Congratulations to the New Participants of SRE 2015!

2014 SRE students are interviewed about their research by the media.

2014 SRE students are interviewed about their research by the media.

NIMBioS is pleased to announce the 16 participants selected for its highly competitive 2015 Summer Research Experience (SRE) program for undergraduates and teachers. Participants were selected from a pool of more than 150 applicants. The program runs for eight weeks, from June 8-July 31. Participants will come to NIMBioS on the Univ. of Tennessee, Knoxville, campus to work in teams with NIMBioS postdocs and UT faculty on research at the interface of mathematics and biology.

2015 SRE participants and their assigned team projects are as follows:

Margaux Hujoel (Mathematics & Computational Biology, Harvey Mudd College); Virginia Parkman (Mathematics, Univ. of Tennessee); and Ayana Wild (Computer Science & Mathematics, Tennessee State Univ.) will work on a project to model canine distemper.

Talon Johnson (Mathematics, Morehouse College); Januka Khanal (Biology, Southeastern Univ.); Michael Rohly (Mathematics & Biology, Columbus State Univ.); and Nick Sirek (Honors Biology & Geology Teacher, L&N STEM Academy, Knoxville, TN) will explore stressors in host-pathogen interactions.

Ashish Gauli (Biology, Fisk Univ.); Nathan Wikle (Mathematics, Truman State Univ.); and Ryan Yan (Mathematical Biology, College of William and Mary) will investigate invasive species movements through global shipping routes.

Mariel Bedell (Biological Sciences, Carnegie Mellon Univ.); Yilin Lin (Applied Mathematics, Emory Univ.); and Emmie Melendez (Mathematics, Univ. of Puerto Rico, Mayaguez) will model the distribution of fluid pressure in the kidney.

Riley Mummah (Biology, Statistics & Mathematics, The Pennsylvania State Univ.); Diya Sashidhar (Applied Mathematics, North Carolina State Univ.); and Jinchuan Wei (Science, Univ. of Minnesota, Twin Cities) will develop mathematical models of Mycobacterium tuberculosis in mice.


Did you like this? Share it:
Posted in SRE | Tagged | Leave a comment

Bat Monitoring Working Group Receives ‘Wings Across the Americas’ Award

The North American Bat Monitoring Program (NABat) working group was hosted by the National Institute for Mathematical and Biological Synthesis in Knoxville, Tenn., to design a program for coordinated bat monitoring across North America. Front row: (L to R) Tushar Kansal, Laura Ellison, Susan Loeb, Tom Rodhouse, Kathi Irvine, Subhash Lele, Robin Russell, Cori Lausen. Back Row: (L to R) Tom Ingersoll, John Reichard, Matthew Clement, Tom Stanley, Wayne Thogmartin, Doug Johnson,Tom Hallam , Patrick Field, and John Sauer.

Bat conservation researchers and their partners associated with a NIMBioS Working Group were recognized yesterday with the U.S. Forest Service Wings Across the Americas Research Award for their contributions to the North American Bat Monitoring Program (NABat).

The award was accepted on behalf of the US Geological Survey contributions to NABat by Anne Kinsinger, USGS associate director for Ecosystems, at the North American Wildlife Resources Conference in Omaha, NE.  USGS partners also recognized were the U.S. Forest Service, National Park Service, U.S. Fish and Wildlife Service, Department of Defense, Environmental Protection Agency, Wildlife Conservation Society, Bat Conservation International, Bat Conservation Trust, Canadian Wildlife Service, University of California, University of Alberta and Colorado Parks and Wildlife.

“Research on bats is important not only because they are vital to the well-being of ecosystems, but also it is in the best interest of the economy due to the importance of bats for pest control and pollination of native and agricultural plants,” Kinsinger said.

Wings Across the Americas is an international program of the U.S. Forest Service that works with a wide range of partners here in the United States and overseas to conserve habitats and populations of birds, bats, butterflies and dragonflies. The award recognizes outstanding conservation work by U.S. Forest Service and partner agencies.

