1
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Albers JL, Ivan LN, Clark BW, Nacci DE, Klingler RH, Thrash A, Steibel JP, Vinas NGR, Carvan MJ, Murphy CA. Impacts on Atlantic Killifish from Neurotoxicants: Genes, Behavior, and Population-Relevant Outcomes. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024. [PMID: 39287556 DOI: 10.1021/acs.est.4c04207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/19/2024]
Abstract
Molecular, cellular, and organismal alterations are important descriptors of toxic effects, but our ability to extrapolate and predict ecological risks is limited by the availability of studies that link measurable end points to adverse population relevant outcomes such as cohort survival and growth. In this study, we used laboratory gene expression and behavior data from two populations of Atlantic killifish Fundulus heteroclitus [one reference site (SCOKF) and one PCB-contaminated site (NBHKF)] to inform individual-based models simulating cohort growth and survival from embryonic exposures to environmentally relevant concentrations of neurotoxicants. Methylmercury exposed SCOKF exhibited brain gene expression changes in the si:ch211-186j3.6, si:dkey-21c1.4, scamp1, and klhl6 genes, which coincided with changes in feeding and swimming behaviors, but our models simulated no growth or survival effects of exposures. PCB126-exposed SCOKF had lower physical activity levels coinciding with a general upregulation in nucleic and cellular brain gene sets (BGS) and downregulation in signaling, nucleic, and cellular BGS. The NBHKF, known to be tolerant to PCBs, had altered swimming behaviors that coincided with 98% fewer altered BGS. Our models simulated PCB126 decreased growth in SCOKF and survival in SCOKF and NBHKF. Overall, our study provides a unique demonstration linking molecular and behavioral data to develop quantitative, testable predictions of ecological risk.
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Affiliation(s)
- Janice L Albers
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, Michigan 48824, United States
| | - Lori N Ivan
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, Michigan 48824, United States
| | - Bryan W Clark
- Office of Research and Development, Center for Environmental Measurement and Modeling, Atlantic Coastal Environmental Sciences Division, U.S. Environmental Protection Agency, Narragansett, Rhode Island 02882, United States
| | - Diane E Nacci
- Office of Research and Development, Center for Environmental Measurement and Modeling, Atlantic Coastal Environmental Sciences Division, U.S. Environmental Protection Agency, Narragansett, Rhode Island 02882, United States
| | - Rebekah H Klingler
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53204, United States
| | - Adam Thrash
- Biocomputing and Biotechnology, Institute for Genomics, Mississippi State University, Starkville, Mississippi 39759, United States
| | - Juan P Steibel
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, Michigan 48824, United States
| | - Natalia Garcia-Reyero Vinas
- Environmental Laboratory, US Army Engineer Research and Development Center, U.S. Army Corps of Engineers, Vicksburg, Mississippi 39180, United States
| | - Michael J Carvan
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53204, United States
| | - Cheryl A Murphy
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, Michigan 48824, United States
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2
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Miller JT, Clark BW, Reid NM, Karchner SI, Roach JL, Hahn ME, Nacci D, Whitehead A. Independently evolved pollution resistance in four killifish populations is largely explained by few variants of large effect. Evol Appl 2024; 17:e13648. [PMID: 38293268 PMCID: PMC10824703 DOI: 10.1111/eva.13648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 01/02/2024] [Accepted: 01/09/2024] [Indexed: 02/01/2024] Open
Abstract
The genetic architecture of phenotypic traits can affect the mode and tempo of trait evolution. Human-altered environments can impose strong natural selection, where successful evolutionary adaptation requires swift and large phenotypic shifts. In these scenarios, theory predicts that adaptation is due to a few adaptive variants of large effect, but empirical studies that have revealed the genetic architecture of rapidly evolved phenotypes are rare, especially for populations inhabiting polluted environments. Fundulus killifish have repeatedly evolved adaptive resistance to extreme pollution in urban estuaries. Prior studies, including genome scans for signatures of natural selection, have revealed some of the genes and pathways important for evolved pollution resistance, and provide context for the genotype-phenotype association studies reported here. We created multiple quantitative trait locus (QTL) mapping families using progenitors from four different resistant populations, and using RAD-seq genetically mapped variation in sensitivity (developmental perturbations) following embryonic exposure to a model toxicant PCB-126. We found that one to two large-effect QTL loci accounted for resistance to PCB-mediated developmental toxicity. QTLs harbored candidate genes that govern the regulation of aryl hydrocarbon receptor (AHR) signaling. One QTL locus was shared across all populations and another was shared across three populations. One QTL locus showed strong signatures of recent natural selection in the corresponding wild population but another QTL locus did not. Some candidate genes for PCB resistance inferred from genome scans in wild populations were identified as QTL, but some key candidate genes were not. We conclude that rapidly evolved resistance to the developmental defects normally caused by PCB-126 is governed by few genes of large effect. However, other aspects of resistance beyond developmental phenotypes may be governed by additional loci, such that comprehensive resistance to PCB-126, and to the mixtures of chemicals that distinguish urban estuaries more broadly, may be more genetically complex.
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Affiliation(s)
- Jeffrey T. Miller
- Department of Environmental Toxicology, Center for Population Biology, Coastal and Marine Sciences InstituteUniversity of California, DavisDavisCaliforniaUSA
- Present address:
Molecular, Cellular, and Biomedical SciencesUniversity of New HampshireDurhamNew HampshireUSA
| | - Bryan W. Clark
- Office of Research and Development, Center for Environmental Measurement and Modeling, Atlantic Coastal Environmental Sciences DivisionUS Environmental Protection AgencyNarragansettRhode IslandUSA
| | - Noah M. Reid
- Department of Molecular & Cell BiologyUniversity of ConnecticutStorrsConnecticutUSA
| | - Sibel I. Karchner
- Biology DepartmentWoods Hole Oceanographic InstitutionWoods HoleMassachusettsUSA
| | - Jennifer L. Roach
- Department of Environmental Toxicology, Center for Population Biology, Coastal and Marine Sciences InstituteUniversity of California, DavisDavisCaliforniaUSA
| | - Mark E. Hahn
- Biology DepartmentWoods Hole Oceanographic InstitutionWoods HoleMassachusettsUSA
| | - Diane Nacci
- Office of Research and Development, Center for Environmental Measurement and Modeling, Atlantic Coastal Environmental Sciences DivisionUS Environmental Protection AgencyNarragansettRhode IslandUSA
| | - Andrew Whitehead
- Department of Environmental Toxicology, Center for Population Biology, Coastal and Marine Sciences InstituteUniversity of California, DavisDavisCaliforniaUSA
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3
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Bhalla D, van Noort V. Molecular Evolution of Aryl Hydrocarbon Receptor Signaling Pathway Genes. J Mol Evol 2023; 91:628-646. [PMID: 37392220 DOI: 10.1007/s00239-023-10124-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 06/13/2023] [Indexed: 07/03/2023]
Abstract
The Aryl hydrocarbon receptor is an ancient transcriptional factor originally discovered as a sensor of dioxin. In addition to its function as a receptor of environmental toxicants, it plays an important role in development. Although a significant amount of research has been carried out to understand the AHR signal transduction pathway and its involvement in species' susceptibility to environmental toxicants, none of them to date has comprehensively studied its evolutionary origins. Studying the evolutionary origins of molecules can inform ancestral relationships of genes. The vertebrate genome has been shaped by two rounds of whole-genome duplications (WGD) at the base of vertebrate evolution approximately 600 million years ago, followed by lineage-specific gene losses, which often complicate the assignment of orthology. It is crucial to understand the evolutionary origins of this transcription factor and its partners, to distinguish orthologs from ancient non-orthologous homologs. In this study, we have investigated the evolutionary origins of proteins involved in the AHR pathway. Our results provide evidence of gene loss and duplications, crucial for understanding the functional connectivity of humans and model species. Multiple studies have shown that 2R-ohnologs (genes and proteins that have survived from the 2R-WGD) are enriched in signaling components relevant to developmental disorders and cancer. Our findings provide a link between the AHR pathway's evolutionary trajectory and its potential mechanistic involvement in pathogenesis.
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Affiliation(s)
- Diksha Bhalla
- Centre of Microbial and Plant Genetics, Faculty of Bioscience Engineering, KU Leuven, Leuven, Belgium.
| | - Vera van Noort
- Centre of Microbial and Plant Genetics, Faculty of Bioscience Engineering, KU Leuven, Leuven, Belgium
- Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
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4
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Oleforuh-Okoleh VU, Sikiru AB, Kakulu II, Fakae BB, Obianwuna UE, Shoyombo AJ, Adeolu AI, Ollor OA, Emeka OC. Improving hydrocarbon toxicity tolerance in poultry: role of genes and antioxidants. Front Genet 2023; 14:1060138. [PMID: 37388938 PMCID: PMC10302211 DOI: 10.3389/fgene.2023.1060138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 05/23/2023] [Indexed: 07/01/2023] Open
Abstract
Sustenance of smallholder poultry production as an alternative source of food security and income is imperative in communities exposed to hydrocarbon pollution. Exposure to hydrocarbon pollutants causes disruption of homeostasis, thereby compromising the genetic potential of the birds. Oxidative stress-mediated dysfunction of the cellular membrane is a contributing factor in the mechanism of hydrocarbon toxicity. Epidemiological studies show that tolerance to hydrocarbon exposure may be caused by the activation of genes that control disease defense pathways like aryl hydrocarbon receptor (AhR) and nuclear factor erythroid 2p45-related factor 2 (Nrf2). Disparity in the mechanism and level of tolerance to hydrocarbon fragments among species may exist and may result in variations in gene expression within individuals of the same species upon exposure. Genomic variability is critical for adaptation and serves as a survival mechanism in response to environmental pollutants. Understanding the interplay of diverse genetic mechanisms in relation to environmental influences is important for exploiting the differences in various genetic variants. Protection against pollutant-induced physiological responses using dietary antioxidants can mitigate homeostasis disruptions. Such intervention may initiate epigenetic modulation relevant to gene expression of hydrocarbon tolerance, enhancing productivity, and possibly future development of hydrocarbon-tolerant breeds.
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Affiliation(s)
| | - Akeem B. Sikiru
- Department of Animal Science, Federal University of Agriculture, Zuru, Kebbi State, Nigeria
| | - Iyenemi I. Kakulu
- Department of Estate Management, Faculty of Environmental Sciences, Rivers State University, Port Harcourt, Nigeria
| | - Barineme B. Fakae
- Department of Animal and Environmental Biology, Rivers State University, Port Harcourt, Rivers State, Nigeria
| | | | - Ayoola J. Shoyombo
- Department of Animal Science, College of Agricultural Science, Landmark University, Omu-aran, Kwara State, Nigeria
| | - Adewale I. Adeolu
- Department of Agriculture, Animal Science Programme, Alex-Ekwueme Federal University, Ikwo, Ebonyi, Nigeria
| | - Ollor A. Ollor
- Department of Medical Laboratory Science, Faculty of Science, Rivers State University, Port Harcourt, Rivers State, Nigeria
| | - Onyinyechi C. Emeka
- Department of Animal Science, Rivers State University, Port Harcourt, Rivers State, Nigeria
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5
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Miller JT, Clark BW, Reid NM, Karchner SI, Roach JL, Hahn ME, Nacci D, Whitehead A. Independently evolved pollution resistance in four killifish populations is largely explained by few variants of large effect. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.07.536079. [PMID: 37066319 PMCID: PMC10104127 DOI: 10.1101/2023.04.07.536079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
The genetic architecture of phenotypic traits can affect the mode and tempo of trait evolution. Human-altered environments can impose strong natural selection, where successful evolutionary adaptation requires swift and large phenotypic shifts. In these scenarios, theory predicts the influence of few adaptive variants of large effect, but empirical studies that have revealed the genetic architecture of rapidly evolved phenotypes are rare, especially for populations inhabiting polluted environments. Fundulus killifish have repeatedly evolved adaptive resistance to extreme pollution in urban estuaries. Prior studies, including genome scans for signatures of natural selection, have revealed some of the genes and pathways important for evolved pollution resistance, and provide context for the genotype-phenotype association studies reported here. We created multiple quantitative trait locus (QTL) mapping families using progenitors from four different resistant populations, and genetically mapped variation in sensitivity (developmental perturbations) following embryonic exposure to a model toxicant PCB-126. We found that a few large-effect QTL loci accounted for resistance to PCB-mediated developmental toxicity. QTLs harbored candidate genes that govern the regulation of aryl hydrocarbon receptor (AHR) signaling, where some (but not all) of these QTL loci were shared across all populations, and some (but not all) of these loci showed signatures of recent natural selection in the corresponding wild population. Some strong candidate genes for PCB resistance inferred from genome scans in wild populations were identified as QTL, but some key candidate genes were not. We conclude that rapidly evolved resistance to the developmental defects normally caused by PCB-126 is governed by few genes of large effect. However, other aspects of resistance beyond developmental phenotypes may be governed by additional loci, such that comprehensive resistance to PCB-126, and to the mixtures of chemicals that distinguish urban estuaries more broadly, may be more genetically complex.
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Affiliation(s)
- Jeffrey T Miller
- Department of Environmental Toxicology, Center for Population Biology, Coastal and Marine Sciences Institute, University of California, Davis, CA
| | - Bryan W Clark
- US Environmental Protection Agency, Office of Research and Development, Center for Environmental Measurement and Modeling, Atlantic Coastal Environmental Sciences Division, Narragansett, RI
| | - Noah M Reid
- Department of Molecular & Cell Biology, University of Connecticut, Storrs, CT
| | - Sibel I Karchner
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA
| | - Jennifer L Roach
- Department of Environmental Toxicology, Center for Population Biology, Coastal and Marine Sciences Institute, University of California, Davis, CA
| | - Mark E Hahn
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA
| | - Diane Nacci
- US Environmental Protection Agency, Office of Research and Development, Center for Environmental Measurement and Modeling, Atlantic Coastal Environmental Sciences Division, Narragansett, RI
| | - Andrew Whitehead
- Department of Environmental Toxicology, Center for Population Biology, Coastal and Marine Sciences Institute, University of California, Davis, CA
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6
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Perdew GH, Esser C, Snyder M, Sherr DH, van den Bogaard EH, McGovern K, Fernández-Salguero PM, Coumoul X, Patterson AD. The Ah Receptor from Toxicity to Therapeutics: Report from the 5th AHR Meeting at Penn State University, USA, June 2022. Int J Mol Sci 2023; 24:5550. [PMID: 36982624 PMCID: PMC10058801 DOI: 10.3390/ijms24065550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 03/10/2023] [Indexed: 03/16/2023] Open
Abstract
The aryl hydrocarbon receptor (AHR) is a sensor of low-molecular-weight molecule signals that originate from environmental exposures, the microbiome, and host metabolism. Building upon initial studies examining anthropogenic chemical exposures, the list of AHR ligands of microbial, diet, and host metabolism origin continues to grow and has provided important clues as to the function of this enigmatic receptor. The AHR has now been shown to be directly involved in numerous biochemical pathways that influence host homeostasis, chronic disease development, and responses to toxic insults. As this field of study has continued to grow, it has become apparent that the AHR is an important novel target for cancer, metabolic diseases, skin conditions, and autoimmune disease. This meeting attempted to cover the scope of basic and applied research being performed to address possible applications of our basic knowledge of this receptor on therapeutic outcomes.
