Records |
Author |
Uzawa, T.; Akiyama, S.; Kimura, T.; Takahashi, S.; Ishimori, K.; Morishima, I.; Fujisawa, T. |
Title |
Collapse and search dynamics of apomyoglobin folding revealed by submillisecond observations of alpha-helical content and compactness |
Type |
Journal Article |
Year |
2004 |
Publication |
Proceedings of the National Academy of Sciences of the United States of America |
Abbreviated Journal |
Proc. Natl. Acad. Sci. U.S.A. |
Volume |
101 |
Issue |
5 |
Pages |
1171-1176 |
Keywords |
Animals; Apoproteins/*chemistry; Circular Dichroism; Cytochromes c/chemistry; Horses; Myoglobin/*chemistry; *Protein Folding; *Protein Structure, Secondary; Scattering, Radiation |
Abstract |
The characterization of protein folding dynamics in terms of secondary and tertiary structures is important in elucidating the features of intraprotein interactions that lead to specific folded structures. Apomyoglobin (apoMb), possessing seven helices termed A-E, G, and H in the native state, has a folding intermediate composed of the A, G, and H helices, whose formation in the submillisecond time domain has not been clearly characterized. In this study, we used a rapid-mixing device combined with circular dichroism and small-angle x-ray scattering to observe the submillisecond folding dynamics of apoMb in terms of helical content (f(H)) and radius of gyration (R(g)), respectively. The folding of apoMb from the acid-unfolded state at pH 2.2 was initiated by a pH jump to 6.0. A significant collapse, corresponding to approximately 50% of the overall change in R(g) from the unfolded to native conformation, was observed within 300 micros after the pH jump. The collapsed intermediate has a f(H) of 33% and a globular shape that involves >80% of all its atoms. Subsequently, a stepwise helix formation was detected, which was interpreted to be associated with a conformational search for the correct tertiary contacts. The characterized folding dynamics of apoMb indicates the importance of the initial collapse event, which is suggested to facilitate the subsequent conformational search and the helix formation leading to the native structure. |
Address |
Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo, Kyoto 615-8510, Japan |
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0027-8424 |
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PMID:14711991 |
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no |
Call Number |
Equine Behaviour @ team @ |
Serial |
3779 |
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Author |
Hoy, R. |
Title |
Animal awareness: The (un)binding of multisensory cues in decision making by animals |
Type |
Journal Article |
Year |
2005 |
Publication |
Proceedings of the National Academy of Sciences of the United States of America |
Abbreviated Journal |
Proc. Natl. Acad. Sci. U.S.A. |
Volume |
102 |
Issue |
7 |
Pages |
2267-2268 |
Keywords |
Animals; Anura/physiology; *Awareness; *Behavior, Animal; Decision Making; Female; Male; Perception; Sensation |
Abstract |
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Address |
Department of Neurobiology and Behavior, 215 Mudd Hall, Cornell University, Ithaca, NY 14850, USA. rrh3@cornell.edu |
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0027-8424 |
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PMID:15703288 |
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no |
Call Number |
Equine Behaviour @ team @ |
Serial |
2821 |
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Author |
Jansen, T.; Forster, P.; Levine, M.A.; Oelke, H.; Hurles, M.; Renfrew, C.; Weber, J.; Olek, K. |
Title |
Mitochondrial DNA and the origins of the domestic horse |
Type |
Journal Article |
Year |
2002 |
Publication |
Proceedings of the National Academy of Sciences of the United States of America |
Abbreviated Journal |
Proc. Natl. Acad. Sci. U.S.A. |
Volume |
99 |
Issue |
16 |
Pages |
10905-10910 |
Keywords |
Animals; Animals, Domestic/classification/*genetics; Base Sequence; DNA, Complementary; *DNA, Mitochondrial; *Evolution, Molecular; Horses/classification/*genetics; Molecular Sequence Data; Phylogeny |
Abstract |
