NIMBioS

NIMBioS Welcomes New Researchers

Posted on August 21, 2013 by Catherine Crawley

New postdoctoral fellows are, from left, Matt Zimmerman, Nick Matze and Sean Hoban.

New postdoctoral fellows are, from left, Matt Zimmerman, Nick Matzke and Sean Hoban.

NIMBioS welcomes several new postdoctoral fellows and sabbatical visitors this fall.

New postdoctoral fellows include Sean Hoban, Nick Matze and Matt Zimmerman, which will bring the total number of postdocs at NIMBioS to 17.

Dr. Hoban comes to NIMBioS from a postdoctoral research position studying the conservation of genetic resources for species survival at the Universita di Ferrara, Italy. Dr. Hoban earned a Ph.D. in biology from the University of Notre Dame in 2010. His NIMBioS project is to develop simulation-based sampling guidelines for conserving the genetic resources of rare or economically important plant species.

Dr. Matzke recently completed his Ph.D. in integrative biology at the University of California, Berkeley. His project aims to unify phylogenetic biogeography and species distribution modeling.

Dr. Zimmerman recently completed his Ph.D. in ecology from the University of California, Davis. His project investigates the evolutionary origins of complex institutions.

New sabbatical fellows are Kathleen Donohue (Biological Sciences, Duke University), Jon Forde (Mathematics and Computer Science, Hobart and William Smith Colleges), and Allan Strand (Grice Marine Laboratory, College of Charleston).

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Testing Protocol Described for Epigenetic Model of Homosexuality

Posted on July 19, 2013 by Catherine Crawley

Subscripted symbols represent one or more epi-marks that influence sensitivity to androgens by the developing genitalia (Ge) or sexually dimorphic brain regions influencing sexual partner preference (Sp) or sexual identity (Si). Lighter symbols represent weaker than average epi-marks and bolder symbols represent stronger than average epi-marks. For more detail, see the full figure in BioEssays.

In a new article released today in BioEssays, the authors that brought the widely circulated article on the epigenetic underpinnings of homosexuality last year provide a new testing protocol for the model.

Last year’s study, published in The Quarterly Review of Biology, provided a mathematical model predicting that sex-specific epi-marks, which are laid down during embryonic stem cell development, can lead to homosexuality when they escape erasure between generations and are transmitted from father to daughter or mother to son. The model predicted that these sex-specific epi-marks can cause reversed effects, such as the feminization of some traits in sons, such as sexual preference, and similarly a partial masculinization of daughters.

Today’s article describes five testable predictions for the model, and suggests that epigenetic profiles of human stem cells can offer the best way to test models of epigenetic-based homosexuality.

The work was conducted by William Rice, Urban Friberg and NIMBioS Associate Director for Scientific Activities Sergey Gavrilets.

Citation: Rice WR, Friberg U, Gavrilets S. 2013. Homosexuality via canalized sexual development: A testing protocol for a new epigenetic model. BioEssays: 35. Published online 19 Jul 2013. DOI 10.1002/bies201200033

Posted in publication, research | Tagged publications, research | Comments Off

Which REU Student Volunteers at an Animal Shelter? Find Out in Our REU Profiles

Posted on July 18, 2013 by Catherine Crawley

Of the 19 undergraduate students participating in this year’s Research Experiences for Undergraduates program, one volunteers in an animal shelter. Many relax after a day of mathematical modeling with endless games of Ultimate Frisbee, while a few have learned some surprising facts about cow behavior.

All have said they would definitely recommend the NIMBioS REU program to other undergraduates. “The opportunity to work on a problem, try new ideas, learn new mathematics and biology, and overcome roadblocks is invaluable. I’m confident my experiences this summer will be important as I transition into graduate school,” writes Kiersten Utsey.

Find out more about our 2013 REU students by reading their Q&A profiles.

Posted in Education/Outreach, REU/REV | Tagged Education, REU/REV | Comments Off

Working Hard and Playing Hard: NIMBioS REU is Halfway

Posted on July 16, 2013 by admin

Created with Admarket’s flickrSLiDR.

We’re at the mid-point of this summer’s 2013 NIMBioS REU program, and already the 2013 class has created some fun memories while working hard. Pool parties with other REU groups, trips to see synchronous fireflies in Great Smoky Mountains National Park and the Knoxville Zoo, and field trips to collect audio recordings of birds and information about cattle movement on a farm are some highlights captured in pictures so far. Plus, the Automatic Detection of Rare Birds from Audio Recordings project elicited some nice media attention from the local public radio station (WUOT), newspapers (Knoxville News Sentinel, Daily Beacon) and television (WBIR).

Off camera, the students have been working hard pouring over literature and computer code. Significant progress is apparent. Last week the students gathered to workshop drafts of posters showing the preliminary results of their research, which they will be presenting to the public on July 19 during the UT STEM REU Symposium (Baker Center Toyota Auditorium, 10am-12pm). Please plan to attend and support our hardworking undergraduates!

