Working Group Publishes Review in American Naturalist

Participants from the March 2016 meeting of the Working Group, Meeting 3 participants: (L to R) Michael Antolin, Joanna Kelly, Andrew Storfer, Katie Lotterhos, Sean Hoban, David Lowry, Laura Reed.

Participants from the March 2016 meeting of the Working Group (L to R) Michael Antolin, Joanna Kelly, Andrew Storfer, Katie Lotterhos, Sean Hoban, David Lowry, Laura Reed.

The work of the NIMBioS Working Group on Computational Landscape Genomics has come to fruition with a synthesis review paper in The American Naturalist.

“Finding the genomic basis of local adaptation: Pitfalls, practical solutions, and future directions” provides a critical assessment of complex approaches to identifying genes that underlie adaptive differentiation of populations.

The Working Group, which has met three times since 2014, consists of experts in genomics, statistics, mathematics, bioinformatics and population genetics. Its chief goal has been to advance analytical and computational methods that integrate both the genomic and the ecological landscapes in order to understand the spatial distribution of adaptive genetic variation.

Lead co-authors are former NIMBioS postdoc Sean Hoban, now a tree conservation biologist at the Morton Arboretum; Joanna Kelley, Biological Sciences, Washington State Univ.; and Katie Lotterhos, Marine and Environmental Sciences, Northeastern Univ. Marine Science Center, Nahant, MA. Working Group co-organizers are Andrew Storfer, Biological Sciences, Washington State Univ.; Gilles Guillot, Applied Mathematics, Technical Univ. of Denmark, Copenhagen; Mike Antolin, Biology, Colorado State Univ., Fort Collins; and Mary Poss, Biology, Penn State Univ., University Park.

NIMBioS Working Groups are chosen to focus on major well-defined scientific questions at the interface between biology and mathematics that require insights from diverse researchers, meeting up to three times over a two-year period. 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.

The next deadline to request support for a Working Group at NIMBioS is Sept. 1. For more information, visit http://www.nimbios.org/workinggroups/

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Special Collection Explores Motivation of Play

Meeting 3 of the Working Group on Play, Evolution, and Sociality. (Back row, L to R): M. Mangel, H. Fouts, B. O'Meara, G. Burghardt, B. Smuts, K. Lewis Graham, G. Cordoni, M. Rehakova, E. Palagi, P. Hammerstein. (Front row, L to R): S. Pellis, J. Auerbach. Not pictured: J. Schank, E. Akcay

Meeting 3 of the Working Group on Play, Evolution, and Sociality. (Back row, L to R): M. Mangel, H. Fouts, B. O’Meara, G. Burghardt, B. Smuts, K. Lewis Graham, G. Cordoni, M. Rehakova, E. Palagi, P. Hammerstein. (Front row, L to R): S. Pellis, J. Auerbach. Not pictured: J. Schank, E. Akcay

Research on what motivates play in mammals, both human and non-human, has been published in a special issue of the journal Behaviour. The nine papers in the special issue are products of the NIMBioS Working Group on Play, Evolution and Sociality.

The nine papers in the special issue include:

  • Motivation of play: from ethological to neurological perspectives by Elisabetta Palagi and Hillary N. Fouts
  • Work-themed play among young children in foraging and farming communities in Central Africa by Hillary N. Fouts, Carin L. Neitzel and Lauren R. Bader
  • Affiliation, dominance and friendship among companion dogs by Rebecca K. Trisko, Aaron A. Sandel and Barbara Smuts
  • Play fighting in Visayan warty pigs (Sus cebifrons): insights on restraint and reciprocity in the maintenance of play by Sergio M. Pellis and Vivien C. Pellis
  • Aggression and hierarchical steepness inhibit social play in adult wolves by Giada Cordoni and Elisabetta Palagi
  • Motivation, development and object play: comparative perspectives with lessons from dogs by Gordon M. Burghardt, Julia D. Albright and Karen M. Davis
  • Metacommunication in social play: the meaning of aggression-like elements is modified by play face in Hanuman langurs (Semnopithecus entellus) by Marek Špinka, Marie Palečková and Milada Řeháková
  • A brain motivated to play: insights into the neurobiology of playfulness by Stephen M. Siviy
  • Stone handling, an object play behaviour in macaques: welfare and neurological health implications of a bio-culturally driven tradition by Charmalie A.D. Nahallage, Jean-Baptiste Leca and Michael A. Huffman

The full special issue can be found at http://booksandjournals.brillonline.com/content/journals/1568539x/153/6-7.

