Mathematical Biology Seminars at UBC



Seminars in year 2004

Mathematical Biology Seminar

Time: Monday, Dec 13, 2004, 2:00 pm
Location: Rm216, PIMS main facility, 1933 West Mall, UBC
Speaker: Raibatak Das Department of Chemistry and Chemical Biology Cornell University, Ithaca, NY.
Title: Real time cross-correlation image analysis of IgE receptor signaling.
Abstract:
Signaling in mast cells and basophils is mediated through IgE and its high affinity cell surface receptor FceRI. Binding and crosslinking of IgE receptor complexes by a cognate multivalent antigen initiates a signaling cascade that culminates in degranulation and the release of various effector molecules by these cells. We probe the early events in this signaling cascade by expressing fluorescent protein chimeras of the tyrosine kinases Lyn and Syk and the tandem SH2 domains of phospholipase-Cg1 in RBL-2H3 mast cells. We use multicolor fluorescence confocal microscopy to observe their dynamics following stimulation with multivalent antigen. A fluorescent tag on the antigen allows us to visualize the plasma membrane localization of the receptor complex. Sequential images are acquired with a time resolution of <5s. We have developed an image analysis scheme that allows us to quantify both the recruitment of fluorescent intracellular proteins to the plasma membrane and their colocalization with the receptor as measured by a cross correlation image analysis. We systematically apply this method to successive images acquired over a 20- 30 minute period during antigen stimulation of live cells at physiologically relevant temperatures. In this seminar I will present the details of this methodolgy and the results from this analysis to quantify in vivo kinetics of the early events in IgE receptor signaling.
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Mathematical Biology Seminar

Wedn Dec 8, 2004 Time: 2:00 pm
Location: Rm216, PIMS main facility, 1933 West Mall, UBC
Speaker: Laurence Ward Dept of Psychology, UBC
Title: On the role of synchronous neural oscillations in cognitive processes.
Abstract: Cognitive neuroscience aims to uncover the brain bases of cognitive processes such as perception, attention, memory, and consciousness. We are making progress in discovering which parts of the brain contribute to the processing requirements of these processes. Brain dynamics, however, must be understood to fill in the gaps, because (1) brain areas change their function from moment to moment and (2) most cognitive processes seem to require the cooperative interaction of several brain areas that might be quite distant from each other. A suggested mechanism for this cooperative interaction is synchronous oscillations at particular frequencies by the neuron populations involved. I will review both empirical evidence that synchronous neural oscillations are involved in cognitive processes and a few of the mathematical models of synchrony in spiking neural networks that are being studied.
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Mathematical Biology Seminar

Wedn Dec 1, 2004 Time: 2:00 pm
Location: Rm216, PIMS main facility, 1933 West Mall, UBC
Speaker: Carl T. Bergstrom Dept of Biology, U Washington
Title: Mathematical models of RNA silencing: An intracellular immune system uses multiple synergistic mechanisms to avoid autoimmunity and pathogen subversion
Abstract: RNA silencing or RNA interference (RNAi), found broadly throughout the eukaryotes, suppresses the expression of "aberrant" genes including those of many viruses and transposons. Like the specific immune system of vertebrates, RNA silencing generates specific responses against foreign elements and rapidly amplifiies these responses to clear or otherwise inactivate the threat. Also like the vertebrate immune system, RNA silencing systems risk (1) making mistakes and mounting undesirable responses against the self, and (2) suffering from subversion or sabotage by pathogens. We develop mathematical models of RNA silencing. We show that like the vertebrate immune system, the RNA silencing pathway provides multiple synergetic safeguards against accidental generation of damaging self-directed reactions, and that these safeguards are implemented so as to minimize the opportunities for subversion by the pathogen. (This research is joint with Rustom Antia, Emory University).

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IAM Colloquium (joint with Mathematical Biology Seminar)

Monday Nov 22, 2004 Time: 3:00 pm
Location: Rm 301, Klinck Building, 6356 Agricultural Rd., UBC
Speaker: Karl P. Hadeler Lehrstuhl Biomathematik, University of Tubingen
Title:Reaction Transport Systems and Applications to Biology
Abstract:
If particles interact and move in space and both processes act on the same time scale, then reaction-diffusion equations are the classical models. On the other hand, there are many situations where detailed information on particle motion is available in terms of direction, speed, mean run length, turning rate, velocity, etc., and a diffusion process, although well suited as an approximation, may be considered as being a rather crude model. If such information is incorporated into models for spread and interaction then one arrives at a hierarchy of reaction transport systems which are typically hyperbolic rather than parabolic.

The most detailed models are based on the general transport operator for particles with position and velocity, special cases are Pearson walks and correlated random walks. Cattaneo systems and nonlinear damped wave equations can be seen as approximations, and of course, reaction-diffusion equations as limiting cases.

