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Donald CE, Sørhus E, Perrichon P, Nakken CL, Goksøyr A, Jørgensen KB, Mayer P, da Silva DAM, Meier S. Co-Exposure of Phenanthrene and the cyp-Inducer 3-Methylchrysene Leads to Altered Biotransformation and Increased Toxicity in Fish Egg and Larvae. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023. [PMID: 37465931 DOI: 10.1021/acs.est.3c02770] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) have frequently been suspected of governing crude oil toxicity because of similar morphological defects in fish. However, PAH concentrations are often not high enough to explain the observed crude oil toxicity. We hypothesize that one PAH can enhance the metabolism and toxicity of another PAH when administered as a mixture. Early life stage Atlantic haddock (Melanogrammus aeglefinus) were in this study exposed to phenanthrene in the presence and absence of 3-methylchrysene that is known to induce the metabolic enzyme cytochrome P450 1A via cyp1a gene expression. Uptake, metabolism, and multiple toxicity endpoints were then measured in a time-course study up to 3 days post-hatching. Passive dosing provided aqueous concentrations ≈180 μg/L for phenanthrene and ≈0.6 μg/L for 3-methylchrysene, which resulted in tissue concentrations ≈60 μg/g ww for phenanthrene and ≈0.15 μg/g ww for 3-methylchrysene. The low concentration of 3-methylchrysene led to the elevated expression of cyp1a but no toxicity. Levels of phenanthrene metabolites were 5-fold higher, and morphological defects and cardiotoxicity were consistently greater when co-exposed to both compounds relative to phenanthrene alone. This work highlights the metabolic activation of PAH toxicity by a co-occurring PAH, which can lead to excess toxicity, synergistic effects, and the overproportional contribution of PAHs to crude oil toxicity.
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Affiliation(s)
- Carey E Donald
- Marine Toxicology, Institute of Marine Research, 5004 Bergen, Norway
| | - Elin Sørhus
- Marine Toxicology, Institute of Marine Research, 5004 Bergen, Norway
| | - Prescilla Perrichon
- Reproduction and Developmental Biology, Institute of Marine Research, Austevoll Research Station, 5392 Storebø, Norway
| | | | - Anders Goksøyr
- Department of Biological Sciences, University of Bergen, 5006 Bergen, Norway
| | - Kåre B Jørgensen
- Department of Chemistry, Bioscience and Environmental Engineering, Faculty of Science and Technology, University of Stavanger, 4021 Stavanger, Norway
| | - Philipp Mayer
- Department of Environmental & Resource Engineering, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Denis A M da Silva
- Environmental Chemistry Program, Northwest Fisheries Science Center (NOAA), Seattle, Washington 98112, United States
| | - Sonnich Meier
- Marine Toxicology, Institute of Marine Research, 5004 Bergen, Norway
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Inwongwan S, Pekkoh J, Pumas C, Sattayawat P. Metabolic network reconstruction of Euglena gracilis: Current state, challenges, and applications. Front Microbiol 2023; 14:1143770. [PMID: 36937274 PMCID: PMC10018167 DOI: 10.3389/fmicb.2023.1143770] [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: 01/13/2023] [Accepted: 02/06/2023] [Indexed: 03/06/2023] Open
Abstract
A metabolic model, representing all biochemical reactions in a cell, is a prerequisite for several approaches in systems biology used to explore the metabolic phenotype of an organism. Despite the use of Euglena in diverse industrial applications and as a biological model, there is limited understanding of its metabolic network capacity. The unavailability of the completed genome data and the highly complex evolution of Euglena are significant obstacles to the reconstruction and analysis of its genome-scale metabolic model. In this mini-review, we discuss the current state and challenges of metabolic network reconstruction in Euglena gracilis. We have collated and present the available relevant data for the metabolic network reconstruction of E. gracilis, which could be used to improve the quality of the metabolic model of E. gracilis. Furthermore, we deliver the potential applications of the model in metabolic engineering. Altogether, it is supposed that this mini-review would facilitate the investigation of metabolic networks in Euglena and further lay out a direction for model-assisted metabolic engineering.