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Affiliation(s)
- Gary H. Perdew
- Department of Veterinary and Biomedical Sciences, Center for Molecular Toxicology and Carcinogenesis, Penn State University, University Park, PA 16802, USA
| | - Charlotte Esser
- IUF-Leibniz Research Institute for Environmental Medicine, Auf’m Hennekamp 50, 40225 Düsseldorf, Germany
| | - Megan Snyder
- Department of Environmental Health, Boston University School of Public Health, 72 East Concord Street, Boston, MA 02118, USA
| | - David H. Sherr
- Department of Environmental Health, Boston University School of Public Health, 72 East Concord Street, Boston, MA 02118, USA
| | - Ellen H. van den Bogaard
- Department of Dermatology, Radboud University Medical Center, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Karen McGovern
- Ikena Oncology, Inc., 645 Summer Street Suite 101, Boston, MA 02210, USA
| | - Pedro M. Fernández-Salguero
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad de Extremadura, Avenida de Elvas s/n, 06071 Badajoz, Spain
- Instituto Universitario de Investigación Biosanitaria de Extremadura (INUBE), Avenida de la Investigación s/n, 06071 Badajoz, Spain
| | - Xavier Coumoul
- INSERM UMR-S1124, 45 rue des Saints-Peères, 75006 Paris, France
| | - Andrew D. Patterson
- Department of Veterinary and Biomedical Sciences, Center for Molecular Toxicology and Carcinogenesis, Penn State University, University Park, PA 16802, USA
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7
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Martin NR, Patel R, Kossack ME, Tian L, Camarillo MA, Cintrón-Rivera LG, Gawdzik JC, Yue MS, Nwagugo FO, Elemans LMH, Plavicki JS. Proper modulation of AHR signaling is necessary for establishing neural connectivity and oligodendrocyte precursor cell development in the embryonic zebrafish brain. Front Mol Neurosci 2022; 15:1032302. [PMID: 36523606 PMCID: PMC9745199 DOI: 10.3389/fnmol.2022.1032302] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 10/24/2022] [Indexed: 12/03/2022] Open
Abstract
2,3,7,8-tetrachlorodibenzo-[p]-dioxin (TCDD) is a persistent global pollutant that exhibits a high affinity for the aryl hydrocarbon receptor (AHR), a ligand activated transcription factor. Epidemiological studies have associated AHR agonist exposure with multiple human neuropathologies. Consistent with the human data, research studies using laboratory models have linked pollutant-induced AHR activation to disruptions in learning and memory as well as motor impairments. Our understanding of endogenous AHR functions in brain development is limited and, correspondingly, scientists are still determining which cell types and brain regions are sensitive to AHR modulation. To identify novel phenotypes resulting from pollutant-induced AHR activation and ahr2 loss of function, we utilized the optically transparent zebrafish model. Early embryonic TCDD exposure impaired embryonic brain morphogenesis, resulted in ventriculomegaly, and disrupted neural connectivity in the optic tectum, habenula, cerebellum, and olfactory bulb. Altered neural network formation was accompanied by reduced expression of synaptic vesicle 2. Loss of ahr2 function also impaired nascent network development, but did not affect gross brain or ventricular morphology. To determine whether neural AHR activation was sufficient to disrupt connectivity, we used the Gal4/UAS system to express a constitutively active AHR specifically in differentiated neurons and observed disruptions only in the cerebellum; thus, suggesting that the phenotypes resulting from global AHR activation likely involve multiple cell types. Consistent with this hypothesis, we found that TCDD exposure reduced the number of oligodendrocyte precursor cells and their derivatives. Together, our findings indicate that proper modulation of AHR signaling is necessary for the growth and maturation of the embryonic zebrafish brain.
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Affiliation(s)
- Nathan R. Martin
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, United States
| | - Ratna Patel
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, United States
| | - Michelle E. Kossack
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, United States
| | - Lucy Tian
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, United States
| | - Manuel A. Camarillo
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, United States
| | - Layra G. Cintrón-Rivera
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, United States
| | - Joseph C. Gawdzik
- Molecular and Environmental Toxicology Center, University of Wisconsin at Madison, Madison, WI, United States,Division of Pharmaceutical Sciences, University of Wisconsin at Madison, Madison, WI, United States
| | - Monica S. Yue
- Molecular and Environmental Toxicology Center, University of Wisconsin at Madison, Madison, WI, United States,Division of Pharmaceutical Sciences, University of Wisconsin at Madison, Madison, WI, United States
| | - Favour O. Nwagugo
- Department of Biology, University of Maryland Baltimore County, Baltimore, MD, United States
| | - Loes M. H. Elemans
- Division of Toxicology, Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, Netherlands
| | - Jessica S. Plavicki
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, United States,*Correspondence: Jessica S. Plavicki,
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8
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Scovil AM, de Jourdan BP, Speers-Roesch B. Intraspecific Variation in the Sublethal Effects of Physically and Chemically Dispersed Crude Oil on Early Life Stages of Atlantic Cod (Gadus morhua). ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2022; 41:1967-1976. [PMID: 35622057 DOI: 10.1002/etc.5394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 02/07/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
The offshore oil industry in Atlantic Canada necessitates a greater understanding of the potential impacts of oil exposure and spill response measures on cold-water marine species. We used a standardized scoring index to characterize sublethal developmental impacts of physically and chemically dispersed crude oil in early life stages of Atlantic cod (Gadus morhua) and assessed intraspecific variation in the response among cod families. Cod (origin: Scotian Shelf, Canada) were laboratory-crossed to produce embryos from five specific families, which were subsequently exposed prehatch to gradient dilutions of a water-accommodated fraction (WAF) and a chemically enhanced WAF (CEWAF; prepared with Corexit 9500A) for 24 h. Postexposure, live embryos were transferred into filtered seawater and monitored to hatch; then, all live fish had sublethal endpoints assessed using the blue-sac disease (BSD) severity index. In both WAF and CEWAF groups, increasing exposure concentrations (measured as total petroleum hydrocarbons) resulted in an increased incidence of BSD symptoms (impaired swimming ability, increased degree of spinal curvature, yolk-sac edemas) in cod across all families. This positive concentration-dependent increase in BSD was similar between physically (WAF) versus chemically (CEWAF) dispersed oil exposures, indicating that dispersant addition does not exacerbate the effect of crude oil on BSD incidence in cod. Sensitivity varied between families, with some families having less BSD than others with increasing exposure concentrations. To our knowledge, our study is the first to demonstrate the occurrence in fishes of intraspecific variation among families in sublethal responses to oil and dispersant exposure. Our results suggest that sublethal effects of crude oil exposure will not be uniformly observed across cod populations and that sensitivity depends on genetic background. Environ Toxicol Chem 2022;41:1967-1976. © 2022 SETAC.
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Affiliation(s)
- Allie M Scovil
- Department of Biological Sciences, University of New Brunswick, Saint John, New Brunswick, Canada
| | | | - Ben Speers-Roesch
- Department of Biological Sciences, University of New Brunswick, Saint John, New Brunswick, Canada
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9
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Zhang W, Xie HQ, Li Y, Zhou M, Zhou Z, Wang R, Hahn ME, Zhao B. The aryl hydrocarbon receptor: A predominant mediator for the toxicity of emerging dioxin-like compounds. JOURNAL OF HAZARDOUS MATERIALS 2022; 426:128084. [PMID: 34952507 PMCID: PMC9039345 DOI: 10.1016/j.jhazmat.2021.128084] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/29/2021] [Accepted: 12/12/2021] [Indexed: 06/01/2023]
Abstract
The aryl hydrocarbon receptor (AHR) is a member of the basic helix-loop-helix/Per-ARNT-Sim (bHLH-PAS) family of transcription factors and has broad biological functions. Early after the identification of the AHR, most studies focused on its roles in regulating the expression of drug-metabolizing enzymes and mediating the toxicity of dioxins and dioxin-like compounds (DLCs). Currently, more diverse functions of AHR have been identified, indicating that AHR is not just a dioxin receptor. Dioxins and DLCs occur ubiquitously and have diverse health/ecological risks. Additional research is required to identify both shared and compound-specific mechanisms, especially for emerging DLCs such as polyhalogenated carbazoles (PHCZs), polychlorinated diphenyl sulfides (PCDPSs), and others, of which only a few investigations have been performed at present. Many of the toxic effects of emerging DLCs were observed to be predominantly mediated by the AHR because of their structural similarity as dioxins, and the in vitro TCDD-relative potencies of certain emerging DLC congeners are comparable to or even greater than the WHO-TEFs of OctaCDD, OctaCDF, and most coplanar PCBs. Due to the close relationship between AHR biology and environmental science, this review begins by providing novel insights into AHR signaling (canonical and non-canonical), AHR's biochemical properties (AHR structure, AHR-ligand interaction, AHR-DNA binding), and the variations during AHR transactivation. Then, AHR ligand classification and the corresponding mechanisms are discussed, especially the shared and compound-specific, AHR-mediated effects and mechanisms of emerging DLCs. Accordingly, a series of in vivo and in vitro toxicity evaluation methods based on the AHR signaling pathway are reviewed. In light of current advances, future research on traditional and emerging DLCs will enhance our understanding of their mechanisms, toxicity, potency, and ecological impacts.
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Affiliation(s)
- Wanglong Zhang
- College of Life Sciences, Qufu Normal University, Qufu, Shandong 273165, China
| | - Heidi Qunhui Xie
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunping Li
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingxi Zhou
- Biology Centre of the Czech Academy of Sciences v.v.i, Institute of Plant Molecular Biology, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Zhiguang Zhou
- State Environmental Protection Key Laboratory of Dioxin Pollution Control, National Research Center for Environmental Analysis and Measurement, Beijing 100029, China
| | - Renjun Wang
- College of Life Sciences, Qufu Normal University, Qufu, Shandong 273165, China
| | - Mark E Hahn
- Biology Department, Woods Hole Oceanographic Institution (WHOI), Woods Hole, MA 02543, USA; Boston University Superfund Research Program, Boston University, Boston, MA 02118, USA
| | - Bin Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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10
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Iannello M, Mezzelani M, Dalla Rovere G, Smits M, Patarnello T, Ciofi C, Carraro L, Boffo L, Ferraresso S, Babbucci M, Mazzariol S, Centelleghe C, Cardazzo B, Carrer C, Varagnolo M, Nardi A, Pittura L, Benedetti M, Fattorini D, Regoli F, Ghiselli F, Gorbi S, Bargelloni L, Milan M. Long-lasting effects of chronic exposure to chemical pollution on the hologenome of the Manila clam. Evol Appl 2021; 14:2864-2880. [PMID: 34950234 PMCID: PMC8674894 DOI: 10.1111/eva.13319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 10/20/2021] [Accepted: 10/28/2021] [Indexed: 12/13/2022] Open
Abstract
Chronic exposure to pollutants affects natural populations, creating specific molecular and biochemical signatures. In the present study, we tested the hypothesis that chronic exposure to pollutants might have substantial effects on the Manila clam hologenome long after removal from contaminated sites. To reach this goal, a highly integrative approach was implemented, combining transcriptome, genetic and microbiota analyses with the evaluation of biochemical and histological profiles of the edible Manila clam Ruditapes philippinarum, as it was transplanted for 6 months from the polluted area of Porto Marghera (PM) to the clean area of Chioggia (Venice lagoon, Italy). One month post-transplantation, PM clams showed several modifications to its resident microbiota, including an overrepresentation of the opportunistic pathogen Arcobacter spp. This may be related to the upregulation of several immune genes in the PM clams, potentially representing a host response to the increased abundance of deleterious bacteria. Six months after transplantation, PM clams demonstrated a lower ability to respond to environmental/physiological stressors related to the summer season, and the hepatopancreas-associated microbiota still showed different compositions among PM and CH clams. This study confirms that different stressors have predictable effects in clams at different biological levels and demonstrates that chronic exposure to pollutants leads to long-lasting effects on the animal hologenome. In addition, no genetic differentiation between samples from the two areas was detected, confirming that PM and CH clams belong to a single population. Overall, the obtained responses were largely reversible and potentially related to phenotypic plasticity rather than genetic adaptation. The results here presented will be functional for the assessment of the environmental risk imposed by chemicals on an economically important bivalve species.