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Graduate Students Connect Biological Data with Mathematical Models

Posted on June 17, 2013 by Catherine Crawley

2013 Summer Graduate Workshop

The 2013 Summer Graduate Workshop, co-sponsored by NIMBioS, the Mathematical Biosciences Institute and the Centre for Applied Mathematics in Bioscience and Medicine, has begun with a full slate of modeling lectures and computer activities scheduled for the two-week program.

The program, which runs from June 17-29, features instructors from across North America whose research expertise is mathematical modeling in biological systems using real data. Some of the techniques to be covered include Maximum likelihood and Bayesian approaches to inference, parameter estimation, model identifiability, uncertainty and sensitivity analysis, and data assimilation. Applications of connecting data to models will come from epidemiology, ecology (including global change biology), evolution, microbiology, physiology, pharmacokinetics, and systems biology.

Activities include lectures, computer exercises and research.

In addition to attending lectures and completing computer activities, each of the 40 participants will work in teams on a specific research project and present findings at the end of the program.

Instructors include Tom Banks, North Carolina State University; Ben Bolker, McMaster University; Ariel Cintron-Arias, East Tennessee State University; Marisa Eisenberg, University of Michigan; Kevin Flores, North Carolina State University; Paul Hurtado, Math Biosciences Institute; Denise Kirschner, University of Michigan; Simeone Marino, University of Michigan; Vasileios Maroulas, University of Tennessee-Knoxville; Kiona Ogle, Arizona State University. Also assisting are NIMBioS Postdoctoral Fellows Jeremy Beaulieu, Jiang Jiang, Keenan Mack, Gesham Magombedze, Calistus Ngonghala, Chris Remien and Dan Ryan.

Posted in Education/Outreach, graduates | Tagged Education, graduates | Comments Off

Day 1: Learning & Fun at REU

Posted on June 11, 2013 by Catherine Crawley

NIMBioS’ new REU students begin their first day.

Nineteen of the country’s top undergraduates in mathematics and biology and related fields began their eight-week journey of research and discovery yesterday with NIMBioS’ Research Experiences for Undergraduates program.

Hailing from colleges and universities across the country, the students will live on the UTK campus and work in teams with NIMBioS postdocs and UT faculty on six different research projects, including mathematical modeling of fetal electrocardiograms; modeling animal disease from coronavirus; automatic detection of rare birds from audio recording; modeling the environmental transmission of E-coli in cattle; modeling protein translation and genome evolution; and modeling animal social network dynamics.

NIMBioS postdoc Arik Kershenbaum (right) introduces REU students to the bird song project.

Day 1 began with introductions and an overview of basic modeling approaches. The students also met their mentors who will guide their work over the next eight weeks. Besides the research, trips to the Knoxville zoo and the Great Smoky Mountains to see the synchronous fireflies are planned. The REU culminates in final presentations of their research.

Posted in Education/Outreach, REU/REV, undergraduates | Tagged Education/Outreach, REU/REV, undergraduates | Comments Off

NIMBioS Introduces Students to the Creative Side of Science

Posted on June 7, 2013 by admin

Adventures in STEM campers show off their plant cell organelle printed using the NIMBioS 3D printer.

Middle school girls experienced the creative side of science this week when they used 3D modeling software to design and print their very own plant cell using NIMBioS’ new 3D printer, as a part of activities in the Adventures in STEM summer camp.

After touring NIMBioS and watching the 3D printer at work, the girls learned how to use a free, 3D modeling software called SketchUp to help design different organelles from a plant cell. After drafting potential artistic interpretations of the organelles, final designs were saved and sent off to be printed in 3D. Each organelle took about half an hour to print. The final step involved combining the organelles into one single plant cell.

The activity was intended to show the campers how scientists use unique tools, like computer software and 3D printers, to visualize and model information.

Campers interview NIMBioS Postdoc Julia Earl.

Among the many other NIMBioS-led activities in Adventures in STEM, the girls also interviewed NIMBioS scientists and mathematicians, learned the basics of disease modeling, and took soil samples to calculate insect biodiversity. The week concluded with presentations to their parents.

This is the second year that NIMBioS has participated in the second-annual week-long Adventures in STEM summer camp, which is also sponsored by CURENT. 4-H was an additional sponsor this year. The camp introduces middle school girls to science, math, and engineering through hands-on activities, labs and team projects at the University of Tennessee.

Created with Admarket’s flickrSLiDR.

To view more pictures, visit the NIMBioS Flickr photostream.

Special thanks to NIMBioS IT Manager Michael Peek, who helped with the 3D printing activity, and to NIMBioS Graduate Research Assistants Marco Martinez and Gwen Iacona for donating their time and expertise during the week.

Posted in Computing, Education/Outreach, gender diversity, Middle School, STEM | Tagged 3D printer, 3D printing, 4-H, cell organelles, CURENT, STEM | Comments Off

Kids Have a Ball With Math and Biology

Posted on May 21, 2013 by admin

Kelly Sturner, NIMBioS Education & Outreach Coordinator, prepares to throw a beach ball Earth into the hands of Andersonville Elementary School Students.

