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NIMBioS Tuesday Seminar Series - 2014

Species montage. In conjunction with the interdisciplinary activities of the National Institute for Mathematical and Biological Synthesis (NIMBioS), a seminar series on topics in mathematical biology will be hosted at NIMBioS every other Tuesday at 3:30 p.m. (unless otherwise noted) in Hallam Auditorium, Room 206, Claxton Building, 1122 Volunteer Blvd. Seminar speakers will focus on their research initiatives at the interface of mathematics and many areas of the life sciences. Light refreshments will be served in Room 206 beginning 30 minutes before each talk. Faculty and students from across the UT community are welcome to join us. The schedule will be supplemented as additional speakers are added.

Video Archive of NIMBioS Seminars

Date Speaker
Topic
  January 2014
Jan 14 Sean Hoban, NIMBioS postdoctoral fellow Video icon. How to plan an effective and efficient population genetics sampling strategy
Jan 30
noon
Tom Hallam, UT Emeritus Professor, Ecology & Evolutionary Biology and Mathematics Video icon. Reflections
  February 2014
Feb 18 Kay Holekamp, Distinguished Professor of Zoology, Michigan State Univ. Video icon. The evolution of intelligence
Feb 25 Virginia Dale, Oak Ridge National Laboratory Corporate Fellow, Landscape Ecology & Regional Analysis Group Video icon. Incorporating Bioenergy Into Sustainable Landscape Designs
Feb 27 Nicole Mideo, Ecology & Evolutionary Biology, Univ. of Toronto Video icon. Explaining the complex lives of malaria parasites
  March 2014
Mar 25 Eugene Koonin*, Evolutionary Genomics Research Group, National Center for Biotechnology Information, Bethesda, MD Video icon. Generalization of the Central Models of Molecular Evolution in the (Post) Genomic Era
  April 2014
Apr 1 Yetta Jager, Environmental Sciences Division, Oak Ridge National Laboratory; adjunct professor in Ecology & Evolutionary Biology, UTK Video icon. Getting the Most Out of Rivers: Sustainable Hydropower Development
Apr 15
CANCELED
Michael Lynch*, Biology, Indiana Univ., Bloomington Mutation, Drift and the Origin of Subcellular Features
Apr 30
Wednesday
Leah Edelstein-Keshet*, Mathematics, Univ. of British Columbia Modeling Chemical Patterns in Cell Motility
  November 2014
Nov 11
Hanna Kokko*, Evolutionary Ecology, Australian National Univ. TBA
Nov 18
Rob Boyd*, School of Human Evolution and Social Change, Arizona State Univ. TBA
*NIMBioS Postdoctoral Fellows Invited Distinguished Visitor

NIMBioS Seminar Abstracts


L. Edelstein-Keshet photo. Time/Date: 3:30 p.m., Wednesday, April 30
Location: Hallam Auditorium, Room 206, Claxton Building, 1122 Volunteer Blvd.
Speaker: Leah Edelstein-Keshet, Mathematics, Univ. of British Columbia
Topic: Modeling Chemical Patterns in Cell Motility
Abstract: In order to fight infection or heal wounds, mammalian cells such as white blood cells (neutrophils or macrophages) crawl in response to chemical signals, a process termed chemotaxis. To do so, they rearrange their internal structure (actin cytoskeleton) to become polarized. Then the front protrudes and the rear retracts to produce motility. How is this process coordinated? Regulating this process are proteins (small GTPases) that form a chemical "prepattern" inside the cell. Interactions and crosstalk between these proteins results in the spontaneous self-organization of the intracellular patterns, and thence the polarization and motility. In this seminar I will describe modeling work in my group that addresses this topic in a sequence of models of various levels of detail. I will also present some computational techniques for understanding what the models predict and examples of work with experimental colleagues to validate the models. Click here for more information. Seminar flyer (pdf).

