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PubMed2002

Self-organization and natural selection in the evolution of complex despotic societies.

Differences between related species are usually explained as separate adaptations produced by individual selection. I discuss in this paper how related species, which differ in many respects, may evolve by a combination of individual selection, self-organization, and group-selection, requiring an evolutionary adaptation of only a single trait. In line with the supposed evolution of despotic species of macaques, we take as a starting point an ancestral species that is egalitarian and mildly aggressive. We suppose it to live in an environment with abundant food and we put the case that, if food becomes scarce and more clumped, natural selection at the level of the individual will favor individuals with a more intense aggression (implying, for instance, biting and fierce fighting). Using an individual-centered model, called DomWorld, I show what happens when the intensity of aggression increases. In DomWorld, group life is represented by artificial individuals that live in a homogeneous world. Individuals are extremely simple: all they do is flock together and, upon meeting one another, they may perform dominance interactions in which the effects of winning and losing are self-reinforcing. When the intensity of aggression in the model is increased, a complex feedback between the hierarchy and spatial structure results; via self-organization, this feedback causes the egalitarian society to change into a despotic one. The many differences between the two types of artificial society closely correspond to those between despotic and egalitarian macaques in the real world. Given that, in the model, the organization changes as a side effect of the change of one single trait proper to an egalitarian society, in the real world a despotic society may also have arisen as a side effect of the mutation of a single trait of an egalitarian species. If groups with different intensities of aggression evolve in this way, they will also have different gradients of hierarchy. When food is scarce, groups with the steepest hierarchy may have the best chance to survive, because at least a small number of individuals in such a group may succeed in producing offspring, whereas in egalitarian societies every individual is at risk of being insufficiently fed to reproduce. Therefore, intrademic group selection (selection within an interbreeding group) may have contributed to the evolution of despotic societies.

Aggression↗
PubMed1996

The role of background in mediating apparent movement.

The spatial structure of the background upon which figures engage in apparent movement has been a neglected variable in research. In this pilot study, the presence of a sine-wave-grating as background had a strong influence on the quality of apparent movement that was perceived by 3 observers.

Attention↗
PubMed2004

Cognitive facilitation associated with Chinese brush handwriting: the case of symmetric and asymmetric Chinese characters.

Chinese calligraphic handwriting involves a process of visual spatial structuring of the characters as well as the motor control of the brush to follow specific character configurations through a projection of the cognitive images of the character. Previous research has shown that Chinese calligraphic handwriting facilitates perceptual and cognitive abilities. Reading Chinese characters with geometric features also facilitates cognitive processing. This study investigated Chinese calligraphic handwriting effect on cognitive facilitation measured by responses to asymmetric and asymmetric Chinese characters. 11 participants performed Chinese calligraphic handwriting for 30 min. and had their reaction time and error rate taken before and after the writing session. The reaction time to asymmetric characters was significantly shortened after Chinese calligraphic handwriting. These results confirm the general Chinese calligraphic handwriting effect on cognitive facilitation, but the asymmetric characters seem to result in greater such effects than the symmetric characters.

Adult↗
PubMed1999

Activating oligomerization as intermediate level of signal transduction: analysis of protein-protein contacts and active sites in several glycolytic enzymes.

A number of enzymes have inactive monomeric and active oligomeric forms. This suggests presence of definite interglobular contact -active site interaction in the enzymes. Although the phenomenon is widely studied in vitro as part of folding process the biological roles of the phenomenon, termed here as "activating oligomerization" are not clearly understood. In this work a procedure for analysis of protein-protein interactions was elaborated. Using spatial structures of several glycolytic enzymes potential role of kinase phosphorylation in regulation of oligomerization of the proteins as well as association of domains in a two-domain protein was assessed. In the enzymes 15-75% of kinase sites (mainly protein kinase C and casein kinase 2 sites) are placed in interglobular contact region(s). Upon being phosphorylated these sites may prevent oligomer formation. In structures of all the enzymes definite evidences of connection between active site and interglobular contact were found. Two structural mechanisms of interglobular contact influence on the active site were proposed. In addition to known mechanism of oligomerization initiated by allosteric metabolites the influence may be also exerted through functional sequence overlap and/or interdomain contact stabilization mechanisms. Implications for regulation of enzyme cellular function(s), signal transduction and metabolic analysis are considered. It is concluded that activating oligomerization may represent an intermediate level of enzyme cellular regulation.

Animals↗
PubMed2001

Detection of shape orientation depends on salient axes of symmetry and elongation: evidence from visual search.

