Superfund Research Program
Research Translation Core
Project Leader: Brad L. Upham
Grant Number: P42ES004911
Funding Period: 2006-2020
The Research Translation Core is developing a Molecular Biology Tool Kit (MBTK) based on software tools developed by the Center’s research in detection of biodegradative activity in the environment. Over the past year, the Core updated the sequence information in the functional gene pipeline / repository (FGPR) component of the MBTK 12 times. This site was accessed by researchers over 1,000 times per month. In addition, researchers are adapting programs that were developed in the Environmental Molecular Analysis Core for analysis of ultra-high-throughput pyrosequencing of environmental dioxygenase genes for the MBTK. These are being developed into a pipeline similar to the one that was developed last year for rRNA sequences; it will be able to process tens to hundreds of thousands of functional gene sequences at a time. The pipeline uses the Hidden Markov Models developed for the FGPR along with the GeneWise Tookit and HMMER to translate and align the sequences. They are also building a tool to provide pairwise distances for the protein sequences. Additional tools from the Core’s existing rRNA pipeline will be used to further process the sequences.
A second annual symposium on "Dioxin Toxicity: Mechanisms, Models, & Potential Health Risks" was held on October 21-22, 2008. Based on both the quality of the lectures by leaders in the field of TCDD toxicology and by the attendance & feedback of both the speakers and attendees, the evaluation of the workshop was deemed a success. With international, national and local speakers, three broad categories of TCDD-related topics were covered. The variety of attendeesmakes it clear that the Core had targeted a broad spectrum of backgrounds, expertise and interests. The pragmatic outcome of the formal and informal feedback during the workshop ensures new and renewed collaborations.
Dr. James Tiedje, co-investigator on the Superfund grant organized a workshop dealing with a potential environmental concern entitled "Pharmaceuticals in the Environment: Current Trends & Research Priorities", November 20, 21, 2008. The Research Translation Core decided to lend support to this workshop in order to discover potential ways in which the biomedical group of the Superfund Project might interact with the environmental engineers who have the technology to analytically detect these pharmaceutics and to remediate them, but do not have the expertise to evaluate the potential human/ecological health risks. Again, the quality of the invited speakers brought this emerging field into a high quality review of this topic.
A presentation of research translation work was made at the meeting in Asilomar, December 7th, 2008 “Development and Application of Functional Gene and Pyrosequencing Pipelines for Analyzing Phylogenetic and Functional Diversity of Contaminated Sites”,Iwai S, Chai B, Wang Q, McGarrell D, Sul W, Cole JR, Hashsham SA, and Trosko JE.