In a series of meetings from 2011 to 2013, the NIMBioS Working Group brought together mathematicians, anthropologists, zoologists, neuroscientists, ecologists, psychologists and other top experts to examine play as a window into cognitive evolution and the rules of sociality.

Until the Working Group was established, the field lacked a mathematical and computational approaches for understanding how play evolves. Using mathematical tools, the group aimed to uncover factors predicting the dynamics, occurrence and trajectory of play in the animal kingdom, as well as explore the ecological, psychological and life history factors that facilitate and maintain play.

The special issue is the second from the Working Group. The first was Adaptive Behavior on the origin and evolution of play issued last November.

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SRE Undergraduates Present at Summer STEM Poster Symposium

SRE participants Kelly Regan (left), Alana Cooper and Emily Horton (right of poster) present their work on dynamic modeling of human emotions.

SRE participants Kelly Regan (left), Alana Cooper and Emily Horton (right of poster) present their work on dynamic modeling of human emotions.

Undergraduates in the NIMBioS Summer Research Experience (SRE) program presented five posters on their projects last week at the University of Tennessee (UT) Summer STEM Poster Symposium. NIMBioS students joined with other undergraduates conducting summer research from other campus programs in engineering, chemistry, computing, life sciences, nursing, psychology, and more. Fifty-seven posters were presented in all.

Since the SRE’s still have two more weeks to the program, only methods and preliminary results were presented. The students reported that the feedback they received from faculty and other students will help them as they continue and begin to wrap up their projects. For some students, it was their first time presenting a research poster of their work, a valuable new experience.

The poster symposium is one that NIMBioS helps co-organize annually with CURENT, an NSF-supported engineering center located at UT. More photos from this year’s symposium are available here.

NIMBioS also hosted visitors for the symposium whom have been spending the summer at East Tennessee State University doing research in math and biology through a summer research experience for undergraduates sponsored by the National Security Agency. After lunch together, the students stayed for a panel discussion on graduate school featuring graduate students in math and biology from UT organized for the SRE program participants.

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STEM Campers Run Like Dinosaurs and Design 3D Models

Adventures in STEM campers 3D print flower models

Campers watch a 3D printer bring their flower model design to life.

Middle school girls from across Tennessee enjoyed trying out different models used in math and science at this year’s Adventures in STEM Camp. The campers used computers to design 3D models of flowers for 3D printing, tested a mathematical model for dinosaur locomotion, and played with Netlogo to learn about agent-based modeling of predator-prey interactions. Fifteen middle school girls participated.

In another activity, girls demonstrated population modeling by pretending to be wolves and deer in an exciting game of “Oh Deer!” They graphed their results outside with sidewalk chalk on one of Knoxville’s Greenways. Other highlights included engineering activities to learn about the power grid, a tour of the UT Veterinary Hospital, and interviews with mathematicians, scientists and engineers.

Campers pose with graphs they created of changing deer and wolf populations from the game "Oh Deer!"

Campers pose with graphs they created of changing deer and wolf populations from the game “Oh Deer!”

NIMBioS and CURENT, an NSF-supported engineering center at UT, have co-organized the week-long day camp since 2012. The camp’s goal is to encourage and inspire middle school girls with STEM interests by delving into a variety of fun hands-on activities, making new friends with shared interests, and by learning about career opportunities in the STEM fields.

Thanks to the many NIMBioS staff, graduate students, and other volunteers that help make this camp possible.

