2001/2003

Jan 27, 2003, 3-4 pm, IAM/Stats seminar Room (301 Leonard Klink bldg), IAM-PIMS Distinguished colloquium speaker: Leon Glass (Physiology, McGill): Dynamics of genetic networks

We study ionic channel proteins which come from distinct but related families. Each of the families can characterized statistically by distributions of amino acids along positions of its sequence; that is, a profile. We build stochastic models to measure similarity and evolutionary distances between the families. Our models take into account correlations between residues at each position and substitution probabilities of one amino acid by another.

The talk will provide an overview of the project and summarize its main results. A hierarchical model that expands upon these simple rules by linking them to different sensory mechanisms, energetic trade-offs and behavioural modes is currently being developed by Dr. Newlands and Prof. Keshet to test alternative hypotheses and to identify unique rule-sets that produce different school formations. To search for realistic survival trade-offs that individuals make while schooling in the wild, simulation results of these individual-based models will be compared to data on the shape and structure of different formations of Atlantic bluefin tuna.

November 14, 2002, 12 - 1 pm, IRC 6: Dr. Ruedi Aebersold Institute for Systems Biology, Seattle UBC Systems Biology Lecture Series

November 7, 2002, 12 - 1 pm, IRC 6: Dr. Tony Pawson Samuel Lunenfeld Research Institute, Toronto UBC Systems Biology Lecture Series

Nov 4, 2002, 3-4 pm, IAM/Stats seminar Room (301 Leonard Klink bldg) David Boal (Physics, SFU): Extraterrestrial cells

October 31, 2002, 12 - 1 pm, IRC 6: Dr. John Aitchison Institute for Systems Biology, Seattle UBC Systems Biology Lecture Series

Oct 25, 2002, 3-4 p.m.,Mathematics Colloquium: MATH ANNEX 1100, Jim Keener (Math, Utah), title: TBA

MATHEMATICS COLLOQUIUM:

Time: Friday, Oct 11, 2002, 3:00 pm

Location: Math Annex 1100

Speaker: Yue Xian Li

Title: A Minimal Network Model for Quadrapedal Locomotion Based on Symmetry and Stability

Abstract:

Four-legged animals move with several distinct patterns of rhythmic leg movements, called gaits. Standard quadrapedal gaits include walk, pace, trot, bound, and gallop. Networks of coupled oscillators have been used to model the central pattern generators (CPGs) that produce these patterns. In these models, symmetric gaits are related to phase-locked states of the network possessing the same symmetries. Pioneer works by Golubitsky et al were based on symmetry analysis that gave conditions for the existence of these states. We show that models based on symmetry alone cannot generate a model circuit of practical use, i.e., a circuit people can actually install in a four-legged robot capable of moving with different gaits. A functioning network should possess not only enough symmetry to guarantee the existence of these solutions but a mechanism to segregate each one of them dynamically. Our new theory, based on the analysis of both the existence and stability of these phase-locked states, allows us to achieve both goals. We show that a minimal network of four identical neurons is capable of generating dynamically independent patterns for all standard quadrapedal gaits. A circuit is designed based on this theory using a realistic neuronal model and synaptic currents. Numerical simulations of this model circuit confirmed the analytical results. (Others involved in part of this work: Drs. Yuqing Wang and Robert Miura)

October 3, 2002, 12 - 1 pm, IRC 6 Dr. Tim Galitski Institute for Systems Biology, Seattle UBC Systems Biology Lecture Series

Sept 30, 2002, 3-4 pm, IAM/Stats seminar Room (301 Leonard Klink bldg) Carl Bergstrom (Zoology, UW): Fighting the antibiotic resestant bacteria in hospitals.

September 19, 2002, 1-2 pm, Wesbrook Building 100, 6174 University Boulevard Dr. Andrew Link Vanderbilt University, Tennessee UBC Systems Biology Lecture Series

September 16, 2002, 3.30-4.30 pm, Instructional Resources Centre 6, 2194 Health Sciences Mall (IRC 6) Dr. John Yates Scripps Institute, La Jolla UBC Systems Biology Lecture Series

September 11, 2-3 pm, Forest Science Centre 1005, 2424 Main Mall Dr. Lee Hood Institute for Systems Biology, Seattle UBC Systems Biology Lecture Series

September 6, 2002, 3-4 p.m., MATH ANNEX 1100, Michael Ward (UBC Math), Beyond Turing: The Stability and Dynamics of Localized Patterns in Reaction-Diffusion Systems (Dept of Mathematics Colloquium).

No Math Biology seminars. Seminars will resume in September.