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Affiliation(s)
- Mariangela Iannello
- Department of Biological, Geological, and Environmental SciencesUniversity of BolognaBolognaItaly
| | - Marica Mezzelani
- Department of Life and Environmental SciencesPolytechnic University of MarcheAnconaItaly
| | - Giulia Dalla Rovere
- Department of Comparative Biomedicine and Food ScienceUniversity of PadovaLegnaroItaly
| | - Morgan Smits
- Department of Comparative Biomedicine and Food ScienceUniversity of PadovaLegnaroItaly
| | - Tomaso Patarnello
- Department of Comparative Biomedicine and Food ScienceUniversity of PadovaLegnaroItaly
| | - Claudio Ciofi
- Department of BiologyUniversity of FlorenceSesto FiorentinoItaly
| | - Lisa Carraro
- Department of Comparative Biomedicine and Food ScienceUniversity of PadovaLegnaroItaly
| | - Luciano Boffo
- Associazione “Vongola Verace di Chioggia”ChioggiaItaly
| | - Serena Ferraresso
- Department of Comparative Biomedicine and Food ScienceUniversity of PadovaLegnaroItaly
| | - Massimiliano Babbucci
- Department of Comparative Biomedicine and Food ScienceUniversity of PadovaLegnaroItaly
| | - Sandro Mazzariol
- Department of Comparative Biomedicine and Food ScienceUniversity of PadovaLegnaroItaly
| | - Cinzia Centelleghe
- Department of Comparative Biomedicine and Food ScienceUniversity of PadovaLegnaroItaly
| | - Barbara Cardazzo
- Department of Comparative Biomedicine and Food ScienceUniversity of PadovaLegnaroItaly
| | - Claudio Carrer
- c/o Magistrato alle Acque di Venezia Ufficio Tecnico Antinquinamento Laboratorio CSMOPadovaItaly
| | | | - Alessandro Nardi
- Department of Life and Environmental SciencesPolytechnic University of MarcheAnconaItaly
| | - Lucia Pittura
- Department of Life and Environmental SciencesPolytechnic University of MarcheAnconaItaly
| | - Maura Benedetti
- Department of Life and Environmental SciencesPolytechnic University of MarcheAnconaItaly
| | - Daniele Fattorini
- Department of Life and Environmental SciencesPolytechnic University of MarcheAnconaItaly
| | - Francesco Regoli
- Department of Life and Environmental SciencesPolytechnic University of MarcheAnconaItaly
| | - Fabrizio Ghiselli
- Department of Biological, Geological, and Environmental SciencesUniversity of BolognaBolognaItaly
| | - Stefania Gorbi
- Department of Life and Environmental SciencesPolytechnic University of MarcheAnconaItaly
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food ScienceUniversity of PadovaLegnaroItaly
| | - Massimo Milan
- Department of Comparative Biomedicine and Food ScienceUniversity of PadovaLegnaroItaly
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11
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Celander MC, Goldstone JV, Brun NR, Clark B, Jayaraman S, Nacci D, Stegeman JJ. Resistance to Cyp3a induction by polychlorinated biphenyls, including non-dioxin-like PCB153, in gills of killifish (Fundulus heteroclitus) from New Bedford Harbor. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2021; 83:103580. [PMID: 33429071 PMCID: PMC8374885 DOI: 10.1016/j.etap.2020.103580] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 11/19/2020] [Accepted: 12/22/2020] [Indexed: 06/12/2023]
Abstract
Previous reports suggested that non-dioxin-like (NDL) PCB153 effects on cytochrome P450 3A (Cyp3a) expression in Atlantic killifish (Fundulus heteroclitus) gills differed between F0 generation fish from a PCB site (New Bedford Harbor; NBH) and a reference site (Scorton Creek; SC). Here, we examined effects of PCB153, dioxin-like (DL) PCB126, or a mixture of both, on Cyp3a56 mRNA in killifish generations removed from the wild, without environmental PCB exposures. PCB126 effects in liver and gills differed between populations, as expected. Gill Cyp3a56 was not affected by either congener in NBH F2 generation fish, but was induced by PCB153 in SC F1 fish, with females showing a greater response. PCB153 did not affect Cyp3a56 in liver of either population. Results suggest a heritable resistance to NDL-PCBs in killifish from NBH, in addition to that reported for DL PCBs. Induction of Cyp3a56 in gills may be a biomarker of exposure to NDL PCBs in fish populations that are not resistant to PCBs.
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Affiliation(s)
- Malin C Celander
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, SE 405 30, Gothenburg, Sweden; Biology Department, MS #32, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA.
| | - Jared V Goldstone
- Biology Department, MS #32, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Nadja R Brun
- Biology Department, MS #32, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Bryan Clark
- United States Environmental Protection Agency, Office of Research and Development, Center for Environmental Measurement and Modeling, Atlantic Coastal Environmental Sciences Division, 27 Tarzwell Drive, Narragansett, RI, 02882, USA
| | - Saro Jayaraman
- United States Environmental Protection Agency, Office of Research and Development, Center for Environmental Measurement and Modeling, Atlantic Coastal Environmental Sciences Division, 27 Tarzwell Drive, Narragansett, RI, 02882, USA
| | - Diane Nacci
- United States Environmental Protection Agency, Office of Research and Development, Center for Environmental Measurement and Modeling, Atlantic Coastal Environmental Sciences Division, 27 Tarzwell Drive, Narragansett, RI, 02882, USA
| | - John J Stegeman
- Biology Department, MS #32, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
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12
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Eskenazi B, Ames J, Rauch S, Signorini S, Brambilla P, Mocarelli P, Siracusa C, Holland N, Warner M. Dioxin exposure associated with fecundability and infertility in mothers and daughters of Seveso, Italy. Hum Reprod 2021; 36:794-807. [PMID: 33367671 PMCID: PMC7891815 DOI: 10.1093/humrep/deaa324] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 10/23/2020] [Indexed: 11/12/2022] Open
Abstract
STUDY QUESTION Is there an association between 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) exposure and fecundability and infertility among Seveso women and their daughters? SUMMARY ANSWER TCDD exposure is associated with a decrease in fecundability and increased risk of infertility in women, as well as their daughters. WHAT IS KNOWN ALREADY In animal studies, maternal exposure to TCDD is associated with decreased fertility in offspring. Effects of TCDD are mediated by activation of the aryl hydrocarbon receptor (AHR) pathway. STUDY DESIGN, SIZE, DURATION The Seveso Women's Health Study (SWHS) has followed 981 women exposed to TCDD in a 1976 accident since 1996. In 2014, we initiated the Seveso Second Generation Study to follow-up their children. PARTICIPANTS/MATERIALS, SETTING, METHODS We obtained information on pregnancy history including time of trying to conceive from SWHS women and their daughters who were 18 years or older. We considered TCDD exposure as initial 1976 serum TCDD concentration and estimated TCDD at pregnancy. We examined relationships of TCDD exposure with time to pregnancy (TTP, the monthly probability of conception within the first 12 months of trying) and infertility (≥12 months of trying to conceive). We also assessed contributions of polymorphisms in the AHR pathway via genetic risk score. MAIN RESULTS AND THE ROLE OF CHANCE Among SWHS women (n = 446), median TTP was 3 months and 18% reported taking ≥12 months to conceive. Initial 1976 TCDD (log10) was associated with longer TTP (adjusted fecundability odds ratio = 0.82; 95% CI 0.68-0.98) and increased risk of infertility (adjusted relative risk = 1.35; 95% CI 1.01-1.79). TCDD at pregnancy yielded similar associations. Among SWHS daughters (n = 66), median TTP was 2 months and 11% reported taking ≥12 months to conceive. Daughters showed similar, but non-significant, associations with maternal TCDD exposure. LIMITATIONS, REASONS FOR CAUTION A limitation of this study is time to pregnancy was reported retrospectively, although previous studies have found women are able to recall time to conception with a high degree of accuracy many years after the fact. The number of SWHS daughters who had a live birth was small and we were unable to examine fecundability of SWHS sons. WIDER IMPLICATIONS OF THE FINDINGS Consistent with previous findings in animal studies, our study found that TCDD exposure may be associated with decreased fertility in Seveso mothers and potentially in their daughters exposed in utero. There may be susceptible genetic subgroups. The literature has largely considered the genetics of the AHR pathway in the context of male fertility but not female fertility, despite strong biological plausibility. These findings should be replicated in larger populations and of different ancestry. Future studies in Seveso should examine the sons and the grandchildren of exposed mothers given the animal literature suggesting potential heritable epigenetic effects. STUDY FUNDING/COMPETING INTEREST(S) This study was supported by grant numbers F06 TW02075-01 from the National Institutes of Health, R01 ES07171 and 2P30-ESO01896-17 from the National Institute of Environmental Health Sciences, R82471 from the U.S. Environmental Protection Agency and #2896 from Regione Lombardia and Fondazione Lombardia Ambiente, Milan, Italy. J.A. was supported by F31ES026488 from the National Institutes of Health. The authors declare they have no actual or potential competing financial interests. TRIAL REGISTRATION NUMBER N/A.
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Affiliation(s)
- Brenda Eskenazi
- Center for Environmental Research and Children’s Health (CERCH), School of Public Health, University of California at Berkeley, Berkeley, CA, USA
| | - Jennifer Ames
- Center for Environmental Research and Children’s Health (CERCH), School of Public Health, University of California at Berkeley, Berkeley, CA, USA
| | - Stephen Rauch
- Center for Environmental Research and Children’s Health (CERCH), School of Public Health, University of California at Berkeley, Berkeley, CA, USA
| | - Stefano Signorini
- Department of Laboratory Medicine, University of Milano-Bicocca, School of Medicine, Hospital of Desio, Desio-Milano, Italy
| | - Paolo Brambilla
- Department of Laboratory Medicine, University of Milano-Bicocca, School of Medicine, Hospital of Desio, Desio-Milano, Italy
| | - Paolo Mocarelli
- Department of Laboratory Medicine, University of Milano-Bicocca, School of Medicine, Hospital of Desio, Desio-Milano, Italy
| | - Claudia Siracusa
- Department of Laboratory Medicine, University of Milano-Bicocca, School of Medicine, Hospital of Desio, Desio-Milano, Italy
| | - Nina Holland
- Center for Environmental Research and Children’s Health (CERCH), School of Public Health, University of California at Berkeley, Berkeley, CA, USA
| | - Marcella Warner
- Center for Environmental Research and Children’s Health (CERCH), School of Public Health, University of California at Berkeley, Berkeley, CA, USA
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13
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Mahringer A, Bernd A, Miller DS, Fricker G. Aryl hydrocarbon receptor ligands increase ABC transporter activity and protein expression in killifish (Fundulus heteroclitus) renal proximal tubules. Biol Chem 2020; 400:1335-1345. [PMID: 30913027 DOI: 10.1515/hsz-2018-0425] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 03/21/2019] [Indexed: 12/15/2022]
Abstract
Many widespread and persistent organic pollutants, for example, 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and some polychlorinated biphenyls, activate the aryl hydrocarbon receptor (AhR) causing it to translocate to the cell nucleus where it transactivates target genes, increasing expression of a number of xenobiotic metabolizing enzymes as well as some transporters. AhR's ability to target transporters within the kidney is essentially unexplored. We show here that exposing isolated killifish (Fundulus heteroclitus) renal proximal tubules to micromolar β-naphthoflavone (BNF) or nanomolar TCDD roughly doubled the transport activity of Multidrug resistance-associated proteins Mrp2 and Mrp4, P-glycoprotein (P-gp) and Breast cancer resistance protein (Bcrp), all ATP-driven xenobiotic efflux pumps and critical determinants of renal xenobiotic excretion. These effects were abolished by actinomycin D and cycloheximide and by the AhR antagonist, α-naphthoflavone, indicating that increased transport activity was dependent on transcription and translation as well as ligand binding to AhR. Quantitative immunostaining of renal tubules exposed to BNF and TCDD showed increased luminal membrane expression of Mrp2, Mrp4, P-gp and Bcrp. Thus, in these renal tubules, the four ABC transporters are targets of AhR action.
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Affiliation(s)
- Anne Mahringer
- Institute of Pharmacy and Molecular Biotechnology, Ruprecht-Karls-University, D-69120 Heidelberg, Germany.,Mount Desert Island Biological Laboratory (MDIBL), Salisbury Cove, ME 04672, USA
| | - Alexandra Bernd
- Institute of Pharmacy and Molecular Biotechnology, Ruprecht-Karls-University, D-69120 Heidelberg, Germany.,Mount Desert Island Biological Laboratory (MDIBL), Salisbury Cove, ME 04672, USA
| | - David S Miller
- Mount Desert Island Biological Laboratory (MDIBL), Salisbury Cove, ME 04672, USA.,Laboratory of Toxicology and Pharmacology and Chemistry, National Institutes of Health/National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Gert Fricker
- Institute of Pharmacy and Molecular Biotechnology, Ruprecht-Karls-University, D-69120 Heidelberg, Germany.,Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04672, USA
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14
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Baldwin WS. Phase 0 of the Xenobiotic Response: Nuclear Receptors and Other Transcription Factors as a First Step in Protection from Xenobiotics. NUCLEAR RECEPTOR RESEARCH 2019; 6:101447. [PMID: 31815118 PMCID: PMC6897393 DOI: 10.32527/2019/101447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
This mini-review examines the crucial importance of transcription factors as a first line of defense in the detoxication of xenobiotics. Key transcription factors that recognize xenobiotics or xenobiotic-induced stress such as reactive oxygen species (ROS), include AhR, PXR, CAR, MTF, Nrf2, NF-κB, and AP-1. These transcription factors constitute a significant portion of the pathways induced by toxicants as they regulate phase I-III detoxication enzymes and transporters as well as other protective proteins such as heat shock proteins, chaperones, and anti-oxidants. Because they are often the first line of defense and induce phase I-III metabolism, could these transcription factors be considered the phase 0 of xenobiotic response?
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Affiliation(s)
- William S Baldwin
- Clemson University, Biological Sciences/Environmental Toxicology, 132 Long Hall, Clemson, SC 29634
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15
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Divergence, evolution and adaptation in ray-finned fish genomes. SCIENCE CHINA-LIFE SCIENCES 2019; 62:1003-1018. [PMID: 31098893 DOI: 10.1007/s11427-018-9499-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 02/12/2019] [Indexed: 02/06/2023]
Abstract
With the rapid development of next-generation sequencing technologies and bioinformatics, over 50 ray-finned fish genomes by far have been sequenced with high quality. The genomic work provides abundant genetic resources for deep understanding of divergence, evolution and adaptation in the fish genomes. They are also instructive for identification of candidate genes for functional verification, molecular breeding, and development of novel marine drugs. As an example of other omics data, the Fish-T1K project generated a big database of fish transcriptomes to integrate with these published fish genomes for potential applications. In this review, we highlight the above-mentioned recent investigations and core topics on the ray-finned fish genome research, with a main goal to obtain a deeper understanding of fish biology for theoretical and practical applications.
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16
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Huang W, Bencic DC, Flick RL, Nacci DE, Clark BW, Burkhard L, Lahren T, Biales AD. Characterization of the Fundulus heteroclitus embryo transcriptional response and development of a gene expression-based fingerprint of exposure for the alternative flame retardant, TBPH (bis (2-ethylhexyl)-tetrabromophthalate). ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 247:696-705. [PMID: 30721860 PMCID: PMC7495336 DOI: 10.1016/j.envpol.2019.01.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 12/18/2018] [Accepted: 01/03/2019] [Indexed: 05/07/2023]
Abstract
Although alternative Flame Retardant (FR) chemicals are expected to be safer than the legacy FRs they replace, their risks to human health and the environment are often poorly characterized. This study used a small volume, fish embryo system to reveal potential mechanisms of action and diagnostic exposure patterns for TBPH (bis (2-ethylhexyl)-tetrabromophthalate), a component of several widely-used commercial products. Two different concentration of TBPH were applied to sensitive early life stages of an ecologically important test species, Fundulus heteroclitus (Atlantic killifish), with a well-annotated genome. Exposed fish embryos were sampled for transcriptomics or chemical analysis of parent compound and primary metabolite or observed for development and survival through larval stage. Global transcript profiling using RNA-seq was conducted (n = 16 per treatment) to provide a non-targeted and statistically robust approach to characterize TBPH gene expression patterns. Transcriptomic analysis revealed a dose-response in the expression of genes associated with a surprisingly limited number of biological pathways, but included the aryl hydrocarbon receptor signal transduction pathway, which is known to respond to several toxicologically-important chemical classes. A transcriptional fingerprint using Random Forests was developed that was able to perfectly discriminate exposed vs. non-exposed individuals in test sets. These results suggest that TBPH has a relatively low potential for developmental toxicity (at least in fishes), despite concerns related to its structural similarities to endocrine disrupting chemicals and that the early life stage Fundulus system may provide a convenient test system for exposure characterization. More broadly, this study advances the usefulness of a biological testing and analysis system utilizing non-targeted transcriptomics profiling and early developmental endpoints that complements current screening methods to characterize chemicals of ecological and human health concern.
