Undergraduates From Across Country Present Research at NIMBioS Conference

IMG_4688 croppedMore than 160 undergraduates and faculty mentors converged in Knoxville, Nov. 16-17, for the fifth annual Undergraduate Research Conference at the Interface of Biology and Mathematics. More than 60 oral and poster presentations were presented, many with multiple collaborating students, on topics from mathematically modeling proteins to image analyses of microscopic worms moving through 3D-printed environments. Participants came from as far away as the University of Hawaii at Hilo, with 29 statues and 70 different institutions represented.

The keynote and featured talks also represented the great range of mathematical biology. Keynote speaker Dr. Mariel Vazquez from San Francisco State University presented her work on “DNA Unlinking by Xer Recombination” where she applies topology to better understand biochemical processes. Later, featured speaker Dr. Andrew Liebhold from the USDA Forest Service gave his talk on “Forest Insect Outbreaks: A Never-Ending Puzzle” about mathematical modeling of forest insect pest dynamics. Dr. Talitha Washington from Howard University and Dr. Joe Bailey from the University of Tennessee both joined in for the career panel to advise students about career paths in math and biology.

The conference also featured a showcase of graduate opportunities and more.

A lively stream of “tweets” took place on Twitter with the hashtag #nimbiosurc. All tweets from the conference are curated on NIMBioS’ Storify page. A full set of photos from the conference can be viewed here.


Created with Admarket’s flickrSLiDR.

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Modeling of Microbial World Comes of Age

Andersen-microbes-Web

Exploring the individuality of microbes

The fruits of the labor of the NIMBioS Investigative Workshop on Individual-Based Ecology of Microbes: Observations and Modeling appear today in an opinion paper in the Proceedings of the National Academy of Sciences. The paper argues that individual-based models are ideal for incorporating the intra-cellular dynamics of synthetic organisms in order to predict their behavior and fitness under various conditions

The paper advocates for what the authors call “microbial Individual-Based Ecology,” a combination of individual-based modeling and experimentation, arguing that this approach will lead to greater insights into ecology and evolution.

“The chance to observe, manipulate and model from first principles, from molecules via individuals to populations, communities, and ecosystems goes far beyond the current basis of ecological and evolutionary theory,” they write.

The Workshop met in June 2011.

Citation: Kreft U, et. al. 2013. Mighty small: Observing and modeling individual microbes becomes big science. Proceedings of the National Academy of Sciences.

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NIMBioS Hosts SHADES Girls in STEM Workshop

Rosalia, local middle school student, shows off the rubber band car in progress.

Rosalia, local middle school student, shows off her rubber band car in progress.

NIMBioS hosted area middle school girls this month for SHADES, an interactive one-day workshop in science and engineering. Girls did many fun and interactive STEM activities including T-shirt chromatography, building model sinkholes, using Geiger counters, creating genetic code bracelets, and making special tapes to measure tree trunk diameter using pi. The day culminated with an engineering design competition where the girls built rubber-band cars. The day was designed to show off fun and interesting applications of STEM to attract girls to science and engineering careers.

Girls using chromatography to create T-shirt designs

Girls using chromatography to create T-shirt designs

SHADES stands for “SHAring ADventures in Engineering and Science.” The annual event is sponsored with the Greater Knoxville Math/Science Coalition, which includes the American Association of University Women (AAUW), American Women in Science (AWIS), Society of Women Engineers (SWE), American Nuclear Society (ANS), Tennessee Society of Professional Engineers (TSPE), and US Women in Nuclear (WIN).

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NIMBioS Celebrates Diversity in STEM at National Conference

Gesham Magombedze, NIMBioS postdoctoral fellow, at the 2013 SACNAS Conference in San Antonio, TX

Gesham Magombedze, NIMBioS postdoctoral fellow, at the 2013 SACNAS Conference in San Antonio, TX

NIMBioS researchers and staff shared their passion for science this month at the 2013 SACNAS Annual Conference, as well as the many opportunities available to diverse STEM students and faculty at NSF math institutes and biology centers. SACNAS, the Society for the Advancement of Chicanos and Native Americans in Science, hosts an annual conference each year promoting STEM and emphasizing mentoring, networking and professional development. This year’s conference in San Antonio, TX, boasted almost 4,000 attendees, 1,000 student presentations, over 300 exhibitors, many scientific symposia and cultural events.

