Measuring and Modeling Stochastic Behavior of Simple Organisms
E. coli, a flagellated bacterium, has a natural behavioral variable-the direction of rotation of its flagellar rotary motor. Monitoring this one-dimensional motor response in reaction to chemical perturbation has been instrumental in understanding how E. coli performs chemotaxis at the genetic, physiological, and computational level. We are applying this experimental strategy to the study of bacterial thermotaxis - a sensory mode that is less well understood. To investigate bacterial thermosensation we subject single cells to well defined thermal stimuli such as impulses of heat produced by an IR laser and discover computational properties of the sensory network from their response.
Higher organisms may have more complicated behavioral outputs because their motions have more degrees of freedom. Here we provide a comprehensive analysis of motor behavior of such an organism -- the nematode C. elegans. Using tracking video-microscopy we capture a worm's image and extract the skeleton of the shape as a head-to-tail ordered collection of tangent angles sampled along the curve. Applying principal components analysis we show that the space of shapes is remarkably low dimensional, with four dimensions accounting for > 95 percent of the shape variance, and that these dimensions align with behaviorally relevant states.
We also partially construct equations of motion and show that the stochastic dynamics within this shape space predicts transitions between attractors corresponding to abrupt reversals in crawling direction. With no free parameters, our inferred stochastic dynamical system generates reversals time scales and stereotyped trajectories in close agreements with experimental observations.