Save the Salamander: Epidemiological Modeling Deployed to Halt Killer Fungus

Fire salamanders in parts of Europe are almost extinct due to the Bsal skin fungus. (Photo: Frank Pasmans)

We like to hear what former NIMBioS postdocs are up to, so we were happy to learn from UT professor Matt Gray that his mentee Angie Peace was recently awarded part of a large $2.5 million grant from the National Science Foundation.

The award will fund research to investigate Batrachochytrium salamandrivorans (Bsal), a flesh-eating fungal pathogen that affects salamanders. Researchers will characterize the  fungus’ epidemiology, host immune responses, and pathogenesis in the red-spotted newt, one of the most widely distributed salamander species in North America. Researchers hope to head off an outbreak of Bsal in North America, which holds the world’s greatest diversity of salamanders. Tennessee alone has 57 species.

Originating from Asia, Basl was first discovered in Europe in the Netherlands in 2008 where it caused mass mortality and drove the infected populations to local extinction. Subsequent laboratory trials showed most European salamander and newt species die within two weeks after infection.

Peace, now an assistant professor of mathematics and statistics at Texas Tech University, was awarded $165,000 to lead the epidemiological modeling associated with the research.

As a NIMBioS postdoc from August 2014 to July 2015, Peace developed mathematical models of essential elements and their interactions under the framework of ecological stoichiometry.

If you have some news about a former NIMBioS postdoc, drop us a line!

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How Will Species Adapt to Climate Change? g2p2pop Seeks Answers

What is g2p2pop? The catchy abbreviation describes a new effort to model genomes to phenomes to populations in a changing climate.

The project grew out of activities of the NIMBioS Working Group on Modeling Organisms-to-Ecosystems, and received a $500,000 Research Coordination Network (RCN) award from the National Science Foundation.

Nika Galic, who works in environmental safety and ecological modeling at Syngenta Crop Protection, was a participant in the Working Group and is co-PI on the grant.

The goal of the RCN is “to assemble a diverse, interdisciplinary, multi-institutional, multinational network of scientists to tackle the urgent challenge of predicting how populations and species of vertebrates will respond to a changing climate by integrating knowledge across levels of biological organization.”

Through up to ten laboratory exchanges and five planned workshops, g2p2pop aims to serve as a platform for building interdisciplinary collaborations. They hope to develop new mechanistic models to extrapolate key processes across levels of organization.

Working Group co-organizer Valery Forbes is co-organizing one of the g2p2pop workshops next summer on “Modeling from Genomes to Phenomes to Populations” at the University of Minnesota.

Membership in the g2p2pop RCN is open to university faculty, students, and postdoctoral scholars, those working in industry, and anyone with an interest in the topic.

PI is Loren Buck, professor of biology at Arizona State University. Along with Galic, the other co-PI is Allyson Hindle, assistant professor of anesthesia at Massachusetts General Hospital/Harvard Medical School.

You can read more about g2p2pop at https://nau.edu/cbi-rcn-g2p2pop/

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Team Science at NIMBioS Produces Top Paper

The last meeting of the Working Group in May 2015. (L to R): James Bever, Jonathan Bauer, Katharine Suding, Allan Strand, Dan Johnson, Kerri Crawford, James Umbanhower, Karen Abbott, Jiang Jiang, Maarten Eppinga, Liza Comita, Keenan Mack. Not Pictured: Mara Baudena.

This is the story of how researchers from different corners of the scientific universe can come together to create new synthesis — it involves two former NIMBioS postdocs, a former sabbatical fellow and the special alchemy of a NIMBioS Working Group.

From 2013 to 2015, empiricists and theoreticians studying plant-soil feedback met at NIMBioS with the goal of better understanding the potential role of the soil community organisms that drive diversity patterns within plant communities. They formed the NIMBioS Working Group on Plant-Soil Feedback.

Biologist Allan Strand from the College of Charleston was on sabbatical at NIMBioS; Jiang Jiang and Keenan Mack were in residence as postdoctoral fellows. All three joined the Working Group.

