| Records |
| Author |
Haruta, N.; Kitagawa, T. |
| Title |
Time-resolved UV resonance Raman investigation of protein folding using a rapid mixer: characterization of kinetic folding intermediates of apomyoglobin |
Type |
Journal Article |
| Year |
2002 |
Publication |
Biochemistry |
Abbreviated Journal |
Biochemistry |
| Volume |
41 |
Issue |
21 |
Pages  |
6595-6604 |
| Keywords |
Animals; Apoproteins/*chemistry; Circular Dichroism; Holoenzymes/chemistry; Horses; Hydrochloric Acid/chemistry; Hydrogen-Ion Concentration; Imidazoles/chemistry; Kinetics; Models, Molecular; Myoglobin/*chemistry; Peptide Fragments/chemistry; *Protein Folding; Protein Structure, Secondary; Spectrum Analysis, Raman/*methods; Tryptophan/*chemistry; Ultraviolet Rays; Whales |
| Abstract |
The 244-nm excited transient UV resonance Raman spectra are observed for the refolding intermediates of horse apomyoglobin (h-apoMb) with a newly constructed mixed flow cell system, and the results are interpreted on the basis of the spectra observed for the equilibrium acid unfolding of the same protein. The dead time of mixing, which was determined with the appearance of UV Raman bands of imidazolium upon mixing of imidazole with acid, was 150 micros under the flow rate that was adopted. The pH-jump experiments of h-apoMb from pH 2.2 to 5.6 conducted with this device demonstrated the presence of three folding intermediates. On the basis of the analysis of W3 and W7 bands of Trp7 and Trp14, the first intermediate, formed before 250 micros, involved incorporation of Trp14 into the alpha-helix from a random coil. The frequency shift of the W3 band of Trp14 observed for this process was reproduced with a model peptide of the A helix when it forms the alpha-helix. In the second intermediate, formed around 1 ms after the start of refolding, the surroundings of both Trp7 and Trp14 were significantly hydrophobic, suggesting the formation of the hydrophobic core. In the third intermediate appearing around 3 ms, the hydrophobicity was relaxed to the same level as that of the pH 4 equilibrium intermediate, which was investigated in detail with the stationary state technique. The change from the third intermediate to the native state needs more time than 40 ms, while the appearance of the native spectrum after the mixing of the same solutions was confirmed separately. |
| Address |
School of Mathematical and Physical Sciences, The Graduate University for Advanced Studies, Myodaiji, Okazaki 444-8585, Japan |
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English |
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Edition |
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0006-2960 |
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| Notes |
PMID:12022863 |
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no |
| Call Number |
Equine Behaviour @ team @ |
Serial |
3785 |
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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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English |
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0027-8424 |
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| Notes |
PMID:16585519 |
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no |
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refbase @ user @ |
Serial |
510 |
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| Author |
Muscatello, G.; Anderson, G.A.; Gilkerson, J.R.; Browning, G.F. |
| Title |
Associations between the ecology of virulent Rhodococcus equi and the epidemiology of R. equi pneumonia on Australian thoroughbred farms |
Type |
Journal Article |
| Year |
2006 |
Publication |
Applied and Environmental Microbiology |
Abbreviated Journal |
Appl Environ Microbiol |
| Volume |
72 |
Issue |
9 |
Pages |
6152-6160 |
| Keywords |
Actinomycetales Infections/epidemiology/microbiology/*veterinary; Air Microbiology; Animal Husbandry; Animals; Animals, Newborn; Australia/epidemiology; Colony Count, Microbial; DNA, Bacterial/genetics; Ecosystem; Horse Diseases/epidemiology/*microbiology; Horses; Pneumonia, Bacterial/epidemiology/microbiology/*veterinary; Rhodococcus equi/genetics/isolation & purification/*pathogenicity; Soil Microbiology; Virulence |
| Abstract |
The ecology of virulent strains of Rhodococcus equi on horse farms is likely to influence the prevalence and severity of R. equi pneumonia in foals. This study examined the association between the ecology of virulent R. equi and the epidemiology of R. equi pneumonia by collecting air and soil samples over two breeding seasons (28 farm-year combinations) on Thoroughbred breeding farms with different reported prevalences of R. equi pneumonia. Colony blotting and DNA hybridization were used to detect and measure concentrations of virulent R. equi. The prevalence of R. equi pneumonia was associated with the airborne burden of virulent R. equi (both the concentration and the proportion of R. equi bacteria that were virulent) but was not associated with the burden of virulent R. equi in the soil. Univariable screening and multivariable model building were used to evaluate the effect of environmental and management factors on virulent R. equi burdens. Lower soil moisture concentrations and lower pasture heights were significantly associated with elevated airborne concentrations of virulent R. equi, as were the holding pens and lanes, which typically were sandy, dry, and devoid of pasture cover. Few variables appeared to influence concentrations of virulent R. equi in soil. Acidic soil conditions may have contributed to an elevated proportion of virulent strains within the R. equi population. Environmental management strategies that aim to reduce the level of exposure of susceptible foals to airborne virulent R. equi are most likely to reduce the impact of R. equi pneumonia on endemically affected farms. |