M. Lynch photo. This seminar has been CANCELED.
Time/Date: 3:30 p.m., Tuesday, April 15
Location: Hallam Auditorium, Room 206, Claxton Building, 1122 Volunteer Blvd.
Speaker: Michael Lynch, Biology, Indiana Univ., Bloomington
Topic: Mutation, Drift and the Origin of Subcellular Features
Abstract: Understanding the mechanisms of evolution and the degree to which phylogenetic generalities exist requires information on the rate at which mutations arise and their effects at the molecular and phenotypic levels. Although procuring such data has been technically challenging, high-throughput genomic sequencing is rapidly expanding our knowledge in this area. Most notably, information on spontaneous mutations, now available in a wide variety of organisms, implies an inverse scaling of the mutation rate (per nucleotide site) with the effective population size of a lineage. The argument will be made that this pattern naturally arises as natural selection pushes the mutation rate down to a lower limit set by the power of random genetic drift rather than by intrinsic molecular limitations on repair mechanisms. This drift-barrier hypothesis has general implications for all aspects of evolution, including the performance of enzymes and the stability of proteins. The fundamental assumption is that as molecular adaptations become more and more refined, the room for subsequent improvement becomes diminishingly small. If this hypothesis is correct, the population-genetic environment imposes a fundamental constraint on the level of perfection that can be achieved by any molecular adaptation, and indeed all adaptations. Additional examples consistent with this hypothesis will be drawn from recent observations on the transcription error rate and on the evolution of the oligomeric states of proteins. Click here for more information. Seminar flyer (pdf).

Y. Jager photo. Time/Date: 3:30 p.m., Tuesday, April 1
Location: Hallam Auditorium, Room 206, Claxton Building, 1122 Volunteer Blvd.
Speaker: Yetta Jager, Environmental Sciences Division, Oak Ridge National Laboratory
Topic: Getting the Most Out of Rivers: Sustainable Hydropower Development
Abstract: What is the best way to arrange dams within river basins to benefit society? Recent interest in this question has grown in response to the world-wide trend toward developing hydropower as a source of renewable energy in Asia and South America and with the movement toward removing unnecessary dams in the US. Hydropower development has rarely been planned with the goal of providing society with a portfolio of ecosystem services into the future. I synthesized a review of river basin design around four questions related to spatial decisions: Is it better to build fewer main stem dams or more tributary dams? Should dams be clustered or distributed among distant subbasins? Where should dams be placed along a river? And at what spatial scale should decisions be made? The following design principles emerged from our review: 1) concentrate dams within a sub-set of tributary watersheds and avoid downstream main stems, 2) disperse freshwater reserves among the remaining tributary catchments, 3) ensure that habitat provided between dams will support and retain production, and 4) formulate spatial decision problems at the scale of large river basins. To illustrate this, I developed a simple model for the American eel (Anguilla rostrata). For a randomly generated river network, I produced a Pareto-optimal frontier of solutions demonstrating where power dams should be located to maximize two objectives: power generation and eel survival. Click here for more information. Seminar flyer (pdf).
Video icon.Watch seminar online.

E. Koonin photo. Time/Date: 3:30 p.m., Tuesday, March 25
Location: Hallam Auditorium, Room 206, Claxton Building, 1122 Volunteer Blvd.
Speaker: Eugene V. Koonin, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, and a NIMBioS Postdoctoral Fellows Invited Distinguished Visitor
Topic: Generalization of the Central Models of Molecular Evolution in the (Post) Genomic Era
Abstract: The advances of comparative genomics and phylogenomics call for replacement of the key models of molecular evolution by a new generation of more general models. The traditional view of a genome of an individual organism or species has been supplanted by the pangenome concept. It has become apparent that the rates of gene loss and gain far exceed the rates of nucleotide substitution, at least in prokaryotes. Therefore, the pangenome, i.e. the entirety of the genes available to a given species, is typically is much larger than any individual genome, extremely dynamic and variable between different groups of microbes. I will present an overview of the genome dynamics and pangenome size estimates across the microbial world. The dynamic genome evolution and the do minance of horizontal gene transfer (HGT) in the evolution of prokaryotes also undermines the classical Tree of Life (TOL) concept. The notion of a single TOL is giving way to the model of a phylogenetic network that, however, can be shown to encompass a tree-like central trend. Further, genome-wide comparison of phylogenetic trees bears on the Molecular Clock model. It has been long known that the Molecular Clock is substantially overdispersed. I will show that the new model of Universal Pacemaker of genome evolution that only requires the conservation of relative rates of gene evolution, in contrast to the conservation of absolute rates inherent in Molecular Clock, yields a better fit to the phylogenomic data for diverse organisms. The new, general models of evolution do not refute the classic models but include them as extreme cases, in a pattern that appears common in the history of science. Click here for more information. Seminar flyer (pdf).
Video icon.Watch seminar online.