The efforts of the Working Group were rewarded this week with a paper in Nature Ecology & Evolution. The study, “Frequency-dependent feedback constrains plant community coexistence,” outlines a new way to mathematically describe the social network that creates and maintains biodiversity in forests. The equation can be applied to plant communities of any number of species, whereas previously, only predictions of pairwise species interaction were possible.

The authors, which included Jiang, Mack and Strand, tested their theory using observations of tree species diversity on more than 200,000 locations in North America.

“We had previously found spatial patterns of seedlings consistent with strong plant-soil feedback in the data. Our new theory enables us to demonstrate that these feedbacks can explain the high diversity of tree species in warm, moist forests in the South East of the United States and the decline in tree diversity in colder and drier forests,” said senior author of the study and Working Group co-organizer James Bever in a press release. Bever is a professor of ecology and evolutionary biology at the University of Kansas.

“To be able to meet with Working Group participants in Knoxville not just once, but four times between 2013 and 2015 was crucial to getting to the bottom of the intriguing problem of how to quantify community-level plant-soil feedback, ” writes lead author and Working Group co-organizer Maarten Eppinga, in a blog post about the paper. Eppinga is an assistant professor of environmental sciences at Utrecht University.

The other authors on the paper—all from the Working Group—are Mara Baudena, an assistant professor of geosciences at Utrecht University, and Daniel J. Johnson, an assistant professor of forest resources and conservation at the University of Florida.

NIMBioS Working Groups are relatively small with no more than 15 participants, focus on a well-defined topic and have well-defined goals and metrics of success. Since 2008 when the institute was established, NIMBioS has hosted 58 Working Groups.

Jiang, who is now a professor in the Department of Soil and Water Conservation at Nanjing Forestry University, China, joined the Working Group during its second meeting. “It was a really good experience with exciting discussions among top scientists in their areas,” he wrote in an email.

For Strand, his sabbatical at NIMBioS changed the way he approaches research, for the better. “I do research differently now after my sabbatical at NIMBioS. Now when I begin a research project, I always think about what team can I assemble to work on this and what data already exists. Before I tended to do this on my own,” Strand said in an interview.

The result? “All of a sudden my publication rate doubled, my funding is better than it was,” he said. “It made me more collaborative and more willing to think about existing data and modeling that.”

Congratulations to the Plant-Soil Feedback Working Group!

Eppinga MB et al. 2018. Frequency-dependent feedback and plant community coexistence. Nature Ecology and Evolution.

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A Decade of Summer Undergrad Research Underway

Undergraduates take the NIMBioS grand tour on the first day of SRE 2018. This year’s program marks the 10th year of SRE.

The NIMBioS Summer Research Experience (SRE) program kicked off yesterday, celebrating a decade of providing students with opportunities to conduct research at the interface of mathematics and biology.

Fifteen undergraduate students from around the country arrived at NIMBioS to begin the program, which runs for eight weeks. With NIMBioS postdocs and UT faculty, they will work on teams tackling a variety of topics, from modeling thousand cankers disease, management of feral cats, to topics related to hunting in tropical forests, using phylogenetics to understand cancer tumor evolution, and predicting mosquito abundance levels in response to the environment.

To mark the first day, students and their mentors met to begin discussing their projects and what they will aim to get accomplished in the eight short weeks.

Although the main focus is research, the students also receive training on mathematical modeling and software, careers, and graduate school, as well as experience working with the media. They also make time for field trips, dinner parties and other social gatherings.

Nationally competitive, the NIMBioS SRE program typically receives more than 100 applicants. Participants have gone on to do amazing things, from publishing their research in academic journals, to winning competitions with their research, to pursuing doctoral studies in at the interface of math and biology. Participants receive a stipend, apartment-style housing, and travel support to Knoxville.

More photos in our SRE Photo Album.

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Nature Paper Sheds Light on Human Brain Evolution

Why did the human brain evolved to its unusually large size? Former NIMBioS GRA Mauricio González-Forero has some answers in a new Nature publication that develops a mechanistic model showing brain expansion was likely driven by ecological, not social, processes.

Roughly six size times larger than expected for its body size, the human brain consumes 20 percent of the body’s energy yet accounts for only 4 percent of its mass. The dominant hypothesis as to why the human brain has evolved this way suggests that challenging social interactions, such as cooperation and competition, were the driving force.

