Grantee Research Project Results
EcoGenoRisk : Identifying Potential Ecological Risks Posed by a Novel Genome
EPA Grant Number: R840207Title: EcoGenoRisk : Identifying Potential Ecological Risks Posed by a Novel Genome
Investigators: Mansfeldt, Cresten
Institution: University of Colorado at Boulder
EPA Project Officer: Callan, Richard
Project Period: July 1, 2021 through June 30, 2024
Project Amount: $337,616
RFA: Assessment Tools for Biotechnology Products (2020) RFA Text | Recipients Lists
Research Category: Chemical Safety for Sustainability , Safer Chemicals
Description:
Synthetic biological (synbio) products pose a unique challenge for effective assessment and mitigation of risks. Unlike the handling of chemical agents, select synbio products maintain the ability to actively replicate within the environment, compounding on the mass and locations required to manage. This proposal focuses on developing an ecological risk assessment for the release of a full synthetic microbial cell (a subset of all synbio organisms) into an environmental matrix by developing the bioinformatic tool EcoGenoRisk.
Objective:
The objective of this proposal is to develop and deploy the Python-based EcoGenoRisk, a bioinformatic tool with three primary aims for the software to deliver: (1) identify those genomes within public databases that negatively respond to the product, display the most similarity genetically to the synbio microorganism, and/or harbor similar or competing pathways, in combination, defining the susceptible populations; (2) identify environmental habitats that are likely to harbor the susceptible populations; and (3) quantify both the likelihood of the synbio microorganism to arrive in the susceptible habitat and the extent of structural or functional disruption experienced by the resident microbial community.
Approach:
The development of EcoGenoRisk focuses on three subfunctions to achieve a risk assessment workflow: HazID, EnvCen, and RiskQ. HazID identifies the susceptible community members within a population. EnvCen then quantifies the population of different environmental matrices that are likely susceptible. Finally, RiskQ then quantifies the overall ecological risk of a synbio microorganism released into various environmental matrices. Each of these functions requires database development and curation, linking to and employing the resources of public bioinformatic and chemoinformatic archives.
Expected Results:
The ultimate outcome of this project is the development and release of EcoGenoRisk, a computational package to compare the novel synbio organism to the available genetic databases, characterizing the risk to known organisms and environments. This bioinformatic system supports the risk assessment of synbio microorganisms by first identifying the presence of a hazard through comparing the modified genomes to wildtype in a combined comparative genetic, pathway, and produced inhibitor analysis (HazID). After identification of a hazard, the habitats most at risk are identified through an ecological census lookup (EcoCen). Finally, the overall risk is characterized by assessing the likelihood of the organism arriving, establishing, and surviving within a given location by considering additional constraints (RiskQ). Combined, EcoGenoRisk will provide the user with an ability to query current genetic databases for predicted risks as the final output. The open-source development of EcoGenoRisk will ensure that users may incorporate the software and approach into other bioinformatic pipelines and link with existing EPA ecological risk assessment tools.
Publications and Presentations:
Publications have been submitted on this project: View all 6 publications for this projectJournal Articles:
Journal Articles have been submitted on this project: View all 1 journal articles for this projectSupplemental Keywords:
Quantitative Risk Assessment, susceptibility, ecological effectsProgress and Final Reports:
The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Conclusions drawn by the principal investigators have not been reviewed by the Agency.