The Langevin (Ornstein-Uhlenbeck) approach leading to semi-linear Kramers equations fits into this scheme. The different levels of this hierarchy can be connected by moment approximations.

For many of these problems the classical questions can be successfully approached: existence and stability of equilibria in bounded domains with Dirichlet or Neumann boundary data, location of the spectrum of the linearized problem, existence and structure of global attractors, existence of travelling front solutions as typical limit elements in unbounded domains, determination of critical speed. The equations can be applied to describe moving microorganisms, epidemic spread, chemotaxis and pattern formation.

The role of coupled (and split) dynamics and of quiescent states has been thoroughly investigated recently.
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Mathematical Biology Seminar

Time: Wednesday, Nov 17, 2004, 2:00 pm
Location: PIMS 216 (near PIMS), 1933 West Mall, UBC
Speaker: Ivan Robert Nabi, Department of Anatomy, Cell Biology & Physiology, University of British Columbia
Title:Autocrine receptor activation and the regulation of tumor cell motility.
Abstract: Autocrine activation of cytokine receptors, where a cell that expresses a cytokine receptor also secretes its ligand, is a common feature of tumor cell progression. Phosphoglucose isomerase (PGI) is a glycolytic enzyme that moonlights as a ubiquitous cytokine under the aliases autocrine motility factor (AMF), neuroleukin and maturation factor. AMF/PGI and its receptor, gp78 or AMF-R, are endocytosed via two pathways (caveolae/rafts and clathrin-coated vesicles) and associate with a mitochondria-associated smooth domain of the endoplasmic reticulum as well as fibronectin fibrils. Both AMF-R and PGI are associated with tumor progression and the complex intracellular trafficking of this receptor/ligand pair may serve to harness and sequester the cytokine potential of PGI, a ubiquitous cellular protein. In another cell model, autocrine activation of the c-Met/HGFR receptor is responsible for the protrusion of actin-rich pseudopodia in an invasive variant of transformed MDCK epithelial cells. These pseudopodia are highly blebbed structures morphologically distinct from lamellipodia whose formation is mediated by Rho/ROCK/p38MAPK signaling within the pseudopodial domain. This signaling pathway is activated in response to microtubule depolymerization. Local autocrine activation of c-Met/HGFR therefore modulates interplay between the actin and microtubule cytoskeletons to regulate not only cell motility but also the nature of the pseudopodial protrusion.

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Mathematical Biology Seminar

Time: Wednesday, Nov 10, 2004, 2:00 pm
Location: PIMS 216 (near PIMS), 1933 West Mall, UBC
Speaker: James D. Johnson, Department of Cellular and Physiological Sciences and Department of Surgery, University of British Columbia
Title:New roles for intracellular calcium stores in pancreatic beta-cells.
Abstract:It is becoming clear that all cell types possess multiple intracellular calcium stores, each with distinct functional properties. We have studied the properties and functional roles of three classes of intracellular calcium stores in human pancreatic beta-cells. We demonstrated for the first time that human beta-cells possess calcium stores sensitive to NAADP. NAADP-sensitive calcium stores initiate calcium signaling and IP3 receptor-dependent calcium oscillations. NAADP-sensitive calcium stores are a critical component of autocrine insulin signaling. Evidence from other studies suggests that NAADP-sensitive calcium stores are located in acidic organelles of the endosomal/lysosomal pathway. We have also shown that human beta-cells possess functional ryanodine receptor (RyR)-gated calcium stores. These calcium stores function in a novel mode of "calcium-induced calcium uptake" during depolarization-induced calcium influx and appear to be located in both ER and endosomal compartments. RyR-gated calcium stores appear to be critical to the regulation of beta-cell apoptosis, possibly through close interactions with mitochondria. Together these studies illustrate the variety of cellular functions that are controlled by specific calcium stores.

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IAM/PIMS Distinguished Colloquium (joint with Mathematical Biology Seminar)

Monday Oct 25, 2004 Time: 3:00 pm
Location: Rm 301, Klinck Building, 6356 Agricultural Rd., UBC
Speaker: Prof Raymond Goldstein Dept of Physics and Inst for Biomedical Sci & Biotechnol, U Arizona
Title:A stirring tale of bacterial swimming and chemotaxis
Abstract: See IAM website

Please note the time and place. There will be no other Mathematical Biology seminar on this week.

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IAM Colloquium (joint with Mathematical Biology Seminar)

Monday Oct 4, 2004 Time: 3:00 pm
Location: Rm 301, Klinck Building, 6356 Agricultural Rd., UBC
Speaker: Robert Guy Dept of Mathematics, University of Utah
Title:Computational modelling of platelet aggregation in large arteries
Abstract: See IAM website

Please note the time and place. There will be no other Mathematical Biology seminar on this week.

