Abstract: This simulation study explores some conditions leading to transitivity within dominance orders. Combinations of three parameters were varied to study their consequences upon hierarchy formation and upon the degree of linearity of resultant structures. The factors studied were: (1) the importance of initial resource holding potentials (RHPs); (2) changes brought in RHPs by successive victories and defeats; and (3) accuracy of RHP assessment made by opponents. Results show that initial differences in RHP always lead to perfectly transitive chains whose rank order reflects the importance of initial differences. Even when simulated animals make important errors while assessing each other during round robin tournaments, emerging dominance structures are perfectly linear and ranks obtained in the structure are highly correlated with initial values in RHPs. Moreover, accumulated experiences of victory and/or defeat alone always lead to perfectly linear hierarchies. Their combination with initial individual differences in RHP led to the same conclusion. Even when assessment was far from being perfect, not only perfect chains were formed but initial values in RHPs significantly influenced rank order when the contribution of victory and defeat to RHP was relatively unimportant. The higher the importance of victory and defeat to RHP as compared to that of initial RHP values, the lower was the correlation between initial RHP values and the ranks order reached by individuals in the resultant hierarchies. In general also, the lower the variation within initial RHPs, the lower was the correlation between initial RHPs and ranks in the hierarchy. At a given level of initial RHP dispersion, increasing the contribution of victory and defeat to RHP diminished the correlation between initial RHP values and obtained ranks. In addition, inaccurate assessment reduced the overall correlation, especially when dispersion of initial RHP values was low and the contribution of victory and defeat relatively unimportant. These results shed some light on the controversy about the respective roles of initial individual attributes and that of patterns of resolution in the formation of animal hierarchies. We present the emergence of social order within closed systems as those simulated here as a case of self-organization.

Abstract: An acid-destabilized form of apomyoglobin, the so-called E state, consists of a set of heterogeneous structures that are all characterized by a stable hydrophobic core composed of 30-40 residues at the intersection of the A, G, and H helices of the protein, with little other secondary structure and no other tertiary structure. Relaxation kinetics studies were carried out to characterize the dynamics of core melting and formation in this protein. The unfolding and/or refolding response is induced by a laser-induced temperature jump between the folded and unfolded forms of E, and structural changes are monitored using the infrared amide I' absorbance at 1648-1651 cm(-1) that reports on the formation of solvent-protected, native-like helix in the core and by fluorescence emission changes from apomyoglobin's Trp14, a measure of burial of the indole group of this residue. The fluorescence kinetics data are monoexponential with a relaxation time of 14 micros. However, infrared kinetics data are best fit to a biexponential function with relaxation times of 14 and 59 micros. These relaxation times are very fast, close to the limits placed on folding reactions by diffusion. The 14 micros relaxation time is weakly temperature dependent and thus represents a pathway that is energetically downhill. The appearance of this relaxation time in both the fluorescence and infrared measurements indicates that this folding event proceeds by a concomitant formation of compact secondary and tertiary structures. The 59 micros relaxation time is much more strongly temperature dependent and has no fluorescence counterpart, indicating an activated process with a large energy barrier wherein nonspecific hydrophobic interactions between helix A and the G and H helices cause some helix burial but Trp14 remains solvent exposed. These results are best fit by a multiple-pathway kinetic model when U collapses to form the various folded core structures of E. Thus, the results suggest very robust dynamics for core formation involving multiple folding pathways and provide significant insight into the primary processes of protein folding.

Abstract: Ground reaction force (GRF) measurements are often normalised to body mass to facilitate inter-individual comparisons. The objective of this study was to explore the effect of a rider on the GRFs and fetlock joint kinematics of trotting horses. The subjects were 5 dressage-trained horses and 3 experienced dressage riders. Ground reaction force measurements and sagittal view videotapes were recorded as the horses trotted at the same velocity in hand (3.49 +/- 0.52 m/s) and with a rider (3.49 +/- 0.46 m/s). Data were time-normalised to stance duration. Ground reaction force measurements were expressed in absolute terms and normalised to the system mass (horse or horse plus rider). All the horses showed changes in the same direction when comparing the ridden condition with the in-hand condition. There was an increase in the absolute peak vertical GRFs of the fore- and hindlimbs with a rider. However, the mass-normalised peak vertical GRFs were lower for the ridden condition, with the peak occurring later in the forelimbs and earlier in the hindlimbs compared with the inhand condition. Maximal fetlock angle and its time of occurrence were similar for the 2 conditions, but the fore fetlock joint was more extended during the later part of the stance phase in ridden horses. The presence of a rider appeared to affect the GRFs and fetlock joint kinematics differently in the fore- and hindlimbs, and the ridden horse did not seem to be equivalent to a proportionately larger horse. This should be considered when normalising for body mass in studies comparing horses in hand and ridden horses.

Abstract: The initial phase of folding for many proteins is presumed to be the collapse of the polypeptide chain from expanded to compact, but still denatured, conformations. Theory and simulations suggest that this collapse may be a two-state transition, characterized by barrier-crossing kinetics, while the collapse of homopolymers is continuous and multi-phasic. We have used a laser temperature-jump with fluorescence spectroscopy to measure the complete time-course of the collapse of denatured cytochrome c with nanosecond time resolution. We find the process to be exponential in time and thermally activated, with an apparent activation energy approximately 9 k(B)T (after correction for solvent viscosity). These results indicate that polypeptide collapse is kinetically a two-state transition. Because of the observed free energy barrier, the time scale of polypeptide collapse is dramatically slower than is predicted by Langevin models for homopolymer collapse.

Abstract: The pressures of developing and maintaining intricate social relationships may have led to the evolution of enhanced cognitive abilities in many nonhuman primates. Knowledge of the dominance ranks and social relationships of other individuals, in particular, is important in evaluating one's position in the rank hierarchy and affiliative networks. Triadic interactions offer an excellent opportunity to examine whether decisions are taken by individuals on the basis of such knowledge. Allogrooming supplants among wild female bonnet macaques (macaca radiata) usually involved the subordinate female of a grooming dyad retreating at the approach of a female dominant to both members of the dyad. In a few exceptional cases, however, the dominant member of the dyad retreated; simple non-cognitive hypotheses involving dyadic rank differences and agonistic relationships failed to explain this phenomenon. Instead, retreat by the dominant individual was positively correlated with the social attractiveness of her subordinate companion (as measured by the duration of grooming received by the latter from other females in the troop). This suggests that not only does an individual evaluate relationships among other females, but does so on the basis of the amount of grooming received by them. Similarly, the frequency of approaches received by any female was correlated with her social attractiveness when she was the dominant member of the dyad, but not when she was the subordinate. This indicated that approaching females might be aware of the relative dominance ranks of the two allogrooming individuals. In logistic regression analyses, the probability of any individual retreating was found to be influenced more by her knowledge of her rank difference with both the other interactants, rather than by their absolute ranks. Moreover, information about social attractiveness appeared to be used in terms of correlated dominance ranks. The nature of knowledge acquired by bonnet macaque females may thus be egotistical in that other individuals are evaluated relative to oneself, integrative in that information about all other interactants is used simultaneously, and hierarchical in the ability to preferentially use certain categories of knowledge for the storage of related information from other domains.