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Michigan State University Superfund Research Program
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MSU Superfund Research Program Newsletter

The MSU Superfund Research Program is pleased to send you the ninth edition of our electronic newsletter. Please take a moment to read over our recent activities.  

For more information on the MSU Superfund Research Program,
please visit: http://iit.msu.edu/superfund/index.html.

In This Newsletter:

Research Spotlight

Research Support Core B: Environmental Molecular Analysis, Michigan State University

The “Environmental Molecular Analysis Core” (EMAC) is an integral part of the MSU Superfund Research Program Center. The primary objectives of EMAC is to provide bioinformatics support for the Center research projects primarily through improved analysis methods for high-throughput gene-targeted metagenomics of microbial populations, support for RNA-Seq analysis of biodegrading strains and microbial communities, and through novel  functional gene metagenome and metatranscriptome enrichment methods. One ongoing example of the EMAC support is the transcriptome analysis of pure cultures of bacterial organisms challenged with free or sorbed 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and its less toxic congener dibenzo-p-dioxin (DD), that resulted in answering important questions regarding bioavailability, gene expression response, toxicology, and other environmental impacts of TCDDs, and possible bioremediation solutions.
 
EMAC has developed critical software tools for outside researchers both as freely available web tools on our public site and as open source software. These include FunGene, a database  of important ecofunctional genes, including dioxin and other biodegradative genes. FunGene includes a pipeline for analysis of gene-targeted metagenomics for dioxin degradation genes to reveal the natural diversity in dioxin and dibenzofuran-degrading microbial communities. Another is the Xander software package, which incorporates a novel method for assembling protein-coding sequences for genes of interest from a metagenomic dataset. In addition to the software package, EMAC has created tutorials and help files. These tutorials walk the new user step-by-step through the process of preparing the necessary protein models for each new gene from the gene sequences in our FunGene database, through post-processing and analysis of the results. The software, source code and tutorials are available for free at https://github.com/rdpstaff/RDPTools. These tools are routinely updated with new genes of interest to the investigators.
 
EMAC has also developed a EcoFunPrimer primer/probe design platform for protein-coding genes. EcoFunPrimer can rapidly design thousands of probes and primer pairs required for in-solution RNA bait-and-capture and for SmartChip  and other massively parallel amplicon qPCR systems. More recent developments include new functions allowing combinations of weighing schemes for reference sequences based on a-priori information, such as the importance of different gene alleles in the target environments, along with the choice of three weighting methods to correct uneven phylogenetic distribution of the reference set.
 
All EMACS software tools are available at no cost through the Research Translation Core.

Dearing Named to EPA Council for Environmental Policy and Technology

Dr. James Dearing, Core Leader of the MSU Superfund Community Engagement Core, and professor and chairperson of the Department of Communication at MSU's College of Communication Arts and Sciences, has accepted an invitation to serve on an advisory council for the U.S. Environmental Protection Agency. Dearing will serve on the EPA’s National Advisory Council for Environmental Policy and Technology, which advises the agency administrator about a range of issues and reports to the EPA on policy challenges.
 
“This will be a way to bring a social science perspective to EPA deliberations,” said Dearing. “Applications of diffusion of innovation theory and scale-up strategies can help the EPA to accelerate the adoption of community-level adaptation and mitigation policies and practices in response to climate change.”
 
Established in 1988, the National Advisory Council for Environmental Policy and Technology is charged with providing expert advice to the EPA administrator on a broad range of issues. These include environmental policy, technology and management issues. The council helps the EPA to gain diverse perspectives from a range of interest groups, including the public, private and nonprofit sectors. Council members serve as representatives from business and industry, academia and nongovernmental organizations, as well as state, tribal and local governments.
 
The council provides the EPA with an efficient and cost-effective forum that can quickly respond to evolving policy challenges. The council meets several times annually.

National Academy Workshop: The Promise of Single Cell and Single Molecule Analysis Tools to Advance Environmental Health Research
 

Workshop & Webcast
March 7-8, 2019; Washington, DC

National Academies of Sciences, Engineering, and Medicine
Keck Center, Room 100
500 Fifth Street NW Washington, DC 20001

Workshop Chaired by MSU’s Dr. Norbert Kaminski
Organizing Committee includes MSU’s Dr. Sudin Bhattacharya


How similar are the cells within a particular tissue? Most analytical tools study cells and their molecular contents in bulk, providing information about the average cell and molecular complexes. Now, emerging findings suggest these traditional approaches could miss important differences between the cells in a sample, rare cell types like cancer stem cells or drug-resistant bacteria, and the opportunity to capture a cell in a fleeting transitional state.

Over the past decade, new single cell and single molecule analysis tools have led to advances that isolate single cells, technologies that can assay each cell's DNA, RNA, proteins, and metabolites, and imaging tools that map cell contents and their molecular interactions. These tools promise new insight on the differences in function between individual cells and molecules, the organization and timing of responses to stimuli, how cells interact as components of a complex system, and how these interactions may change with age, disease, and exposure to environmental stressors.

This workshop will explore the current status of this rapidly evolving field of study, review the preliminary use of single cell and single molecule analysis tools in environmental health studies, and investigate the resources needed to make the data generated most useful to the biomedical and public health fields and to regulatory decision makers.