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IAM Colloquium (joint with Mathematical Biology Seminar)

NOTE RESCHEDULED TIME AND PLACE
Monday Sept 27, 2004 Time: 12:00 noon
Location: Rm 110, PIMS, 1933 West Mall, UBC
Speaker: Alex Mogilner Dept of Mathematics and Center for Genetics and Development, UC Davis
Title:Monte Carlo simulations and probabilistic analysis shed light on how microtubules search in space
Abstract: See IAM website

Please note the time and place. There will be no other Mathematical Biology seminar on this week.
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Mathematical Biology Seminar

Time: Wedn Sept 22, 2004 2:00 pm
Location: Rm216, PIMS main facility, 1933 West Mall, UBC
Speaker: Anders Carlsson, Dept of Physics, Washington University (St. Louis)
Title:Structure of Branched Actin Networks in Solution
Abstract:
The growth of branched networks of the protein actin is crucial for numerous cellular process. A kinetic polymerization model is developed which includes the basic growth and topological events in the growth of branched actin networks in aqueous solution. The main events include filament growth and depolymerization,branching along filament sides and/or ends, debranching, capping of filament ends by the branching catalyst Arp2/3 complex and capping protein, and uncapping. The unknown rate parameters in the model are fit to the measured polymerization kinetics of actin solutions containing Arp2/3 complex and capping protein. The quality of fit demonstrates that side branching dominates over end branching, and indicates that a decay process occurs which reduces the branching probability over time. The structure of the solution is followed as a function of time. Both analytic theory and computer simulations indicate that an initial "branching explosion" occurs, after which the filaments become much less branched.
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Mathematical Biology Seminar

Time: Wednesday, Sept 15, 2004, 2:00 pm
Location: WMAX 240 (near PIMS), 1933 West Mall, UBC
Speaker: Edwin Munro, Zoology, University of Washington
Title:Dynamics of cell polarization in the early C. elegans embryo: regulatory gene networks meet cortical mechanics.
Abstract:
In the past several years, the PAR proteins have emerged as conserved regulators of cellular polarity in a variety of different cellular and organismal contexts. In all these cases, PAR proteins are themselves asymmetrically distributed. Thus a key to understanding how cells polarize is to comprehend how cells establish and then stably maintain asymmetric distributions of PAR proteins. We are using a combination of experimental and computational approaches to address this question in the context of the early C. elegans embryo. In C. elegans embryos, PAR asymmetries emerge in response to a transient cue supplied by the sperm at fertilization. Recent experimental work from our lab and others suggests that a network of interactions among PAR proteins, and between PAR proteins and a contractile actomyosin cortex, govern the response to this cue: Cortical flows caused by a local weakening of the cortex near the point of sperm entry transport PAR proteins to establish and maintain their asymmetric distributions; at the same time, PAR proteins feed back upon the cortex to regulate contractile dynamics, cortical flow and thus their own distributions. Building on these results, we have developed a computational model that couples regulatory gene network dynamics to cortical mechanics to explore how robust mechanisms for the establishment and maintenance of PAR polarities could emerge from known interactions among PAR proteins and the cortex.
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Special Afternoon in Mathematical Biology

Date: Wedn Aug 18, 2:00 pm
Location: WMAX 240 (Near PIMS), 1933 West Mall, UBC
We will have several guests speaking on this afternoon:

Time: 2:00 pm
Speakers: Hannah McKenzie (Dalhousie University) and Isaac Holloway (UBC)
Title:Modelling a Yellow Fever Outbreak
Abstract:
Yellow Fever is a viral disease present in Africa and the Americas. It is has a complex transmission cycle which includes primates, humans, and mosquitoes. In this talk we present a biologically meaningful model of a Yellow Fever outbreak based on the common SIR model. This model is then used to fit data from an outbreak in Senegal in 2002, and to investigate the effects of the model parameters on an outbreak.

We would like to acknowledge the sponsors of the 3rd Annual PIMS-MITACS Mathematical Biology Summer Workshop (Edmonton AB, May 2004) for encouraging this research.

Time: 2:40- 3:40 pm
Rebecca Tyson and summer students working in her group at Okanagan University College will present some of their research during this time slot.

Speaker: Brock Nyquist student, Okanagan University College
Title:Modelling tree squirrel population dynamics in a managed forest
Abstract:Managed forests are subject to periodic clearcutting. Squirrels living in the area which is clearcut all perish, and there is a long period of time when no squirrels are able to live in the clearcut. Eventually, as the forest grows back, squirrels are able to survive and successfully reproduce in the second growth forest. We present a model of the squirrel population dynamics in a managed forest and examine how clearcut size and frequency affect the viability of the squirrel population as a whole. The results should be useful in future models of endangered or threatened species living in managed forests.