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Affiliation(s)
- Weichun Huang
- U.S. EPA Office of Research and Development, National Exposure Research Laboratory, 26 W. Martin Luther King Dr., Cincinnati, OH, 45268, USA
| | - David C Bencic
- U.S. EPA Office of Research and Development, National Exposure Research Laboratory, 26 W. Martin Luther King Dr., Cincinnati, OH, 45268, USA
| | - Robert L Flick
- U.S. EPA Office of Research and Development, National Exposure Research Laboratory, 26 W. Martin Luther King Dr., Cincinnati, OH, 45268, USA
| | - Diane E Nacci
- U.S. EPA National Health and Environmental Effects Research Laboratory, 27 Tarzwell Drive Narragansett, RI, 02882, USA
| | - Bryan W Clark
- U.S. EPA National Health and Environmental Effects Research Laboratory, 27 Tarzwell Drive Narragansett, RI, 02882, USA
| | - Lawrence Burkhard
- U.S. EPA National Health and Environmental Effects Research Laboratory, 6201 Congdon Boulevard, Duluth, MN, 55804, USA
| | - Tylor Lahren
- U.S. EPA National Health and Environmental Effects Research Laboratory, 6201 Congdon Boulevard, Duluth, MN, 55804, USA
| | - Adam D Biales
- U.S. EPA Office of Research and Development, National Exposure Research Laboratory, 26 W. Martin Luther King Dr., Cincinnati, OH, 45268, USA.
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17
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Evolutionary Toxicogenomics of the Striped Killifish ( Fundulus majalis) in the New Bedford Harbor (Massachusetts, USA). Int J Mol Sci 2019; 20:ijms20051129. [PMID: 30841640 PMCID: PMC6429206 DOI: 10.3390/ijms20051129] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/18/2019] [Accepted: 02/23/2019] [Indexed: 12/27/2022] Open
Abstract
In this paper, we used a Genotyping-by-Sequencing (GBS) approach to find and genotype more than 4000 genome-wide SNPs (Single Nucleotide Polymorphisms) from striped killifish exposed to a variety of polychlorinated biphenyls (PCBs) and other aromatic pollutants in New Bedford Harbor (NBH, Massachusetts, USA). The aims of this study were to identify the genetic consequences of exposure to aquatic pollutants and detect genes that may be under selection. Low genetic diversity (HE and π) was found in the site exposed to the highest pollution level, but the pattern of genetic diversity did not match the pollution levels. Extensive connectivity was detected among sampling sites, which suggests that balanced gene flow may explain the lack of genetic variation in response to pollution levels. Tests for selection identified 539 candidate outliers, but many of the candidate outliers were not shared among tests. Differences among test results likely reflect different test assumptions and the complex pollutant mixture. Potentially, selectively important loci are associated with 151 SNPs, and enrichment analysis suggests a likely involvement of these genes with pollutants that occur in NBH. This result suggests that selective processes at genes targeted by pollutants may be occurring, even at a small geographical scale, and may allow the local striped killifish to resist the high pollution levels.
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18
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Goodale BC, Hampton TH, Ford EN, Jackson CE, Shaw JR, Stanton BA, King BL. Profiling microRNA expression in Atlantic killifish (Fundulus heteroclitus) gill and responses to arsenic and hyperosmotic stress. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2019; 206:142-153. [PMID: 30476744 PMCID: PMC6298807 DOI: 10.1016/j.aquatox.2018.11.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 11/09/2018] [Accepted: 11/09/2018] [Indexed: 06/09/2023]
Abstract
The Atlantic killifish (Fundulus heteroclitus), native to estuarine areas of the Atlantic coast of the United States, has become a valuable ecotoxicological model as a result of its ability to acclimate to rapid environmental changes and adapt to polluted habitats. MicroRNAs (miRNAs) are highly conserved small RNAs that regulate gene expression and play critical roles in stress responses in a variety of organisms. Global miRNA expression in killifish and the potential roles miRNA have in environmental acclimation have yet to be characterized. Accordingly, we profiled miRNA expression in killifish gill for the first time and identified a small group of highly expressed, well-conserved miRNAs as well as 16 novel miRNAs not yet identified in other organisms. Killifish respond to large fluctuations in salinity with rapid changes in gene expression and protein trafficking to maintain osmotic balance, followed by a secondary phase of gene and protein expression changes that enable remodeling of the gills. Arsenic, a major environmental toxicant, was previously shown to inhibit gene expression responses in killifish gill, as well the ability of killifish to acclimate to a rapid increase in salinity. Thus, we examined the individual and combined effects of salinity and arsenic on miRNA expression in killifish gill. Using small RNA sequencing, we identified 270 miRNAs expressed in killifish, and found that miR-135b was differentially expressed in response to arsenic and at 24 h following transfer to salt water. Predicted targets of miR-135b are involved in ion transport, cell motility and migration, GTPase mediated signal transduction and organelle assembly. Consistent with previous studies of these two environmental stressors, we found a significant interaction (i.e., arsenic dependent salinity effect), whereby killifish exposed to arsenic exhibited an opposite response in miR-135b expression at 24 h post hyperosmotic challenge compared to controls. By examining mRNA expression of predicted miRNA targets during salinity acclimation and arsenic exposure, we found that miR-135b targets were significantly more likely to decrease during salinity acclimation than non-targets. Our identification of a significant interaction effect of arsenic and salinity on miR-135b expression supports the hypothesis that arsenic alters upstream regulators of stress response networks, which may adversely affect the killifish response to osmotic stress. The characterization of miRNAs in this ecotoxicological model will be a valuable resource for future studies investigating the role of miRNAs in response to environmental stress.
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Affiliation(s)
- Britton C Goodale
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, United States.
| | - Thomas H Hampton
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, United States
| | - Emily N Ford
- Department of Physical and Biological Sciences, Western New England University, Springfield, MA 01119, United States
| | - Craig E Jackson
- School of Public and Environmental Affairs, Indiana University, Bloomington, IN 47405, United States
| | - Joseph R Shaw
- School of Public and Environmental Affairs, Indiana University, Bloomington, IN 47405, United States
| | - Bruce A Stanton
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, United States
| | - Benjamin L King
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469, United States
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19
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Glazer L, Kido Soule MC, Longnecker K, Kujawinski EB, Aluru N. Hepatic metabolite profiling of polychlorinated biphenyl (PCB)-resistant and sensitive populations of Atlantic killifish (Fundulus heteroclitus). AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2018; 205:114-122. [PMID: 30368057 PMCID: PMC6246827 DOI: 10.1016/j.aquatox.2018.10.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 10/09/2018] [Accepted: 10/15/2018] [Indexed: 06/08/2023]
Abstract
Atlantic killifish inhabiting polluted sites along the east coast of the U.S. have evolved resistance to toxic effects of contaminants. One such contaminated site is the Acushnet River estuary, near New Bedford Harbor (NBH), Massachusetts, which is characterized by very high PCB concentrations in the sediments and in the tissues of resident killifish. Though killifish at this site appear to be thriving, the metabolic costs of survival in a highly contaminated environment are not well understood. In this study we compared the hepatic metabolite profiles of resistant (NBH) and sensitive populations (Scorton Creek (SC), Sandwich, MA) using a targeted metabolomics approach in which polar metabolites were extracted from adult fish livers and quantified. Our results revealed differences in the levels of several metabolites between fish from the two sites. The majority of these metabolites are associated with one-carbon metabolism, an important pathway that supports multiple physiological processes including DNA and protein methylation, nucleic acid biosynthesis and amino acid metabolism. We measured the gene expression of DNA methylation (DNA methyltransferase 1, dnmt1) and demethylation genes (Ten-Eleven Translocation (TET) genes) in the two populations, and observed lower levels of dnmt1 and higher levels of TET gene expression in the NBH livers, suggesting possible differences in DNA methylation profiles. Consistent with this, the two populations differed significantly in the levels of 5-methylcytosine and 5-hydroxymethylcytosine nucleotides. Overall, our results suggest that the unique hepatic metabolite signatures observed in NBH and SC reflect the adaptive mechanisms for survival in their respective habitats.
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Affiliation(s)
- Lilah Glazer
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, United States; School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Melissa C Kido Soule
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, United States
| | - Krista Longnecker
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, United States
| | - Elizabeth B Kujawinski
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, United States
| | - Neelakanteswar Aluru
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, United States.
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20
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Osterberg JS, Cammen KM, Schultz TF, Clark BW, Di Giulio RT. Genome-wide scan reveals signatures of selection related to pollution adaptation in non-model estuarine Atlantic killifish (Fundulus heteroclitus). AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2018; 200:73-82. [PMID: 29727773 PMCID: PMC6957077 DOI: 10.1016/j.aquatox.2018.04.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 04/21/2018] [Accepted: 04/24/2018] [Indexed: 05/09/2023]
Abstract
In many human-altered ecosystems, organisms are increasingly faced with more diverse and complex environmental stressors and pollutant mixtures, to which the adaptations necessary to survive exposure are likely to be numerous and varied. Improving our understanding of the molecular mechanisms that underlie complex polygenic adaptations in natural settings requires significant toxicological, biochemical, physiological, and genomic data rarely available for non-model organisms. Here, we build upon two decades of study of adaptation to anthropogenic pollutants in a population of Atlantic killifish (Fundulus heteroclitus) that inhabits the creosote-contaminated Atlantic Wood Industries Superfund (AW) site on the Elizabeth River, Virginia in the United States. To better understand the genotypes that underlie previously characterized resistance to PCBs and PAHs, we performed Restriction site-Associated DNA sequencing (RADseq) on killifish from AW and two relatively clean reference sites (King's Creek-KC, and Mains Creek-MC). Across the genome, we analyzed over 83,000 loci and 12,000 single nucleotide polymorphisms (SNPs). Shared across both comparisons of killifish from polluted (AW) and relatively unpolluted (KC and MC) sites, we found eight genomic regions with smoothed FST values significantly (p < 0.001) elevated above background. Using the recently published F. heteroclitus reference genome, we identified candidate genes in these significant regions involved in the AHR pathway (e.g. AIP, ARNT1c), as well as genes relating to cardiac structure and function. These genes represent both previously characterized and potentially novel molecular adaptations involved with various aspects of resistance to these environmental toxins.
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Affiliation(s)
- J S Osterberg
- Duke University, Nicholas School of the Environment, Duke Superfund Research Center, Durham, NC, 27708, USA; Duke University, Nicholas School of the Environment, Duke Marine Lab, Beaufort, NC, 28516, USA.
| | - K M Cammen
- Duke University, Nicholas School of the Environment, Duke Marine Lab, Beaufort, NC, 28516, USA
| | - T F Schultz
- Duke University, Nicholas School of the Environment, Duke Marine Lab, Beaufort, NC, 28516, USA
| | - B W Clark
- Duke University, Nicholas School of the Environment, Duke Superfund Research Center, Durham, NC, 27708, USA
| | - R T Di Giulio
- Duke University, Nicholas School of the Environment, Duke Superfund Research Center, Durham, NC, 27708, USA
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Hamilton PB, Rolshausen G, Uren Webster TM, Tyler CR. Adaptive capabilities and fitness consequences associated with pollution exposure in fish. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2016.0042. [PMID: 27920387 PMCID: PMC5182438 DOI: 10.1098/rstb.2016.0042] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/08/2016] [Indexed: 12/22/2022] Open
Abstract
Many fish populations are exposed to harmful levels of chemical pollution and selection pressures associated with these exposures have led to the evolution of tolerance. Our understanding of the physiological basis for these adaptations is limited, but they are likely to include processes involved with the absorption, distribution, metabolism and/or excretion of the target chemical. Other potential adaptive mechanisms include enhancements in antioxidant responses, an increased capacity for DNA and/or tissue repair and alterations to the life cycle of fish that enable earlier reproduction. Analysis of single-nucleotide polymorphism frequencies has shown that tolerance to hydrocarbon pollutants in both marine and estuarine fish species involves alteration in the expression of the xenobiotic metabolism enzyme CYP1A. In this review, we present novel data showing also that variants of the CYP1A gene have been under selection in guppies living in Trinidadian rivers heavily polluted with crude oil. Potential costs associated with these adaptations could reduce fitness in unpolluted water conditions. Integrating knowledge of local adaptation to pollution is an important future consideration in conservation practices such as for successful restocking, and improving connectivity within river systems.This article is part of the themed issue 'Human influences on evolution, and the ecological and societal consequences'.
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Affiliation(s)
- Patrick B Hamilton
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
| | - Gregor Rolshausen
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Tamsyn M Uren Webster
- Department of Biosciences, Swansea University, Wallace Building, Swansea SA2 8PP, UK
| | - Charles R Tyler
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
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22
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Hale MD, Galligan TM, Rainwater TR, Moore BC, Wilkinson PM, Guillette LJ, Parrott BB. AHR and CYP1A expression link historical contamination events to modern day developmental effects in the American alligator. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2017; 230:1050-1061. [PMID: 28764121 DOI: 10.1016/j.envpol.2017.07.065] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 07/16/2017] [Accepted: 07/19/2017] [Indexed: 05/16/2023]
Abstract
The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor that initiates a transcriptional pathway responsible for the expression of CYP1A subfamily members, key to the metabolism of xenobiotic compounds. Toxic planar halogenated aromatic hydrocarbons, including dioxin and PCBs, are capable of activating the AHR, and while dioxin and PCB inputs into the environment have been dramatically curbed following strict regulatory efforts in the United States, they persist in the environment and exposures remain relevant today. Little is known regarding the effects that long-term chronic exposures to dioxin or dioxin-like compounds might have on the development and subsequent health of offspring from exposed individuals, nor is much known regarding AHR expression in reptilians. Here, we characterize AHR and CYP1A gene expression in embryonic and juvenile specimen of a long-lived, apex predator, the American alligator (Alligator mississippiensis), and investigate variation in gene expression profiles in offspring collected from sites conveying differential exposures to environmental contaminants. Both age- and tissue-dependent patterning of AHR isoform expression are detected. We characterize two downstream transcriptional targets of the AHR, CYP1A1 and CYP1A2, and describe conserved elements of their genomic architecture. When comparisons across different sites are made, hepatic expression of CYP1A2, a direct target of the AHR, appears elevated in embryos from a site associated with a dioxin point source and previously characterized PCB contamination. Elevated CYP1A2 expression is not persistent, as site-specific variation was absent in juveniles originating from field-collected eggs but reared under lab conditions. Our results illustrate the patterning of AHR gene expression in a long-lived environmental model species, and indicate a potential contemporary influence of historical contamination. This research presents a novel opportunity to link contamination events to critical genetic pathways during embryonic development, and carries significant potential to inform our understanding of potential health effects in wildlife and humans.