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Affiliation(s)
- Sahutchai Inwongwan
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Research Center of Microbial Diversity and Sustainable Utilizations, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Jeeraporn Pekkoh
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Research Center of Microbial Diversity and Sustainable Utilizations, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Chayakorn Pumas
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Research Center in Bioresources for Agriculture, Industry and Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Pachara Sattayawat
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Research Center of Microbial Diversity and Sustainable Utilizations, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Research Center in Bioresources for Agriculture, Industry and Medicine, Chiang Mai University, Chiang Mai, Thailand
- *Correspondence: Pachara Sattayawat,
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Passi A, Tibocha-Bonilla JD, Kumar M, Tec-Campos D, Zengler K, Zuniga C. Genome-Scale Metabolic Modeling Enables In-Depth Understanding of Big Data. Metabolites 2021; 12:14. [PMID: 35050136 PMCID: PMC8778254 DOI: 10.3390/metabo12010014] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/18/2021] [Accepted: 12/20/2021] [Indexed: 11/16/2022] Open
Abstract
Genome-scale metabolic models (GEMs) enable the mathematical simulation of the metabolism of archaea, bacteria, and eukaryotic organisms. GEMs quantitatively define a relationship between genotype and phenotype by contextualizing different types of Big Data (e.g., genomics, metabolomics, and transcriptomics). In this review, we analyze the available Big Data useful for metabolic modeling and compile the available GEM reconstruction tools that integrate Big Data. We also discuss recent applications in industry and research that include predicting phenotypes, elucidating metabolic pathways, producing industry-relevant chemicals, identifying drug targets, and generating knowledge to better understand host-associated diseases. In addition to the up-to-date review of GEMs currently available, we assessed a plethora of tools for developing new GEMs that include macromolecular expression and dynamic resolution. Finally, we provide a perspective in emerging areas, such as annotation, data managing, and machine learning, in which GEMs will play a key role in the further utilization of Big Data.
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Affiliation(s)
- Anurag Passi
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0760, USA; (A.P.); (M.K.); (D.T.-C.); (K.Z.)
| | - Juan D. Tibocha-Bonilla
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0760, USA;
| | - Manish Kumar
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0760, USA; (A.P.); (M.K.); (D.T.-C.); (K.Z.)
| | - Diego Tec-Campos
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0760, USA; (A.P.); (M.K.); (D.T.-C.); (K.Z.)
- Facultad de Ingeniería Química, Campus de Ciencias Exactas e Ingenierías, Universidad Autónoma de Yucatán, Merida 97203, Yucatan, Mexico
| | - Karsten Zengler
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0760, USA; (A.P.); (M.K.); (D.T.-C.); (K.Z.)
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093-0412, USA
- Center for Microbiome Innovation, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0403, USA
| | - Cristal Zuniga
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0760, USA; (A.P.); (M.K.); (D.T.-C.); (K.Z.)
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Sørhus E, Meier S, Donald CE, Furmanek T, Edvardsen RB, Lie KK. Cardiac dysfunction affects eye development and vision by reducing supply of lipids in fish. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 800:149460. [PMID: 34391158 DOI: 10.1016/j.scitotenv.2021.149460] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 07/31/2021] [Accepted: 07/31/2021] [Indexed: 06/13/2023]
Abstract
Developing organisms are especially vulnerable to environmental stressors. Crude oil exposure in early life stages of fish result in multiple functional and developmental defects, including cardiac dysfunction and abnormal and smaller eyes. Phenanthrene (Phe) has a reversible impact on cardiac function, and under exposure Phe reduces cardiac contractility. Exposure to a known L-type channel blocker, nicardipine hydrochloride (Nic) also disrupts cardiac function and creates eye deformities. We aimed to investigate whether cardiac dysfunction was the major underlying mechanism of crude oil-, Phe- and Nic-induced eye malformations. We exposed Atlantic haddock (Melanogrammus aeglefinus) early embryos to Nic and crude oil (Oil) and late embryos/early larvae to Phe exposure. All three exposures resulted in cardiac abnormalities and lead to severe, eye, jaw and spinal deformities at early larval stages. At 3 days post hatching, larvae from the exposures and corresponding controls were dissected. Eyes, trunk, head and yolk sac were subjected to lipid profiling, and eyes were also subjected to transcriptomic profiling. Among most enriched pathways in the eye transcriptomes were fatty acid metabolism, calcium signaling and phototransduction. Changes in lipid profiles and the transcriptome suggested that the dysfunctional and abnormal eyes in our exposures were due to both disruption of signaling pathways and insufficient supply of essential fatty acids and other nutrients form the yolk.
