A Report of some sessions at the Annual
Meeting
Raymond Mejia
The SMB Annual Meeting was held at the University
of Toronto July 13-17. It was held in conjunction with SIAM's
Annual and Discrete Mathematics Meetings. The meeting was well
attended; by my estimate over 1000 registered, and over 100 attendees
participated in the SMB meeting/poster session/reception on Wednesday
evening at the Fields Institute.
A brief summary of each talk is included where possible.
An introduction to what genomics is included current
efforts in information science and chemistry, the goal to understand
the cellular operating system and organisms as well as diagnosis
and treatment of disease, and methods used: informatics as well
as the physical and biological sciences. The rudiments of biotechnology
included informatics and chemistry of DNA, hybridization, and
the polymerase chain reaction. The mathematical perspective included
information processing as central to genomics plus experimental
design, analysis and examples of applications.
Genetic mapping was described, including recombination,
linkage maps, markers and traits followed by microsatellite genotyping,
laboratory experiments and data interpretation methods and examples.
Radiation hybrid mapping discussed included association
of DNA markers to locations, mathematical methods used and sample
maps.
That small drug molecules must bind to a particular
site on a large receptor protein is an essential step to producing
a desired biological response in drug discovery. The speaker
presented an objective way of finding a range of models that deduce
receptor site's shape and energetics of interaction to predict
the binding of other molecules with estimated uncertainties.
Approaches to gene mapping using nonparametric statistics
and open problems were discussed.
Combinatorial problems that arise in radiation hybrid
mapping, sequence-tagged-site mapping and restriction mapping
were discussed as well as combinatorial problems that arise in
the analysis of gene expression data.
Lila Kari, in "DNA Computing: Arrival of Biological Mathematics", addressed two questions proposed by Adleman [Molecular computation of solutions to combinatorial problems. Science. 1994 Nov 11; 266(5187): 1021-1024], namely: - Does EVERY computing problem have a DNA-based solution? and
- Is it possible, at least theoretically, to construct programmable "test-tube" DNA computers?
Ramit Mehr, in "Modelling the Metadynamics of Lymphocyte Repertoires", described how receptor genes rearrange from segment libraries to create highly diverse repertoires to recognize most antigens. The biology was described for modelling repertoire metadynamics, from the stochastic generation of new clones, through competition between clones, through competition between clones to emergent properties including learning and memory.
Sharon Crook, in "Modelling Cortical Oscillations with Networks of Coupled Phase Oscillators", used such models to examine mechanisms that affect cortical dynamics. Graciela Cerezo, in "Modelling the Distributional Dynamics of a Clam Population along the Coasts of Argentina", presented a model of the life cycle of Mesodesma mactroides integrated with a model of the physical environment. Results of a discrete model and a continuous model that couples the coastal population dynamics of the species with transport processes in the ocean were shown, as was how these may help to create restoration and conservation of the species.
Harold Layton, in "Oscillations in the Tubuloglomerular Feedback System", described a model of the TGF pathway that shows oscillations arising from two distributed delays; namely, the time for fluid to travel up the thick ascending loop of Henle, and the time for macula densa cells to sense the fluid composition delivered to the distal tubules. Model results predict that for a sufficiently large feedback loop gain magnitude, the oscillations have the potential to decouple water and NaCl delivery to the distal nephron. John Milton, in ";Multistability in Neural Computer Devices (NCD)", discussed multistability in prototype NCDs involving Aplysia motoneurons and the human pupil light reflex. Jacques Belair, in "Timing and Delays in Drug Administration", described the need to take into account time delays due to circulation in the design of theraputic drug treatments. Examples were given of both beneficial as well as undesirable oscillations due to treatment strategies.
Ramit Mehr, in "Modeling B Cell Repertoire Shift",
described how antibodies dominating the secondary immune response
are often produced by different B cell lineage from that which
dominated the primary response. A mathematical model and computer
simulations of the dynamics of competing B cell clones was used
to examine the various hypotheses that attempt to explain repertoire
shift. In combination with experimental data, the suggestion
was made that differentiation of mature B cells and their earlier
development may use the same mechanisms.
James Sneyd, in "Talking with Nonlinear Waves:
Coordination in Cell Populations", described how the theory
of nonlinear waves can be used to study intracellular communication,
and how the mathematical problems differ for different cell types.
Examples included cardiac tissue, the liver, the hippocampus,
and the trachea.
Michael Savageau, in "Function, Design and Evolution
of Gene Circuitry", presented a quantitative theory to predict
selection of the mode of control as well as minimum, maximum and
nominal values for gene cycle time in an organism.
William Ditto, in "Unstable Fixed Points in
Biological Systems: Tips, Traps and Techniques", demonstrated
control of fixed points in human atrial and canine ventricular
fibrilation and in rat hippocampal slices.
James Collins, in "Noise-Enhanced Dynamics in
Sensory Neurons", showed how noise can enhance the detection
and transmission of weak signals in certain nonlinear systems.
Stochastic resonance behavior was demonstrated in single model
neurons, networks of model neurons, rat cutaneous motor neurons
and the human-touch sensation system.
Timothy Lewis, in "The Effects of Nonexcitable
Regions on Signal Propagation in Excitable Media: Propagation
Failure and Reflection", demonstrated and gave examples of
dynamical mechanisms that form the basis of arrythmia-generating
phenomena of propagation failure and reflection in a cardiac tissue
model.
Arthur Sherman, in "Heterogeneous Patterns of
Pancreatic Beta-Cell Activity Studied with Modelling and Dynamic
Current Clamp" describes how pancreatic islet response might
be constructed from isolated cell activity,
Gregory Smith, in "Fourier Analysis of Sinusoidally
Driven Thalamocortical Relay Neurons and a Minimal Integrate-and-Fire-or-Burst
Model", showed results of a minimal IFB model that reproduces
many of the features of thalamocortical relay cell responses to
sinusoidal current injection. The model is constrained using
Fourier analysis of intracellular records from cat thalamic slices
and experimental observations.
Gerda de Vries, in
Rebecca Tyson,
Carl Panetta, in
Jonathan Bell, in
Jonathan Rubin, in |

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