ET&C Best Paper of 2023

Abstract

WINNER OF THE 2023 BEST PAPER AWARD:

Genes-to-Pathways Species Conservation Analysis: Enabling the Exploration of Conservation of Biological Pathways and Processes Across Species

Claudia Rivetti, Jade Houghton, Danilo Basili, Geoff Hodges, and Bruno Campos

DOI:doi.org/10.1002/etc.5600

The development of the Genes-to-Pathways Species Conservation Analysis (G2P-SCAN), a novel R package designed to enhance the understanding of cross-species conservation of biological pathways, is a major leap forward towards integrating computational biology approaches into safety assessments. By integrating data from multiple databases and focusing on gene orthologs, protein families, entities, and reactions, G2P-SCAN offers a comprehensive tool for analyzing the conservation of biological processes across various species. This methodology supports the reduction of animal testing by enabling more accurate species extrapolation and risk assessment.

The paper's significance lies in its potential to improve the accessibility and synthesis of genomic data, thus facilitating the application of mechanistically based data in ecological risk assessments. The authors demonstrate the utility of G2P-SCAN through five case studies, validating its effectiveness in identifying conservation and susceptibility at the pathway level across different species. This work not only advances scientific understanding but also aligns with global regulatory shifts towards new approach methodologies (NAMs), promoting the use of computational and cell-based approaches in safety assessments.

REFERENCE

Rivetti, C., Houghton, J., Basili, D., Hodges, G., & Campos, B. (2023), Genes-to-pathways species conservation analysis: Enabling the exploration of conservation of biological pathways and processes across species. Environmental Toxicology and Chemistry, 42, 1152–1166.

Jana Asselmann

Ghent University

Ghent, Belgium

Best Paper Award winner Claudia Rivetti.

Models used to predict chemical bioaccumulation in fish from in vitro biotransformation rates require accurate estimates of blood–water partitioning and chemical volume of distribution

Leslie J. Saunders and John W. Nichols

DOI:10.1002/etc.5503

Arsenic and mercury distribution in an aquatic food chain: Importance of femtoplankton and picoplankton filtration fractions

Abdullah M. Alowaifeer, Scott Clingenpeel, Jinjun Kan, Patricia E. Bigelow, Masafumi Yoshinaga, Brian Bothner, and Timothy R. McDermott

DOI:10.1002/etc.5516

Sublethal exposure of per- and polyfluoroalkyl substances of varying chain length and polar functionality results in distinct metabolic responses in Daphnia magna

Lisa M. Labine, Erico A. Oliveira Pereira, Sonya Kleywegt, Karl J. Jobst, André J. Simpson, and Myrna J. Simpson

DOI:10.1002/etc.5517

Prioritizing pesticides of potential concern and identifying potential mixture effects in great lakes tributaries using passive samplers

Luke C. Loken, Steven R. Corsi, David A. Alvarez, Gerald T. Ankley, Austin K. Baldwin, Brett R. Blackwell, Laura A. De Cicco, Michele A. Nott, Samantha K. Oliver, and Daniel L. Villeneuve

DOI:10.1002/etc.5491

Development of a new polar organic chemical integrative sampler for 1,4-dioxane using silicone membrane as a diffusion barrier

Kazushi Noro, Satoshi Endo, Daisuke Inoue, Natsumi Suzuki, Hiroshi Kameoka, Junko Ono, Satoshi Nakamura, and Yoshinori Yabuki

DOI:10.1002/etc.5518

Combining in vitro and in silico new approach methods to investigate type 3 iodothyronine deiodinase chemical inhibition across species

Sally A. Mayasich, Michael R. Goldsmith, Kali Z. Mattingly, and Carlie A. LaLone

DOI:10.1002/etc.5591

Salmonid pituitary cells as a test system for identifying endocrine-disrupting compounds

Louisa Harding, Irvin R. Schultz, Graham Young, and Penny Swanson

DOI:10.1002/etc.5644

Changes in temperature alter the toxicity of polycyclic aromatic compounds to American lobster (Homarus americanus) larvae