In their model, González-Forero and co-author Andy Gardner found evidence instead that environmental challenges, such as finding food, are key in driving brain-size evolution.

A Marie Curie Fellow of Evolutionary Biology at the University of St Andrews, González-Forero was a NIMBioS GRA from 2010 to 2012. He earned a Ph.D. in ecology and evolutionary biology in 2013, conducting research in the lab of Sergey Gavrilets focused on mathematical modeling of the evolution of sociality.

González-Forero wrote a detailed article for The Conservation about the Nature paper, which can be found here. The paper has already received widespread attention in mainstream media.

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TN State Assembly Honors Director Gross

(L to R): University of Tennessee Interim Provost and Senior Vice Chancellor John Zomchick, Interim Chancellor Wayne Davis, Dan Simberloff, Louis Gross, David Mandrus, and State Rep. Eddie Smith. Photo Credit: Erik Campos/UT

NIMBioS Director Louis Gross was honored on Friday when State Representative Eddie Smith presented Gross, along with two other UT professors, a resolution commending them for recent achievements.

House Joint Resolution No. 1013 honors Gross, noting his venerable list of academic and professional achievements, in particular as a recent recipient of the 2018 SEC Faculty Achievement Award. The James R. Cox and Alvin and Sally Beaman Distinguished Professor of Ecology and Evolutionary Biology and Mathematics, Gross also directs the Institute for Environmental Modeling.

Also noted was Gross’ service to the Knoxville community, which includes volunteering as a sound engineer for concerts at the Laurel Theater and volunteering for Jubilee Community Arts and Community Shares.

The Resolution states, “Dr. Louis Gross epitomizes the spirit and commitment that are characteristic of a true Tennessean.”

The Resolution was officially adopted by the Tennessee House of Representatives on April 11.

Other UT faculty honored were David Mandrus, the Jerry and Kay Henry Endowed Professor in Materials Science and Engineering and Daniel Simberloff, the Gore Hunger Professor of Environmental Studies.

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French Connection: NIMBioS, CESAB Discuss New Collaborations Across the Pond

CESAB Director Alison Specht visits the drone at NIMBioS’ Spatial Analysis Lab with Director Louis Gross.

New collaborations and conversations about future directions took place last week at NIMBioS with a visit from Alison Specht, the director of the Centre for the Synthesis and Analysis of Biodiversity (CESAB) in Provence, France. Specht met with NIMBioS Director Louis Gross to discuss possible projects and how the plans for NIMBioS sustainability have led to the development of the National Institute for STEM Evaluation and Research, the Spatial Analysis Lab, and the Center for the Dynamics of Social Complexity. They also compared recent papers that each co-authored using theories for human behavior to investigate impacts on data reuse (Specht) and climate change (Gross). Specht was visiting the University of Tennessee to continue work with DataONE, the Data Observation Network for Earth.

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Landmark Collaborations Lead to UT Successes via NIMBioS

In recent years, NIMBioS has developed productive partnerships with faculty in many units at the University of Tennessee, collaborating on and helping manage a variety of sponsored projects. Totaling more than $3.2 million, these grants, contracts and cooperative agreements span interdisciplinary research, from modeling infectious disease to evaluation of STEM education to analysis of issues of concern in conservation and environmental science.

“NIMBioS is experienced in helping faculty build new interdisciplinary research and education efforts and has the capacity and resources to foster successful proposals to diverse funding agencies,” said NIMBioS Director Louis Gross.

Why do UT faculty partner with NIMBioS to develop proposals? Benefits of partnering with NIMBioS include tapping into the guidance of the NIMBioS Leadership Team and staff. Since 2009, the Leadership Team has been successful in managing the first major NSF-funded center-scale activity at UT Knoxville — NIMBioS — and has also brought in over 20 externally-funded projects to UT Knoxville from a diverse collection of federal agencies. Many on the Leadership Team have also served as reviewers for these agencies and so can lend this expertise in proposal development.

NIMBioS has consistently received outstanding ratings from the well over 6,000 visitors that it has supported over the past decade. The staff is experienced in managing every aspect of logistics for any activities that could be developed as a part of a proposal, from small 10-person Working Groups, to major Conferences with over 200 attendees. Logistically, NIMBioS staff takes care of all the details of managing meals, travel and lodging, while allowing organizers of activities to focus on the science and education components of their project.