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Affiliation(s)
- Elin Sørhus
- Insititue of Marine Research, Nordnesgaten 50, 5005 Bergen, Norway.
| | - Sonnich Meier
- Insititue of Marine Research, Nordnesgaten 50, 5005 Bergen, Norway
| | - Carey E Donald
- Insititue of Marine Research, Nordnesgaten 50, 5005 Bergen, Norway
| | - Tomasz Furmanek
- Insititue of Marine Research, Nordnesgaten 50, 5005 Bergen, Norway
| | - Rolf B Edvardsen
- Insititue of Marine Research, Nordnesgaten 50, 5005 Bergen, Norway
| | - Kai K Lie
- Insititue of Marine Research, Nordnesgaten 50, 5005 Bergen, Norway
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Eide M, Zhang X, Karlsen OA, Goldstone JV, Stegeman J, Jonassen I, Goksøyr A. The chemical defensome of five model teleost fish. Sci Rep 2021; 11:10546. [PMID: 34006915 PMCID: PMC8131381 DOI: 10.1038/s41598-021-89948-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 05/04/2021] [Indexed: 12/13/2022] Open
Abstract
How an organism copes with chemicals is largely determined by the genes and proteins that collectively function to defend against, detoxify and eliminate chemical stressors. This integrative network includes receptors and transcription factors, biotransformation enzymes, transporters, antioxidants, and metal- and heat-responsive genes, and is collectively known as the chemical defensome. Teleost fish is the largest group of vertebrate species and can provide valuable insights into the evolution and functional diversity of defensome genes. We have previously shown that the xenosensing pregnane x receptor (pxr, nr1i2) is lost in many teleost species, including Atlantic cod (Gadus morhua) and three-spined stickleback (Gasterosteus aculeatus), but it is not known if compensatory mechanisms or signaling pathways have evolved in its absence. In this study, we compared the genes comprising the chemical defensome of five fish species that span the teleosteii evolutionary branch often used as model species in toxicological studies and environmental monitoring programs: zebrafish (Danio rerio), medaka (Oryzias latipes), Atlantic killifish (Fundulus heteroclitus), Atlantic cod, and three-spined stickleback. Genome mining revealed evolved differences in the number and composition of defensome genes that can have implication for how these species sense and respond to environmental pollutants, but we did not observe any candidates of compensatory mechanisms or pathways in cod and stickleback in the absence of pxr. The results indicate that knowledge regarding the diversity and function of the defensome will be important for toxicological testing and risk assessment studies.
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Affiliation(s)
- Marta Eide
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Xiaokang Zhang
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital-Radiumhospitalet, Oslo, Norway
| | - Odd André Karlsen
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Jared V Goldstone
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - John Stegeman
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Inge Jonassen
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Anders Goksøyr
- Department of Biological Sciences, University of Bergen, Bergen, Norway.
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Zhang X, Jonassen I, Goksøyr A. Machine Learning Approaches for Biomarker Discovery Using Gene Expression Data. Bioinformatics 2021. [DOI: 10.36255/exonpublications.bioinformatics.2021.ch4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
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