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Affiliation(s)
- Matthew D Hale
- Savannah River Ecology Laboratory, P.O. Drawer E, Aiken, SC 29802, United States; Odum School of Ecology, University of Georgia, Athens, GA 30602, United States
| | - Thomas M Galligan
- Marine Biomedicine and Environmental Sciences Program, Hollings Marine Laboratory and the Medical University of South Carolina, Charleston, SC 29412, United States
| | - Thomas R Rainwater
- Tom Yawkey Wildlife Center & Belle W. Baruch Institute of Coastal Ecology and Forest Science, Clemson University, Georgetown, SC 29442, United States
| | - Brandon C Moore
- Department of Biology, Sewanee: the University of the South, Sewanee, TN 37383, United States
| | - Philip M Wilkinson
- Tom Yawkey Wildlife Center Heritage Preserve, South Carolina Department of Natural Resources, Georgetown, SC 29440, United States
| | - Louis J Guillette
- Marine Biomedicine and Environmental Sciences Program, Hollings Marine Laboratory and the Medical University of South Carolina, Charleston, SC 29412, United States
| | - Benjamin B Parrott
- Savannah River Ecology Laboratory, P.O. Drawer E, Aiken, SC 29802, United States; Odum School of Ecology, University of Georgia, Athens, GA 30602, United States.
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23
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Conservation Evo-Devo: Preserving Biodiversity by Understanding Its Origins. Trends Ecol Evol 2017; 32:746-759. [DOI: 10.1016/j.tree.2017.07.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 06/27/2017] [Accepted: 07/03/2017] [Indexed: 02/01/2023]
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24
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Baldwin WS, Boswell WT, Ginjupalli G, Litoff EJ. Annotation of the Nuclear Receptors in an Estuarine Fish species, Fundulus heteroclitus. NUCLEAR RECEPTOR RESEARCH 2017; 4. [PMID: 28804711 DOI: 10.11131/2017/101285] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The nuclear receptors (NRs) are ligand-dependent transcription factors that respond to various internal as well as external cues such as nutrients, pheromones, and steroid hormones that play crucial roles in regulation and maintenance of homeostasis and orchestrating the physiological and stress responses of an organism. We annotated the Fundulus heteroclitus (mummichog; Atlantic killifish) nuclear receptors. Mummichog are a non-migratory, estuarine fish with a limited home range often used in environmental research as a field model for studying ecological and evolutionary responses to variable environmental conditions such as salinity, oxygen, temperature, pH, and toxic compounds because of their hardiness. F. heteroclitus have at least 74 NRs spanning all seven gene subfamilies. F. heteroclitus is unique in that no RXRα member was found within the genome. Interestingly, some of the NRs are highly conserved between species, while others show a higher degree of divergence such as PXR, SF1, and ARα. Fundulus like other fish species show expansion of the RAR (NR1B), Rev-erb (NR1D), ROR (NR1F), COUPTF (NR2F), ERR (NR3B), RXR (NR2B), and to a lesser extent the NGF (NR4A), and NR3C steroid receptors (GR/AR). Of particular interest is the co-expansion of opposing NRs, Reverb-ROR, and RAR/RXR-COUPTF.
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Affiliation(s)
- William S Baldwin
- Biological Sciences, Clemson University, Clemson, SC 29634.,Environmental Toxicology Program, Clemson University, Clemson, SC 29634
| | | | - Gautam Ginjupalli
- Environmental Toxicology Program, Clemson University, Clemson, SC 29634
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25
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Yakub M, Tiffin P. Living in the city: urban environments shape the evolution of a native annual plant. GLOBAL CHANGE BIOLOGY 2017; 23:2082-2089. [PMID: 27718531 DOI: 10.1111/gcb.13528] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 09/11/2016] [Indexed: 06/06/2023]
Abstract
Urban environments are warmer, have higher levels of atmospheric CO2 and have altered patterns of disturbance and precipitation than nearby rural areas. These differences can be important for plant growth and are likely to create distinct selective environments. We planted a common garden experiment with seeds collected from natural populations of the native annual plant Lepidium virginicum, growing in five urban and nearby rural areas in the northern United States to determine whether and how urban populations differ from those from surrounding rural areas. When grown in a common environment, plants grown from seeds collected from urban areas bolted sooner, grew larger, had fewer leaves, had an extended time between bolting and flowering, and produced more seeds than plants grown from seeds collected from rural areas. Interestingly, the rural populations exhibited larger phenotypic differences from one another than urban populations. Surprisingly, genomic data revealed that the majority of individuals in each of the urban populations were more closely related to individuals from other urban populations than they were to geographically proximate rural areas - the one exception being urban and rural populations from New York which were nearly identical. Taken together, our results suggest that selection in urban environments favors different traits than selection in rural environments and that these differences can drive adaptation and shape population structure.
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Affiliation(s)
- Mohamed Yakub
- Department of Plant and Microbial Biology, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN, 55108, USA
| | - Peter Tiffin
- Department of Plant and Microbial Biology, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN, 55108, USA
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26
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Whitehead A, Clark BW, Reid NM, Hahn ME, Nacci D. When evolution is the solution to pollution: Key principles, and lessons from rapid repeated adaptation of killifish ( Fundulus heteroclitus) populations. Evol Appl 2017; 10:762-783. [PMID: 29151869 PMCID: PMC5680427 DOI: 10.1111/eva.12470] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 02/10/2017] [Indexed: 12/18/2022] Open
Abstract
For most species, evolutionary adaptation is not expected to be sufficiently rapid to buffer the effects of human‐mediated environmental changes, including environmental pollution. Here we review how key features of populations, the characteristics of environmental pollution, and the genetic architecture underlying adaptive traits, may interact to shape the likelihood of evolutionary rescue from pollution. Large populations of Atlantic killifish (Fundulus heteroclitus) persist in some of the most contaminated estuaries of the United States, and killifish studies have provided some of the first insights into the types of genomic changes that enable rapid evolutionary rescue from complexly degraded environments. We describe how selection by industrial pollutants and other stressors has acted on multiple populations of killifish and posit that extreme nucleotide diversity uniquely positions this species for successful evolutionary adaptation. Mechanistic studies have identified some of the genetic underpinnings of adaptation to a well‐studied class of toxic pollutants; however, multiple genetic regions under selection in wild populations seem to reflect more complex responses to diverse native stressors and/or compensatory responses to primary adaptation. The discovery of these pollution‐adapted killifish populations suggests that the evolutionary influence of anthropogenic stressors as selective agents occurs widely. Yet adaptation to chemical pollution in terrestrial and aquatic vertebrate wildlife may rarely be a successful “solution to pollution” because potentially adaptive phenotypes may be complex and incur fitness costs, and therefore be unlikely to evolve quickly enough, especially in species with small population sizes.
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Affiliation(s)
- Andrew Whitehead
- Department of Environmental Toxicology University of California Davis Davis CA USA
| | - Bryan W Clark
- Atlantic Ecology Division National Health and Environmental Effects Research Laboratory Office of Research and Development Oak Ridge Institute for Science and Education US Environmental Protection Agency Narragansett RI USA
| | - Noah M Reid
- Department of Molecular and Cell Biology University of Connecticut Storrs CT USA
| | - Mark E Hahn
- Department of Biology Woods Hole Oceanographic Institution Woods Hole MA USA.,Superfund Research Program Boston University Boston MA USA
| | - Diane Nacci
- Atlantic Ecology Division National Health and Environmental Effects Research Laboratory Office of Research and Development US Environmental Protection Agency Narragansett RI USA
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27
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Leung MCK, Procter AC, Goldstone JV, Foox J, DeSalle R, Mattingly CJ, Siddall ME, Timme-Laragy AR. Applying evolutionary genetics to developmental toxicology and risk assessment. Reprod Toxicol 2017; 69:174-186. [PMID: 28267574 PMCID: PMC5829367 DOI: 10.1016/j.reprotox.2017.03.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 02/27/2017] [Accepted: 03/02/2017] [Indexed: 12/26/2022]
Abstract
Evolutionary thinking continues to challenge our views on health and disease. Yet, there is a communication gap between evolutionary biologists and toxicologists in recognizing the connections among developmental pathways, high-throughput screening, and birth defects in humans. To increase our capability in identifying potential developmental toxicants in humans, we propose to apply evolutionary genetics to improve the experimental design and data interpretation with various in vitro and whole-organism models. We review five molecular systems of stress response and update 18 consensual cell-cell signaling pathways that are the hallmark for early development, organogenesis, and differentiation; and revisit the principles of teratology in light of recent advances in high-throughput screening, big data techniques, and systems toxicology. Multiscale systems modeling plays an integral role in the evolutionary approach to cross-species extrapolation. Phylogenetic analysis and comparative bioinformatics are both valuable tools in identifying and validating the molecular initiating events that account for adverse developmental outcomes in humans. The discordance of susceptibility between test species and humans (ontogeny) reflects their differences in evolutionary history (phylogeny). This synthesis not only can lead to novel applications in developmental toxicity and risk assessment, but also can pave the way for applying an evo-devo perspective to the study of developmental origins of health and disease.
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Affiliation(s)
- Maxwell C K Leung
- Nicholas School of the Environment, Duke University, Durham, NC, United States.
| | - Andrew C Procter
- Institute for Advanced Analytics, North Carolina State University, Raleigh, NC, United States
| | - Jared V Goldstone
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Jonathan Foox
- Department of Invertebrate Zoology, American Museum of Natural History, New York, New York, United States
| | - Robert DeSalle
- Department of Invertebrate Zoology, American Museum of Natural History, New York, New York, United States
| | - Carolyn J Mattingly
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States
| | - Mark E Siddall
- Department of Invertebrate Zoology, American Museum of Natural History, New York, New York, United States
| | - Alicia R Timme-Laragy
- Department of Environmental Health Sciences, University of Massachusetts, Amherst, MA, United States
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28
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Uren Webster TM, Williams TD, Katsiadaki I, Lange A, Lewis C, Shears JA, Tyler CR, Santos EM. Hepatic transcriptional responses to copper in the three-spined stickleback are affected by their pollution exposure history. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2017; 184:26-36. [PMID: 28081447 DOI: 10.1016/j.aquatox.2016.12.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 12/05/2016] [Accepted: 12/28/2016] [Indexed: 06/06/2023]
Abstract
Some fish populations inhabiting contaminated environments show evidence of increased chemical tolerance, however the mechanisms contributing to this tolerance, and whether this is heritable, are poorly understood. We investigated the responses of two populations of wild three-spined stickleback (Gasterosteus aculeatus) with different histories of contaminant exposure to an oestrogen and copper, two widespread aquatic pollutants. Male stickleback originating from two sites, the River Aire, with a history of complex pollution discharges, and Siblyback Lake, with a history of metal contamination, were depurated and then exposed to copper (46μg/L) and the synthetic oestrogen ethinyloestradiol (22ng/L). The hepatic transcriptomic response was compared between the two populations and to a reference population with no known history of exposure (Houghton Springs, Dorset). Gene responses included those typical for both copper and oestrogen, with no discernable difference in response to oestrogen between populations. There was, however, some difference in the magnitude of response to copper between populations. Siblyback fish showed an elevated baseline transcription of genes encoding metallothioneins and a lower level of metallothionein induction following copper exposure, compared to those from the River Aire. Similarly, a further experiment with an F1 generation of Siblyback fish bred in the laboratory found evidence for elevated transcription of genes encoding metallothioneins in unexposed fish, together with an altered transcriptional response to 125μg/L copper, compared with F1 fish originating from the clean reference population exposed to the same copper concentration. These data suggest that the stickleback from Siblyback Lake have a differential response to copper, which is inherited by the F1 generation in laboratory conditions, and for which the underlying mechanism may include an elevation of baseline transcription of genes encoding metallothioneins. The genetic and/or epigenetic mechanisms contributing to this inherited alteration of metallothionein transcription have yet to be established.
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Affiliation(s)
- Tamsyn M Uren Webster
- Biosciences, College of Life & Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK; Biosciences, College of Science, Swansea University, Swansea SA2 8PP, UK.
| | - Tim D Williams
- School of Biosciences, The University of Birmingham, Birmingham B15 2TT, UK
| | - Ioanna Katsiadaki
- Centre for Environment, Fisheries and Aquaculture Science, Cefas Weymouth Laboratory, Weymouth DT4 8UB, UK
| | - Anke Lange
- Biosciences, College of Life & Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
| | - Ceri Lewis
- Biosciences, College of Life & Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
| | - Janice A Shears
- Biosciences, College of Life & Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
| | - Charles R Tyler
- Biosciences, College of Life & Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
| | - Eduarda M Santos
- Biosciences, College of Life & Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK.
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29
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Oziolor EM, Bickham JW, Matson CW. Evolutionary toxicology in an omics world. Evol Appl 2017; 10:752-761. [PMID: 29151868 PMCID: PMC5680431 DOI: 10.1111/eva.12462] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Accepted: 01/13/2017] [Indexed: 12/11/2022] Open
Abstract
Evolutionary toxicology is a young field that has grown rapidly in the past two decades. The potential of this field comes from the ability to link chemical contamination to multigenerational and population-wide effects in various species. The advancements and rapidly decreasing costs of -omic tools are improving the power and resolution of evolutionary toxicology studies. In this manuscript, we aim to address the trajectories and perspectives for conducting evolutionary toxicology studies with -omic approaches. We discuss the complementarity of using multiple -omic tools (genomics, eDNA, transcriptomics, proteomics, and metabolomics) for utility in understanding the toxicological relevance of adaptive responses in populations. In addition, we discuss phenotypic plasticity and its relevance to transcriptomic studies in toxicology. As evolutionary toxicology grows and expands its capacity to link toxicology with population-wide end points, we emphasize the applications of such studies in answering questions about ecological and population health, as well as future applicability to regulation. Thus, we aim to emphasize the enormous potential for evolutionary toxicology in an -omics world and give perspectives on the directions of future investigations.