Speaker: Kyle Newton Student, Okanagan University College
Title:Assessing the effect of pheromone traps on the spatial distribution of moths
Abstract:When measuring dispersal of moths in the field, Mass-Mark-Recapture is a commonly used method in which large numbers of moths are marked, released in the field, and then recaptured in traps. The traps used are often pheromone traps, which are attractive to male moths within a certain area. It is well accepted among field ecologists that pheromone traps mustn't be so strong that the natural dispersal behaviour of the moths is significantly altered. On the other hand, if the traps are too weak so few moths are caught that the results are difficult to interpret. It is not clear however, what is the optimum trap strength. We present an individual-based model of moth movement which we use to quantitatively assess the effect of attractive traps on moth dispersal characteristics.

Speaker: Justin-Hebert Student, Okanagan University College
Title:Modelling nematode swimming
Abstract:We present a three dimensional model of nematode structure which allows us to generate swimming motion as a result of coordinated contractions of nematode muscle. Muscle characteristics are carefully modeled so as to represent actual muscle properties as closely as possible.

Speaker: Rebecca Tyson Professor, Okanagan University College
Title:Codling Moth Dispersal
Abstract:We present a model for the spatial movement of codling moths over a heterogeneous landscape including orchards and open areas. The codling moth is a pome fruit pest of economic importance in temperate regions of the world, and sterile insect release control methods in the Okanagan Valley have not had anywhere near the success rate which was predicted. By modelling codling moth dispersal we hope to gain a clearer understanding of how these moths move around in heterogeneous landscapes, leading hopefully to more successful control.
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Mathematical Biology Seminar

Date: Wednesday Aug 11, 2004, 2:00 pm
Location: WMAX 240 (Near PIMS), 1933 West Mall, UBC
Speaker: James Keener, Dept of mathematics, University of Utah
Title:A Model for Length Control of Flagellar Hooks of Salmonella typhimurium
Abstract: We present a mathematical model for the growth and length regulation of the hook component of the flagellar motor of Salmonella typhimurium. Under the assumption that the molecular constituents are translocated into the nascent filament by an ATP-ase and then move by molecular diffusion to the growing end, where they polymerize into the growing tube, we find that there is a detectable transition from secretion limited growth to diffusion limited growth. We propose that this transition can be detected by the secretant FliK, allowing FliK to interact with FlhB thereby changing the secretion target of the type III secretion machinery and terminating the growth of the hook.
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Mathematical Biology Seminar

Date: Wednesday Aug 4, 2004
Location: WMAX 240 (Near PIMS), 1933 West Mall, UBC
There will be two consecutive talks on this day by the following disstinguished speakers:
Time: 2:00-2:40 pm
Speaker: J K Percus, Courant Institute and Physics Dept, New York University
Title: Small Population Effects in Stochastic Population Dynamics
Abstract: We focus on several biologically relevant situations in which small populations play a significant qualitative role, and take some first steps to incorporate such situations in the continuous dynamics format that has been so elegantly developed in the past. We first describe a small number of model systems in which the influence of small populations is evident. Then we analyze in detail a toy model, exactly solvable, that suggests a path towards the attainment of our goal, and follow this by a formal vehicle for doing so. Application to the model systems, and comparison with numerical solutions, indicate the potential utility of this approach.
Time: 2:50-3:30 pm
Speaker: Ora E Percus, Courant Institute of Mathematical Sciences, New York University
Title: Can Two Wrongs Make a Right? Coin Tossing Games and Parrondo's Paradox
Abstract: A number of natural and man-made activities can be cast in the form of various one-person games, and many of these appear as sequences of transitions without memory, or Markov chains. It has been observed, initially with surprise, that losing "games" can often be combined by selection, or even randomly, to result in winning games. Here, we present the analysis of such questions in concise mathematical form (exemplified by one nearly trivial case and one which has received a fair amount of prior study), showing that two wrongs can indeed make a right - but also that two rights can make a wrong!
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Mathematical Biology Seminar