Anna Michelle Lawing, NIMBioS postdoctoral fellow, presents at a symposium at the SACNAS conference.

Anna Michelle Lawing, NIMBioS postdoctoral fellow, presents at a symposium at the SACNAS conference.

NIMBioS kicked off its participation with the Modern Math Workshop, an annual pre-conference event sponsored by all of the NSF Mathematical Sciences Institutes. During the workshop, NIMBioS postdoctoral fellow Gesham Magombedze presented “Modeling the Immune Response of Cattle Suffering from Johne’s Disease.” Later and during the conference itself, NIMBioS postdoctoral fellow Anna Michelle Lawing spoke about her work on “Using Evolutionary Biology to Inform Our Understanding of Species and Community Responses to Environmental Change” during a “Hot Topics in Evolution and Ecology” symposium. Lawing presented alongside researchers from NESCent and NCEAS, two other biology synthesis centers, to a packed room of mostly undergraduates. Later, she answered questions about climate change during a screening of science documentary Chasing Ice during SACNAS’ Evolution/Ecology Movie Night.

Notably missing from the conference were many government agencies due to the federal government shutdown. Cliff Poodry, Director of Training, Workforce Development, and Diversity at the National Institutes of Health, was unable to give his invited keynote address, and many other presenters and exhibitors were unable to attend. The disappointment of the SACNAS organization with the situation was expressed in this news video clip from Fox San Antonio.

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Tylenol Scares: New Method May Help Make Life-Saving Decision

Tylenol_rapid_release_pills

“They tell you it’s medicine. They don’t tell you it can kill you.” — David Baumle, father of 12-year-old Davy Baumle who died from acute liver failure caused by acetaminophen.

A recent in-depth investigation by This American Life radio program and ProPublica looks at the underreported dangers of overdosing on Tylenol, especially with regard to children. David Baumle tells ProPublica about the death of his son Davy who took Maximum Strength Tylenol Sore Throat over several days accidentally ingesting a lethal dose.

Acetaminophen is the leading cause of acute liver failure in the U.S. When taken at the recommended dose, however, it is safe and works well, eliminating aches and pains and reducing fever with few side effects.

A chemical antidote to acetaminophen poisoning does exist, but it is only effective if administered within eight hours of an overdose. As ProPublica reports, in one study, people who attempted suicide with acetaminophen and later regretted their action often made it to a hospital in time, whereas people who overdosed by accident were often unaware they have been poisoned. Part of the problem is that acetaminophen is found in many over-the-counter medicines in the U.S., an estimated 600 medicines, so sometimes people are unaware they have taken it. Overdose symptoms take several days to develop and resemble those of the flu. By then, it is too late for the antidote to work.

If liver damage is severe enough and the antidote is not administered early enough, the only life saving treatment is liver transplantation. Determining which patients need a transplant and which will recover is a major problem in treating patients with acetaminophen overdose.

Dr. Chris Remien

Dr. Chris Remien

NIMBioS postdoc Chris Remien and his research partners have developed a novel method to determine which patients will benefit from liver transplant in these instances. Rather than relying on purely statistical methods, Remien’s method is based on a dynamic model of acetaminophen metabolism and cellular damage.

In addition to making predictions on the need for a transplant, the model also explains the threshold with respect to acetaminophen intake and liver damage.

“There is a simple threshold in the model because of how the liver processes acetaminophen, so that there is either very little liver damage or rapid damage, which may explain why patients who chronically overuse acetaminophen can eventually develop rapid liver damage,” Remien explained.

The model has shown promise in a set of 53 patients from the University of Utah, but it still needs to be validated in a larger multi-center study before it can be used by physicians.

“We are currently collecting more data and collaborating with other groups in order to validate our method,” Remien said.

Collaborating on the project are Norman Sussman, Associate Professor of Surgery at Baylor College of Medicine and Fred Adler, Professor of Mathematics and Biology at the University of Utah.

For more information about Remien’s model, view his seminar talk here.

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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 Sciencecafe.org 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

Lake_Okeechobee1

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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