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Affiliation(s)
- Elias M Oziolor
- Department of Environmental Science Center for Reservoir and Aquatic Systems Research (CRASR), and the Institute for Biomedical Studies Baylor University Waco TX USA
| | - John W Bickham
- Department of Wildlife and Fisheries Science Texas A&M University College Station TX USA
| | - Cole W Matson
- Department of Environmental Science Center for Reservoir and Aquatic Systems Research (CRASR), and the Institute for Biomedical Studies Baylor University Waco TX USA
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30
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Hahn ME, Karchner SI, Merson RR. Diversity as Opportunity: Insights from 600 Million Years of AHR Evolution. CURRENT OPINION IN TOXICOLOGY 2017; 2:58-71. [PMID: 28286876 DOI: 10.1016/j.cotox.2017.02.003] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The aryl hydrocarbon receptor (AHR) was for many years of interest only to pharmacologists and toxicologists. However, this protein has fundamental roles in biology that are being revealed through studies in diverse animal species. The AHR is an ancient protein. AHR homologs exist in most major groups of modern bilaterian animals, including deuterostomes (chordates, hemichordates, echinoderms) and the two major clades of protostome invertebrates [ecdysozoans (e.g. arthropods and nematodes) and lophotrochozoans (e.g. molluscs and annelids)]. AHR homologs also have been identified in cnidarians such as the sea anemone Nematostella and in the genome of Trichoplax, a placozoan. Bilaterians, cnidarians, and placozoans form the clade Eumetazoa, whose last common ancestor lived approximately 600 million years ago (MYA). The presence of AHR homologs in modern representatives of all these groups indicates that the original eumetazoan animal possessed an AHR homolog. Studies in invertebrates and vertebrates reveal parallel functions of AHR in the development and function of sensory neural systems, suggesting that these may be ancestral roles. Vertebrate animals are characterized by the expansion and diversification of AHRs, via gene and genome duplications, from the ancestral protoAHR into at least five classes of AHR-like proteins: AHR, AHR1, AHR2, AHR3, and AHRR. The evolution of multiple AHRs in vertebrates coincided with the acquisition of high-affinity binding of halogenated and polynuclear aromatic hydrocarbons and the emergence of adaptive functions involving regulation of xenobiotic-metabolizing enzymes and roles in adaptive immunity. The existence of multiple AHRs may have facilitated subfunction partitioning and specialization of specific AHR types in some taxa. Additional research in diverse model and non-model species will continue to enrich our understanding of AHR and its pleiotropic roles in biology and toxicology.
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Affiliation(s)
- Mark E Hahn
- Biology Department, Woods Hole Oceanographic Institution, MS-32, Woods Hole, MA 02543, USA
| | - Sibel I Karchner
- Biology Department, Woods Hole Oceanographic Institution, MS-32, Woods Hole, MA 02543, USA
| | - Rebeka R Merson
- Biology Department, Rhode Island College, 600 Mt. Pleasant Avenue, 251 Fogarty Life Sciences, Providence, RI 02908
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32
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Reid NM, Proestou DA, Clark BW, Warren WC, Colbourne JK, Shaw JR, Karchner SI, Hahn ME, Nacci D, Oleksiak MF, Crawford DL, Whitehead A. The genomic landscape of rapid repeated evolutionary adaptation to toxic pollution in wild fish. Science 2016; 354:1305-1308. [PMID: 27940876 PMCID: PMC5206662 DOI: 10.1126/science.aah4993] [Citation(s) in RCA: 256] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 10/31/2016] [Indexed: 01/20/2023]
Abstract
Atlantic killifish populations have rapidly adapted to normally lethal levels of pollution in four urban estuaries. Through analysis of 384 whole killifish genome sequences and comparative transcriptomics in four pairs of sensitive and tolerant populations, we identify the aryl hydrocarbon receptor-based signaling pathway as a shared target of selection. This suggests evolutionary constraint on adaptive solutions to complex toxicant mixtures at each site. However, distinct molecular variants apparently contribute to adaptive pathway modification among tolerant populations. Selection also targets other toxicity-mediating genes and genes of connected signaling pathways; this indicates complex tolerance phenotypes and potentially compensatory adaptations. Molecular changes are consistent with selection on standing genetic variation. In killifish, high nucleotide diversity has likely been a crucial substrate for selective sweeps to propel rapid adaptation.
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Affiliation(s)
- Noah M Reid
- Department of Environmental Toxicology, University of California, Davis, CA 95616, USA
| | - Dina A Proestou
- Agricultural Research Service, U.S. Department of Agriculture, Kingston, RI 02881, USA
| | - Bryan W Clark
- Oak Ridge Institute for Science and Education, Office of Research and Development, U.S. Environmental Protection Agency, Narragansett, RI 02882, USA
| | - Wesley C Warren
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - John K Colbourne
- School of Biosciences, University of Birmingham, Edgbaston B15 2TT, UK
| | - Joseph R Shaw
- School of Biosciences, University of Birmingham, Edgbaston B15 2TT, UK
- School of Public and Environmental Affairs, Indiana University, Bloomington, IN 47405, USA
| | - Sibel I Karchner
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
- Boston University Superfund Research Program, Boston University, Boston, MA 02118, USA
| | - Mark E Hahn
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
- Boston University Superfund Research Program, Boston University, Boston, MA 02118, USA
| | - Diane Nacci
- Office of Research and Development, U.S. Environmental Protection Agency, Narragansett, RI 02882, USA
| | - Marjorie F Oleksiak
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL 33149, USA
| | - Douglas L Crawford
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL 33149, USA
| | - Andrew Whitehead
- Department of Environmental Toxicology, University of California, Davis, CA 95616, USA.
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33
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Nacci D, Proestou D, Champlin D, Martinson J, Waits ER. Genetic basis for rapidly evolved tolerance in the wild: adaptation to toxic pollutants by an estuarine fish species. Mol Ecol 2016; 25:5467-5482. [DOI: 10.1111/mec.13848] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 08/22/2016] [Accepted: 08/30/2016] [Indexed: 01/28/2023]
Affiliation(s)
- Diane Nacci
- U.S. Environmental Protection Agency Office of Research and Development National Health and Environmental Effects Research Laboratory Atlantic Ecology Division 27 Tarzwell Dr. Narragansett RI 02882 USA
| | - Dina Proestou
- U.S. Environmental Protection Agency Office of Research and Development National Health and Environmental Effects Research Laboratory Atlantic Ecology Division 27 Tarzwell Dr. Narragansett RI 02882 USA
| | - Denise Champlin
- U.S. Environmental Protection Agency Office of Research and Development National Health and Environmental Effects Research Laboratory Atlantic Ecology Division 27 Tarzwell Dr. Narragansett RI 02882 USA
| | - John Martinson
- U.S. Environmental Protection Agency Office of Research and Development National Exposure Research Laboratory Ecological Exposure Research Division 26 W. Martin Luther King Dr. Cincinnati OH 45268 USA
| | - Eric R. Waits
- U.S. Environmental Protection Agency Office of Research and Development National Exposure Research Laboratory Ecological Exposure Research Division 26 W. Martin Luther King Dr. Cincinnati OH 45268 USA
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Wojdylo JV, Vogelbein W, Bain LJ, Rice CD. AHR-related activities in a creosote-adapted population of adult atlantic killifish, Fundulus heteroclitus, two decades post-EPA superfund status at the Atlantic Wood Site, Portsmouth, VA USA. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2016; 177:74-85. [PMID: 27262937 PMCID: PMC4967385 DOI: 10.1016/j.aquatox.2016.05.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 05/17/2016] [Accepted: 05/21/2016] [Indexed: 05/04/2023]
Abstract
Atlantic killifish, Fundulus heteroclitus, are adapted to creosote-based PAHs at the US EPA Superfund site known as Atlantic Wood (AW) on the southern branch of the Elizabeth River, VA USA. Subsequent to the discovery of the AW population in the early 1990s, these fish were shown to be recalcitrant to CYP1A induction by PAHs under experimental conditions, and even to the time of this study, killifish embryos collected from the AW site are resistant to developmental deformities typically associated with exposure to PAHs in reference fish. Historically, however, 90 +% of the adult killifish at this site have proliferative hepatic lesions including cancer of varying severity. Several PAHs at this site are known to be ligands for the aryl hydrocarbon receptor (AHR). In this study, AHR-related activities in AW fish collected between 2011 and 2013 were re-examined nearly 2 decades after first discovery. This study shows that CYP1A mRNA expression is three-fold higher in intestines of AW killifish compared to a reference population. Using immunohistochemistry, CYP1A staining in intestines was uniformly positive compared to negative staining in reference fish. Livers of AW killifish were examined by IHC to show that CYP1A and AHR2 protein expression reflect lesions-specific patterns, probably representing differences in intrinsic cellular physiology of the spectrum of proliferative lesions comprising the hepatocarcinogenic process. We also found that COX2 mRNA expression levels were higher in AW fish livers compared to those in the reference population, suggesting a state of chronic inflammation. Overall, these findings suggest that adult AW fish are responsive to AHR signaling, and do express CYP1A and AHR2 proteins in intestines at a level above what was observed in the reference population.
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Affiliation(s)
- Josephine V Wojdylo
- Department of Biological Sciences, Environmental Toxicology Graduate Program, Clemson University, Clemson, SC 29634, USA
| | | | - Lisa J Bain
- Department of Biological Sciences, Environmental Toxicology Graduate Program, Clemson University, Clemson, SC 29634, USA
| | - Charles D Rice
- Department of Biological Sciences, Environmental Toxicology Graduate Program, Clemson University, Clemson, SC 29634, USA.
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Planchart A, Mattingly CJ, Allen D, Ceger P, Casey W, Hinton D, Kanungo J, Kullman SW, Tal T, Bondesson M, Burgess SM, Sullivan C, Kim C, Behl M, Padilla S, Reif DM, Tanguay RL, Hamm J. Advancing toxicology research using in vivo high throughput toxicology with small fish models. ALTEX 2016; 33:435-452. [PMID: 27328013 PMCID: PMC5270630 DOI: 10.14573/altex.1601281] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Accepted: 05/31/2016] [Indexed: 12/18/2022]
Abstract
Small freshwater fish models, especially zebrafish, offer advantages over traditional rodent models, including low maintenance and husbandry costs, high fecundity, genetic diversity, physiology similar to that of traditional biomedical models, and reduced animal welfare concerns. The Collaborative Workshop on Aquatic Models and 21st Century Toxicology was held at North Carolina State University on May 5-6, 2014, in Raleigh, North Carolina, USA. Participants discussed the ways in which small fish are being used as models to screen toxicants and understand mechanisms of toxicity. Workshop participants agreed that the lack of standardized protocols is an impediment to broader acceptance of these models, whereas development of standardized protocols, validation, and subsequent regulatory acceptance would facilitate greater usage. Given the advantages and increasing application of small fish models, there was widespread interest in follow-up workshops to review and discuss developments in their use. In this article, we summarize the recommendations formulated by workshop participants to enhance the utility of small fish species in toxicology studies, as well as many of the advances in the field of toxicology that resulted from using small fish species, including advances in developmental toxicology, cardiovascular toxicology, neurotoxicology, and immunotoxicology. We alsoreview many emerging issues that will benefit from using small fish species, especially zebrafish, and new technologies that will enable using these organisms to yield results unprecedented in their information content to better understand how toxicants affect development and health.
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Affiliation(s)
- Antonio Planchart
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
| | - Carolyn J. Mattingly
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
| | - David Allen
- Integrated Laboratory Systems, Inc., Research Triangle Park, NC, USA
| | - Patricia Ceger
- Integrated Laboratory Systems, Inc., Research Triangle Park, NC, USA
| | - Warren Casey
- National Toxicology Program Interagency Center for the Evaluation of Alternative Toxicological Methods, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - David Hinton
- Nicholas School of the Environment, Duke University, Durham, NC, USA
| | - Jyotshna Kanungo
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
| | - Seth W. Kullman
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
| | - Tamara Tal
- Integrated Systems Toxicology Division, National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Maria Bondesson
- Department of Pharmacological and Pharmaceutical Sciences, University of Houston, Houston, TX, USA
| | | | - Con Sullivan
- Department of Molecular & Biomedical Sciences, University of Maine, Orono, ME, USA
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, ME, USA
| | - Carol Kim
- Department of Molecular & Biomedical Sciences, University of Maine, Orono, ME, USA
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, ME, USA
| | - Mamta Behl
- Division of National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Stephanie Padilla
- Integrated Systems Toxicology Division, National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - David M. Reif
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
| | - Robert L. Tanguay
- Department of Environmental & Molecular Toxicology, Oregon State University, Corvallis, OR, USA
| | - Jon Hamm
- Integrated Laboratory Systems, Inc., Research Triangle Park, NC, USA
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Oziolor EM, Dubansky B, Burggren WW, Matson CW. Cross-resistance in Gulf killifish (Fundulus grandis) populations resistant to dioxin-like compounds. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2016; 175:222-231. [PMID: 27064400 DOI: 10.1016/j.aquatox.2016.03.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 03/18/2016] [Accepted: 03/21/2016] [Indexed: 06/05/2023]
Abstract
The Houston Ship Channel (HSC) in Houston, Texas is an aquatic environment with a long history of contamination, including polychlorinated dibenzodioxins (PCDD), polychlorinated dibenzofurans (PCDF), polychlorinated biphenyls (PCBs), polycyclic aromatic hydrocarbons (PAHs), and heavy metals. Populations of Gulf killifish (Fundulus grandis) from the HSC have adapted to resist developmental cardiac deformities caused by dioxin-like compounds (DLCs). Contaminants in the HSC have acted as a strong selective pressure on resident Gulf killifish populations. Rapid adaptation can lead to fitness costs, some as a direct result of the mechanisms involved in the adaptive process, whereas other adaptations may be more general. To explore potential fitness costs, we evaluated two Gulf killifish populations with documented resistance to DLC-induced cardiac teratogenesis (Patrick Bayou and Vince Bayou), and one previously characterized reference population (Gangs Bayou). We also characterized a previously unstudied population from Galveston Bay as an additional reference population (Smith Point). We tested the sensitivity of F1 larvae from these four populations to two classes of pesticides (pyrethroid (permethrin) and carbamate (carbaryl)) and two model pro-oxidants (tert-butyl hydroquinone (tBHQ) and tert-butyl hydroperoxide (tBOOH)). In addition, we explored their responses to hypoxia and measured resting metabolic rates (M.O2). Both adapted populations were cross-resistant to the toxicity of carbaryl and both pro-oxidants tested. There were no population differences in sensitivity to permethrin. On the other hand, one reference population (Gangs Bayou) was less sensitive to hypoxia, and maintained a lower M.O2 . However, there were no differences in hypoxia tolerance or resting metabolic rate between the second reference and the two adapted populations. This investigation emphasizes the importance of including multiple reference populations to clearly link fitness costs or cross-resistance to pollution adaptation, rather than to unrelated environmental or ecological differences. When compared to previous literature on adapted populations of Fundulus heteroclitus, we see a mixture of similarities and differences, suggesting that F. grandis adapted phenotypes likely involve multiple mechanisms, which may not be completely consistent among adapted populations.
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Affiliation(s)
- Elias M Oziolor
- Department of Environmental Science, Center for Reservoir and Aquatic Systems Research (CRASR) and the Institute for Biomedical Studies, Baylor University, Waco, TX 76798, USA
| | - Benjamin Dubansky
- Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA
| | - Warren W Burggren
- Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA
| | - Cole W Matson
- Department of Environmental Science, Center for Reservoir and Aquatic Systems Research (CRASR) and the Institute for Biomedical Studies, Baylor University, Waco, TX 76798, USA.