Time: Wednesday July 28, 2004 2:00 pm
Location: WMAX 240 (Near PIMS), 1933 West Mall, UBC
Speaker: Edward Green, Centre for Mathematical Medicine, University of Nottingham
Title:Mathematical modelling of liver cell aggregation in vitro
Abstract:
Currently, there are few successful treatments for chronic liver disease apart from organ transplant. A shortage of donors means that the health of many patients deteriorates whilst they are waiting for surgery. In order to alleviate these difficulties, tissue engineers are now attempting to grow functional liver tissue in vitro, with the eventual aim of implantation into patients. When seeded onto an extracellular matrix in vitro under suitable conditions, liver cells will form multicellular spheroids. These show improved viability and functionality compared to cells grown in monolayer culture. However, at present the mechanisms of spheroid formation are not well understood. Working closely with the Tissue Engineering Group at Nottingham, we aim to gain greater insight by developing a mathematical model for the early stages of the aggregation process; it is hoped that this will help tissue engineers to ascertain optimal culture conditions. I will introduce a multiphase continuum model which concentrates on the roles of cell-cell and cell-extracellular matrix interactions in the aggregation process. Model predictions will be presented and shown to display excellent qualitative agreement with experimental results. This project is joint work with Prof. Helen Byrne and Dr Sarah Waters (Centre for Mathematical Medicine) and Prof. Kevin Shakesheff (Tissue Engineering Group).
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Mathematical Biology Seminar

Monday July 26, 2004 Time: 3:00 pm
Location: WMAX 240 (Near PIMS), 1933 West Mall, UBC
Speaker: Rustom Antia Dept of Biology, Emory University, Atlanta
Title:Modeling the dynamics of CD8 responses
Abstract:
I will focus on some of the potential ways in which mathematical models can contribute to our understanding of the CD8 immune response and immunological memory. I will describe some of the theoretical and experimental results which have led us to re-evaluate the earlier "predator-prey" models of immune responses in favor of models in which the immune response is described as a developmental process. I will spend some time describing some of the major problems which remain.
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Mathematical Biology Seminar

Time: Wednesday July 21, 2004 2:00 pm
Location: WMAX 240 (Near PIMS), 1933 West Mall, UBC
Speaker: Ehud Meron, Department of Solar Energy & Environmental Physics and Department of Physics, Ben Gurion University
Title: Ecosystem Engineers: From pattern formation to habitat creation.
Abstract:
Habitat and species richness in drylands are affected by the dynamics of a few key species, termed "ecosystem engineers". These species modulate the landscape and redistribute the water resources so as to allow the introduction of other species. A mathematical model is developed for a pair of ecosystem engineers commonly found in drylands: plants forming symmetry breaking vegetation patterns and cyanobacteria forming soil-crusts. The model highlights conditions for habitat creation and for high habitat richness, and suggests a novel mechanism for species loss events as a result of environmental changes.
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Mathematical Biology Seminar

Time: Tuesday May 25, 2004 2:30 PM
Location: Math Annex 1102, UBC
Speaker: Raibatak Das, Department of Chemistry and Chemical Biology, Cornell University.
Title:Biophysical Investigations of Mast Cell Signaling
Abstract:
Our laboratory employs a diversity of biophysical, biochemical and cell biological techniques in an effort to understand mast cell signaling mediated through IgE and its high affinity cell surface receptor Fc-epsilon-RI. Binding and crosslinking of the receptors by a cognate multivalent antigen initiates a signal cascade that culminates in degranulation and the release of various effecter molecules by these cells. We are examining the dynamics of molecules involved in this signaling pathway and the role of the plasma membrane in modulating their interactions. We use structurally well-defined nanometer length scale ligands to probe the binding of IgE to its antigens and we have described this binding using realistic mathematical models. We utilize fluorescence spectroscopy and quantitative fluorescent imaging of live cells to characterize the interactions between the cell surface receptor and other membrane bound and intracellular signaling proteins. We also use model membrane systems as a basis for understanding the role of lipid rafts - ordered domains in the plasma membrane hypothesized to segregate signaling molecules by their preferential partitioning. This talk will describe some of our recent results in these areas.
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Mathematical Biology Seminar

Time:Wednesday May 12th, 2004, 2:00 pm
Location: WMAX 240 (near PIMS), 1933 West Mall, UBC
Speaker: Franziska Michor, Program for Evolutionary Dynamics, Harvard University
Title:Somatic evolution of cancer
Abstract:
Evolutionary concepts such as mutation and selection can best be described when formulated as mathematical equations. Cancer arises as a consequence of somatic evolution. Therefore, a mathematical approach can be used to understand the process of cancer initiation and progression. But what are the fundamental principles that govern the dynamics of activating oncogenes and inactivating tumor suppressor genes in populations of reproducing cells? And how does a quantitative theory of somatic mutation and selection help us to evaluate the role of genetic instability?
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Mathematical Biology Seminar

