Superfund Research Program
Research Translation Core
Project Leader: Brad L. Upham
Grant Number: P42ES004911
Funding Period: 2006-2020
To support projects involved in identifying biodegradation genes and detecting biodegradative activity in natural environments, the Core developed a set of molecular-biology tools to facilitate generating, collecting, and analyzing 16S rRNA and functional-gene data through high-throughput sequencing technologies. These tools include the Functional Gene Pipeline/Repository (FGRP), which offers interactive display and analysis tools, along with monthly updated Hidden Markov Models (HMM) searches of the National Center for Biotechnology Information (NCBI) protein database, and the Pyrosequencing Pipeline, which provides a collection of fast workflow-oriented tools for handling sequence data related to 16S rRNA gene and genes serving important functional roles in contaminant degradation (e.g., oxygenases and dehalogenases). These two pipelines together are capable of serving projects handling high-throughput sequencing data for a variety of important research tasks, such as homology analysis of the marker genes, primer design, as well as quality-controlled data preprocessing, sequence alignment and clustering, classification, tree building, calculations of ecological metrics, etc. Recent work has focused on a major upgrade to the FGRP. This includes a new relational database back-end, the adoption of a new update strategy, and an upgraded Web interface.
This year, the Core decided to plan for another workshop to meet the SBR's new mission ("Partnering with USEPA and ATSDR to Improve the use of Superfund Research Program Science") to help facilitate better communication within each Superfund Program Project, between the various Superfund Programs and the Administrating Superfund Program, and between EPA and ATDSR. The Core's preliminary plan was to co-sponsor a workshop on the "Interaction of human gut micro-flora's role in modulating the toxicity of environmental toxicants and in modulating the risk to various human diseases," to be held at Research Triangle Park. Organizational plans are still ongoing.
In addition, in response to "broaden Core B's [the Research Translation Core's] mission to include more typical 'outreach activities,'" the Core has contacted various stakeholders in the State of Michigan in order to identify common research and applied goals concerning TCDD-like environmental contaminants. The ultimate results for any mutually agreed-upon goals will have to be considered within the constraints of no increase in the Core's budget.