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PubMed1992

The differentiation of rhythmic structure.

Listeners judged whether two five-tone nonmetric rhythms were the same or different. Each rhythm was presented one, two, or four times to study the process of perceptual differentiation. The results indicated that the listeners perceived these rhythms in terms of the grouping of the tones, and not in terms of the timing between the groups. Two rhythms that had the same perceptual grouping were judged as being identical, even if the timing between the groups was different. The perception of the groupings of tones developed gradually. If each rhythm was presented only once, then the listeners had only a global percept, focused on groups (runs) of three elements, and often judged two different rhythms as being identical. If the rhythms were presented two or four times, then the grouping of the tones became more differentiated and the listeners were less likely to judge different patterns as being identical. Thus, perception of auditory rhythmic structure appears to follow the same developmental process as the perception of visual spatial structure.

Adult↗

PubMed2006

Spatial autocorrelation in two Iris pumila populations estimated on morphological data from natural clones and their samples grown in two different habitats.

Morphological data from two Iris pumila populations (measured on native clones, on their replants into the same habitat, and on their transplants into alternative habitat) were combined with native clones spatial position and spatial autocorrelations (SA) were calculated. Naturally growing I. pumila clones revealed significant SA that were positive on small distances and negative on medium ones in both open Hillock and shaded Woodland populations. No significant SA were detected when calculated with original clone positions, but with morphometric data from replants into the experimental plot in the same habitat. Some significant SA were, however, detected when morphometric data from transplants to alternative habitat were used. Detected SA on I. pumila clones were primarilly a consequence of spatial structuring of environmental factors but also, in lesser degree, a result of genetic spatial arrangements (most probably due to patterns of gene flow).

Adaptation, Physiological↗

PubMed1982

[Lysine-rich histones of Crenomytilis grayanus].

Two lysin-rich histone fractions essentially differing in molecular weights were isolated from mature gonads of the Crenomytilis grayanus. Apart from differences in the length of the polypeptide chains, the proteins revealed some similar properties. They possess high positive charge due to a high content of lysin and arginine. Both histones are similar to histone H5 by the number of arginine, serine and alanine residues. Tyrosine residues essential for the tertiary structure of lysin-rich histones occupy similar positions in these proteins. The spatial structure of H1 molecules of Cr. grayanus is identical in terms of the size and amino acid composition of the globular fragments of both proteins. The larger size of one of the proteins is presumably due to an increased C-terminal domain enriched with lysine, alanine and proline residues. The presence of a globular region in the lysin-rich histones is indicative of a universal three-domain organization of histones H1 and H5. The presence of all the hydrophobic and the bulk of aromatic amino acids in this part of the molecule and certain rigidity of the amino acid composition as well as localization of the whole alpha-helix are typical for the proteins of the given class.

Amino Acids↗

PubMed2002

Experimental study of the dimensionality of black-eye patterns.

The spatial structure of one type of Turing pattern named "black eyes" is studied in experiments using the chlorite-iodide-malonic acid reaction in spatial open reactor. The purpose of the work is to verify (or falsify) two possible theoretical interpretations of black-eye pattern formation: the projection of a body-centered-cubic (bcc) structure onto the plane vertical to the body diagonal and the spatial resonance of larger wave vectors with the fundamental ones. The latter happens when the mode of the larger wave vectors becomes linearly unstable, as the system goes far beyond the onset of Turing bifurcation. Our experimental results give evidence that black-eye patterns are not a projection of the bcc structure, so that the interpretation of a three-dimensional structure can be ruled out. The observations in the experiment also suggest another possible mechanism for the formation of black eyes.

Journal Article↗

PubMed1998

Spatio-temporal vernier acuity.