Time: Wedn May 5, 2004, 2:00 pm
Location: WMAX 240 (near PIMS), 1933 West Mall, UBC
Speaker: Leah Keshet, Dept of Mathematics, UBC
Title:Macrophages in animals prone to Type 1 diabetes are defective
Abstract:
I will present a summary of work done in colaboration with SFU experimentalists on the function of macrophages. In Previous work, Finegood, O'Brien et al showed that in animals prone to autoimmune diabetes, immune cells called macrophages are poor at their function of clearing up debris by phagocytosis. We modeled the process and used the experimental data to refine our understanding of what parts of the function is defective, and to what extent. The modelling work had been initiated by Marek Labecki (UBC). Models suggested ways of improving experimental design, and recent data was collected by Mitsu Komba (SFU). This project is joint work with Stan Maree and Cheryl Dyck, and was supported by MITACS and by CIHR-JDRF funds to Diane Finegood.
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Mathematical Biology Seminar

Time: Wedn April 28, 2004, 2:00 pm
Location: WMAX 240 (Near PIMS), 1933 West Mall, UBC
Speaker: Steven Viscido School of Aquatic and Fishery Sciences, University of Washington
Title:Emergent properties of fish schools: a comparison of observation and theory
Abstract: In animal groups, emergent properties result from individuals' reaction to stimuli from neighbors. Because such reactions are embedded within a social matrix, group members' responses are coupled, and indirect interactions can affect group structure. I will compare statistical properties of groups such as nearest-neighbor distance and group polarity generated by simulations of theoretical traffic rules, with the characteristics of real schooling fish, determined with computerized video tracking, and discuss how the two approaches complement one another.
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Second Semi-Annual MITACS Biomedical team meeting Day

Time: Monday, April 19, 2004, 9:00 am -- 3:30 pm
Location: Rm216, PIMS main facility, 1933 West Mall, UBC
Speakers: MITACS students and faculty
Abstract: Details of the schedule here.
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Mathematical Biology Seminar

Time: Wedn April 14, 2004, 2:00 pm
Location: Rm216, PIMS main facility, 1933 West Mall, UBC
Speaker: Donald Ludwig
Title:Biodiversity and Precaution
Abstract:
"Biodiversity" is a new concept that is used to argue for conservation. Unfortunately, the concept is awkward to define, and has few implications that have been demonstrated by ecological research. A study of human impacts on ecosystem services would be more to the point. In light of our substantial ignorance of how ecosystem services are maintained, we should adopt a policy of meddling as little as possible with things we do not understand.
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There will be no seminar on April 7 to allow students time to study for exams.

Mathematical Biology Seminar

Time: Wedn March 31, 2004, 2:00 pm
Location: Room 216, PIMS main facility, 1933 West Mall, UBC
Speaker: Yue Xian Li Dept of Mathematics, UBC
Title:Models of ideal schooling behaviour
Abstract:
In this talk I will describe models for ideal schooling behaviour, in which the individuals try to maintain positions along a regular lattice, and where they also move at the same velocity. I will describe conditions for the existence and stability of such "perfect schools". In 1D, full analysis is possible. In 2D, the challenge is greater, but simulations and ideas about the extensions will be presented.
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Mathematical Biology Seminar

Time: Wedn March 24, 2004, 2:00 pm
Location: Room 216, PIMS main facility, 1933 West Mall, UBC
Speaker: Michael Gilchrist University of New Mexico
Title:Modeling host-parasite coevolution and intra vs. inter-host selection through the use of nested models
Abstract:
(1) Parasites within a host generally face a trade-off between reproducing at a high rate to facilitate transmission between hosts and illiciting a rapid host immune response and/or harming their their host. Conversely, hosts face a trade-off between having an immune response which can rapidly respond to an infection and one which responds too strongly, wasting resources and potentially damaging the host. To address how natural selection shapes parasite replication and host immune response rates I have developed a novel framework for modeling host-parasite coevolution The framework consists of a set of coupled models. In the within-host model, the dynamics of a parasitic infection are determined by both the parasite's replication rate within a host and the host's immune response rate. This within-host model was nested in an age-structured, epidemiology model. By coupling these two models I am able to explore how the optimal parasite replication rate changes with the host's immune response rate and vice versa.
(2) Natural selection often acts at multiple levels. For example, natural selection occurs within a host, favoring parasites that produce the greatest number of offspring. Simultaneously, natural selection occurs between hosts, favoring parasites that lead to the greatest number of newly infected hosts. Currently, I am using a set of nested within-host and epidemiology models to understanding what conditions the selective forces at these two scales conflict with one another and how such conflicts are resolved.
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Mathematical Biology Seminar

Time: Wedn March 17, 2004, 2:00 pm
Location: Room 216, PIMS main facility, 1933 West Mall, UBC
Speaker: Carlos Castillo-Chavez Arizona State University
Title:Cross - immunity as a mechanism for multiple strain coexistence: The case of influenza A
Abstract:
Cross - immunity (a natural partially effective vaccine) can enhance coexistence between competing strains of the flu. Furthermore, public health measures (quarantine) can destabilize an established strain, producing oscillations. The joint impact of both factors is explored with some interesting and not totally obvious outcomes. This is the result of joint work with Miriam Nuno, Cornell University, Zhilan Feng, Purdue University, and Maia Martcheva, University of Florida.