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Cotter KA, Nacci D, Champlin D, Yeo AT, Gilmore TD, Callard GV. Adaptive Significance of ERα Splice Variants in Killifish (Fundulus heteroclitus) Resident in an Estrogenic Environment. Endocrinology 2016; 157:2294-308. [PMID: 27070100 DOI: 10.1210/en.2016-1052] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The possibility that chronic, multigenerational exposure to environmental estrogens selects for adaptive hormone-response phenotypes is a critical unanswered question. Embryos/larvae of killifish from an estrogenic-polluted environment (New Bedford Harbor, MA [NBH]) compared with those from a reference site overexpress estrogen receptor alpha (ERα) mRNA but are hyporesponsive to estradiol. Analysis of ERα mRNAs in the two populations revealed differences in splicing of the gene encoding ERα (esr1). Here we tested the transactivation functions of four differentially expressed ERα mRNAs and tracked their association with the hyporesponsive phenotype for three generations after transfer of NBH parents to a clean environment. Deletion variants ERαΔ6 and ERαΔ6-8 were specific to NBH killifish, had dominant negative functions in an in vitro reporter assay, and were heritable. Morpholino-mediated induction of ERαΔ6 mRNA in zebrafish embryos verified its role as a dominant negative ER on natural estrogen-responsive promoters. Alternate long (ERαL) and short (ERαS) 5'-variants were similar transcriptionally but differed in estrogen responsiveness (ERαS ≫ ERαL). ERαS accounted for high total ERα expression in first generation (F1) NBH embryos/larvae but this trait was abolished by transfer to clean water. By contrast, the hyporesponsive phenotype of F1 NBH embryos/larvae persisted after long-term laboratory holding but reverted to a normal or hyper-responsive phenotype after two or three generations, suggesting the acquisition of physiological or biochemical traits that compensate for ongoing expression of negative-acting ERαΔ6 and ERαΔ6-8 isoforms. We conclude that a heritable change in the pattern of alternative splicing of ERα pre-mRNA is part of a genetic adaptive response to estrogens in a polluted environment.
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Affiliation(s)
- Kellie A Cotter
- Department of Biology (K.A.C., A.T.Y., T.D.G., G.V.C.), Boston University, Boston, Massachusetts 02215; and Office of Research and Development (D.N., D.C.), National Health and Environmental Effects Research Laboratory, Atlantic Ecology Division, U.S. Environmental Protection Agency, Narragansett, Rhode Island 02882
| | - Diane Nacci
- Department of Biology (K.A.C., A.T.Y., T.D.G., G.V.C.), Boston University, Boston, Massachusetts 02215; and Office of Research and Development (D.N., D.C.), National Health and Environmental Effects Research Laboratory, Atlantic Ecology Division, U.S. Environmental Protection Agency, Narragansett, Rhode Island 02882
| | - Denise Champlin
- Department of Biology (K.A.C., A.T.Y., T.D.G., G.V.C.), Boston University, Boston, Massachusetts 02215; and Office of Research and Development (D.N., D.C.), National Health and Environmental Effects Research Laboratory, Atlantic Ecology Division, U.S. Environmental Protection Agency, Narragansett, Rhode Island 02882
| | - Alan T Yeo
- Department of Biology (K.A.C., A.T.Y., T.D.G., G.V.C.), Boston University, Boston, Massachusetts 02215; and Office of Research and Development (D.N., D.C.), National Health and Environmental Effects Research Laboratory, Atlantic Ecology Division, U.S. Environmental Protection Agency, Narragansett, Rhode Island 02882
| | - Thomas D Gilmore
- Department of Biology (K.A.C., A.T.Y., T.D.G., G.V.C.), Boston University, Boston, Massachusetts 02215; and Office of Research and Development (D.N., D.C.), National Health and Environmental Effects Research Laboratory, Atlantic Ecology Division, U.S. Environmental Protection Agency, Narragansett, Rhode Island 02882
| | - Gloria V Callard
- Department of Biology (K.A.C., A.T.Y., T.D.G., G.V.C.), Boston University, Boston, Massachusetts 02215; and Office of Research and Development (D.N., D.C.), National Health and Environmental Effects Research Laboratory, Atlantic Ecology Division, U.S. Environmental Protection Agency, Narragansett, Rhode Island 02882
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Braasch I, Gehrke AR, Smith JJ, Kawasaki K, Manousaki T, Pasquier J, Amores A, Desvignes T, Batzel P, Catchen J, Berlin AM, Campbell MS, Barrell D, Martin KJ, Mulley JF, Ravi V, Lee AP, Nakamura T, Chalopin D, Fan S, Wcisel D, Cañestro C, Sydes J, Beaudry FEG, Sun Y, Hertel J, Beam MJ, Fasold M, Ishiyama M, Johnson J, Kehr S, Lara M, Letaw JH, Litman GW, Litman RT, Mikami M, Ota T, Saha NR, Williams L, Stadler PF, Wang H, Taylor JS, Fontenot Q, Ferrara A, Searle SMJ, Aken B, Yandell M, Schneider I, Yoder JA, Volff JN, Meyer A, Amemiya CT, Venkatesh B, Holland PWH, Guiguen Y, Bobe J, Shubin NH, Di Palma F, Alföldi J, Lindblad-Toh K, Postlethwait JH. The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. Nat Genet 2016; 48:427-37. [PMID: 26950095 PMCID: PMC4817229 DOI: 10.1038/ng.3526] [Citation(s) in RCA: 403] [Impact Index Per Article: 50.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 02/12/2016] [Indexed: 12/16/2022]
Abstract
To connect human biology to fish biomedical models, we sequenced the genome of spotted gar (Lepisosteus oculatus), whose lineage diverged from teleosts before teleost genome duplication (TGD). The slowly evolving gar genome has conserved in content and size many entire chromosomes from bony vertebrate ancestors. Gar bridges teleosts to tetrapods by illuminating the evolution of immunity, mineralization and development (mediated, for example, by Hox, ParaHox and microRNA genes). Numerous conserved noncoding elements (CNEs; often cis regulatory) undetectable in direct human-teleost comparisons become apparent using gar: functional studies uncovered conserved roles for such cryptic CNEs, facilitating annotation of sequences identified in human genome-wide association studies. Transcriptomic analyses showed that the sums of expression domains and expression levels for duplicated teleost genes often approximate the patterns and levels of expression for gar genes, consistent with subfunctionalization. The gar genome provides a resource for understanding evolution after genome duplication, the origin of vertebrate genomes and the function of human regulatory sequences.
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Affiliation(s)
- Ingo Braasch
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, USA
| | - Andrew R Gehrke
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, Illinois, USA
| | - Jeramiah J Smith
- Department of Biology, University of Kentucky, Lexington, Kentucky, USA
| | - Kazuhiko Kawasaki
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Tereza Manousaki
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Greece
| | - Jeremy Pasquier
- Institut National de la Recherche Agronomique (INRA), UR1037 Laboratoire de Physiologie et Génomique des Poissons (LPGP), Campus de Beaulieu, Rennes, France
| | - Angel Amores
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, USA
| | - Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, USA
| | - Peter Batzel
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, USA
| | - Julian Catchen
- Department of Animal Biology, University of Illinois, Urbana-Champaign, Illinois, USA
| | - Aaron M Berlin
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Michael S Campbell
- Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah, USA
| | - Daniel Barrell
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Kyle J Martin
- Department of Zoology, University of Oxford, Oxford, UK
| | - John F Mulley
- School of Biological Sciences, Bangor University, Bangor, UK
| | - Vydianathan Ravi
- Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Alison P Lee
- Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Tetsuya Nakamura
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, Illinois, USA
| | - Domitille Chalopin
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Shaohua Fan
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Dustin Wcisel
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, North Carolina, USA
- Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, North Carolina, USA
| | - Cristian Cañestro
- Departament de Genètica, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Barcelona, Spain
| | - Jason Sydes
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, USA
| | - Felix E G Beaudry
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Yi Sun
- Center for Circadian Clocks, Soochow University, Suzhou, China
- School of Biology and Basic Medical Sciences, Medical College, Soochow University, Suzhou, China
| | - Jana Hertel
- Bioinformatics Group, Department of Computer Science, Universität Leipzig, Leipzig, Germany
| | - Michael J Beam
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, USA
| | - Mario Fasold
- Bioinformatics Group, Department of Computer Science, Universität Leipzig, Leipzig, Germany
| | - Mikio Ishiyama
- Department of Dental Hygiene, Nippon Dental University College at Niigata, Niigata, Japan
| | - Jeremy Johnson
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Steffi Kehr
- Bioinformatics Group, Department of Computer Science, Universität Leipzig, Leipzig, Germany
| | - Marcia Lara
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - John H Letaw
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, USA
| | - Gary W Litman
- Department of Pediatrics, University of South Florida Morsani College of Medicine, St. Petersburg, Florida, USA
| | - Ronda T Litman
- Department of Pediatrics, University of South Florida Morsani College of Medicine, St. Petersburg, Florida, USA
| | - Masato Mikami
- Department of Microbiology, Nippon Dental University School of Life Dentistry at Niigata, Niigata, Japan
| | - Tatsuya Ota
- Department of Evolutionary Studies of Biosystems, SOKENDAI (Graduate University for Advanced Studies), Hayama, Japan
| | - Nil Ratan Saha
- Molecular Genetics Program, Benaroya Research Institute, Seattle, Washington, USA
| | - Louise Williams
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, Universität Leipzig, Leipzig, Germany
| | - Han Wang
- Center for Circadian Clocks, Soochow University, Suzhou, China
- School of Biology and Basic Medical Sciences, Medical College, Soochow University, Suzhou, China
| | - John S Taylor
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Quenton Fontenot
- Department of Biological Sciences, Nicholls State University, Thibodaux, Louisiana, USA
| | - Allyse Ferrara
- Department of Biological Sciences, Nicholls State University, Thibodaux, Louisiana, USA
| | - Stephen M J Searle
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Bronwen Aken
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Mark Yandell
- Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah, USA
| | - Igor Schneider
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem, Brazil
| | - Jeffrey A Yoder
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, North Carolina, USA
- Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, North Carolina, USA
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Germany
- International Max Planck Research School for Organismal Biology, University of Konstanz, Konstanz, Germany
| | - Chris T Amemiya
- Molecular Genetics Program, Benaroya Research Institute, Seattle, Washington, USA
| | - Byrappa Venkatesh
- Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore
| | | | - Yann Guiguen
- Institut National de la Recherche Agronomique (INRA), UR1037 Laboratoire de Physiologie et Génomique des Poissons (LPGP), Campus de Beaulieu, Rennes, France
| | - Julien Bobe
- Institut National de la Recherche Agronomique (INRA), UR1037 Laboratoire de Physiologie et Génomique des Poissons (LPGP), Campus de Beaulieu, Rennes, France
| | - Neil H Shubin
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, Illinois, USA
| | | | - Jessica Alföldi
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
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Cotter KA, Nacci D, Champlin D, Chuprin J, Callard GV. Cloning of multiple ERα mRNA variants in killifish (Fundulus heteroclitus), and differential expression by tissue type, stage of reproduction, and estrogen exposure in fish from polluted and unpolluted environments. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2015; 159:184-197. [PMID: 25550165 PMCID: PMC4300264 DOI: 10.1016/j.aquatox.2014.12.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Revised: 12/11/2014] [Accepted: 12/12/2014] [Indexed: 06/04/2023]
Abstract
To test the hypothesis that alternative splicing could be an adaptive mechanism for populations subject to multi-generational estrogenic exposures, we compared estrogen receptor alpha (ERα) splicing variants in two populations of killifish (Fundulus heteroclitus): one resident in an estrogenic polluted environment (New Bedford Harbor, NBH, MA, USA) and one from a relatively uncontaminated reference site (Scorton Creek, SC, MA, USA). In total we identified 19 ERα variants, each with deletions of one or more coding exons. Four of the variants with potential functional relevance were analyzed by qPCR to test for population differences in expression by tissue type, site, sex, seasonal reproductive status and estrogen treatment. Significantly, a 5'-truncated short form variant (ERαS) was highly expressed in liver and ovary, and was associated with seasonal reproductive activity in SC but not NBH fish. Both ERαS and the full-length long variant (ERαL) were estrogen-inducible (ERαS>ERαL) but the induction response was lower in NBH than in SC fish. In contrast, NBH killifish were hyper-responsive to estrogen as measured by expression of two other estrogen responsive genes: vitellogenin (Vtg) and aromatase B (AroB). Most strikingly, two ERα deletion variants (Δ6 and Δ6-8), lacking ligand binding and activation function domains, were identified in a subset of NBH fish, where they were associated with reduced responsiveness to estrogen treatment. Together, these results support the hypothesis that alternative splicing of the esr1 gene of killifish could be an autoregulatory mechanism by which estrogen modulates the differential expression of ERα, and suggests a novel and adaptive mechanistic response to xenoestrogenic exposure.
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Affiliation(s)
- Kellie A Cotter
- Boston University Department of Biology, 5 Cummington Mall, Boston, MA 02215, USA
| | - Diane Nacci
- US Environmental Protection Agency, Office of Research and Development, National Health and Environmental Effects Research Laboratory, Atlantic Ecology Division, 27 Tarzwell Drive, Narragansett, RI 02882, USA
| | - Denise Champlin
- US Environmental Protection Agency, Office of Research and Development, National Health and Environmental Effects Research Laboratory, Atlantic Ecology Division, 27 Tarzwell Drive, Narragansett, RI 02882, USA
| | - Jane Chuprin
- Boston University Department of Biology, 5 Cummington Mall, Boston, MA 02215, USA
| | - Gloria V Callard
- Boston University Department of Biology, 5 Cummington Mall, Boston, MA 02215, USA.
