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Your Environment. Your Health.

Progress Reports: Michigan State University: Research Translation Core

Superfund Research Program

Research Translation Core

Project Leader: Brad L. Upham
Grant Number: P42ES004911
Funding Period: 2006-2020
View this project in the NIH Research Portfolio Online Reporting Tools (RePORT)

Learn More About the Grantee

Visit the grantee's eNewsletter page Visit the grantee's eNewsletter page

Progress Reports

Year:   2019  2018  2017  2016  2015  2014  2013  2012  2011  2010  2009  2008  2007  2006 

The Research Translation Core (RTC) has developed a 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 individually 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 receiving a package of results when the process is completed. The RTC has also expanded MBTR to cover more genes that are important in biodegradation and other natural processes, such as ppo (coding for laccase) and carA (coding for carbazole dioxygenase). The FGPipeline and other MBTR tools together have facilitated bioinformatics tasks required by the project.

The RTC's mission has also been broadened to engage additional stakeholders in a bidirectional manner. MSU investigators met with representatives from Michigan's Department of Environmental Quality and Department of Agriculture and are presently organizing a joint seminar series between MSU and environmental scientists from the state agencies. The RTC also organized a new Community Engagement Core (CEC) to be implemented in the renewal of the program and will be integrally involved in CEC activities. Plans were also drafted to implement an educational program for medical students and residents in the College of Human Medicine's community based-program at Michigan State University's Midland and Flint campuses with the intent of training future physicians on environmental issues relevant to their communities. During this funding period, specific activities in addressing the education of medical students in environmental health were conducted by Dr. Trosko in which he helped organize a symposium with Dr. Reza Nassiri, Director of MSU's Institute of International Health, titled "Diminishing Latin America's Inequalities: Land, Food and Human Health Strategies," April 20-21, 2011, with the goal of educating medical students in Chipas and Yucatan, Mexico and Brazil (Universidade Federal da Bahia, Salvador, Brazil). In addition, Dr. Trosko worked with The Seoul National University School of Medicine to teleconference to several South Korean-affiliated medical schools and university hospitals a lecture on "The Role of Physicians to Educate their Patients on the Role of Environmental Toxicants in Human Diseases" (September 20, 2011).

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