In addition, NIMBioS has access to a network of more than 5,000 connections around the world in quantitative and life science areas and can readily publicize research successes through its established science communication channels.

NIMBioS also offers expert advice on choosing an evaluator appropriate for any proposal or project, though the National Institute for STEM Evaluation and Research (NISER), which is part of NIMBioS. The NISER staff can directly assist by serving as the evaluator of a project and by assisting investigators to develop the evaluation section of proposals for external support.

For projects with a spatial analysis component, NIMBioS has a set of tools to assist spatial analysis of environmental systems, including a drone that can collect photos and multispectral data, a terrestrial LIDAR system, and expertise in software to analyze the data arising from projects. The Spatial Analysis Lab (SAL) has a standard set of charges for its services that can be specified as appropriate in a proposal or used for currently funded projects.

For those needing some support for modeling projects, NIMBioS is also developing the Mathematical Modeling Consulting Center. Although in its early stages, the MMCC is ready to help. Are you thinking of getting a project started that might benefit from modeling, but you’re unsure how to start? Please contact MMCC Director Nina Fefferman at nina.h.fefferman@gmail.com.

For proposals submitted through NIMBioS, the Institute works with the principal investigators to provide accounting and management services as needed and to develop an indirect cost sharing agreement that can potentially provide more flexibility in planning the project than might be obtained otherwise.

Finally, through NIMBioS, PIs have access to a group of highly successful quantitative researchers with broad skills in mathematical modeling, mathematical biology, spatial data analysis, data science, coding and high performance computing who can serve as collaborators on proposals or be consultants.

We invite UT faculty to partner with NIMBioS and to learn how NIMBioS can help you build new initiatives at the forefront of scholarship. Please contact NIMBioS Director Louis Gross at gross@nimbios.org.

For a full list of current awards at NIMBioS through UT faculty, visit http://www.nimbios.org/UTpartner.

 

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Students with Disabilities Reach Out to High Schoolers

Julia Williams, junior at UT and member of the UT-NIMBioS STEM Alliance

When Julia Williams was a high school student in Nashville, she aspired to study science in college. But with her diagnosis of ADHD, she wondered about the unique challenges she might encounter and didn’t know who to turn to for answers.

Today students like Williams, now a junior in microbiology at UT, can find those answers by turning to groups like the UT-NIMBioS STEM Alliance, which aims to improve the success of students with disabilities in the STEM disciplines.

At a Meet-Greet-&-Eat event held last week at the L&N STEM Academy in Knoxville, Williams and other members from the STEM Alliance chatted over pizza and cookies with  high school students with disabilities who are interested in the STEM fields. The UT students shared tips and resources based on their own experiences in navigating STEM majors on the college campus. UT faculty and staff who work with students with disabilities also attended and shared resources. About 20 high schoolers attended.

“This event was really empowering for our students,” said Lucinda Parramore, Special Education Department Chair at the L&N STEM Academy. “The UT students shared very insightful, personal, and realistic stories about their own experiences in college and how it relates to their disability. For a student with a disability, having peers here talking with them, being honest about their experiences, was encouraging and really lends credibility.”

After the meeting, Parramore said that a parent of one of the high school students told her that the meeting was particularly inspirational for her son. Prior to the meeting, the student had worried a lot about his ability to succeed in college, but hearing from college students was inspirational and showed a path toward success.

Williams has been involved in the UT-NIMBioS STEM Alliance since she was sophomore at UT and says it has been a invaluable resource in learning how to advocate for herself. The group has also helped her know her rights around disclosing her disability and for getting learning accommodations based on the Americans with Disabilities Act. She said it is something she wished she had available to her when she was in high school considering taking on a difficult college major.

“I didn’t know anything about what to expect. It was hard to find any information or who to talk to. Some people even discouraged me from going into microbiology, but it doesn’t have to be that way,” Williams said.