Danielle Philibert, Sarah Marteinson, and Benjamin de Jourdan

DOI:10.1002/etc.5719

Application of ion mobility spectrometry–mass spectrometry for compositional characterization and fingerprinting of a library of diverse crude oil samples

Alexandra C. Cordova, James N. Dodds, Han-Hsuan D. Tsai, Dillon T. Lloyd, Alina T. Roman-Hubers, Fred A. Wright, Weihsueh A. Chiu, Thomas J. McDonald, Rui Zhu, Galen Newman, and Ivan Rusyn

DOI:10.1002/etc.5727

Metal mixture toxicity of Ni, Cu, and Zn in freshwater algal communities and the correlation of single-species sensitivities among single metals: A comparative analysis

Andreas Fettweis, Simon Hansul, Karel De Schamphelaere, and Erik Smolders

DOI:10.1002/etc.5735

Alowaifeer, A. M., Clingenpeel, S., Kan, J., Bigelow, P. E., Yoshinaga, M., Bothner, B., & McDermott, T. R. (2023). Arsenic and mercury distribution in an aquatic food chain: Importance of femtoplankton and picoplankton filtration fractions. Environmental Toxicology and Chemistry, 42, 225–241. https://doi.org/10.1002/etc.5516

Brix, K. V., Tear, L., DeForest, D. K., & Adams, W. J. (2023). Development of multiple linear regression models for predicting chronic iron toxicity to aquatic organisms. Environmental Toxicology and Chemistry, 42, 1386–1400. https://doi.org/10.1002/etc.5623

Chung, J., Lee, J.-H., Hwang, D.-S., Park, D.-H., An, Y.-J., Yeom, D.-H., Park, T.-J., & Choi, J. (2023). Comparison of the estimation methods from acute to chronic biotic ligand model-based predicted no-effect concentrations for nickel in freshwater species. Environmental Toxicology and Chemistry, 42, 914–927. https://doi.org/10.1002/etc.5572

Cordova, A. C., Dodds, J. N., Tsai, H.-H. D., Lloyd, D. T., Roman-Hubers, A. T., Wright, F. A., Chiu, W. A., McDonald, T. J., Zhu, R., Newman, G., & Rusyn, I. (2023). Application of ion mobility spectrometry–mass spectrometry for compositional characterization and fingerprinting of a library of diverse crude oil samples. Environmental Toxicology and Chemistry, 42, 2336–2349. https://doi.org/10.1002/etc.5727

Doering, J. A., Tillitt, D. E., & Wiseman, S. (2023). Reevaluation of 2,3,7,8-tetrachlorodibenzo-p-dioxin equivalency factors for dioxin-like polychlorinated dibenzo-p-dioxins, polychlorinated dibenzofurans, and polychlorinated biphenyls for fishes. Environmental Toxicology and Chemistry, 42, 2215–2228. https://doi.org/10.1002/etc.5690

Fettweis, A., Hansul, S., Schamphelaere, K. D., & Smolders, E. (2023). Metal mixture toxicity of Ni, Cu, and Zn in freshwater algal communities and the correlation of single-species sensitivities among single metals: A comparative analysis. Environmental Toxicology and Chemistry, 42, 2666–2683. https://doi.org/10.1002/etc.5735

Harding, L., Schultz, I. R., Young, G., & Swanson, P. (2023). Salmonid pituitary cells as a test system for identifying endocrine-disrupting compounds. Environmental Toxicology and Chemistry, 42, 1730–1742. https://doi.org/10.1002/etc.5644

Ji, X., Arenas, C. E. D., Perez, A. S. C., Giesy, J. P., & Brinkmann, M. (2023). Predicting the kinetics of resupply of organic pollutants from sediments using diffusive gradients in thin film samplers and their bioavailability to aquatic invertebrates. Environmental Toxicology and Chemistry, 42, 1696–1708. https://doi.org/10.1002/etc.5681

Jeninga, A. J., Wallace, Z., Victoria, S., Harrahy, E., & King-Heiden, T. C. (2023). Chronic exposure to environmentally relevant concentrations of imidacloprid impact survival and ecologically relevant behaviors of fathead minnow larvae. Environmental Toxicology and Chemistry, 42, 2184–2192. https://doi.org/10.1002/etc.5710