The novelty of the NABat program is a vision for collaborative monitoring of an imperiled species group with a sound statistical underpinning allowing for species distribution modeling across broad geographic regions. Researchers provide expertise on statistical survey design, statistical analysis of bat acoustic and colony count data and database development informed by experience with many wildlife species such as bats, birds and amphibians.

NABat was developed in conjunction with specialists from other agencies, universities and NGOs in the United States, Canada, the United Kingdom and Mexico in response to growing concerns over threats to bats from continuing and emerging stressors including habitat loss and fragmentation, white-nose syndrome, wind energy development and climate change.  There are currently no national programs to monitor and track bat populations in North America, and NABat seeks to assist in development of such programs that will provide managers and policy makers with the information they need to effectively manage bat populations, detect early warning signs of population declines and estimate extinction risk.

Efforts to date include four workshops and discussions supported by NIMBioS and the Landscape Conservation Cooperatives National Council to develop a national monitoring program. The workshops were attended by scientists and researchers from multiple agencies including FWS, USGS, USFS, NPS, University of Calgary and the Canadian Wildlife Service.  The framework for NABat, “A Plan for a North American Bat Monitoring Program (NABat)” will be published in May 2015.


Did you like this? Share it:
Posted in awards, Wildlife | Tagged , | Comments Off

Peace of Cake: NIMBioS Postdoc Revealed as Top Baker


Dr. Peace and her winningest cake.

NIMBioS postdoc Angie Peace knows a little something about food web dynamics, and she also knows how to make the best kind of food: cake! Peace’s cake took 1st place this week in the Biogeography Cake Contest for UTK’s Darwin Day.

Judged on taste and scientific merit, Peace’s cake had four circular layers of alternating chocolate and red velvet with creme cheese frosting. The theme was biogeographical phylogenetics. Four different panels around the sides of the cake illustrated evolution through time with small cake islands for continents and red liquorice for phylogenetic trees. Toblerone chocolate served nicely as mountains on the top. Peace won $50 for her cake.

As a NIMBioS postdoc, Peace uses mathematical modeling to determine the effect of phosphorus pollution from fertilization run-off on the food web dynamics of freshwater lakes.

She confesses to being a life-long baker, and she is often asked to bake birthday cakes for friends. “When I was a kid, I always wanted an Easy Bake Oven, but my mom wouldn’t let me get one and so I had to use the real oven instead,” Peace said. Apparently, the lessons learned in the kitchen at a young age paid off.

Dr. Peace's cake had four panels of continents and phylogenetic trees depicting evolution through time.

Dr. Peace’s cake had four panels of chocolate continents and licorice phylogenetic trees depicting evolution through time.


Did you like this? Share it:
Posted in awards, competitions, postdocs | Tagged , | Comments Off

NIMBioS Hits 5,000 Mark

NIMBioS at the University of Tennessee, Knoxville

NIMBioS at the University of Tennessee, Knoxville

Since our first activity in March 2009, more than 5,000 visitors have participated in NIMBioS research and educational opportunities. We recently surpassed the 5,000 mark with last week’s Investigative Workshop on Lymphoid Cells in Acute Inflammation.

NIMBioS was established in September 2008 with support from the National Science Foundation, the U.S. Department of Homeland Security, and the U.S. Department of Agriculture with additional support from The University of Tennessee, Knoxville. Today, we are a NSF Synthesis Center supported through NSF’s Biological Sciences Directorate via a Cooperative Agreement with UT totaling more than $35 million over ten years.

NIMBioS supports Working Groups, which focus on major well-defined scientific questions at the interface between biology and mathematics; Investigative Workshops, which focus on broad topics and which summarize/synthesize the state of the art and identify future directions; Postdoctoral Fellowships; Sabbatical Fellowships; short-term visits; and a wide array of education and outreach activities for K-12 students and teachers, undergraduate and graduate students, university and college faculty, professional industry audiences, and the general public.