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Gräns J, Wassmur B, Fernández-Santoscoy M, Zanette J, Woodin BR, Karchner SI, Nacci DE, Champlin D, Jayaraman S, Hahn ME, Stegeman JJ, Celander MC. Regulation of pregnane-X-receptor, CYP3A and P-glycoprotein genes in the PCB-resistant killifish (Fundulus heteroclitus) population from New Bedford Harbor. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2015; 159:198-207. [PMID: 25553538 PMCID: PMC4311260 DOI: 10.1016/j.aquatox.2014.12.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 12/10/2014] [Accepted: 12/12/2014] [Indexed: 05/12/2023]
Abstract
Killifish survive and reproduce in the New Bedford Harbor (NBH) in Massachusetts (MA), USA, a site severely contaminated with polychlorinated biphenyls (PCBs) for decades. Levels of 22 different PCB congeners were analyzed in liver from killifish collected in 2008. Concentrations of dioxin-like PCBs in liver of NBH killifish were ∼400 times higher, and the levels of non-dioxin-like PCBs ∼3000 times higher than in killifish from a reference site, Scorton Creek (SC), MA. The NBH killifish are known to be resistant to the toxicity of dioxin-like compounds and to have a reduced aryl hydrocarbon receptor (AhR) signaling response. Little is known about the responses of these fish to non-dioxin-like PCBs, which are at extraordinarily high levels in NBH fish. In mammals, some non-dioxin-like PCB congeners act through nuclear receptor 1I2, the pregnane-X-receptor (PXR). To explore this pathway in killifish, a PXR cDNA was sequenced and its molecular phylogenetic relationship to other vertebrate PXRs was determined. Killifish were also collected in 2009 from NBH and SC, and after four months in the laboratory they were injected with a single dose of either the dioxin-like PCB 126 (an AhR agonist) or the non-dioxin-like PCB 153 (a mammalian PXR agonist). Gills and liver were sampled three days after injection and transcript levels of genes encoding PXR, cytochrome P450 3A (CYP3A), P-glycoprotein (Pgp), AhR2 and cytochrome P450 1A (CYP1A) were measured by quantitative PCR. As expected, there was little effect of PCB exposure on mRNA expression of AhR2 or CYP1A in liver and gills of NBH fish. In NBH fish, but not in SC fish, there was increased mRNA expression of hepatic PXR, CYP3A and Pgp upon exposure to either of the two PCB congeners. However, basal PXR and Pgp mRNA levels in liver of NBH fish were significantly lower than in SC fish. A different pattern was seen in gills, where there were no differences in basal mRNA expression of these genes between the two populations. In SC fish, but not in NBH fish, there was increased mRNA expression of branchial PXR and CYP3A upon exposure to PCB126 and of CYP3A upon exposure to PCB153. The results suggest a difference between the two populations in non-AhR transcription factor signaling in liver and gills, and that this could involve killifish PXR. It also implies possible cross-regulatory interactions between that factor (presumably PXR) and AhR2 in liver of these fish.
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Affiliation(s)
- Johanna Gräns
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, SE 405 30 Gothenburg, Sweden
| | - Britt Wassmur
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, SE 405 30 Gothenburg, Sweden
| | - María Fernández-Santoscoy
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, SE 405 30 Gothenburg, Sweden
| | - Juliano Zanette
- Biology Department, MS #32, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Bruce R Woodin
- Biology Department, MS #32, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Sibel I Karchner
- Biology Department, MS #32, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Diane E Nacci
- Office of Research and Development, National Health and Environmental Effects Research Laboratory, Atlantic Ecology Division, United States Environmental Protection Agency, 27 Tarzwell Drive, Narragansett, RI 02882, USA
| | - Denise Champlin
- Office of Research and Development, National Health and Environmental Effects Research Laboratory, Atlantic Ecology Division, United States Environmental Protection Agency, 27 Tarzwell Drive, Narragansett, RI 02882, USA
| | - Saro Jayaraman
- Office of Research and Development, National Health and Environmental Effects Research Laboratory, Atlantic Ecology Division, United States Environmental Protection Agency, 27 Tarzwell Drive, Narragansett, RI 02882, USA
| | - Mark E Hahn
- Biology Department, MS #32, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - John J Stegeman
- Biology Department, MS #32, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Malin C Celander
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, SE 405 30 Gothenburg, Sweden.
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Aluru N, Karchner SI, Franks DG, Nacci D, Champlin D, Hahn ME. Targeted mutagenesis of aryl hydrocarbon receptor 2a and 2b genes in Atlantic killifish (Fundulus heteroclitus). AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2015; 158:192-201. [PMID: 25481785 PMCID: PMC4272816 DOI: 10.1016/j.aquatox.2014.11.016] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 11/17/2014] [Accepted: 11/18/2014] [Indexed: 06/04/2023]
Abstract
Understanding molecular mechanisms of toxicity is facilitated by experimental manipulations, such as disruption of function by gene targeting, that are especially challenging in non-standard model species with limited genomic resources. While loss-of-function approaches have included gene knock-down using morpholino-modified oligonucleotides and random mutagenesis using mutagens or retroviruses, more recent approaches include targeted mutagenesis using zinc finger nuclease (ZFN), transcription activator-like effector nuclease (TALENs) and clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 technology. These latter methods provide more accessible opportunities to explore gene function in non-traditional model species. To facilitate evaluation of toxic mechanisms for important categories of aryl hydrocarbon pollutants, whose actions are known to be receptor mediated, we used ZFN and CRISPR-Cas9 approaches to generate aryl hydrocarbon receptor 2a (AHR2a) and AHR2b gene mutations in Atlantic killifish (Fundulus heteroclitus) embryos. This killifish is a particularly valuable non-traditional model, with multiple paralogs of AHR whose functions are not well characterized. In addition, some populations of this species have evolved resistance to toxicants such as halogenated aromatic hydrocarbons. AHR-null killifish will be valuable for characterizing the role of the individual AHR paralogs in evolved resistance, as well as in normal development. We first used five-finger ZFNs targeting exons 1 and 3 of AHR2a. Subsequently, CRISPR-Cas9 guide RNAs were designed to target regions in exon 2 and 3 of AHR2a and AHR2b. We successfully induced frameshift mutations in AHR2a exon 3 with ZFN and CRISPR-Cas9 guide RNAs, with mutation frequencies of 10% and 16%, respectively. In AHR2b, mutations were induced using CRISPR-Cas9 guide RNAs targeting sites in both exon 2 (17%) and exon 3 (63%). We screened AHR2b exon 2 CRISPR-Cas9-injected embryos for off-target effects in AHR paralogs. No mutations were observed in closely related AHR genes (AHR1a, AHR1b, AHR2a, AHRR) in the CRISPR-Cas9-injected embryos. Overall, our results demonstrate that targeted genome-editing methods are efficient in inducing mutations at specific loci in embryos of a non-traditional model species, without detectable off-target effects in paralogous genes.
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Affiliation(s)
- Neelakanteswar Aluru
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA; Superfund Research Program, Boston University School of Public Health, Boston, MA, USA.
| | - Sibel I Karchner
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA; Superfund Research Program, Boston University School of Public Health, Boston, MA, USA
| | - Diana G Franks
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA; Superfund Research Program, Boston University School of Public Health, Boston, MA, USA
| | - Diane Nacci
- Office of Research and Development, National Health and Environmental Effects Research Laboratory, Atlantic Ecology Division, Environmental Protection Agency, Narragansett, RI 02882, USA
| | - Denise Champlin
- Office of Research and Development, National Health and Environmental Effects Research Laboratory, Atlantic Ecology Division, Environmental Protection Agency, Narragansett, RI 02882, USA
| | - Mark E Hahn
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA; Superfund Research Program, Boston University School of Public Health, Boston, MA, USA
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Bugel SM, Bonventre JA, White LA, Tanguay RL, Cooper KR. Chronic exposure of killifish to a highly polluted environment desensitizes estrogen-responsive reproductive and biomarker genes. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2014; 152:222-231. [PMID: 24794048 PMCID: PMC4084733 DOI: 10.1016/j.aquatox.2014.04.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Revised: 04/08/2014] [Accepted: 04/09/2014] [Indexed: 06/03/2023]
Abstract
Reproductive and endocrine disruption is commonly reported in aquatic species exposed to complex contaminant mixtures. We previously reported that Atlantic killifish (Fundulus heteroclitus) from the chronically contaminated Newark Bay, NJ, exhibit multiple endocrine disrupting effects, including inhibition of vitellogenesis (yolk protein synthesis) in females and false negative vitellogenin biomarker responses in males. Here, we characterized the effects on estrogen signaling and the transcriptional regulation of estrogen-responsive genes in this model population. First, a dose-response study tested the hypothesis that reproductive biomarkers (vtg1, vtg2, chg H, chg Hm, chg L) in Newark Bay killifish are relatively less sensitive to 17β-estradiol at the transcriptional level, relative to a reference (Tuckerton, NJ) population. The second study assessed expression for various metabolism (cyp1a, cyp3a30, mdr) and estrogen receptor (ER α, ER βa, ER βb) genes under basal and estrogen treatment conditions in both populations. Hepatic metabolism of 17β-estradiol was also evaluated in vitro as an integrated endpoint for adverse effects on metabolism. In the third study, gene methylation was evaluated for promoters of vtg1 (8 CpGs) and vtg2 (10 CpGs) in both populations, and vtg1 promoter sequences were examined for single nucleotide polymorphism (SNPs). Overall, these studies show that multi-chemical exposures at Newark Bay have desensitized all reproductive biomarkers tested to estrogen. For example, at 10ng/g 17β-estradiol, inhibition of gene induction ranged from 62% to 97% for all genes tested in the Newark Bay population, relative to induction levels in the reference population. The basis for this recalcitrant phenotype could not be explained by a change in 17β-estradiol metabolism, nuclear estrogen receptor expression, promoter methylation (gene silencing) or SNPs, all of which were unaltered and normal in the Newark Bay population. The decreased transcriptional sensitivity of estrogen-responsive genes is suggestive of a broad effect on estrogen receptor pathway signaling, and provides insight into the mechanisms of the endocrine disrupting effects in the Newark Bay population.
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Affiliation(s)
- Sean M Bugel
- Department of Environmental and Molecular Toxicology, Environmental Health Sciences Center, Oregon State University, Corvallis, OR 97331, United States.
| | - Josephine A Bonventre
- Department of Environmental and Molecular Toxicology, Environmental Health Sciences Center, Oregon State University, Corvallis, OR 97331, United States
| | - Lori A White
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, United States
| | - Robert L Tanguay
- Department of Environmental and Molecular Toxicology, Environmental Health Sciences Center, Oregon State University, Corvallis, OR 97331, United States
| | - Keith R Cooper
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, United States
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Varian-Ramos CW, Swaddle JP, Cristol DA. Mercury reduces avian reproductive success and imposes selection: an experimental study with adult- or lifetime-exposure in zebra finch. PLoS One 2014; 9:e95674. [PMID: 24759822 PMCID: PMC3997408 DOI: 10.1371/journal.pone.0095674] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2013] [Accepted: 03/31/2014] [Indexed: 02/06/2023] Open
Abstract
Mercury is a global pollutant that biomagnifies in food webs, placing wildlife at risk of reduced reproductive fitness and survival. Songbirds are the most diverse branch of the avian evolutionary tree; many are suffering persistent and serious population declines and we know that songbirds are frequently exposed to mercury pollution. Our objective was to determine the effects of environmentally relevant doses of mercury on reproductive success of songbirds exposed throughout their lives or only as adults. The two modes of exposure simulated philopatric species versus dispersive species, and are particularly relevant because of the heightened mercury-sensitivity of developing nervous systems. We performed a dosing study with dietary methylmercury in a model songbird species, the zebra finch (Taeniopygia guttata), at doses from 0.3 – 2.4 parts per million. Birds were exposed to mercury either as adults only or throughout their lives. All doses of mercury reduced reproductive success, with the lowest dose reducing the number of independent offspring produced in one year by 16% and the highest dose, representing approximately half the lethal dose for this species, causing a 50% reduction. While mercury did not affect clutch size or survivorship, it had the most consistent effect on the proportion of chicks that fledged from the nest, regardless of mode of exposure. Among birds exposed as adults, mercury caused a steep increase in the latency to re-nest after loss of a clutch. Birds exposed for their entire lifetimes, which were necessarily the offspring of dosed parents, had up to 50% lower reproductive success than adult-exposed birds at low doses of methylmercury, but increased reproductive success at high doses, suggesting selection for mercury tolerance at the highest level of exposure. Our results indicate that mercury levels in prey items at contaminated sites pose a significant threat to populations of songbirds through reduced reproductive success.
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Affiliation(s)
- Claire W. Varian-Ramos
- Biology Department, Colorado State University – Pueblo, Pueblo, Colorado, United States of America
- * E-mail:
| | - John P. Swaddle
- Institute for Integrative Bird Behavior Studies, Biology Department, The College of William and Mary, Williamsburg, Virginia, United States of America
| | - Daniel A. Cristol
- Institute for Integrative Bird Behavior Studies, Biology Department, The College of William and Mary, Williamsburg, Virginia, United States of America
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Proestou DA, Flight P, Champlin D, Nacci D. Targeted approach to identify genetic loci associated with evolved dioxin tolerance in Atlantic killifish (Fundulus heteroclitus). BMC Evol Biol 2014; 14:7. [PMID: 24422627 PMCID: PMC4029433 DOI: 10.1186/1471-2148-14-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 12/30/2013] [Indexed: 11/10/2022] Open
Abstract
Background The most toxic aromatic hydrocarbon pollutants are categorized as dioxin-like compounds (DLCs) to which extreme tolerance has evolved independently and contemporaneously in (at least) four populations of Atlantic killifish (Fundulus heteroclitus). Surprisingly, the magnitude and phenotype of DLC tolerance is similar among these killifish populations that have adapted to varied, but highly aromatic hydrocarbon-contaminated urban/industrialized estuaries of the US Atlantic coast. Multiple tolerant and neighboring sensitive killifish populations were compared with the expectation that genetic loci associated with DLC tolerance would be revealed. Results Since the aryl hydrocarbon receptor (AHR) pathway partly or fully mediates DLC toxicity in vertebrates, single nucleotide polymorphisms (SNPs) from 42 genes associated with the AHR pathway were identified to serve as targeted markers. Wild fish (N = 36/37) from four highly tolerant killifish populations and four nearby sensitive populations were genotyped using 59 SNP markers. Similar to other killifish population genetic analyses, strong genetic differentiation among populations was detected, consistent with isolation by distance models. When DLC-sensitive populations were pooled and compared to pooled DLC-tolerant populations, multi-locus analyses did not distinguish the two groups. However, pairwise comparisons of nearby tolerant and sensitive populations revealed high differentiation among sensitive and tolerant populations at these specific loci: AHR 1 and 2, cathepsin Z, the cytochrome P450s (CYP1A and 3A30), and the NADH dehydrogenase subunits. In addition, significant shifts in minor allele frequency were observed at AHR2 and CYP1A loci across most sensitive/tolerant pairs, but only AHR2 exhibited shifts in the same direction across all pairs. Conclusions The observed differences in allelic composition at the AHR2 and CYP1A SNP loci were identified as significant among paired sensitive/tolerant populations of Atlantic killifish with multiple statistical tests. The genetic patterns reported here lend support to the argument that AHR2 and CYP1A play a role in the adaptive response to extreme DLC contamination. Additional functional assays are required to isolate the exact mechanism of DLC tolerance.
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Affiliation(s)
- Dina A Proestou
- US Environmental Protection Agency, Office of Research and Development, National Health and Environmental Effects Research Laboratory, Atlantic Ecology Division, 27 Tarzwell Drive, Narragansett, RI 02882, USA.
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