Grantee Research Project Results
2023 Progress Report: 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: Packard, Benjamin H
Project Period: July 1, 2021 through April 22, 2025
Project Period Covered by this Report: July 1, 2022 through June 30,2023
Project Amount: $337,616
RFA: Assessment Tools for Biotechnology Products (2020) RFA Text | Recipients Lists
Research Category: Safer Chemicals , Chemical Safety for Sustainability
Objective:
The primary objective of this proposal is to develop and deploy the Python-based EcoGenoRisk, a bioinformatic tool with three aims for the software to deliver:
- Identify those genomes within public databases that negatively respond to the product, display the most similarity genetically to the synbio organism, and/or harbor similar or competing pathways to define susceptible populations;
- Identify environmental habitats that are likely to harbor the susceptible populations; and
- 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.
Progress Summary:
Within the reporting period, the coding effort focused on releasing the HazID portion of EcoGenoRisk. HazID has three main functions: NicheOverlap, CompetitorFind, and PoisInhibitor. NicheOverlap focuses on the direct displacement by the synbio microorganism overlapping and outcompeting with a given niche. CompetitorFind identifies similar, competing, or mitigating pathways in response to the presence of the synbio microorganism. Finally, PoisInhibitor finds those enzymes that respond negatively to the product of the synbio microorganism.
The main results in this reporting period are as follows: (1) a script and public release of HazID, (2) an automatically updating genome database, (3) an automatically updating EC number database, (4) a test-run of HazID on an external dataset, and (5) demonstration of CompetitorFind and PoisInhibitor.
Future Activities:
The main future research and development activities planned for the next reporting period continue the tasks identified in the timeline (Figure 1). After the current release of HazID, the developmental effort will switch to EcoCen and the curation of metagenomes. The main targeted outputs during this period are two papers and the attendance of two conferences. With Anna Ulanova successfully completing, John Docter was recruited as a PhD student and will lead the completion of the project.
Journal Articles on this Report : 1 Displayed | Download in RIS Format
| Other project views: | All 9 publications | 1 publications in selected types | All 1 journal articles |
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Ulanova A, Mansfeldt C. EcoGenoRisk:Developing a computational ecological risk assessment tool for synthetic biology. Environmental Pollution 2024:123647. |
R840207 (2023) R840207 (2024) |
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Supplemental Keywords:
functional classification, phenotypic classification
Relevant Websites:
Git Hub CU Boulder, Exit CMBM-GEM Labs Exit
Progress and Final Reports:
Original AbstractThe 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.