Since our first activity in 2009 (Training the Trainers: High-Performance Computing Tutorial for Computational Science Professionals Collaborating with Biologists), NIMBioS has hosted more than 5,000 participants from 789 institutions in 53 countries and all 50 U.S. states and has supported 34 Working Groups, 32 Investigative Workshops, 37 Postdoctoral Fellows, 13 Sabbatical Fellows, over 200 short-term visitors, and more than 200 education and outreach activities. Activities have led to the publication of more than 370 peer-reviewed articles on topics across the breadth of quantitative biology. Publications resulting from NIMBioS activities have appeared in top national and international journals with high impact factors, including Nature, Science, Ecology Letters, Trends in Ecology and Evolution, PLOS Biology, Systematic Biology, and the Proceedings of the National Academy of Sciences.

One research area of particular emphasis at NIMBioS has been modeling animal
infectious diseases, such as white-nose syndrome in bats, pseudo-rabies virus in feral swine, Toxoplasma gondii in cats, and vector-transmitted diseases such as malaria in mosquitoes and humans. As a leading international center for animal infectious disease modeling, NIMBioS has contributed significantly to global needs in analyzing the potential spread, impact and control of diseases that can move from animals to humans, such as West Nile virus, anthrax, swine flu and mad cow disease.

NIMBioS has carried out extensive evaluations of the variety of activities it has supported which has led to peer-reviewed publications on the methods used at NIMBioS to foster interdisciplinary research and education. NIMBioS has made available many of the products of its activities through its website and a variety of social media outlets. Available products include more than 50 video interviews of researchers and educators discussing their experiences in mathematical biology and more than 100 videos of research and tutorial presentations at NIMBioS.

Did you like this? Share it:
Posted in Education/Outreach, research | Tagged , | Comments Off

Evolution Featured at Tennessee Teacher Conference

Mike Knapp, biology teacher at Hardin Valley High School, sets up a demonstration of his lactose intolerance lab while teachers are in discussion.

Mike Knapp (upper left), biology teacher at Hardin Valley High School, sets up a demonstration of his lactose intolerance lab while teachers discuss.

While socio-cultural forces continue to pressure teachers not to talk about evolution through intimidation and confusing laws, many science teachers remain committed in the face of adversity to helping each other teach their students the scientific consensus of evolution as an important unifying concept in science. A session on how to teach the evolution of the lactose tolerance gene drew 40 middle and high school science teachers and pre-service teachers into a packed room at the statewide Tennessee Science Teachers’ Association Conference last week. The session was jointly supported by NIMBioS and Darwin Day Tennessee.

Discussing the evolution of lactose tolerance with students presents an interesting case because it demonstrates how human culture can be a selective agent of evolution. Also, students can relate to the subject matter personally, since most of the world’s population, mostly people of non-European ancestry, can’t tolerate lactose in dairy into adulthood. Hardin Valley Academy biology teacher Mike Knapp introduced teachers to the lab that he uses with his own students, using cups of milk, Lactaid pills and glucose test strips to learn about the effect of enzymes on breaking down lactose into glucose.

Whitaker Hoskins, a graduate student at the University of Tennessee, co-presented a guided non-fiction reading on lactose tolerance from “Before the Dawn” by Nicolas Wade. Hoskins said interacting with the teachers was the highlight of his session during last week’s conference. He also spoke to teachers about the many events planned for February as a part of Darwin Day Tennessee surrounding Darwin’s birthday, including a day-long teacher workshop on teaching evolution which will be hosted at NIMBioS on February 7, 2015. Look for more details about signing up for this workshop coming soon to the Darwin Day Tennessee website.

The National Center for Science Education (NCSE) and the Howard Hughes Medical Institute (HHMI) donated teacher packets, videos and books to the teachers attending the session.

Did you like this? Share it:
Posted in conference, Education/Outreach, evolution, high school, Middle School, STEM, Teachers | Tagged , , , , , , | Comments Off

Two Days of STEM Fun: Over 100 Middle School Students, Teachers & Parents Visit NIMBioS

Elizabeth Hobson, NIMBioS postdoctoral fellow (standing, black shirt) helping visiting students from Greenback School with an image analysis activity

Elizabeth Hobson, NIMBioS postdoctoral fellow (standing, black shirt) helping visiting students from Greenback School with an image analysis activity.

