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Church, R. M. (1997). Quantitative models of animal learning and cognition. J Exp Psychol Anim Behav Process, 23(4), 379–389.
Abstract: This article reviews the prerequisites for quantitative models of animal learning and cognition, describes the types of models, provides a rationale for the development of such quantitative models, describes criteria for their evaluation, and makes recommendations for the next generation of quantitative models. A modular approach to the development of models is described in which a procedure is considered as a generator of stimuli and a model is considered as a generator of responses. The goal is to develop models that, in combination with many different procedures, produce sequences of times of occurrence of events (stimuli and responses) that are indistinguishable from those produced by the animal under many experimental procedures and data analysis techniques.
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Clayton, H. M., Lanovaz, J. L., Schamhardt, H. C., & van Wessum, R. (1999). The effects of a rider's mass on ground reaction forces and fetlock kinematics at the trot. Equine Vet J Suppl, 30, 218–221.
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.
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Gulotta, M., Gilmanshin, R., Buscher, T. C., Callender, R. H., & Dyer, R. B. (2001). Core formation in apomyoglobin: probing the upper reaches of the folding energy landscape. Biochemistry, 40(17), 5137–5143.
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.
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Hagen, S. J., & Eaton, W. A. (2000). Two-state expansion and collapse of a polypeptide. J Mol Biol, 301(4), 1019–1027.
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.
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Polverini, E., Cugini, G., Annoni, F., Abbruzzetti, S., Viappiani, C., & Gensch, T. (2006). Molten globule formation in apomyoglobin monitored by the fluorescent probe Nile Red. Biochemistry, 45(16), 5111–5121.
Abstract: The interaction of nile red (NR) with apomyoglobin (ApoMb) in the native (pH 7) and molten globule (pH 4) states was investigated using experimental and computational methods. NR binds to hydrophobic locations in ApoMb with higher affinity (K(d) = 25 +/- 5 microM) in the native state than in the molten globule state (K(d) = 52 +/- 5 microM). In the molten globule state, NR is located in a more hydrophobic environment. The dye does not bind to the holoprotein, suggesting that the binding site is located at the heme pocket. In addition to monitoring steady-state properties, the fluorescence emission of NR is capable of tracking submillisecond, time-resolved structural rearrangements of the protein, induced by a nanosecond pH jump. Molecular dynamics simulations were run on ApoMb at neutral pH and at pH 4. The structure obtained for the molten globule state is consistent with the experimentally available structural data. The docking of NR with the crystal structure shows that the ligand binds into the binding pocket of the heme group, with an orientation bringing the planar ring system of NR to overlap with the position of two of the heme porphyrin rings in Mb. The docking of NR with the ApoMb structure at pH 4 shows that the dye binds to the heme pocket with a slightly less favorable binding energy, in keeping with the experimental K(d) value. Under these conditions, NR is positioned in a different orientation, reaching a more hydrophobic environment in agreement with the spectroscopic data.
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Sinha, A. (1998). Knowledge acquired and decisions made: triadic interactions during allogrooming in wild bonnet macaques, Macaca radiata. Philos Trans R Soc Lond B Biol Sci, 353(1368), 619–631.
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.
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Viscido, S. V., Miller, M., & Wethey, D. S. (2001). The response of a selfish herd to an attack from outside the group perimeter. J. Theor. Biol., 208(3), 315–328.
Abstract: According to the selfish herd hypothesis, animals can decrease predation risk by moving toward one another if the predator can appear anywhere and will attack the nearest target. Previous studies have shown that aggregations can form using simple movement rules designed to decrease each animal's Domain of Danger. However, if the predator attacks from outside the group's perimeter, these simple movement rules might not lead to aggregation. To test whether simple selfish movement rules would decrease predation risk for those situations when the predator attacks from outside the flock perimeter, we constructed a computer model that allowed flocks of 75 simulated fiddler crabs to react to one another, and to a predator attacking from 7 m away. We attacked simulated crab flocks with predators of different sizes and attack speeds, and computed relative predation risk after 120 time steps. Final trajectories showed flight toward the center of the flock, but curving away from the predator. Path curvature depended on the predator's size and approach speed. The average crab experienced a greater decrease in predation risk when the predator was small or slow moving. Regardless of the predator's size and speed, however, predation risk always decreased as long as crabs took their flock-mates into account. We conclude that, even when flight away from an external predator occurs, the selfish avoidance of danger can lead to aggregation.
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Watanabe, S., & Troje, N. F. (2006). Towards a “virtual pigeon”: a new technique for investigating avian social perception. Anim. Cogn., 9(4), 271–279.
Abstract: The purpose of the present study is to examine the applicability of a computer-generated, virtual animal to study animal cognition. Pigeons were trained to discriminate between movies of a real pigeon and a rat. Then, they were tested with movies of the computer-generated (CG) pigeon. Subjects showed generalization to the CG pigeon, however, they also responded to modified versions in which the CG pigeon was showing impossible movement, namely hopping and walking without its head bobbing. Hence, the pigeons did not attend to these particular details of the display. When they were trained to discriminate between the normal and the modified version of the CG pigeon, they were able to learn the discrimination. The results of an additional partial occlusion test suggest that the subjects used head movement as a cue for the usual vs. unusual CG pigeon discrimination.
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