The UT-NIMBioS STEM Alliance also provides scholarship funds to students. Usually meeting bi-weekly throughout the semester, the group holds discussions with speakers on professional development topics, such as careers, resume writing, mentorship, graduate schools and internships. The group also has informal gatherings to share ideas and provide support.

Due the success of last week’s meeting, Parramore hopes to have more meetings with the UT-NIMBioS STEM Alliance and expand it to other Knoxville schools that focus on STEM. She also aspires to develop a mentor program with the college students.

“Having older peers share so openly about their disabilities with the high school students is really empowering. They help mitigate concerns [that the high schoolers] might have about how to succeed in college and help them know about what support is out there,” Parramore said.

Representatives from the Knox County Schools system also attended the Meet-Eat-&-Greet at L&N, including Mike Scripa who works with students with disabilities throughout Knox County. Scripa found the meeting beneficial.

“I was impressed by the maturity of the members of the support group. Their message was empowering and relatable,” he said. “I felt that it provided our students with clarity regarding the importance of seeking helpful relationships in support of their transition goals, regardless of their disability.”

If you or someone you know might be interested in becoming involved with the UT-NIMBioS STEM Alliance, visit its website for more information or contact advisor Suzanne Lenhart (slenhart@tennessee.edu) or NIMBioS Education Coordinator Greg Wiggins (wiggybug@nimbios.org).

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NIMBioS Sweep: Spring Awards Round-up

As the spring semester winds down here on the UT campus, congratulations are in order for a number of NIMBioS-affiliated faculty and staff who received accolades for service and academics.

Suzanne Lenhart
Associate Director for Education and Outreach

At the UT Mathematics Department Honors Day Events, NIMBioS Associate Director for Education & Outreach Suzanne Lenhart was nominated for a 2018 End-of-Year Service Award by the Math Graduate Students Committee. The award honors “outstanding contribution to graduate students not directly related to duties as an instructor of record (eg. advising, mentoring).” In nominating Lenhart, graduate students wrote: “This incredible individual works tirelessly to make sure she is taking care of the needs of everyone with whom she works with. The help and path she has put myself and many others on is very deserving of a service award.”

“Dr. Lenhart is an excellent mentor and helps tremendously in the navigation research, professional development and networking. Despite her very busy schedule, she always makes time for students,” wrote another graduate student.

(L to R): UT math professor Morwen Thistlethwaite, Sam Duchscherer, and Louis Gross at the UT Mathematics Department Honors Day Events.

Graduate students also made their mark. The Mathematics Department honored Samantha Duchscherer who received the Yueh-er, Hong-hsu & Clarence Cheng Kuo Fellowship Award for her master’s thesis, “Classifying Building Usages: A Machine Learning Approach on Building Extractions.” Duchscherer was supported by a contract to NIMBioS and her thesis advisor is NIMBioS Director Louis J. Gross. Following graduation this spring, Duchscherer has accepted a position as a post masters research associate with the Geographic Information Science and Technology  group at Oak Ridge National Laboratory.

 

NIMBioS GRA Danielle Burton

Over at the Chancellor’s Honors Banquet, NIMBioS Graduate Research Assistant Danielle Burton  was awarded the LGBTQ Student Leadership Award, given by the Commission for LGBT People to a student who demonstrates a commitment to advancing lesbian, gay, bisexual, and transgender issues on campus. Burton is a doctoral candidate in mathematics whose research focuses on optimal control of difference equations describing populations and on examining the effects of processes such as harvesting or dispersal on individual or coupled populations. More details here.

 

(L to R): Faculty Advisor Beth Schussler and her student Miranda Chen at the Chancellor’s Honors Banquet. Photo Credit: Marilyn Kallet

Miranda Chen, a doctoral student in ecology & evolutionary biology, was awarded a Chancellor’s Citation for Extraordinary Community Service for her contributions to the university community through leadership and service. During the spring semester, Chen conducted an independent study with the National Institute for STEM Evaluation and Research (NISER) at NIMBioS. She also helped NISER with evaluating the Possibilities in Post-Secondary Education & Science (PiPES) program. She is working with NISER to write a paper for The Qualitative Report Journal that includes best practices in the evaluation of STEM education outreach programs using qualitative data from multiple stakeholders. Chen will continue her research this summer with NISER and NIMBioS.

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