NIMBioS hosted two events for middle school students last week that resulted in over 100 students, parents and teachers visiting the institute. On the agenda were fun activities to inspire students to pursue higher education in science, technology, engineering and math (STEM). The first event was a field trip by 7th graders from Greenback School in Loudon County, TN, which brought 60 students and three teachers for a day learning about biodiversity and computer image analysis, touring the university library, and building windmills and doing engineering lab tours at CURENT, an engineering center across campus.

Greenback School students took fun photos in the Studio at the University of Tennessee Library during a tour there. Later Eric Carr, NIMBioS High Performance Computing Specialist, ran some image altering MATLAB code that the students had learned about on the photos.

Greenback School students took fun photos in the Studio at the University of Tennessee Library during a tour there. Later Eric Carr, NIMBioS High Performance Computing Specialist, ran image altering edge-detection MATLAB code that the students had learned about on the photos.

NIMBioS also co-hosted SHADES, Sharing Adventures in Engineering & Science, a STEM symposium for 6th and 7th grade girls. The annual event organized by the Greater Knoxville Math/Science Coalition had 34 student participants from the greater Knoxville area, plus parents, Girl Scout Troop leaders, and teachers. Volunteers from Oak Ridge National Laboratory, the University of Tennessee, NIMBioS, and TNSCORE all contributed activities. Highlights included T-shirt chromatography, using Geiger counters, and an engineering competition using fuel cell model cars.

A number of NIMBioS volunteers contributed to the event by helping out the Education & Outreach staff. Special thanks to Eric Carr, NIMBioS HPC Specialist, for putting together a great activity on image analysis, to volunteer helpers and NIMBioS postdoctoral fellows Amiyaal Ilany, Elizabeth Hobson, Jeremy Beaulieu and NIMBioS graduate assistant Ben Levy.

Participants at SHADES sort plastic insects for an activity on using probability to measure biodiversity.

Participants at SHADES sort plastic insects for an activity on using probability to measure biodiversity.

Did you like this? Share it:
Posted in Diversity, Education/Outreach, gender diversity, GRAs, Middle School, postdocs, STEM, Teachers | Tagged , , , , , , , | Comments Off

The Bat Cave at NIMBioS

Little brown bat visits NIMBioS

Little brown bat visits NIMBioS

Literally and figuratively speaking, both, this little brown bat knows a good and safe spot when he sees it. The bat found refuge today on the wall outside the entrance to NIMBioS, where inside scientists have worked feverishly to save the bats from the deadly white-nose syndrome. See here and here.

We’re happy to report that this little brown appeared to be in good health.


Did you like this? Share it:
Posted in Wildlife | Tagged | Comments Off

Math for Cholera, Drug Discovery, Environment & More at 2014 NIMBioS Undergraduate Research Conference

Julia Martinez from the College of Charleston talks about her research on the effects of antimicrobials on shrimp to a group at the NIMBioS Undergraduate Research Conference

Juita Martinez from the College of Charleston talks about her research on the effects of antimicrobial pollutants on shrimp to a group at the 2014 NIMBioS Undergraduate Research Conference

More than 100 undergraduates and faculty in math, biology and related fields convened in Knoxville at the weekend to share research and network at the 6th Annual NIMBioS Undergraduate Research Conference at the Interface of Mathematics and Biology.

Highlights of the conference included keynote presentations by Joseph Tien of The Ohio State University (“Cholera Dynamics: Blackboard, Bedside, Bench”) and Jeremy Smith of University of Tennessee and Oak Ridge National Laboratory (“Computer Simulation for Renewable Energy, Environmental Science & Drug Design”). Later, the two joined Suzanne Lenhart, NIMBioS Associate Director for Education & Outreach, for a Q&A session on careers and graduate school. Other highlights were the student talks themselves — over 50 student poster and oral presentations on using mathematics and computer science to tackle questions in biology from the tiniest scale (genes, proteins, biomolecules) to the largest (ecology of interacting populations). View more photos from the conference on our Flickr page, and highlights and tweets via Storify.

Save the date! The next NIMBioS URC will be Nov 21-22, 2015. Come back, present new work, and bring new students, friends and colleagues!

