Salerno's model of DNA reanalysed: could solitons have biological significance?

We investigate the sequence-dependent behaviour of localised excitations in a toy, nonlinear model of DNA base-pair opening originally proposed by Salerno. Specifically we ask whether ``breather'' solitons could play a role in the facilitated location of promoters by RNA polymerase. In an effective potential formalism, we find excellent correlation between potential minima and {\em Escherichia coli} promoter recognition sites in the T7 bacteriophage genome. Evidence for a similar relationship between phage promoters and downstream coding regions is found and alternative reasons for links between AT richness and transcriptionally-significant sites are discussed. Consideration of the soliton energy of translocation provides a novel dynamical picture of sliding: steep potential gradients correspond to deterministic motion, while ``flat'' regions, corresponding to homogeneous AT or GC content, are governed by random, thermal motion. Finally we demonstrate an interesting equivalence between planar, breather solitons and the helical motion of a sliding protein ``particle'' about a bent DNA axis.Comment: Latex file 20 pages, 5 figures. Manuscript of paper to appear in J. Biol. Phys., accepted 02/09/0

The relationship between observing behavior and food-key response rates under mixed and multiple schedules of reinforcement

Pigeons were trained under an observing response procedure in which pecks on one key (food key) were reinforced under a mixed fixed-interval 30-sec extinction schedule. A response on a second (observing) key replaced the mixed-schedule stimulus with either of two multiple-schedule stimuli (red and green keylights) for 5 sec. Observing response rates were positively correlated with food-key response rates in the presence of multiple-schedule stimuli and inversely related to food-key response rates in the presence of mixed-schedule stimuli. These results suggest that observing response output is controlled not only by the stimuli produced by observing responses but also by the stimuli in the presence of which observing responses occur. The possibility that observing responses alter the probability of reinforcement is advanced