| Address |
School of Veterinary Science, The University of Melbourne, Parkville, Victoria 3010, Australia. mug@unimelb.edu.au |
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English |
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Edition |
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| ISSN |
0099-2240 |
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| Notes |
PMID:16957241 |
Approved |
no |
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Equine Behaviour @ team @ |
Serial |
2622 |
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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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English |
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0027-8424 |
ISBN |
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Conference |
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| Notes |
PMID:11331768 |
Approved |
no |
| Call Number |
Equine Behaviour @ team @ |
Serial |
2822 |
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| Author |
Mettke-Hofmann, C.; Gwinner, E. |
| Title |
Long-term memory for a life on the move |
Type |
Journal Article |
| Year |
2003 |
Publication |
Proceedings of the National Academy of Sciences of the United States of America |
Abbreviated Journal |
Proc. Natl. Acad. Sci. U.S.A. |
| Volume |
100 |
Issue |
10 |
Pages |
5863-5866 |
| Keywords |
Animals; Germany; Israel; Memory/*physiology; Models, Biological; Periodicity; Songbirds/*physiology |
| Abstract |
Evidence is accumulating that cognitive abilities are shaped by the specific ecological conditions to which animals are exposed. Long-distance migratory birds may provide a striking example of this. Field observations have shown that, at least in some species, a substantial proportion of individuals return to the same breeding, wintering, and stopover sites in successive years. This observation suggests that migrants have evolved special cognitive abilities that enable them to accomplish these feats. Here we show that memory of a particular feeding site persisted for at least 12 months in a long-distance migrant, whereas a closely related nonmigrant could remember such a site for only 2 weeks. Thus, it seems that the migratory lifestyle has influenced the learning and memorizing capacities of migratory birds. These results build a bridge between field observations suggesting special memorization feats of migratory birds and previous neuroanatomical results from the same two species indicating an increase in relative hippocampal size from the first to the second year of life in the migrant but not in the nonmigrant. |
| Address |
Max Planck Research Centre for Ornithology, Department of Biological Rhythms and Behaviour, Von-der-Tann-Strasse 7, 82346 Andechs, Germany. mettke-hofmann@erl.ornithol.mpg.de |
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English |
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0027-8424 |
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| Notes |
PMID:12719527 |
Approved |
no |
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refbase @ user @ |
Serial |
511 |
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| Author |
Amé, J.-M.; Halloy, J.; Rivault, C.; Detrain, C.; Deneubourg, J.L. |
| Title |
Collegial decision making based on social amplification leads to optimal group formation |
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 |
15 |
Pages |
5835-5840 |
| Keywords |
Animals; Blattellidae/*physiology; Choice Behavior; Decision Making; Leadership; *Social Behavior |
| Abstract |
Group-living animals are often faced with choosing between one or more alternative resource sites. A central question in such collective decision making includes determining which individuals induce the decision and when. This experimental and theoretical study of shelter selection by cockroach groups demonstrates that choices can emerge through nonlinear interaction dynamics between equal individuals without perfect knowledge or leadership. We identify a simple mechanism whereby a decision is taken on the move with limited information and signaling and without comparison of available opportunities. This mechanism leads to optimal mean benefit for group individuals. Our model points to a generic self-organized collective decision-making process independent of animal species. |
| Address |
Service d'Ecologie Sociale CP231, Universite Libre de Bruxelles, Avenue F. D. Roosevelt 50, B-1050 Brussels, Belgium |
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English |
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0027-8424 |
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| Notes |
PMID:16581903 |
Approved |
no |
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Equine Behaviour @ team @ |
Serial |
2042 |
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| Author |
Ballew, R.M.; Sabelko, J.; Gruebele, M. |
| Title |
Direct observation of fast protein folding: the initial collapse of apomyoglobin |
Type |
Journal Article |
| Year |
1996 |
Publication |
Proceedings of the National Academy of Sciences of the United States of America |
Abbreviated Journal |