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NIMBioS Teaches the Teachers

Tennessee elementary school teachers measure hip height learned how Alexander's Formula is used to model how fast dinosaurs could move based on their stride length, determined from fossilized footprints, and based on their hip height, determined from fossilized bones. The teachers then took on the role of pretending to be bipedal dinosaurs and performed trials by running outside

Tennessee elementary school teachers measure hip height as a part of an exercise learning how to use Alexander’s Formula to model dinosaur speed. The exercise was part of a workshop training math teachers in ways students can connect math and biology in the classroom.

Tennessee math teachers went back to the classroom this month to learn creative and engaging ways to connect mathematics with biology, led by the NIMBioS Education and Outreach team.

NIMBioS Associate Director for Education and Outreach Suzanne Lenhart, Education and Outreach Coordinator Kelly Sturner, and undergraduate intern Virginia Parkman traveled to Jacksboro Middle School in Campbell County, TN, yesterday to lead a one-day workshop for 23 area elementary and middle-school math teachers. The workshop was part of a longer Tennessee Department of Education “Math Counts II” Workshop.

In this lesson, teachers designing animal shelter cage arrangements.

In this lesson, teachers use array-thinking to design the placement of cages in animal shelters.

The NIMBioS team organized and presented interactive applications of math for grades 3-8, covering modeling, measurement and applications of geometry and array-thinking. Grades 3-5 teachers designed how cages might be arranged in different arrays in an animal shelter to minimize the spread of canine distemper virus. Grades 6-8 teachers learned how Alexander’s Formula is used to model how fast dinosaurs could move based on their stride length, determined from fossilized footprints, and based on their hip height, determined from fossilized bones. The teachers then took on the role of pretending to be bipedal dinosaurs and performed trials by running outside and measuring hip heights. They compared their data to what Alexander’s formula would predict.

In early June, Lenhart and Sturner traveled to Campbell County High School in Jacksboro, TN, for two days as a part of a longer workshop for high school math teachers called “Connecting Math and STEM Through Modeling.” Seventeen math teachers from Campbell County and surrounding counties participated in exercises designed to improve teachers’ understanding of math modeling in the real world. Using resources from Moody’s Mega Math Challenge, Lenhart and Sturner presented the steps involved in using real-world data to generate a modeling equation. Teachers worked in groups and then presented their own model solutions and shared how they might do simple modeling cases with their students.

The workshops were supported by two different grants to Lynn Hodge, associate professor of math education at UT-Knoxville, and Gale Stanley, a retired Campbell County science teacher and currently president of the Tennessee Science Teacher’s Association.

 

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SRE Team Publishes in Frontiers in Microbiology

(From left) Winode Handagama, Magaret McDaniel and Nitin Krishna

(From left) Winode Handagama, Magaret McDaniel and Nitin Krishna

Congratulations to the three students who participated in the 2014 Summer Research Experiences project on mathematical modeling of granuloma formation in Johne’s disease. The team, along with its mentors, has published their results in Frontiers in Microbiology.

“Quantifying limits on replication, death, and quiescence of Mycobacterium tuberculosis in mice” investigates the limits of the rates of bacterial replication, death, and quiescence during Mtb infection in mice. The study found no significant correlation between estimated rates of Mtb replication and death, suggesting the decline in the rates was driven by independent mechanisms. The study also found that the data could not be explained by assuming that bacteria do not die, suggesting that some removal of bacteria from lungs of the mice had to occur even though the total bacterial counts in these mice always increased over time. The study also showed that to explain the data the majority of bacterial cells (at least 60%) must be replicating in the chronic phase of infection, further challenging widespread belief of nonreplicating Mtb in latency.

Co-authors are Margaret McDaniel, who at the time of the program was a student in biochemistry, cellular and molecular biology and mathematics at UT-Knoxville; Nitin Krishna, who was a student in mathematics at the University of Chicago; Winode Handagama, who was a student in biochemistry at Maryville College; along with their mentors: Shigetoshi Eda in the Department of Forestry, Wildlife and Fisheries, UT-Knoxville, and Vitaly Ganusov in the Department of Microbiology, UT-Knoxville.