Did you like this? Share it:
Posted in conference, Education/Outreach, undergraduates | Tagged , , , , | Comments Off

Postdoc Shares Latest Research with National Seed Bank


The seed bank at the National Center for Genetic Resources Preservation (NCGRP)

Picture a library but instead of books, thousands upon thousands of seed packets on every shelf. The USDA’s National Center for Genetic Resource Preservation in Ft. Collins, CO, is a secure 5,000-square-foot storage facility for more than half a million seed samples from over 8,000 species of interest to sustainable agriculture, successful restoration, and endangered species preservation, and is adding more specimens every day.

NCGRP scientists travel to remote parts of the world to gather wild strawberries, apples, wheat, and other species in order to introduce new, useful traits into crop breeding programs. They also gather common tree and grass species for restoring degraded or burned land. The facility partners with local and national agencies around the world to “back-up” other important seed collections. The seeds are stored in a tornado proof shelter, some of them in large steel tanks full of liquid nitrogen and others in long rows of giant shelves in rooms at freezing temperature, all meticulously labeled and accessible for future needs.

NIMBioS postdoctoral fellow Sean Hoban recently visited the NCGRP to share his newest research results in a seminar with scientists there and at Colorado State University. Hoban studies how to optimally plan collections of new seeds, using cutting edge computational and mathematical models. While the storage facility is huge, the need for seed saving is great, and thus there is need for efficient collections that capture the most biodiversity in a minimum collection size.

Sean Hoban visits Medicine Bow National Forest in Wyoming,  one of the many places from where the US Forest Service is sending seeds to the National Center for Genetic Resource Preservation seed bank in Ft. Collins, CO.

Sean Hoban visits Medicine Bow National Forest in Wyoming, one of the many places from where the US Forest Service is sending seeds to the National Center for Genetic Resource Preservation seed bank in Ft. Collins, CO.

Hoban’s work has helped show where to collect from and how much seed to collect. He is now working to custom design seed collections, including collections from native Tennessee species, like the endangered butternut tree and several endangered Trillium species, found throughout the Appalachians and eastern forests.

“It was exciting to see this national seed facility firsthand, which helped me better understand the opportunities and challenges of these collections,” Hoban said. “It was also great to connect my mathematical work on species’ genetic diversity to the work of other researchers involved in seed collections, aspects that complement mine. Now we can integrate genetics with geography, climate data, plant traits and much more.”

The next stop on Hoban’s “seed-saving tour” is the Rancha Santa Anna Botanic Garden near Los Angeles, followed by an “Advancing Ex Situ Conservation” workshop at the San Diego Zoo for researchers from zoos and botanic gardens across the US.

“This will be a planning meeting for next steps in the science and practice of saving, breeding, and reintroducing rare species,” Hoban said.

Other stops on the tour include the College of Charleston and the Missouri Botanic Garden.

“It is important to take our theoretical research and apply it to real challenges in society. I’m very glad that NIMBioS encourages and helps postdoctoral fellows to do so,” Hoban said.

Aside from his seed-saving talks and travels, Hoban is also developing new models of genetic diversity of rare species and working on a related project to model resistance to diseases and pests to help save eastern hardwood forest species, such as ash trees and hemlock.

Hoban’s most recent publication is “Optimal sampling of seeds from plant populations for ex-situ conservation of genetic biodiversity, considering realistic population structure” in Biological Conservation. Click here to read more.

Did you like this? Share it:
Posted in postdocs, research | Tagged , | Comments Off

NIMBioS Fall Hike: Grotto Falls and Brushy Mountain

Smokies-fall 116One of the great perks of working at NIMBioS is the number of folks who love to get outside and climb up mountains together. On Saturday, NIMBioS friends and families ventured into the beautiful autumnal scenery in the Great Smoky Mountains National Park for a hike on Trillium Gap Trail to Grotto Falls and Brushy Mountain. Smokies-fall 016The waterfall was a perfect for those wishing to do a short hike, while some of us continued on to the top of Brushy Mountain. We finished the day by gathering for post-hike refreshments at the Fox & Parrot British tavern. Click here for more photos — most were taken by the amazing and talented in-house photographer and NIMBioS postdoc Clemente Aguilar.

Did you like this? Share it:
Posted in hikes | Tagged | Comments Off