Three experiments investigated the role of the global spatial structure of two-dimensional (2-D) shapes in terms of symmetry and elongation on visual search for shape orientation. Experiment 1 demonstrated the often reported orientation search asymmetry (i.e., a faster detection of a tilted target among vertical distractors than the reverse) for the global orientation of 2-D polygons that possess a salient, "principal" axis of symmetry or elongation. Moreover, the search asymmetry depended on the orientation of the principal axis, rather than on the orientation of local contours. Further exploration of this effect with polygons (Experiment 2) showed that the search asymmetry for global orientation occurred for shapes containing an axis of symmetry; elongation, on the other hand, did not seem to be crucial. Finally, Experiment 3 demonstrated orientation search asymmetries with shapes composed of curved rather than straight contours: Here, the search asymmetry occurred as a function of the orientation of both axes of symmetry and elongation. Overall, search for global orientation was less efficient than search for local orientation. The results suggest that the perception of the global orientation of shapes is mediated by axis-based descriptions in terms of perceptually salient axes of symmetry and elongation.

Attention↗
PubMed2003

Egocentric and geocentric frames of reference in memory of large-scale space.

This experiment investigated the frames of reference used in memory to represent the spatial structure of a large-scale outdoor environment. Participants learned the locations of eight objects in an unfamiliar city park by walking through the park on one of two prescribed paths that encircled a large rectangular building. The aligned path was oriented with the building; the misaligned path was rotated by 45 degrees. Later, participants pointed to target objects from imagined vantage points using their memories. Pointing accuracy was higher in the aligned than in the misaligned path group, and the patterns of results differed: In the aligned condition, accuracy was higher for imagined headings parallel to legs of the path and for an imagined heading oriented toward a nearby lake, a salient landmark. In the misaligned condition, pointing accuracy was highest for the imagined heading oriented toward the lake, and decreased monotonically with angular distance. These results indicated that locations of objects were mentally represented in terms of frames of reference defined by the environment but selected on the basis of egocentric experience.

Female↗
PubMed1994

Inhibition of return to object-based and environment-based locations.

Inhibition of return (IOR) has been described in terms of two functional components. The location-based component is associated with descriptions of spatially fixed, environmental locations; the object-based component is associated with more abstract descriptions of spatially invariant objects. In the present study, we hypothesized that the location-based component may also be associated with descriptions of spatially invariant objects because, like environment-based descriptions, object-based descriptions have an intrinsic spatial structure. To test this hypothesis, we employed a computer-generated depiction of a brick that rotated in depth between the presentations of cue and target. The results of four experiments showed that IOR accrued to locations that remained fixed with respect to the brick as well as the environment, suggesting that both object-based and environment-based descriptions can influence location-based IOR.

Attention↗
PubMedDate not supplied

[A new approach to calculation of the energy from van der Waals interactions in macromolecular proteins. Dielectric permeability as a physical parameter for calculations].

The problem in the calculation of Van der Waals interactions in protein globules based on the theory of condensed media was considered. The Van der Waals interactions are represented as energies of interaction of regions with a uniform density distribution. A definition of the local dielectric constant as a function of coefficients of absorption of molecular groups with a particular conformation was introduced. The applicability of this approach was estimated. The theory enables one to circumvent the problems arising in calculations based on pairwise additive approximation. The methods provides a high accuracy in determining the local features of spatial structures of globular proteins and physicochemical characteristics of their constituent amino acids and molecular groups.

Models, Chemical↗
PubMed1999

[3'-Deoxy-3'-fluoro analogs of core trimers of 2-5A: effect on lytic activity of human NK-lymphocytes].

The effect of core trimers, (2'-5')-analogues of oligoadenylic acid containing 9-(3-deoxy-3-fluoro-beta-D-xylofuranosyl)adenine (AF) and 3'-deoxy-3'-fluoroadenosine (AF) in various positions of the oligomer chain, on the lytic activity of human natural killer cells (NK cells) was studied in three different ways. The cellular cytotoxicity was determined using a highly sensitive nonradioactive approach employing a chelate europium-diethylenetriamino-pentaacetic acid complex (Eu-DTPA). It was shown that all fluorodeoxyanalogues enhance the lytic activity of intact NK lymphocytes, which follows from the lysis rate constant k2. At the same time, the substitution of either the central adenosine fragment or (to a greater extent) the 5'-terminal residue of (2'-5')A3 with AF causes a decrease in the number of active NK cells, which, unlike the case of the natural core trimer, leads to a loss of the capacity to increase the activity of NK. By contrast, isomeric ribo-analogues. (2'-5')(AF)A2 and (2'-5')A(AF)A, and trimers with the 2'(3')-terminal nucleotide substituted by AF or AF increased the activity of NK cells with an effectiveness close to or higher than the natural trimer (2'-5')A3. Inasmuch as isomeric xylo- and ribo-3'-deoxy-3'-fluoroanalogues of (2'-5')A3 are stereochemically modified oligomers, the data unambiguously suggest that the spatial structure of these trimers affects the increase in the lytic activity of NK cells.