I will consider two such horizontal gradients of phytoplankton. By means of a simple model, I will present analytical calculations of the induced velocities to ascertain whether the differential heating effects are significant. Finally, I will discuss the potential for the induced velocities to act as a mechanism for enhancing the supply of nutrients into the near-surface waters, such that the phytoplankton may (speculatively) modify the physical environment to 'feed themselves'.

A spatially-explicit, individual-based model of bluefin tuna whereby interacting individuals coexist on a spatially heterogeneous ocean landscape will be presented. The model represents the population dynamics of schooling bluefin tuna seasonally resident in an important Northwestern Atlantic commercial fishing area. The model is structured based on new results obtained from the analysis of acoustic tracking, satellite tagging and survey data. Individual tuna move by adjusting their orientation and speed, responding to oceanographic gradients and the prey concentration. Foraging (intensive search) and travel (extensive search), two separable behavioural modes of movement are distinguished by different turning rates and cross-correlation strength between movement parameters. The movement dynamics of schools is considered to be a stochastic process whereby individual fish perceive and continually adjust their modes based upon an incomplete identification of the modes of their

Selected results from analyses of new experimental data and model simulations will be presented. The talk will end by outlining several improvements required and two aspects of the model where further collaborative research will be focused.

We are investigating novel approaches to media optimization through monitoring the gene expression profile of cells in culture. It is hypothesized that cells experiencing a particular limitation will exhibit a characteristic gene expression profile corresponding to that limitation. We have analyzed human TF-1 cells under glucose limitation and also literature data on yeast cells under amino acid limitations. The expression level of genes in the pathways relevant to these two nutrients were analyzed at several times following exposure to the particular limitation. Ultimately, the knowledge developed here should lead to the development of a diagnostic tool for monitoring and optimizing cell culture.

This work was carried out in collaboration with Prof. Paulien Hogeweg at the Department of Theoretical Biology/Bioinformatics, Utrecht University, the Netherlands.

We use three different approaches to understand the problem of cytoskeleton reorganization and pigment aggregation. First, a 2D Monte Carlo simulation of microtubule and pigment dynamics provides evidence for the mechanism we propose. Next, we derive a system of non-linear diffusion-advection equations (1D) that describes the system under a particular parameter regime. The steady state solution to this system, which can be calculated analytically, has the desired "centered" structure. Finally, numerical simulation of an intergo-differential equation that describes a second parameter regime also demonstrates the centering behaviour we seek to explain.

This work was carried out in collaboration with Alex Mogilner (University of California at Davis, Mathematics) and Vladimir Rodionov (University of Connecticut, Physiology).

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Using their data, we here develop a number of ordinary differential equation models, to explore the possible underlying mechanisms of the affinity maturation, as well as the modulation of the progression by APLs. We show that a rich set of known immunological interactions could explain the observed data, as long as they fulfill certain essential characteristics, either directly or indirectly. Such a model study forces to make implicit assumptions explicit, which allows us to test the feasibility of competing explanations, and leads to suggestions for experiments to discriminate between them.

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I will present a mechanochemical analysis of a crawling cell and describe a finite element model wherein (a) localized protein polymerization and bundling generate the force for extension, and (b) energy stored in the gel formed from the polymers at the leading edge is subsequently used to produce the contraction that pulls the rear of the cell forward. While this model has features of general interest, I apply it to a specific example, the crawling of the nematode sperm cell. These cells crawl using a specialized "major sperm protein", rather than actin, in their cytoskeleton. Their simplicity provides a 'stripped down' version of a crawling cell in which to examine the basic mechanism of cell locomotion, independent of other cellular functions. I show how results of the models and simulations, based on realistic values of known biological parameters agree with the experimental observations.

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Title: Part II. Development of the Nervous System of the Gut

The main focus of this project was the development of mathematical models describing different aspects of protein transport in HFBRs. The models were validated using protein concentration data collected during cell-free HFBR experiments. A one-dimensional Krogh cylinder model was employed to analyse hindered transmembrane transport relevant to the leakage of smaller proteins from the ECS. A two-dimensional porous medium model (PMM) was used to simulate open-shell operations such as product harvesting from the ECS. An extended, three-dimensional PMM formulation permitted a more advanced analysis of gravity-influenced free-convective ECS protein transport at different HFBR orientations.

We have simulated the whole developmental process using a hybrid cellular automata/partial differential equation model. In the model, individual cells are represented as a group of connected automata, i.e. the basic scale of the model is subcellular. Therefore amoebae can slide past one another, and deform themselves and adjoining amoebae by means of small changes in their boundaries.

With our model we have been able to reproduce and understand the dynamics that emerge during the morphogenesis. I will show that cyclic AMP signalling (which is a special kind of exitable medium) and differential adhesion are sufficient to produce many self-organizing and self-correcting properties, and how the entire development is enacted by means of the above mentioned building blocks.