| Literature DB >> 34551147 |
Carlie A LaLone1, Niladri Basu2, Patience Browne3, Stephen W Edwards4, Michelle Embry5, Fiona Sewell6, Geoff Hodges7.
Abstract
Entities:
Keywords: Chemical regulation; Computational toxicology; Predictive toxicology; Species extrapolation
Mesh:
Year: 2021 PMID: 34551147 PMCID: PMC9161440 DOI: 10.1002/etc.5214
Source DB: PubMed Journal: Environ Toxicol Chem ISSN: 0730-7268 Impact factor: 4.218
Figure 1The recognized complexity for meaningful extrapolation of toxicity knowledge across species includes both toxicokinetic and toxicodynamic considerations.
Bioinformatics approaches that could be applied to challenges in cross‐species extrapolation, aligning with biological levels of organization in the adverse outcome pathway framework
| Level of biological organization | Approaches | Examples |
|---|---|---|
| Molecular | Sequence conservation of molecular targets | SeqAPASS ( |
| Conservation of biological pathways | ECOdrug ( | |
| Seq2Fun ( | ||
| Cellular | Conservation of cell types within conserved tissues/organs | MetaboAnalyst ( |
| Conservation of different biological pathways within a cell type | BMDExpress ( | |
| FastBMD ( | ||
| NetworkAnalyst ( | ||
| EcoToxXplorer ( | ||
| OmicsNet ( | ||
| Tissue/organ | Conservation of tissues and organs | The Monarch Initiative ( |
| Phenotypic relationships among species | ||
| Organism | Phylogenetic relationships among species | T‐Rex ( |
| MEGAX ( | ||
| PhyML ( | ||
| RAxML ( | ||
| NGPhylogeny ( | ||
| IQTree ( | ||
| Population | Population‐sequencing approaches | VSEARCH ( |
| Metabarcoding | SWARM ( |
| Term | Definition |
| Adverse outcome pathway | Conceptual construct that portrays existing knowledge concerning the linkage between a direct molecular initiating event (e.g., a molecular interaction between a xenobiotic and a specific biomolecule) and an adverse outcome at a biological level of organization relevant to risk assessment. |
| Bioinformatics | The collection, organization, storage, analysis, and synthesis of biological information using computers commonly applied to ‐omics data such as molecular genetics, genomics, and proteomics. |
| Cytotoxic burst | Stress responses are activated in a nonspecific way at concentrations close to cell death. |
| One Health | Collaborative effort of multiple disciplines—working locally, nationally, and globally—to attain optimal health for people, animals, and the environment. |
| Species extrapolation | The act of using existing knowledge about one species to estimate, predict, project, or infer the effect, impact, or trajectory of another species. |
| Species sensitivity distribution | A cumulative probability distribution of a chemical's toxicity measurements obtained from single‐species bioassays of various species that can be used to estimate the ecotoxicological impacts of a chemical. |
| Systematic literature review | A predefined, systematic method whereby literature is assembled, reviewed, and assessed using standardized techniques. |
| Taxonomic domain of applicability | In the context of the adverse outcome pathway framework, it defines how broadly across taxa/species/subspecies the pathway knowledge is applicable based on conservation of structure and function. |
| Toxicokinetics | The rate of uptake, excretion, and metabolism of a chemical in an organism. |
| Toxicodynamics | The dynamic interaction of a chemical with a biological target resulting in a biological effect. |
| New approach methodologies (NAMs) | An umbrella term used to capture approaches or assays that reduce animal use and improve toxicokinetic or toxicodynamic knowledge of chemicals. They include in silico, in chemico, in vitro assays, omics, and toxicokinetic and exposure prediction. |
| Metabarcoding | The barcoding of DNA/RNA for the simultaneous identification of many taxa within the same sample. |
| Organisation for Economic Co‐operation and Development (OECD) | An intergovernmental economic organisation with 37 member countries that works cooperatively to establish evidence‐based international standards and find solutions to an array of social, economic, and environmental challenges. |
| Registration, Evaluation, Authorisation and Restriction of Chemicals (REACH) | A regulation of the European Union that was adopted to improve the protection of human health and the environment from the risks that can be posed by chemicals. |