCID: PMC8459276 DOI: 10.1002/eap.2384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 04/28/2021] [Accepted: 05/26/2021] [Indexed: 06/12/2023]
Abstract
Ecological forecasts are quantitative tools that can guide ecosystem management. The coemergence of extensive environmental monitoring and quantitative frameworks allows for widespread development and continued improvement of ecological forecasting systems. We use a relatively simple estuarine hypoxia model to demonstrate advances in addressing some of the most critical challenges and opportunities of contemporary ecological forecasting, including predictive accuracy, uncertainty characterization, and management relevance. We explore the impacts of different combinations of forecast metrics, drivers, and driver time windows on predictive performance. We also incorporate multiple sets of state-variable observations from different sources and separately quantify model prediction error and measurement uncertainty through a flexible Bayesian hierarchical framework. Results illustrate the benefits of (1) adopting forecast metrics and drivers that strike an optimal balance between predictability and relevance to management, (2) incorporating multiple data sources in the calibration data set to separate and propagate different sources of uncertainty, and (3) using the model in scenario mode to probabilistically evaluate the effects of alternative management decisions on future ecosystem state. In the Chesapeake Bay, the subject of this case study, we find that average summer or total annual hypoxia metrics are more predictable than monthly metrics and that measurement error represents an important source of uncertainty. Application of the model in scenario mode suggests that absent watershed management actions over the past decades, long-term average hypoxia would have increased by 7% compared to 1985. Conversely, the model projects that if management goals currently in place to restore the Bay are met, long-term average hypoxia would eventually decrease by 32% with respect to the mid-1980s.
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Affiliation(s)
- Donald Scavia
- School for Environment and SustainabilityUniversity of MichiganAnn ArborMichigan48103USA
| | - Isabella Bertani
- Chesapeake Bay Program OfficeUniversity of Maryland Center for Environmental ScienceAnnapolisMaryland21403USA
| | - Jeremy M. Testa
- Chesapeake Biological LaboratoryUniversity of Maryland Center for Environmental ScienceSolomonsMaryland20688USA
| | | | - Joel D. Blomquist
- U.S. Geological Survey, Water Observing Systems ProgramBaltimoreMaryland21228USA
| | | | - Lewis C. Linker
- U.S. EPA Chesapeake Bay Program OfficeAnnapolisMaryland21403USA
| | | | - Rebecca R. Murphy
- Chesapeake Bay Program OfficeUniversity of Maryland Center for Environmental ScienceAnnapolisMaryland21403USA
| | - Gary W. Shenk
- U.S. Geological Survey Chesapeake Bay Program OfficeAnnapolisMaryland21403USA
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