Kast, C., Droz, B., & Kilchenmann, V. (2023). Toxicity of coumaphos residues in beeswax foundation to the honey bee brood. Environmental Toxicology and Chemistry, 42, 1816–1822. https://doi.org/10.1002/etc.5645

Labine, L. M., Oliveira Pereira, E. A., Kleywegt, S., Jobst, K. J., Simpson, A. J., & Simpson, M. J. (2023). Sublethal exposure of per- and polyfluoroalkyl substances of varying chain length and polar functionality results in distinct metabolic responses in Daphnia magna. Environmental Toxicology and Chemistry, 42, 242–256. https://doi.org/10.1002/etc.5517

Loken, L. C., Corsi, S. R., Alvarez, D. A., Ankley, G. T., Baldwin, A. K., Blackwell, B. R., De Cicco, L. A., Nott, M. A., Oliver, S. K., & Villeneuve, D. L. (2023). Prioritizing pesticides of potential concern and identifying potential mixture effects in Great Lakes tributaries using passive samplers. Environmental Toxicology and Chemistry, 42, 340–366. https://doi.org/10.1002/etc.5491

Mayasich, S. A., Goldsmith, M. R., Mattingly, K. Z., & LaLone, C. A. (2023). Combining in vitro and in silico new approach methods to investigate type 3 iodothyronine deiodinase chemical inhibition across species. Environmental Toxicology and Chemistry, 42, 1032–1048. https://doi.org/10.1002/etc.5591

Noro, K., Endo, S., Inoue, D., Suzuki, N., Kameoka, H., Ono, J., Nakamura, S., & Yabuki, Y. (2023). Development of a new polar organic chemical integrative sampler for 1,4-dioxane using silicone membrane as a diffusion barrier. Environmental Toxicology and Chemistry, 42, 296–302. https://doi.org/10.1002/etc.5518

Philibert, D., Marteinson, S., & de Jourdan, B. (2023). Changes in temperature alter the toxicity of polycyclic aromatic compounds to American lobster (Homarus americanus) larvae. Environmental Toxicology and Chemistry, 42, 2389–2399. https://doi.org/10.1002/etc.5719

Rivetti, C., Houghton, J., Basili, D., Hodges, G., & Campos, B. (2023). Genes-to-pathways species conservation analysis: Enabling the exploration of conservation of biological pathways and processes across species. Environmental Toxicology and Chemistry, 42, 1152–1166. https://doi.org/10.1002/etc.5600

Saunders, L. J., & Nichols, J. W. (2023). Models used to predict chemical bioaccumulation in fish from in vitro biotransformation rates require accurate estimates of blood–water partitioning and chemical volume of distribution. Environmental Toxicology and Chemistry, 42, 33–45. https://doi.org/10.1002/etc.5503

Schöfer, N., Ackermann, J., Hoheneder, J., Hofferberth, J., & Ruther, J. (2023). Sublethal effects of four insecticides targeting cholinergic neurons on partner and host finding in the parasitic wasp Nasonia vitripennis. Environmental Toxicology and Chemistry, 42, 2400–2411. https://doi.org/10.1002/etc.5721

Suski, J. G., Chanov, M. K., Heron, C. G., Field, J. A., & Salice, C. J. (2023). Ecotoxicity and accumulation of perfluorononanoic acid in the fathead minnow (Pimephales promelas) and an approach to developing protective thresholds in the aquatic environment through species sensitivity distribution. Environmental Toxicology and Chemistry, 42, 2229–2236. https://doi.org/10.1002/etc.5692

Trapp, S., Shi, J., & Zeng, L. (2023). Generic model for plant uptake of ionizable pharmaceuticals and personal care products. Environmental Toxicology and Chemistry, 42, 793–804. https://doi.org/10.1002/etc.5582

Wagner-Deyriès, M., Varignier, L., Revel, M., Delhaye, T., Rondeau, D., Coutellec, M.-A., & McCairns, R. J. S. (2023). Variation of tolerance to isothiazolinones among Daphnia pulex clones. Environmental Toxicology and Chemistry, 42, 805–814. https://doi.org/10.1002/etc.5564