N. Mideo photo. Time/Date: 3:30 p.m., Thursday, February 27
Location: Hallam Auditorium, Room 206, Claxton Building, 1122 Volunteer Blvd.
Speaker: Nicole Mideo, Ecology & Evolutionary Biology, Univ. of Toronto
Topic: Explaining the complex lives of malaria parasites
Abstract: Despite a wealth of biomedical research into the pathogenesis of infectious diseases, little is known about the basic biology of their etiological agents. For many parasites, we lack satisfying answers to questions such as: what is it specifically about the interaction between hosts and parasites that results in disease symptoms? How do these interactions differ between closely related parasite strains or species? And, which factors have shaped parasite traits that determine harm to host and infectiousness? Using a combination of theoretical and experimental approaches, my work has revealed processes that underlie within-host dynamics of experimental rodent malaria infections and how differences in these processes give rise to the variation observed in patterns of disease across parasite genotypes. I will present results that demonstrate the importance of resource availability and competition and show that such 'bottom-up' mechanisms can explain phenomena that are often attributed to immune-mediated processes. Finally, I will show how verbal hypotheses pervading the literature to explain why malaria parasites seem to invest so little in reproduction (transmission) do not stand up to formal, mathematical scrutiny. Click here for more information. Seminar flyer (pdf).
Video icon.Watch seminar online.

V. Dale photo. Time/Date: 3:30 p.m., Tuesday, February 25
Location: Hallam Auditorium, Room 206, Claxton Building, 1122 Volunteer Blvd.
Speaker: Virginia Dale, Director, Center for BioEnergy Sustainability, ORNL; Adjunct Faculty, Ecology & Evolutionary Biology, UTK
Topic: Incorporating Bioenergy Into Sustainable Landscape Designs
Abstract: A spatially explicit collaborative plan for resource allocation and management, landscape design involves multiple scales, fits into existing systems, and maintains or enhances services. We describe an approach for landscape design that focuses on bioenergy production systems, which integrates into other components of the land, environment and socioeconomic system. The design for a particular area is developed with the involvement of key stakeholders. Appropriately applied, landscape design can guide choices toward more sustainable provision of bioenergy and other services. This approach encapsulates monitoring and assessment of a suite of indicators for soil quality, water quality and quantity, greenhouse gases, biodiversity, air quality, and productivity as well as socioeconomic considerations. The landscape design approach requires attention to site selection and environmental effects when making choices about locations, type(s) of feedstock, transport of feedstock to the refinery, refinery processing, and distribution of bioenergy products and services. The approach includes monitoring and reporting of measures of sustainability along the bioenergy supply chain and within specific contexts. Landscape designs must be implemented in a way that is doable from the perspective of producers along the supply chain. Hence, clear communication of environmental and socioeconomic opportunities and concerns is required to participants in production and users of the energy. Click here for more information. Seminar flyer (pdf).
Video icon.Watch seminar online.