Please note that Carlos Castillo-Chavez will also give a IAM Colloquium, on Tuesday March 16, 2004 at 3:00 pm in Math 203
Title: Multiple time scales in the dynamics of tuberculosis
Abstract: Tuberculosis is transmitted by close and casual contacts. In this talk I will look at the transmission dynamics of tuberculosis on generalized households. Emphasis will be put on the modeling challenges and the use of time scales to reduce the dimensionality of a complex model. This work has been carried out in collaboration with Baojun Song, Montclair State University (New Jersey), and Juan Aparicio, Universidad Metropolitana (Puerto Rico).
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Mathematical Biology Seminar

Time: Wedn March 10, 2004, 2:00 pm
Location: Room 216, PIMS main facility, 1933 West Mall, UBC
Speakers: Andrew MacDougall, Botany, UBC (and Leah Keshet, Math, UBC in a supporting role).
Title:Predictable unpredictability in a disturbance-dependent ecosystem
Abstract:
Fire is assumed to stabilize grassland communities by offsetting competitive displacement. Species loss in grassland remnants is often attributed to increased competition due to fire suppression, and this leads to the use of prescribed burning for restoration. We examined the effects of fire on stability by monitoring its impact on productivity in an oak savanna ecosystem where fire has been absent for 150+ years. Four years of summer burning caused a substantial decrease of perennial grasses and a concomitant increase of non-grass species (forbs).
Given the decline in grasses and increase in forbs, we predicted that fire would create a forb-dominated community that was as stable with repeated burning as the grass-dominated community with its long-term absence. Our data did not support this hypothesis. Total production dropped in the savanna, as the increase in forb production was unable to match the former output by the grasses. Due to substantial differences in litter quality and quantity, it is predicted that perennial forb species will be incapable of supporting annual burning over time.
Because burning does not completely eliminate the more abundant perennial grass species, they would be predicted to increase in response to the decreased occurrence of fire. At the site level, therefore, the savanna community is predicted to oscillate through time between grass- and forb-dominated assemblages. The interaction of soil depth and annual climatic variations are predicted to deflect this oscillation into further unpredictability. Prior to the extensive loss of habitat in this ecosystem beginning in the 1840s, the stability of this savanna was probably best defined at the regional level due to the fire-induced variability in forbs and grasses at the site level. Although burning in remnant areas could re-establish this oscillation, many native species no longer have regional distributions and may be highly vulnerable to its effects.
Some preliminary modelling ideas on this ecological problem will be presented by the second speaker at the conclusion of this talk.
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Mathematical Biology Seminar

Time: Wedn Mar 3, 2004, 2:00 pm
Location: WMAX 240, (**near PIMS**), 1933 West Mall, UBC
Speaker: Colin Clark Dept of Mathematics, UBC
Title:Fisheries Management: the problem of excess capacity
Abstract: Severe, even disastrous overfishing continues to plague ocean fisheries worldwide, including some cases where intensive management has been in force. One proposed remedy is for governments to buy back excess fleet capacity (and sink it). But previous buyback programs, though costing many millions, have had little effect. This talk uses dynamic models to investigate the economics of buybacks. The main prediction is that buyback programs are all but guaranteed to fail (and to be extremely expensive) unless they are accompanied by rigorous incentive-altering devices such as IFQs (Individual Fishing Quotas).
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Mathematical Biology Seminar

Time: Wedn Feb 25, 2004, 2:00 pm
Location: NOTE ROOM: Math Annex 1102, UBC
Speaker: Rachel Bearon School of Oceanography, University of Washington
Title:Swimming micro-organisms: from individual trajectories to population distributions
Abstract:
Many single-celled micro-organisms are motile. Understanding swimming behaviour is necessary to predict the spatial-temporal dynamics of a population in its natural environment. I will present experimental data on the swimming behaviour of Heterosigma akashiwo, a harmful alga, which forms dense aggregations associated with fish-kill. I will then discuss model predictions for the spatial distribution of swimming cells in ambient fluid flows.
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There will be no seminar over spring break.

Mathematical Biology Seminar

Time: Wedn Feb 11, 2003, 2:00 pm
Location: WMAX 240, (**near PIMS**), 1933 West Mall, UBC
Speaker: Adriana Dawes, Dept of Mathematics, UBC
Title:The establishment of cell polarity in the early C. elegans embryo
Abstract: A central question in the field of development is how a single cell with one genome produces numerous differentiated cells in the mature organism. One way that an organism can achieve cellular diversity is through asymmetric division and protein localization. In C. elegans, our model organism, cell fate specification begins at the one cell stage as an initially unpolarized cell establishes anterior/posterior specification. Once the anterior/posterior axis is established, specific proteins are localized to opposite ends of the cell. This protein distribution is maintained to first cleavage, when the single celled embryo divides asymmetrically. We use experiments and modelling to understand how feedback loops between proteins and the actomyosin mesh at the cell cortex establish cell polarity leading up to first cleavage.