Held in Washington D.C. and webcast live, the workshop will include presentations and panel discussions on topics such as:
  • What does single cell and single molecule analysis enable researchers to do better, for example in terms of precision, accuracy, and speed?
  • What kinds of environmental health questions or challenges could be explored with single cell and single molecule detection tools and analysis?
  • What are the key goals to advance or improve single cell and single molecule tools, particularly as they pertain to environmental health research and decision needs?
  • What are the key barriers or limitations to the use of data emerging from the use of single cell and single molecule detection tools, for example in terms of standards, comparability across technologies, and the limit of detection uncertainties?
For more information and to register, please visit: http://nas-sites.org/emergingscience/the-promise-of-single-cell-and-single-molecule-analysis/.

MSU Researcher Awarded Best Postdoctoral Presentation from the SOT Immunotoxicology Specialty Section


Dr. Lance Blevins, Project 1, has been selected to receive the Best Postdoctoral Presentation from the Immunotoxicology Specialty Section of the SOT for his paper titled, "Identification and Characterization of a Sensitive Immunologic Target of TCDD: CD5⁺ Innate-like B Cells”.  Using human primary peripheral blood B cells, Dr. Blevins demonstrates the preferential sensitivity of CD5+ innate-like B cells to aryl hydrocarbon receptor (AHR) activation and provides insight into mechanisms associated with AHR activation in human B cells. Others who contributed to this work include Jiajun Zhou, Nick Wawee, Robert Crawford, Sudin Bhattacharya and Norbert E Kaminski. Dr. Blevins will be presenting this paper on Wednesday, March 13 at 3:45 pm at the SOT Annual Meeting.

MSU SRP Researchers Win 2019 Best Paper Award in Applying Risk Assessment

Researchers Qiang Zhang, Sudin Bhattacharya and Rory Connolly from Research Support Core A: Computational Modeling of Mammalian Biomolecular Responses have received the 2019 Best Paper Award in Applying Risk Assessment  from the SOT Risk Assessment Specialty Section for their paper, "Bridging the Data Gap From in vitro Toxicity Testing to Chemical Safety Assessment Through Computational Modeling," which was published in Frontiers in Public Health in September of 2018. 

https://www.frontiersin.org/articles/10.3389/fpubh.2018.00261/full 

Dr. Sudin Bhattacharya Presents Webinar for ASCCT 


Dr. Sudin Bhattacharya presented a webinar for the American Society for Cellular and Computational Toxicology (ASCCT) on February 21, 2019 titled, “Integrating Genomics and Epigenomics into Predictive Toxicology of the Aryl Hydrocarbon Receptor (AHR)." You can view Dr. Bhattacharya’s presentation at: https://www.youtube.com/watch?v=3CGLDzhNCqc, at the 37:37 mark.  

Postdoctoral Trainee Nault Attends Bio-Trac Single Cell RNA-Seq Workshop


Rance Nault, postdoctoral trainee working with Projects 1, 2, and 3, attended the Bio-Trac Single Cell RNA-Seq Workshop in Germantown, Maryland, December 10-13, 2018. Single-cell sequencing is an emerging technique which allows the evaluation of gene expression with unprecedented resolution.

Through hands-on training during the workshop, Nault developed the critical skills to perform both wet lab and computational analysis. "Developing these skills is essential for the use of these tools in my own research applying toxicogenomics in the evaluation of AhR-mediated fatty liver disease pathogenesis and enabling the dissection of mechanisms at the cellular level," said Nault.

Article Spotlight

 

Researchers from Project 6: Geochemical Controls on the Sorption, Bioavailability, Formation and Long-term Environmental Fate of Polychlorinated Dibenzo-p-Dioxins (PCDDs), recently published a research article titled, "Quantification and characterization of dissolved organic carbon from biochars," in Geoderma. 

Abstract: 
Dissolved organic carbon (DOC) in biochars is critical to carbon dynamics and contaminant transport in soils. This study aimed to develop a robust and easy method to characterize and quantify the biochar-DOC, using water-, acid-, and base-extractable DOC samples (WEOC, AEOC, and BEOC respectively) from 46 biochars produced from diverse feedstocks and pyrolysis conditions. BEOC concentrations were the highest (2.3–139 mg-C/g-biochar), followed by WEOC (0.5–40 mg-C/g-biochar) and AEOC (0.2–23 mg-C/g-biochar). Fast-pyrolysis biochars generally had higher DOC concentrations than slow-pyrolysis biochars. DOC concentrations in slow-pyrolysis biochars decreased exponentially with increasing pyrolysis temperature from 300 to 600 °C. The solid-state 13C NMR showed that biochar-DOC had abundant small fused-ring aromatics, aliphatic C, and carboxyl C. Biochar-DOC included an acid-precipitated (AP) fraction of higher molecular weight and aromaticity and an acid-soluble (AS) fraction of lower molecular weight and aromaticity. BEOC generally had a greater AP fraction than WEOC and AEOC. Molecular weight, aromaticity and composition of AEOC and BEOC differed from those of more environmentally-relevant WEOC, suggesting that the acid- and base-extraction may not produce the DOC released in real soils. Finally, a quick, easy and robust UV–vis spectrometric method was developed to measure the composition and concentrations of WEOC in diverse biochar samples (R2 = 0.96, n = 46).
https://www.sciencedirect.com/science/article/pii/S0016706118307614

MSU SRP Virtual Lab Meetings Spring 2019

Two MSU SRP Virtual Lab Meetings have been scheduled for spring 2019:

  • Tuesday, March 26 - Gerben Zylstra, Project 5
  • Tuesday, April 30 - Jeff Cox, Community Engagement Core
Both meetings will take place at 12:00 noon Eastern Time in 162 Food Safety and Toxicology Building, MSU and can be joined by affiliates at Purdue and Rutgers by using Zoom. Zoom information will be distributed prior to the events.
Copyright © *|2019|* *|Michigan State University Superfund Research Program|*, All rights reserved.

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