Cytotoxicity, Immunologic↗
PubMed1999

[Effect of infrared rays on the eye in progressive myopia].

In the submitted paper the authors pay attention to infrared radiation close to visible light is intensely absorbed by haemoglobin, melanin and xanthophyll whereby part of the radiation energy is transformed into heat. The authors present three series of experiments where they investigated by different methods changes in the vitreous body after exposure to light, infrared radiation or raised temperature. They assume that on the defocused eye with a myopic conus which developed as a result of an inborn inadequate closure of the optic cup the light can cause a rise of temperature in the vitreous body. This leads to metabolic changes characterized by increased activity of lysosomal enzymes causing loss of the spatial structure of hyaluronic acid and collagen biomolecules. Penetration of the altered vitreous fluid thought the conus can lead to degradation of the interstitial substances of the sclera. Suitable absorption glasses filtering infrared light close to visible light could reduce the hyperthermia of the vitreous body.

Humans↗
PubMed1999

Model of the active site of firefly luciferase.

A model for the spatial structure of firefly luciferase--ATP--luciferin complex is suggested using the coordinates of unliganded luciferase and the enzyme--substrate complex of the adenylating subunit of gramicidin S synthetase known from the literature. Conformational changes in luciferase can occur during substrate binding resulting in a relative orientation of two luciferase domains similar to that in case of the AMP--phenylalanine--synthetase complex. The model is consistent with data on the physicochemical properties of firefly luciferase and its complexes with the substrates.

Adenosine Triphosphate↗
PubMed1999

[Mechanism of action of aspartic proteases. III. Conformational characteristics of HIV-1 protease inhibitor JG-365].

A set of conformations was shown to be characteristic of the free-state spatial structure of substrate-like inhibitor JG-365 for aspartic protease from HIV-1. Among them, the lowest-energy conformations have a folded form of the peptide backbone. The inhibitor has a noncleavable hydroxyethylamine group with an additional chiral center in its structure. Our calculations showed that only the S-isomer of the inhibitor displays conformational characteristics that practically coincide with those of the native substrate for HIV-1 protease. One of the calculated conformations with a completely extended main chain and a relative energy of 9.5 kcal/mol very closely mimics the experimentally observed structure of the inhibitor in the enzyme-inhibitor complex. The realization of this structure is unlikely for a free inhibitor, because it has only a small number of interresidual noncovalent interactions in the extended conformation; these are presumably compensated for by intermolecular interactions at the active site of the enzyme.

Aspartic Acid Endopeptidases↗
PubMed1999

[Mechanism of action of aspartic proteases. IV.Conformational characteristics of a substrate and an inhibitor of rhizopuspepsin ].

On the basis of theoretical conformational analysis of separate peptide fragments, the conformational characteristics of two substrates and a substrate-like inhibitor of aspartic protease rhizopuspepsin were studied. It was shown that the spatial structure of these molecules is described by several families of conformations, the transition between which does not require the overcoming of high energy barriers. It was assumed that the stabilization of beta-structural conformations experimentally observed in inhibitor complexes is due to the greater predisposition of extended structures to the formation of effective intermolecular contacts with amino acid residues of the active site of the enzyme.

Aspartic Acid Endopeptidases↗
PubMedDate not supplied

[Models of radiation dispersion in medical laser tomographic system].

The prospects for developing a new noninvasive medical diagnostic technique, such as optical (laser) tomography of biological tissues largely depend on the feasibility of designing an adequate mathematical model for the reconstruction of images of the spatial structure of objects that are in the highly scattering medium (HSM). The basic difficulty is that it is necessary to effectively describe the physical properties and the propagation pattern of photons of different types in such a medium. This review considers methods for describing the distribution of laser ultrashort pulses in HSM with particular emphasis on a new nonstationary two-flux model of radiation transfer.

Diffusion↗
PubMedDate not supplied

[Conformational features of a pentapeptide as an element of the active center of human immunoglobulin E].

The spatial structures of human immunoglobulin E pentapeptide Asp-Ser-Asp-Pro-Arg and some of its related peptides were investigated by the method of theoretical conformational analysis. These synthetic peptides have the capacity to inhibit the binding of immunoglobulin E to the mast cells of the skin. The results of the calculations and the data on biological activity of these peptides were used for determination their energy-dependent conformational characteristics that provide their specific interaction with receptors of mast cells.