The place and date of the domestication of the horse has long been a matter for debate among archaeologists. To determine whether horses were domesticated from one or several ancestral horse populations, we sequenced the mitochondrial D-loop for 318 horses from 25 oriental and European breeds, including American mustangs. Adding these sequences to previously published data, the total comes to 652, the largest currently available database. From these sequences, a phylogenetic network was constructed that showed that most of the 93 different mitochondrial (mt)DNA types grouped into 17 distinct phylogenetic clusters. Several of the clusters correspond to breeds and/or geographic areas, notably cluster A2, which is specific to Przewalski's horses, cluster C1, which is distinctive for northern European ponies, and cluster D1, which is well represented in Iberian and northwest African breeds. A consideration of the horse mtDNA mutation rate together with the archaeological timeframe for domestication requires at least 77 successfully breeding mares recruited from the wild. The extensive genetic diversity of these 77 ancestral mares leads us to conclude that several distinct horse populations were involved in the domestication of the horse. |
Address |
Biopsytec Analytik GmbH, Marie-Curie-Strasse 1, 53359 Rheinbach, Germany. jansen@biopsytec.com |
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0027-8424 |
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Notes |
PMID:12130666 |
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no |
Call Number |
refbase @ user @ |
Serial |
772 |
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Author |
Scheffer, M.; van Nes, E.H. |
Title |
Self-organized similarity, the evolutionary emergence of groups of similar species |
Type |
Journal Article |
Year |
2006 |
Publication |
Proceedings of the National Academy of Sciences of the United States of America |
Abbreviated Journal |
Proc. Natl. Acad. Sci. U.S.A. |
Volume |
103 |
Issue |
16 |
Pages |
6230-6235 |
Keywords |
Animals; *Competitive Behavior; *Ecosystem; *Evolution; *Models, Biological |
Abstract |
Ecologists have long been puzzled by the fact that there are so many similar species in nature. Here we show that self-organized clusters of look-a-likes may emerge spontaneously from coevolution of competitors. The explanation is that there are two alternative ways to survive together: being sufficiently different or being sufficiently similar. Using a model based on classical competition theory, we demonstrate a tendency for evolutionary emergence of regularly spaced lumps of similar species along a niche axis. Indeed, such lumpy patterns are commonly observed in size distributions of organisms ranging from algae, zooplankton, and beetles to birds and mammals, and could not be well explained by earlier theory. Our results suggest that these patterns may represent self-constructed niches emerging from competitive interactions. A corollary of our findings is that, whereas in species-poor communities sympatric speciation and invasion of open niches is possible, species-saturated communities may be characterized by convergent evolution and invasion by look-a-likes. |
Address |
Aquatic Ecology and Water Quality Management Group, Department of Environmental Sciences, Wageningen University, P.O. Box 8080, 6700 DD, Wageningen, The Netherlands. marten.scheffer@wur.nl |
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0027-8424 |
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Notes |
PMID:16585519 |
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no |
Call Number |
refbase @ user @ |
Serial |
510 |
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Author |
Reiss, D.; Marino, L. |
Title |
Mirror self-recognition in the bottlenose dolphin: a case of cognitive convergence |
Type |
Journal Article |
Year |
2001 |
Publication |
Proceedings of the National Academy of Sciences of the United States of America |
Abbreviated Journal |
Proc. Natl. Acad. Sci. U.S.A. |
Volume |
98 |
Issue |
10 |
Pages |
5937-5942 |
Keywords |
Animals; *Cognition; Dolphins/*physiology; *Visual Perception |
Abstract |
The ability to recognize oneself in a mirror is an exceedingly rare capacity in the animal kingdom. To date, only humans and great apes have shown convincing evidence of mirror self-recognition. Two dolphins were exposed to reflective surfaces, and both demonstrated responses consistent with the use of the mirror to investigate marked parts of the body. This ability to use a mirror to inspect parts of the body is a striking example of evolutionary convergence with great apes and humans. |
Address |
Osborn Laboratories of Marine Sciences, New York Aquarium, Wildlife Conservation Society, Brooklyn, NY 11224, USA. dlr28@columbia.edu |
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0027-8424 |
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PMID:11331768 |
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no |
Call Number |
Equine Behaviour @ team @ |
Serial |
2822 |
