Superfund Research Program

Research Translation Core

Project Leader: Brad L. Upham
Grant Number: P42ES004911
Funding Period: 2006-2021

Project-Specific Links

Final Progress Reports

Year:   2020  2012 

The Research Translation Core (RTC) continued to develop the new analysis pipeline, the FGPipeline, to incorporate into the “Molecular Biology Tools Repository” (MBTR), which was designed to support the project goals in identifying biodegradation genes and detecting biodegradative activity in natural environments. The FGPipeline integrates sequence analysis tools that can be run individual or together as a workflow available on the FGPipeline website. Integrated in this pipeline are components for estimating sequencing error rates from control sequences (Mock Community Analysis), a tool for translating nucleotide sequences to protein with frameshift detection and correction (FrameBot), generating rapid alignment (HMMER3) of high-throughput reads to protein Hidden Markov Models (HMMs), and performing clustering analysis with scaled-up capacity (mcClust). This pipeline workflow option allows researchers to carry out the whole line of essential analysis tasks by entering raw sequencing data through the web page at once and receive a package of results when the process is completed. The researchers have added to the repository 18 new genes, which code for proteins involved in important eco-functions such as biogeochemical cycles (cbh1, cellobiohydrolase), cycling of toxic environmental contaminants (arsA, arsenical pump-driving ATPase), plant pathogenicity, and biosynthesis of antibiotics and toxic chemicals (hcnA1, hydrogen cyanide synthase), and metabolism of aromatic compounds (pqsA, benzoate CoA ligase). Dr. Upham and his research team have strengthened user support by incorporating FunGene tools into RDP’s new interactive procedural tutorials and created a wiki to increase cooperation with the research community.

The RTC’s mission has also been broadened to engage additional stakeholders in a bidirectional manner. The RTC has established a relationship with Michigan’s Department of Environmental Quality (MDEQ), Michigan Department of Agriculture, and the USEPA, and coordinated a collaborative effort between the Geochemical Controls on the Adsorption, Bioavailability, and Long-term Environmental Fate of Dioxins, PCBs, and PAHs project (Project 7) and MDEQ where MDEQ will provide environmental sediments from the Tittabawassee-Saginaw river basin contaminated with dioxin and other AhR-agonists to Project 7’s research efforts. The RTC was also active initiating connections with the Midland-Saginaw communities for the new Community Engagement Core (CEC). In particular, Dr. Upham attended the Tittabawassee-Saginaw River Community Advisory Group (Midland-CAG) meetings that are held bimonthly where he networked with the participants, and is coordinating with this CAG to present a program overview of the SRP center at one of their bimonthly meetings. As the research team advances its CEC efforts, this CAG group will be an instrumental partner. In addition, the chair of this Midland-CAG, Dr. Deborah Huntley, has agreed to be a member of MSU’s SRP External Advisory Committee. RTC and the Computational Modeling of Mammalian Biomolecular Responses Core co-coordinated a short course (Pharmacology 980-1 credit) on “Computational Systems Biology and Dose Response Modeling” that was held May 22-24 at Michigan State University, which provided excellent translational activities of the SRP center. Dr. Upham also presented an abstract and poster at the Partnerships for Environmental Public Health Conference-“Strengthening a Dynamic Environmental Public Health Network for Tomorrow," March 7, 2012, Bethesda, MD, and moderated a session on “Developing Partnerships with State Governments”.