K. Holekamp photo. Time/Date: 3:30 p.m., Tuesday, February 18
Location: Hallam Auditorium, Room 206, Claxton Building, 1122 Volunteer Blvd.
Speaker: Kay Holekamp, Distinguished Professor of Zoology, Michigan State Univ.
Topic: The Evolution of Intelligence
Abstract: Despite huge metabolic costs of neural tissue, some mammals and birds exhibit relatively large brain:body ratios and relatively sophisticated cognitive abilities. However, it is not clear whether big brains and great intelligence have generally evolved to cope with social complexity, complexity in the physical environment, neither or both. Primatologists have claimed that non-primate animals rarely form aggregations that impose rigorous cognitive demands and that their evolutionary success seldom depends on intelligence. They have therefore concluded that non-primate animals have no need to solve social problems that require knowledge of kinship, rank, or past history of give-and-take, as do many primates. Here I evaluate this assertion in light of recent data from non-primate mammals, focusing in particular on mammalian carnivores. It appears that that there has been remarkable convergence between primates and non-primate mammals with respect to the selection pressures, particularly social complexity, favoring the evolution of intelligence. However, recent data also suggest that the evolution of brains and behavioral flexibility has been considerably less constrained in primates than in mammalian carnivores. Recent work suggests that both social and non-social variables shape brain evolution, as do phylogenetic relationships and recent history. Click here for more information. Seminar flyer (pdf).
Video icon.Watch seminar online.

T. Hallam photo. This seminar has been rescheduled for noon, Thursday, January 30
Time/Date: 12:00 p.m., Thursday, January 30
Location: Hallam Auditorium, Room 206, Claxton Building, 1122 Volunteer Blvd.
Speaker: Tom Hallam, University of Tennessee Professor Emeritus
Topic: Reflections
Abstract: Join us for a special talk with the esteemed Tom Guy Hallam, Professor Emeritus of UT's Departments of Ecology and Environmental Biology and Mathematics, to be held in the newly renovated Tom Hallam Auditorium at NIMBioS. Dr. Hallam received his Ph.D. from the University of Missouri in 1965 and began his career as a faculty member in the Department of Mathematics at Florida State University, working in the area of comparison theorems for ordinary differential equations. While at Florida State, he initiated a mathematical modeling course. As his interest in applying mathematics to environmental problems took off, he began taking courses in oceanography and ecology. In 1977, Hallam accepted a joint professorship at UT. During the 1980s and 1990s, Hallam's research group integrated ecotoxicology and population dynamics into a watershed quality assessment tool for the U.S. Environmental Protection Agency. His research in using mathematical models to solve problems in ecotoxicology and ecology inspired him to begin an interdisciplinary program at UT combining mathematics and biology. The program seeks to apply mathematical theory to problems in the biological sciences. Dr. Hallam's talk will cover recollections and comments about the earlier days of mathematical and theoretical ecology, the history of theoretical and computational biology at UT; the talented faculty and graduate students who have been associated with the program, which culminated in NIMBioS. Dr. Hallam's seminar may also cover topics related to white nose syndrome and AIDS. Click here for more information. Seminar flyer (pdf).
Video icon.Watch seminar online.


S. Hoban photo. Time/Date: 3:30 p.m., Tuesday, January 14
Location: Room 205, Claxton Building, 1122 Volunteer Blvd.
Speaker: Sean Hoban, NIMBioS postdoctoral fellow
Topic: How to plan an effective and efficient population genetics sampling strategy: Markers, samples, and spatial considerations
Abstract: Genetic biodiversity contributes to species' evolutionary potential, ecosystem function, and human prosperity (e.g., agriculture). Preserving genetic resources during rapid environmental change is a pressing scientific and societal challenge. To meet this challenge, it is important to ensure that conservation researchers utilize well-designed and robust analytical methods and sampling/monitoring protocols. Unfortunately, many genetic studies are undertaken without knowledge of how many populations, genetic markers or individuals are needed. With colleagues, I developed software (Hoban et al. 2013, Methods in Ecology and Evolution) that calculates power of proposed sampling strategies for five study goals, including performing genetic assignment tests, using ancient DNA, and detecting genetic differentiation. I will explain how I used the software to highlight several concerns seldom considered during study planning: (a) power is rarely a linear function of adding markers/samples; (b) power is situation (species and history) specific; (c) some signals are too weak to detect. I will also explain my current interests in planning ex situ conservation collections (e.g., seed banks). At NIMBioS, I plan to optimize seed sampling from plant populations under local and range-wide population structure, while considering various strategies including those that are spatially biased or otherwise restricted. This project will result in general guidelines as well as software for customizing collections to particular species. Click here for more information. Seminar flyer (pdf).
Video icon.Watch seminar online.


NIMBioS Seminar Archive

  2013
  2012
  2011
  2010
  2009