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Author |
Chase, I.D.; Tovey, C.; Spangler-Martin, D.; Manfredonia, M. |
Title |
Individual differences versus social dynamics in the formation of animal dominance hierarchies |
Type |
Journal Article |
Year |
2002 |
Publication |
Proceedings of the National Academy of Sciences of the United States of America |
Abbreviated Journal |
Proc. Natl. Acad. Sci. U.S.A. |
Volume |
99 |
Issue |
8 |
Pages |
5744-5749 |
Keywords |
Animals; *Behavior, Animal; Fishes; Humans; *Social Behavior; *Social Dominance |
Abstract |
Linear hierarchies, the classical pecking-order structures, are formed readily in both nature and the laboratory in a great range of species including humans. However, the probability of getting linear structures by chance alone is quite low. In this paper we investigate the two hypotheses that are proposed most often to explain linear hierarchies: they are predetermined by differences in the attributes of animals, or they are produced by the dynamics of social interaction, i.e., they are self-organizing. We evaluate these hypotheses using cichlid fish as model animals, and although differences in attributes play a significant part, we find that social interaction is necessary for high proportions of groups with linear hierarchies. Our results suggest that dominance hierarchy formation is a much richer and more complex phenomenon than previously thought, and we explore the implications of these results for evolutionary biology, the social sciences, and the use of animal models in understanding human social organization. |
Address |
Department of Sociology, State University of New York, Stony Brook, NY 11794-4356, USA. Ichase@notes.cc.sunysb.edu |
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0027-8424 |
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Notes |
PMID:11960030 |
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no |
Call Number |
refbase @ user @ |
Serial |
442 |
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Author |
Hauser, M.D.; Kralik, J.; Botto-Mahan, C.; Garrett, M.; Oser, J. |
Title |
Self-recognition in primates: phylogeny and the salience of species-typical features |
Type |
Journal Article |
Year |
1995 |
Publication |
Proceedings of the National Academy of Sciences of the United States of America |
Abbreviated Journal |
Proc. Natl. Acad. Sci. U.S.A. |
Volume |
92 |
Issue |
23 |
Pages |
10811-10814 |
Keywords |
Animals; *Behavior, Animal; *Cognition; Discrimination (Psychology); Exploratory Behavior; Female; Hair Color; Male; Phylogeny; Psychology, Comparative; Research Design; Saguinus/*psychology; *Self Concept; Species Specificity; Touch; *Visual Perception |
Abstract |
Self-recognition has been explored in nonlinguistic organisms by recording whether individuals touch a dye-marked area on visually inaccessible parts of their face while looking in a mirror or inspect parts of their body while using the mirror's reflection. Only chimpanzees, gorillas, orangutans, and humans over the age of approximately 2 years consistently evidence self-directed mirror-guided behavior without experimenter training. To evaluate the inferred phylogenetic gap between hominoids and other animals, a modified dye-mark test was conducted with cotton-top tamarins (Saguinus oedipus), a New World monkey species. The white hair on the tamarins' head was color-dyed, thereby significantly altering a visually distinctive species-typical feature. Only individuals with dyed hair and prior mirror exposure touched their head while looking in the mirror. They looked longer in the mirror than controls, and some individuals used the mirror to observe visually inaccessible body parts. Prior failures to pass the mirror test may have been due to methodological problems, rather than to phylogenetic differences in the capacity for self-recognition. Specifically, an individual's sensitivity to experimentally modified parts of its body may depend crucially on the relative saliency of the modified part (e.g., face versus hair). Moreover, and in contrast to previous claims, we suggest that the mirror test may not be sufficient for assessing the concept of self or mental state attribution in nonlinguistic organisms. |
Address |
Department of Anthropology, Harvard University, Cambridge, MA 02138, USA |
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0027-8424 |
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PMID:7479889 |
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no |
Call Number |
Equine Behaviour @ team @ |
Serial |
2825 |
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Author |