McDaniel is now a graduate student in immunology at the University of Texas Southwestern Medical School. Her research includes how Mtb triggers a prolonged inflammatory signal.

Krishna is now a junior at the University of Chicago. He is currently a participant in Williams College SMALL Mathematics REU program, studying fluid dynamics and partial differential equations.

Handagama recently graduated from Maryville College.

The publication is available online at http://journal.frontiersin.org/article/10.3389/fmicb.2016.00862/full

Eighteen undergraduates and two high school teachers participated in the 2014 Summer Research Experience at NIMBioS, June 9-August 1. During the eight-week program, participants lived on campus at the University of Tennessee, Knoxville, and worked in teams with NIMBioS postdocs and UT faculty to conduct research at the interface of mathematics and biology. The award included a stipend, housing and some funding to support travel.

More information about NIMBioS’ SRE can be found at http://www.nimbios.org/sre/. Currently, 16 undergraduates are participating in the program, working in teams on five different research projects.

 

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Working Group Publishes New Habitat Management Guide

The NIMBioS Working Group on Habitat for Migratory Species enjoys a visit to the mountains during its last meeting at NIMBioS in May. (From left) Chris Welsh, Julia Earl, Christine Sample, Sam Nicol, xx , Gary McCracken, Wayne Thogmartin, Richard Erickson, xx. Seated, from left, Ruscena Wiederholt, Paula Federico, xx, Laura Lopez-Hoffman, Darius Semmens.

The NIMBioS Working Group on Habitat for Migratory Species enjoys a visit to the mountains during its last meeting at NIMBioS in May. (From left) NIMBioS Deputy Director and tour guide Chris Welsh, Julia Earl, Christine Sample, Sam Nicol, Brady Mattsson, Gary McCracken, Wayne Thogmartin, Richard Erickson, Tyler Flockhart. (Seated from left) Ruscena Wiederholt, Paula Federico, Jay Diffendorfer, Laura Lopez-Hoffman, Darius Semmens.

A new management guide for selecting habitat- and patch-specific metrics in spatially-structured populations was published yesterday in Ecological Indicators. The paper is a result of efforts by the NIMBioS Working Group on Habitat for Migratory Species.

The paper reviews the many ways to measure the contribution of a habitat to a population. Some populations, like migratory birds, use many different areas during their lifetimes, making managing such populations a challenge. Which areas should be managed? Not all areas are necessarily equal.

The Group asked the question: What is the best way to measure the value of a habitat to a population, given a particular management objective?

The paper reviews techniques to measure contributions from an applied, management point of view and argues that the best metric for a situation depends on the management goal.

The Working Group began meeting in 2014 and has met four times at NIMBioS, concluding its final meeting in May 2016. Co-organizers are Wayne Thogmartin, Jay Diffendorfer, Ruscena Wiederholt, and Brady Mattsson.

The paper can be viewed at this link for up to 50 days: http://authors.elsevier.com/a/1TAOl_,3LxxlYWs

Nicol S et. al. A management-oriented framework for selecting metrics used to assess habitat- and path-specific quality in spatially structured populations. Ecological Indicators 69: 792-802. DOI:10.1016/j.ecolind.2016.05.027

 

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NIMBioS Welcomes New Postdocs

(From left) Sarah Flanagan, Sergei Tarasov, Nourridine Siewe

(From left) Sarah Flanagan, Sergei Tarasov, Nourridine Siewe

Several new postdoctoral fellows will begin their research soon at NIMBioS.

Joining in the summer are Sarah Flanagan, Nourridine Siewe, and Sergei Tarasov. Flanagan (Biology, Texas A&M Univ.) will develop new predictive approaches for next-generation sequencing population genomics studies. Siewe (Mathematics, Howard Univ.) will develop mathematical models of visceral leishmaniasis and malaria co-infection to improve the diagnosis and treatment process. Tarasov (Mathematics and Natural Sciences, Univ. of Oslo) will model and explore the evolution of anatomy ontologies using innovative stochastic processes and two focal groups of insects: dung beetles and wasps.

