Superfund Research Program
Research Translation Core
Project Leader: Brad L. Upham
Grant Number: P42ES004911
Funding Period: 2006-2020
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Progress Reports
Year: 2019 2018 2017 2016 2015 2014 2013 2012 2011 2010 2009 2008 2007 2006
A “Molecular Biology Tools Repository” (MBTR) was developed to support projects identifying biodegradation genes and detecting biodegradative activity in natural environments. The researchers integrated three sets of dnx gene sequences (coding for dioxin dioxygenase) into their Functional Gene Pipeline/Repository (FGRP). The FGRP includes interactive display and analysis tools, along with monthly updated Hidden Markov Models (HMM) searches of the NCBI protein database for related protein sequences. In the last year, Core researchers also integrated updated versions of analysis tools they originally developed for processing gene-targeted metagenomics sequence data as part of their Pyrosequencing Pipeline. These tools were designed to facilitate analysis of gene-targeted metagenomic sequences from current generation high-throughput short-read sequencing technologies. Included in this site are components for estimating sequencing error rates from control reference sequences, rapid alignment of high throughput reads to protein HMMs, with a built-in function for frame shift detection/correction, and performing clustering analysis with scaled-up capacity. This service makes it possible to perform most essential analysis tasks needed for processing gene-targeted metagenomics sequence data for dxn and other genes involved in biodegradation.
This year, the Research Translation Core (RTC) organized a workshop, "Health Consequences from Xenobiotic–Gut Microbiome-Host Interactions" to meet the SRP's new mission of "Partnering with USEPA and ATSDR to Improve the use of Superfund Research Program Science" and to help facilitate better communication within each Superfund Program project, as well as between the various Superfund Programs, the Environmental Protection Agency, and the Agency for Toxic Substances and Disease Registry. The meeting was considered a success on a "cutting-edge" environmental health issue. It was held at NIEHS in Research Triangle Park, N.C., on November 17-18, 2010, with a total of 84 registrants (54 from academia, 21 from government agencies, and 9 from the private sector). In addition to oral presentations from leading scientists in the field, three breakout sessions were conducted to discuss (1) the significance of the human microbiome in the toxicology of environmental contaminants and (2) future directions of this field in environmental health. The discussions were summarized and are currently being prepared for a commentary to be submitted to Environmental Health Perspectives.
The RTC mission has also been broadened to engage additional stakeholders in a bidirectional manner. Michigan State University (MSU) investigators met twice with representatives from Michigan’s Department of Natural Resources and Environment (DNRE) and once with EPA’s Region 5. MSU-SRP investigators are now a recognized resource for MI-DNRE in research on AhR agonist toxicology and bioremediation. Equally important, MSU-SRP research cores have learned critical historical, social, and technical environmental issues pertinent to high priority sites in Michigan contaminated with TCDD-like compounds. These discussions are now influencing current research directives of the SRP research cores, in particular those interested in bioavailability issues involving real sediments found at contaminated sites. The last meeting also included two representatives from EPA’s Region 5, and further efforts are being made for bidirectional partnerships with that group. Dr. James Tiedje presented SRP-related results to the ATSDR’s seminar series (10/20/10).