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SeqAPASS as a prioritization tool, applied to pharmaceuticals and their environmental safety
Citation:
Lalone, C. SeqAPASS as a prioritization tool, applied to pharmaceuticals and their environmental safety. Ghent University, Virtual, NC, March 10, 2023. https://doi.org/10.23645/epacomptox.24602322
Impact/Purpose:
The lecture for Ghent University Environmental Toxicology and Aquatic Ecology course 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 in the context of pharmaceuticals in the environment.
Description:
Bioinformatics is the combination of information science, mathematics, and biology to answer biological questions, typically pertaining to the exploration of large volumes of DNA and/or amino acid sequence data. The major advantages of such approaches are that complex data can be queried, extracted, stored, organized, annotated, visualized, and interpreted rapidly using computers. The science of bioinformatics has been greatly enhanced in the fields of drug discovery and development paving the way for exciting opportunities to apply these methods to challenges in ecotoxicology. In particular, ecotoxicology aims to understand the effects of chemical stressors to the diversity of life in the environment. That is over an estimated + 8 million eukaryotic species on earth. Recognizing that it is impossible to generate toxicity data for all species that may be exposed to chemicals in the environment, there are bioinformatics approaches that have been developed that can be used to extrapolate knowledge from toxicity data generated with model organisms to the diversity of species. Specifically, the US Environmental Protection Agency’s Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS; https://seqapass.epa.gov/seqapass/) was created using bioinformatics approaches to streamline a process for evaluating protein sequence similarity to predict chemical susceptibility across the diversity of species. The web-based tool was developed to generate a transparent and user-friendly method for users with a basic understanding of biology to generate meaningful data to extrapolated knowledge across species for research and decision-making. During this lecture the SeqAPASS tool and methods will be described along with brief descriptions of demonstrated applications for current environmental challenges relative to pharmaceuticals in the environment. Overall, the lecture will be used as a means to illustrate that the science of ecotoxicology is primed for the integration of bioinformatics approaches in its toolbox for cross species extrapolation. The contents of this abstract neither constitute nor reflect official US EPA policy.
URLs/Downloads:
DOI: SeqAPASS as a prioritization tool, applied to pharmaceuticals and their environmental safety
PRESENTATION.PDF (PDF, NA pp, 10076.158 KB, about PDF)