Dolphin Communication on the Menu for Science Café

NIMBioS Posdoctoral Fellow Arik Kershenbaum answers questions from the audience at the Science Cafe.

NIMBioS Posdoctoral Fellow Arik Kershenbaum answers questions from the audience at the Science Cafe.

NIMBioS Postdoctoral Fellow Arik Kershenbaum led a lively discussion on the topic “Can We Talk to Dolphins?” at a Knoxville Science Café last week. All members of the community were invited.

“Science Cafés are events that take place in casual settings such as pubs and coffeehouses, are open to everyone, and feature an engaging conversation with a scientist about a particular topic,” according to Nova’s website. The event last week is a part of a series of Science Cafés sponsored by the Spirit & Truth Fellowship of Knoxville and held at a local nature center.

After watching a series of short clips from a Nova science documentary on dolphin communication, the audience asked Kershenbaum questions about how animals communicate. Kershenbaum is an expert on analyzing the vocal communications of animals. One question from the audience about whether animals could perhaps communicate telepathically led to an interesting discussion about forms of non-verbal communication in animals.

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NIMBioS Researchers Attend National Academies Workshop

Gesham Magombedze

Gesham Magombedze

Pelagie Favi

Pelagie Favi

The National Academies’ Committee on Key Challenge Areas for Convergence and Health meets this week for a workshop in Washington, DC, and two NIMBioS researchers are attending.

Invited to attend with a travel award are NIMBioS Postdoctoral Fellow Gesham Magombedze and NIMBioS Graduate Research Assistant Pelagie Favi. Magombedze’s research focuses on understanding the immunological interaction between host-pathogen in Johne’s disease. Favi, a doctoral student in materials science and engineering, designs bacterial cellulose scaffolds for tissue engineering of stem cells.

The two-day workshop brings together scientists involved in transdisciplinary research, leaders from academia and industry, and representatives of foundations and agencies to discuss how convergence in the life sciences can be facilitated through institutional policies, structures and networks.


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Ernest Brothers Selected for Leadership Knoxville Class of 2014

Dr. Ernest Brothers

Dr. Ernest Brothers

Congratulations to Ernest Brothers, NIMBioS Associate Director for Diversity Enhancement, for being selected to join the 2014 class of Leadership Knoxville.

Leadership Knoxville, a non-profit training progam begun in 1985, brings together about 50 leaders from around the Knoxville region to a 10-month, intensive study of the community, its history, opportunities and challenges. Through a nomination process, participants are selected based on the nominee’s interest, demonstrated leadership to greater Knoxville and leadership capabilities. Participants commit to Leadership Knoxville’s goal of serving as “catalysts for positive change” in the greater Knoxville area.

Dr. Brothers is an assistant dean in UTK’s Graduate School, overseeing the Office of Graduate Training and Mentorship. In his role at NIMBioS, Dr. Brothers helps further NIMBioS’ goals to increase underrepresented minorities in the sciences.

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NIMBioS REU’s Talk Cows and Hyenas at MBI Capstone Conference

From L to R: Monica Napoles, Brutus Buckeye, Jacob Lambert and Jocelyn Keung take a break at the MBI Capstone Conference

(From L to R): Monica Napoles, Jacob Lambert and Jocelyn Keung take a break with The Ohio State University’s mascot Brutus Buckeye at the MBI Capstone Conference.

Three 2013 NIMBioS REU students traveled to Columbus, Ohio last month to share their work in epidemiology and social network modeling at the Mathematical Biosciences Institute Undergraduate Research Capstone Conference. The conference drew REU students from across the country. Jacob Lambert from University of Tennessee presented a poster about his group project on modeling animal social network dynamics in hyenas. Jocelyn Keung from University of North Carolina and Monica Napoles from Humboldt State University presented a poster from their group project: an agent-based model of E. coli transmission in cattle.

Keung’s first academic conference, the experience helped her think about the most effective ways to present math biology research to an audience representing diverse backgrounds and math biology expertise. Keung said she particularly enjoyed networking with graduate school representatives at the event and  learning about the different ways that math and biology intersect.

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Solving South Florida’s Polluted Water Problem


Mathematical modeling is used to help solve the problem of the polluted waters of Lake Okeechobee.

The New York Times published a science story this week focusing on the challenges of water management in South Florida, especially at Lake Okeechobee with its 80-year-old earthen dike and polluted water. Climate change – in this case, unusually heavy rain – has caused “the most significant threat” to the lake with its three major estuaries bearing the brunt of the deluge.

NIMBioS postdoctoral fellow Jiang Jiang’s research focuses on ways mathematical modeling can help inform scientific management of ecosystems like Lake Okeechobee. Jiang focuses on developing models that can help predict changes to coastal vegetation due to storm surges, which occur as a result of increased frequency of hurricanes and other extreme weather.

South Florida suffered through extreme drought during the dry season of 2010, Jiang explains. But last May, downpours hit, bringing Lake Okeechobee’s water to record levels.

One of the ways officials dealt with the deluge was to release billions of gallons of the lake’s polluted water into the estuaries to the east and west, overwhelming the estuaries, which rely on a natural balance of salt and fresh water. Salinity in the eastern estuary is now at zero percent, which kills marine life and threatens the sea grasses and reefs that help sustain the estuaries.

In response, officials plan to send some of the water south toward the Everglades, where it should flow naturally. But Lake Okeechobee’s phosphorous levels, which cause algae to bloom, are far higher than permissible. So to protect the Everglades, the water must be filtered and treated, unlike the water that is pushed to the east and west estuaries.
“The habitat is fragile to these kinds of disturbances,” Jiang said.

Modeling techniques developed by Jiang and his colleagues are among the first to couple vegetation dynamics with soil hydrology and salinity to study the factors that affect coastal vegetation in ecotones, areas where vegetation changes abruptly, such as mangroves to hardwood hammocks. Salinity appears to be the critical factor separating vegetation communities, and a self-reinforcing feedback is the main mechanism for creating sharp coastal boundaries and maintaining the ecological resilience of the ecotones according to Jiang’s research.

Jiang’s models are just part of the adaptive management approach that the South Florida Water Management District has utilized. Another tool has been the ATLSS project or Across Trophic Level System Simulation, which offers a suite of models that can be used specifically for hydrology scenarios. NIMBioS Director Louis Gross is the principal investigator on ATLSS.

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NIMBioS Welcomes New Researchers

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

Screen Shot 2013-07-19 at 2.29.53 PM

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



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

profilecollageOf 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.

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Working Hard and Playing Hard: NIMBioS REU is Halfway

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

2013 Summer Graduate Workshop

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 projects.

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.

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