Amino Acid Sequence↗
PubMedDate not supplied

[Study of the complex formation of daunomycin with deoxytetranucleotides with bases of differing sequence in an aqueous solution by 1H-NMR spectroscopy].

The complex formation of the antibiotic daunomycin with deoxytetranucleotides of different base sequence in the chain, 5'-d(GpCpGpC), 5'-d(CpGpCpG), and 5'-d(TpGpCpA) in aqueous salt solution was studied by 1D and 2D (2M-TOCSY and 2M-NOESY) 1H-NMR spectroscopy. Concentration and temperature dependences of proton chemical shifts of molecules were measured. Based on these dependences, reaction equilibrium constants, relative content of various complexes depending on concentration and temperature, limiting values of chemical shifts of protons of daunomycin incorporated in various complexes, and the thermodynamic parameters delta H and delta S of complex formation were calculated. The analysis of the results enables the conclusion that the sites of predominant intercalation of daunomycin are triplet nucleotide sequences, the binding sites of the antibiotic with three consecutive GC pairs in the tetranucleotide duplex being more preferential. Daunomycin exhibits no sequence specificity upon binding to the single-stranded deoxynucleotide sequence. From the calculated values of induced chemical shifts of daunomycin protons and 2M-NOE data, the most probable spatial structures of complexes (1:2) of the antibiotic with deoxytetranucleotides were constructed. The binding of the second daunomycin molecule to both the single-stranded and duplex form of tetramers is of pronounced anticooperative mode, which is explained by the presence in the antibiotic of a positively charged amino sugar residue, which poses considerable steric constraints for the insertion of the second antibiotic molecule into the short tetranucleotide sequence. The results were compared with the data obtained under identical experimental conditions for typical intercalators proflavine and ethidium bromide.

Antibiotics, Antineoplastic↗
PubMed2000

High root concentration and uneven ectomycorrhizal diversity near Sarcodes sanguinea (Ericaceae): a cheater that stimulates its victims?

Sarcodes sanguinea is a nonphotosynthetic mycoheterotrophic plant that obtains all of its fixed carbon from neighboring trees through a shared ectomycorrhizal fungus. We studied the spatial structuring of this tripartite symbiosis in a forest where Sarcodes is abundant, and its only fungal and photosynthetic plant associates are Rhizopogon ellenae and Abies magnifica, respectively. We found disproportionately high concentrations of Abies roots adjacent to Sarcodes roots compared to the surrounding soil. Rhizopogon ellenae colonizes the vast majority of those Abies roots (86-98%), and its abundance tends to decrease with increasing distance from Sarcodes plants. At 500 cm from Sarcodes plants we did not detect R. ellenae, and the ectomycorrhizal community instead was dominated by members of the Russulaceae and Thelephoraceae, which are commonly dominant in other California pinaceous forests. The highly clumped distribution of Abies-R. ellenae ectomycorrhizas indicates that Sarcodes plants either establish within pre-existing clumps, or they stimulate clump formation. Several lines of evidence favor the latter interpretation, suggesting an unexpected mutualistic aspect to the symbiosis. However, the mechanism involved remains unknown.

Journal Article↗
PubMedDate not supplied

[The role of single amino acid residues of the immunodominant continuous epitope of cytochrome P450CAM (CYP101) 312LKKGDQ317 in recognition by specific antibodies].

As it has been shown previously the site 311-318 of bacterial cytochrome P450cam (CYP101) contains an immunodominant continuous B-epitope. In order to investigate the role of single amino acid residues in antibody binding antigenic hexapeptide 312LKKGDQ317 analogues including single amino acid replacements were synthesized using Multipin technology. Antibodies from three anti-P450cam polyclonal rabbit sera interacted similarly to these peptides. The residue G315 was found to play a significant role in antibody recognition; any replacement leads there to considerable decrease of antibody binding. Residues L312, K313 and D316 occurred to be partly replaceable, whereas K314 and Q317 were not essential in recognition. These results correspond to known spatial structure of P450cam molecule. In its 312-317 site the polypeptide chain makes a turn and so some water-accessible atoms form a compact surface cluster including side chain atoms of K313 and D316, O-atom of K314 and C alpha-atom of G315, which present reliable Ig binding site. Side chain of K314 outlying from this cluster does not participate in the interaction. The received data permit to consider that the continuous epitope 312-317 of P450cam is conformationally dependent.

Amino Acids↗