Catch! Kelly Sturner, NIMBioS Education & Outreach Coordinator, prepares to throw an inflatable globe into the hands of Andersonville Elementary School students.

How can you use an Earth beach ball to estimate the area of forest on our planet’s surface? Andersonville Elementary School students figured this out and more at the interface of math and biology on their visit last week to the University of Tennessee.

One hundred and fifty 4th-6th grade students filled the auditorium at the university’s library, excited about the fun-filled day ahead of them meeting scientists and eating pizza. , NIMBioS Associate Director for Education & Outreach Suzanne Lenhart began the NIMBioS math biology session by talking about her work studying various diseases, including whether cats make people crazy (or rather, the effects of toxoplasmosis gondii on humans). Then, NIMBioS Education & Outreach Coordinator Kelly Sturner talked about her work as a soil ecologist and how she used math to study ecosystems such as forests.

The forest surface area on the inflatable globe was estimated using probability and tossing two identical balls around the auditorium, an idea modified from the environmental education curriculum designers at Project Learning Tree. The rest of the forest-math activities were modified from the NIMBioS education module Measuring a Forest.

Children reach for the Earth ball as it flies through the air. When they catch it, if their right index finger falls on green (forest), Sturner records it as well as the total number of tosses.

Posted in ecology, Education/Outreach, Elementary School, STEM, viruses | Tagged ecology, Education, Education/Outreach, leadership, STEM, viruses | Comments Off

Gresham Middle Students Visit NIMBioS

Posted on May 15, 2013 by admin

A group of Gresham students, teachers and chaperones posed for the camera -- a Matlab edge detection software has transformed this image.

Gresham Middle School students, teachers and chaperones visit NIMBioS. A Matlab edge detection code transformed this image to give it a cartoon-like quality.

Local middle school students took their learning beyond the bounds of their classroom on a visit to NIMBioS last week. Fifty students from Gresham Middle School‘s Beta Club, along with teachers and parent chaperones, visited the institute and participated in hands-on activities exploring the connections between math and biology.

In one activity, designed and presented by NIMBioS High Performance Computing Specialist Eric Carr, students learned how computer code can help analyze images for biological applications. For the image lab, students explored how one could use the software to figure out the basal area of leaves. The students changed parameters for the program in Matlab to improve detection and imported images of leaves taken with webcams.

In a second activity, NIMBioS Associate Director for Education & Outreach Suzanne Lenhart explored with students the properties of platonic solids and how they relate to the structure of viruses. Students built solids from plastic triangles and made their own origami solids to take home.

Postdoctoral fellows Ryan Martin and Jeremy Beaulieu both helped with the activities.

Students finished out their visit to the University of Tennessee with a trip to CURENT, an engineering research center on campus, where they toured engineering labs. TNSCORE, another engineering research center on campus, was also involved in the visit and helped the students build small solar-powered cars.

Posted in Computing, Education/Outreach, Leadership, Middle School, postdocs, STEM, tools, viruses | Tagged computing, Education, Education/Outreach, leadership, postdocs, STEM, teachers, viruses | Comments Off

Discover Birds Program Makes the Grade

Posted on April 30, 2013 by admin

NIMBioS Deputy Director Chris Welsh tells Sevierville Primary second graders about his passion for birds at a Discover Birds school visit in April. Photo Credit: discoverbirds.blogspot.com

In light of the success of the Discover Birds program among Tennessee elementary schools, the Tennessee Ornithological Society (TOS) voted at their annual meeting in Knoxville last weekend to order a second printing of the popular Discover Birds activity book.

The program appears to be meeting its primary goals of getting elementary school-aged children excited about birds and science. “The excitement and enthusiasm you see from the kids is a real thrill,” said Chris Welsh, NIMBioS deputy director and Discover Birds volunteer.

Welsh recently visited two local elementary schools with the program. At Sevierville Primary in April, 215 second grade students viewed a slide show about birds and examined feathers, owl pellets and other bird-related objects. Welsh joined other volunteers to lead students on bird walks on the school grounds where students spotted an American Robin sitting on a nest and Tree Swallows visiting nest boxes, as well as many other birds. More details and photos about the school visit are available at the Tennessee Ornithological Society Discover Birds blog.

Nearly all 1,000 activity books from the first printing have now been distributed with most having been donated to classrooms and teachers. NIMBioS contributed math-bird activities to the 36-page activity book. The math-related activities developed by NIMBioS for Discover Birds, along with illustrations by Vickie Henderson, are freely available for download here. For more information about how to obtain the Discover Birds activity book or to request a visit at your school, contact the Knoxville Chapter of the Ornithological Society.

Posted in Education/Outreach, Leadership, STEM, Wildlife | Tagged ecology, Education, Education/Outreach, leadership, publications, STEM, teachers, wildlife | Comments Off