Bergstrom, C.T.; Lachmann, M. |
Title |
Signaling among relatives. III. Talk is cheap |
Type |
Journal Article |
Year |
1998 |
Publication |
Proceedings of the National Academy of Sciences of the United States of America |
Abbreviated Journal |
Proc. Natl. Acad. Sci. U.S.A. |
Volume |
95 |
Issue |
9 |
Pages |
5100-5105 |
Keywords |
Animal Communication; Animals; Costs and Cost Analysis; *Evolution; Interpersonal Relations; Models, Biological |
Abstract |
The Sir Philip Sidney game has been used by numerous authors to show how signal cost can facilitate honest signaling among relatives. Here, we demonstrate that, in this game, honest cost-free signals are possible as well, under very general conditions. Moreover, these cost-free signals are better for all participants than the previously explored alternatives. Recent empirical evidence suggests that begging is energetically inexpensive for nestling birds; this finding led some researchers to question the applicability of the costly signaling framework to nestling begging. Our results show that cost-free or inexpensive signals, as observed empirically, fall within the framework of signaling theory. |
Address |
Department of Biological Sciences, Stanford University, Stanford, CA 94305, USA. carl@charles.stanford.edu |
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0027-8424 |
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PMID:9560235 |
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no |
Call Number |
refbase @ user @ |
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561 |
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Author |
Griffin, D.R. |
Title |
Animals know more than we used to think |
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Year |
2001 |
Publication |
Proceedings of the National Academy of Sciences of the United States of America |
Abbreviated Journal |
Proc. Natl. Acad. Sci. U.S.A. |
Volume |
98 |
Issue |
9 |
Pages |
4833-4834 |
Keywords |
Animal Communication; Animals; Attention/physiology; Brain/physiology; Choice Behavior/physiology; Cognition/*physiology; Humans; Macaca mulatta/physiology/*psychology; Memory/*physiology; Optic Disk/physiology; Psychological Tests |
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0027-8424 |
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PMID:11320232 |
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Equine Behaviour @ team @ |
Serial |
2823 |
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Author |
Proops, L.; McComb, K.; Reby, D. |
Title |
Cross-modal individual recognition in domestic horses (Equus caballus) |
Type |
Journal Article |
Year |
2009 |
Publication |
Proceedings of the National Academy of Sciences of the United States of America |
Abbreviated Journal |
Proc. Natl. Acad. Sci. U.S.A. |
Volume |
106 |
Issue |
3 |
Pages |
947-951 |
Keywords |
animal cognition vocal communication social behavior playback experiment expectancy violation |
Abstract |
Individual recognition is considered a complex process and, although it is believed to be widespread across animal taxa, the cognitive mechanisms underlying this ability are poorly understood. An essential feature of individual recognition in humans is that it is cross-modal, allowing the matching of current sensory cues to identity with stored information about that specific individual from other modalities. Here, we use a cross-modal expectancy violation paradigm to provide a clear and systematic demonstration of cross-modal individual recognition in a nonhuman animal: the domestic horse. Subjects watched a herd member being led past them before the individual went of view, and a call from that or a different associate was played from a loudspeaker positioned close to the point of disappearance. When horses were shown one associate and then the call of a different associate was played, they responded more quickly and looked significantly longer in the direction of the call than when the call matched the herd member just seen, an indication that the incongruent combination violated their expectations. Thus, horses appear to possess a cross-modal representation of known individuals containing unique auditory and visual/olfactory information. Our paradigm could provide a powerful way to study individual recognition across a wide range of species. |
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10.1073/pnas.0809127105 |
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Equine Behaviour @ team @ |
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4689 |
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