** We are using this facility temporarily. Please do not enter the seminar room via the main office of this department (SCARP). Please use the door similar to room 216 for entry/exit.

Mathematical Biology Seminar

Time: Wedn Feb 4, 2004, 2:00 pm
Location:WMAX 240, (**near PIMS**) 1933 West Mall, UBC
Speaker: Judith Miller Mathematics Dept, Georgetown U.
Title:A finite locus effect diffusion model for the evolution of a quantitative trait
Abstract:
A quantitative trait is a continuous random variable. Examples include the height of a human, the oil content of a corn plant, and the number of bristles on the abdomen of a fruit fly. The value of a quantitative trait in an individual is generally determined by contributions from numerous loci (genes), as well as environmental factors and genetic-environmental interactions.

We construct a diffusion model for the joint distribution of absolute locus (gene) effect sizes and allele frequencies for loci contributing to an additive quantitative trait, and present basic results about solutions of the model. It is a "mesoscale" model in that it explicitly incorporates a finite number of loci with finite (i.e. non-infinitesimal) effects, but does not track the evolution of allele frequencies at specific loci. The model is designed to approximate a discrete model exactly in the limit as both population size and the number of loci affecting the trait tend to infinity. For the case when all loci have the same effect size, formal multiple-timescale asymptotics are used to make accurate predictions of the long-time response of the population trait mean to selection. For the case where loci can take on either of two distinct effect sizes, not necessarily with equal probability, numerical solutions of the system confirm that response to selection of a quantitative trait is insensitive to the variability of the distribution of effect sizes.

** We are using this facility temporarily. Please do not enter the seminar room via the main office of this department (SCARP). Please use the door similar to room 216 for entry/exit.
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Mathematical Biology Seminar

Time: Wedn Jan 28, 2004, 2:00 pm
Location: WMAX 240, (**near PIMS**), 1933 West Mall, UBC
Speaker: Eric Cytrynbaum, Dept of Mathematics UC Davis & UBC
Title:Experimental and computational studies of mitotis spindle morphorphogenesis
Abstract: Mitosis, the process by which a cell segregates two identical copies of its genome in preparation for division, is fundamental to cell replication and hence to life as we know it. In order to separate the two copies of the genome, a self-assembling protein machine, the mitotic spindle, employs several force generating molecules known as molecular motors. These motors, through interaction with spindle microtubules (semi-rigid protein filaments), aid in spindle assembly as well as chromosome segregation.

In this talk, I will describe a computational model of the formation of the mitotic spindle at the onset of mitosis. The model describes the growth dynamics of microtubules, the behaviour of dynein and Ncd (molecular motors) and elucidates the role of the nucleus in setting the stage for spindle formation. In addition, I will describe a series of recently completed experiments that underly some of the assumptions of the model and outline some planned experiments that will test out many of the model-based predictions.

** We are using this facility temporarily. Please do not enter the seminar room via the main office of this department (SCARP). Please use the door similar to room 216 for entry/exit.

Mathematical Biology Seminar

Time: Thurs Jan 15, 2004, ** 3:30 pm**
Location: Room 1101 Mathematics Annex, UBC
Speaker: Robert M. Miura, Departments of Mathematical Sciences and Biomedical Engineering, New Jersey Institute of Technology
Title: Spreading Depression: A Paradigm for Understanding Basic Brain Mechanisms
Abstract: Although we know a lot about the many different mechanisms that are operative at the cellular level, we know very little about how they conspire to yield a normal functioning brain. We can gain a lot of new information about how the normal brain functions by studying extreme phenomena, e.g., spreading cortical depression. Spreading depression (SD) has been recognized as a pathological brain phenomenon for 60 years and has been investigated with extensive experimental and theoretical studies. In spite of these, we know very little about how SD is instigated and propagated. It has possible links with a number of diseases. In this talk, I will describe spreading depression and indicate some new directions for modelling.

** We are using this facility temporarily. Please do not enter the seminar room via the main office of this department (SCARP). Please use the door similar to room 216 for entry/exit.

Acknowledgements:

This seminar series is supported by the Mathematics for Information Technology and Complex Systems (MITACS) NCE, by PIMS, and by NSERC grants to UBC faculty. We are very grateful to PIMS and to the PIMS staff for (a) providing space and seminar facilities (b) organizing and providing refreshments and (c) handling local arrangements for visiting speakers.