Proc. Natl. Acad. Sci. U.S.A. |
| Volume |
93 |
Issue |
12 |
Pages |
5759-5764 |
| Keywords |
Animals; Apoproteins/*chemistry; Circular Dichroism; Horses; Kinetics; Muscle, Skeletal/chemistry; Myoglobin/*chemistry; *Protein Folding; Spectrometry, Fluorescence; Spectrophotometry, Infrared; Temperature |
| Abstract |
The rapid refolding dynamics of apomyoglobin are followed by a new temperature-jump fluorescence technique on a 15-ns to 0.5-ms time scale in vitro. The apparatus measures the protein-folding history in a single sweep in standard aqueous buffers. The earliest steps during folding to a compact state are observed and are complete in under 20 micros. Experiments on mutants and consideration of steady-state CD and fluorescence spectra indicate that the observed microsecond phase monitors assembly of an A x (H x G) helix subunit. Measurements at different viscosities indicate diffusive behavior even at low viscosities, in agreement with motions of a solvent-exposed protein during the initial collapse. |
| Address |
School of Chemical Sciences and Beckman Institute for Advanced Science and Technology, University of Illinois, Urbana, 61801, USA |
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English |
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0027-8424 |
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| Notes |
PMID:8650166 |
Approved |
no |
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Equine Behaviour @ team @ |
Serial |
3798 |
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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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English |
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0027-8424 |
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| Notes |
PMID:11960030 |
Approved |
no |
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refbase @ user @ |
Serial |
442 |
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| Author |
Hampton, R.R. |
| Title |
Rhesus monkeys know when they remember |
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 |
9 |
Pages |
5359-5362 |
| Keywords |
Animals; Choice Behavior/physiology; Cognition/*physiology; Cues; Food Preferences/psychology; Macaca mulatta/*physiology/*psychology; Male; Memory/*physiology; Probability; Psychological Tests; Reproducibility of Results; Sensitivity and Specificity |
| Abstract |
Humans are consciously aware of some memories and can make verbal reports about these memories. Other memories cannot be brought to consciousness, even though they influence behavior. This conspicuous difference in access to memories is central in taxonomies of human memory systems but has been difficult to document in animal studies, suggesting that some forms of memory may be unique to humans. Here I show that rhesus macaque monkeys can report the presence or absence of memory. Although it is probably impossible to document subjective, conscious properties of memory in nonverbal animals, this result objectively demonstrates an important functional parallel with human conscious memory. Animals able to discern the presence and absence of memory should improve accuracy if allowed to decline memory tests when they have forgotten, and should decline tests most frequently when memory is attenuated experimentally. One of two monkeys examined unequivocally met these criteria under all test conditions, whereas the second monkey met them in all but one case. Probe tests were used to rule out “cueing” by a wide variety of environmental and behavioral stimuli, leaving detection of the absence of memory per se as the most likely mechanism underlying the monkeys' abilities to selectively decline memory tests when they had forgotten. |
| Address |
Section on the Neurobiology of Learning and Memory, Laboratory of Neuropsychology, National Institute of Mental Health, Building 49, Room 1B-80, Bethesda, MD 20892, USA. robert@ln.nimh.nih.gov |
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English |
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0027-8424 |
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| Notes |
PMID:11274360 |
Approved |
no |
| Call Number |
Equine Behaviour @ team @ |
Serial |
2824 |
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| Author |
Gulotta, M.; Gilmanshin, R.; Buscher, T.C.; Callender, R.H.; Dyer, R.B. |
| Title |
Core formation in apomyoglobin: probing the upper reaches of the folding energy landscape |
Type |
Journal Article |
| Year |
2001 |
Publication |
Biochemistry |
Abbreviated Journal |
Biochemistry |
| Volume |
40 |
Issue |
17 |
Pages |
5137-5143 |
| Keywords |
Animals; Apoproteins/*chemistry; Computer Simulation; Horses; Hydrogen-Ion Concentration; Kinetics; Models, Molecular; Myoglobin/*chemistry; *Protein Folding; Protein Structure, Secondary; Protein Structure, Tertiary; Spectrometry, Fluorescence/instrumentation/methods; Thermodynamics; Tryptophan/chemistry |
| 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. |
| Address |
Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA |
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English |
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Edition |
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0006-2960 |
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| Notes |
PMID:11318635 |
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no |
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Equine Behaviour @ team @ |
Serial |
3789 |
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