Hauser, M. D., Kralik, J., Botto-Mahan, C., Garrett, M., & Oser, J. (1995). Self-recognition in primates: phylogeny and the salience of species-typical features. Proc. Natl. Acad. Sci. U.S.A., 92(23), 10811–10814.
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.
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Uzawa, T., Akiyama, S., Kimura, T., Takahashi, S., Ishimori, K., Morishima, I., et al. (2004). Collapse and search dynamics of apomyoglobin folding revealed by submillisecond observations of alpha-helical content and compactness. Proc. Natl. Acad. Sci. U.S.A., 101(5), 1171–1176.
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.
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Ballew, R. M., Sabelko, J., & Gruebele, M. (1996). Direct observation of fast protein folding: the initial collapse of apomyoglobin. Proc. Natl. Acad. Sci. U.S.A., 93(12), 5759–5764.
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.
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Hostikka, S. L., Eddy, R. L., Byers, M. G., Hoyhtya, M., Shows, T. B., & Tryggvason, K. (1990). Identification of a distinct type IV collagen alpha chain with restricted kidney distribution and assignment of its gene to the locus of X chromosome-linked Alport syndrome. Proc. Natl. Acad. Sci. U.S.A., 87(4), 1606–1610.
Abstract: We have identified and extensively characterized a type IV collagen alpha chain, referred to as alpha 5(IV). Four overlapping cDNA clones isolated contain an open reading frame for 543 amino acid residues of the carboxyl-terminal end of a collagenous domain, a 229-residue carboxyl-terminal noncollagenous domain, and 1201 base pairs coding for a 3' untranslated region. The collagenous Gly-Xaa-Yaa repeat sequence has five imperfections that coincide with those in the corresponding region of the alpha 1(IV) chain. The noncollagenous domain has 12 conserved cysteine residues and 83% and 63% sequence identity with the noncollagenous domains of the alpha 1(IV) and alpha 2(IV) chains, respectively. The alpha 5(IV) chain has less sequence identity with the putative bovine alpha 3(IV) and alpha 4(IV) chains. Antiserum against an alpha 5(IV) synthetic peptide stained a polypeptide chain of about 185 kDa by immunoblot analysis and immunolocalization of the chain in human kidney was almost completely restricted to the glomerulus. The gene was assigned to the Xq22 locus by somatic cell hybrids and in situ hybridization. This may be identical or close to the locus of the X chromosome-linked Alport syndrome that is believed to be a type IV collagen disease.
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Lee, R. D. (2003). Rethinking the evolutionary theory of aging: transfers, not births, shape senescence in social species. Proc Natl Acad Sci U S A, 100(16), 9637–9642.
Abstract: The classic evolutionary theory of aging explains why mortality rises with age: as individuals grow older, less lifetime fertility remains, so continued survival contributes less to reproductive fitness. However, successful reproduction often involves intergenerational transfers as well as fertility. In the formal theory offered here, age-specific selective pressure on mortality depends on a weighted average of remaining fertility (the classic effect) and remaining intergenerational transfers to be made to others. For species at the optimal quantity-investment tradeoff for offspring, only the transfer effect shapes mortality, explaining postreproductive survival and why juvenile mortality declines with age. It also explains the evolution of lower fertility, longer life, and increased investments in offspring.
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