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A vision for the role of bioinformatics in species extrapolation for chemical safety
Citation:
LaLone, C. A vision for the role of bioinformatics in species extrapolation for chemical safety. 2021 Midwest Chapter Society of Environmental Toxicology and Chemistry/Northland Society of Toxicology Joint Meeting, Duluth, MN, April 29 - 30, 2021. https://doi.org/10.23645/epacomptox.14485332
Impact/Purpose:
This presentation will be the Keynote seminar for the Midwest Chapter Society of Environmental Toxicology and Chemistry/Northland Society of Toxicology Joint Meeting. The seminar will discuss the need for understanding the effects of chemical across the diversity of life and the impracticality of generating such data without the use of predictive approaches. The utility of computational approaches that answer questions about biology (termed bioinformatics), typically using DNA and protein information, will be described. The primary example will focus on the development and application of the US EPA Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) tool for predicting chemical susceptibility across species and the evolution of the tool from sequence-based predictions to incorporating structural and functional information. Strengths of bioinformatics approaches along with challenges will be discussed.
Description:
Modernization of chemical safety evaluations with more efficient and rapid, yet scientifically sound, approaches to protect human and ecological health are necessary to keep pace with the development of new chemicals. Historically and with the advent of high-throughput approaches such as cell-based screening bioassays and transcriptomics, select model organisms are used to provide necessary chemical toxicity data. Model organisms are traditionally selected due to ease of maintenance and due to well-characterized genomes, which does not necessarily imply they are the best surrogates for extrapolation of toxicity data to all species needing protection. The US EPA Sequence Alignment to Predict Across Species Susceptibility tool was created to extrapolate knowledge from a known chemical interaction in one species to hundreds of species by comparing protein sequence information. The intent of the SeqAPASS tool is to continue to advance species comparisons at the molecular level, moving from sequence to structure to function as bioinformatics approaches evolve to better understand and predict chemical-protein interactions. This presentation will describe the utility of bioinformatics for species extrapolation using the SeqAPASS tool as an example, describing advances being incorporated in the tool and case examples describing its applications for predicting chemical susceptibility across species.
URLs/Downloads:
DOI: A vision for the role of bioinformatics in species extrapolation for chemical safety
LALONE_VISION FOR EXTRAPOLATION-SLIDES.PDF (PDF, NA pp, 5521.824 KB, about PDF)