Lauren Smith, currently a Gaylord Donnelley Postdoctoral Environmental Fellow at Yale Univ., joins NIMBioS as a postdoc in October. Smith proposes research that examines invasive plants in food-webs and the indirect effects on native communities and ecosystems.

Joining in early 2017 are Andrew Rominger and Oyita Udiani. Rominger (Environmental Science, Policy & Management, Univ. of California, Berkeley) will use bio-collections data and hierarchical models to examine large-scale questions in ecology and evolution. Udiani (Applied Mathematics, Arizona State Univ.) will develop a novel game-theoretical approach to learning in models of animal behavior.

NIMBioS postdoc Robin Taylor (Educational Psychology, Educational Research Methods and Analysis, Auburn University, 2012) began her fellowship last month. As a NIMBioS Postdoctoral Fellow in Science Education Research and Evaluation for NIMBioS Evaluation Services, she is helping to development and validate a Quantitative Biology Concept Inventory, which is designed to assess the efficacy of using real-world biology examples to enhance student understanding of quantitative concepts in college-level calculus courses.

For more information about the NIMBioS Postdoctoral Fellowship, visit http://www.nimbios.org/postdocs/

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NIMBioS, UT Welcome New Faculty

Dr. Tian Hong

Dr. Tian Hong

Dr. Monica "Mona" Papes

Dr. Monica “Mona” Papes

NIMBioS welcomes two new NIMBioS-affiliated assistant professors to the University of Tennessee, Knoxville, beginning in January 2017.

Tian Hong will join the Department of Biochemistry and Cellular and Molecular Biology as assistant professor of computational biology. Hong’s research focuses on mathematical modeling of cellular heterogeneity and plasticity and its application in understanding immune response, development and cancer progression. Hong is currently a postdoctoral fellow in the Department of Mathematics at the University of California, Irvine.

Monica Papes will join the Department of Ecology and Evolutionary Biology as an assistant professor in spatial biology. Papes’ research focuses on theoretical and applied investigations centered on species’ distributions. She uses ecological niche modeling techniques with GIS and remote sensing tools to study the factors that shape species’ geographic distributions. Papes is currently an assistant professor in the Department of Integrative Biology at Oklahoma State University.

As both Hong’s and Papes’ research intersects the focus of NIMBioS, both will be affiliated with NIMBioS. Faculty members on the NIMBioS leadership team served on the hiring committees.

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NIMBioS Hosts Field Trip for Rural Middle School Students

IMG_4787

Greenback School sixth graders release their “organisms” back into the “habitat” during the capture-recapture simulation.

Nearly 50 sixth graders and their teachers from Greenback School visited NIMBioS last week for an exciting day of STEM and getting a taste of the college experience. The rural school located about 30 miles southeast of NIMBioS.

Beginning with a mock “university class,” students did a fun hands-on activity created by NIMBioS postdoc Elizabeth Hobson. Students simulated the capture-recapture method of sampling organisms in the wild by using tupperware bins, beans and pine bedding. The activity showed the usefulness of math for doing ecological research.

Next, students headed across the street to Hodges Library for a tour and an introduction to the University of Tennessee’s six-story university library and all of its resources. The students returned to NIMBioS for a pizza lunch, since pizza is an important part of the college experience. Lastly, students walked across campus, past the new Student Union, Neyland Stadium, and UT’s Hill to the Min Kao Computer Science and Engineering building, where students toured energy and robotics engineering labs associated with CURENT, the Center for Ultra-Wide-Area Resilient Electric Energy Transmission Networks, an NSF Engineering Research Center at UT.

More photos from this fun day are posted on our Flickr photo album.

Hobson (left) with Greenback School Students

Hobson (left) with Greenback School students

 

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