The study of space-time vernier (STV) provides information on the spatio-temporal structure of the visual system in the same way that the classical spatio-spatial vernier (SSV) provides information on its spatial structure. The transposition of a SSV task into a STV one yields the following experimental format: an object (in the present case a Gaussian Blob) drifts with a constant velocity, V, disappears at x0, t0 and reappears after a variable duration delta t at a position x1 +/- delta x with x1 the correct position (given a constant V) and delta x the minimum (positive and negative) spatial offset discriminable from x0, i.e. the STV threshold. Observer's task is to specify whether the reappearance position is ahead of, or behind x1. The STV functions of delta t measured for 1, 5 and 10 deg/s reference velocities are linear with non-zero spatial and temporal intercepts at the origin. We refer to these x and t intercepts as dynamic dmin and tmin. Dynamic dmin is the smallest instantaneous displacement (infinite velocity) discriminable from a continuous drift, V. Dynamic tmin is the shortest 'motion stop' discriminable from the same continuous drift, V. To our knowledge these quantities have not yet been assessed. Estimated dynamic dmin increases with V. whereas tmin is more or less V independent suggesting that the motion sensors presumably involved in the STV task have peak spatial frequencies inversely proportional with V and a temporal frequency characteristic independent of V (at least within the studied range). The observed STV linearity with the spatio-temporal separation implies that the STV task is equivalent to a velocity discrimination. Two additional observations yield support to this conclusion. (i) The slopes of these functions yield velocities very similar to those discriminable from the reference V in a standard V-discrimination experiment. (ii) The predicted STV performances based on a decomposition of the task into two velocity discrimination tasks run as independent experiments are reasonably accurate.

Depth Perception↗

PubMed1995

Three-dimensional structure of ectatomin from Ectatomma tuberculatum ant venom.

Two-dimensional 1H NMR techniques were used to determine the spatial structure of ectatomin, a toxin from the venom of the ant Ectatomma tuberculatum. Nearly complete proton resonance assignments for two chains of ectatomin (37 and 34 amino acid residues, respectively) were obtained using 2D TOCSY, DQF-COSY and NOESY experiments. The cross-peak volumes in NOESY spectra were used to define the local structure of the protein and generate accurate proton-proton distance constraints employing the MARDIGRAS program. Disulfide bonds were located by analyzing the global fold of ectatomin, calculated with the distance geometry program DIANA. These data, combined with data on the rate of exchange of amide protons with deuterium, were used to obtain a final set of 20 structures by DIANA. These structures were refined by unrestrained energy minimization using the CHARMm program. The resulting rms deviations over 20 structures (excluding the mobile N- and c-termini of each chain) are 0.75 A for backbone heavy atoms, and 1.25 A for all heavy atoms. The conformations of the two chains are similar. Each chain consists of two alpha-helices and a hinge region of four residues; this forms a hairpin structure which is stabilized by disulfide bridges. The hinge regions of the two chains are connected together by a third disulfide bridge. Thus, ectatomin forms a four-alpha-helical bundle structure.

Amino Acid Sequence↗

PubMed2003

Specificity and phenetic relationships of iron- and manganese-containing superoxide dismutases on the basis of structure and sequence comparisons.

The iron- and manganese-containing superoxide dismutases (Fe/Mn-SOD) share the same chemical function and spatial structure but can be distinguished according to their modes of oligomerization and their metal ion specificity. They appear as homodimers or homotetramers and usually require a specific metal for activity. On the basis of 261 aligned SOD sequences and 12 superimposed x-ray structures, two phenetic trees were constructed, one sequence-based and the other structure-based. Their comparison reveals the imperfect correlation of sequence and structural changes; hyperthermophilicity requires the largest sequence alterations, whereas dimer/tetramer and manganese/iron specificities are induced by the most sizable structural differences within the monomers. A systematic investigation of sequence and structure characteristics conserved in all aligned SOD sequences or in subsets sharing common oligomeric and/or metal specificities was performed. Several residues were identified as guaranteeing the common function and dimeric conformation, others as determining the tetramer formation, and yet others as potentially responsible for metal specificity. Some form cation-pi interactions between an aromatic ring and a fully or partially positively charged group, suggesting that these interactions play a significant role in the structure and function of SOD enzymes. Dimer/tetramer- and iron/manganese-specific fingerprints were derived from the set of conserved residues; they can be used to propose selected residue substitutions in view of the experimental validation of our in silico derived hypotheses.

Amino Acid Sequence↗

PubMed1987

Vision beyond the resolution limit: aliasing in the periphery.

Pattern resolution is generally considered a prerequisite for spatial vision because details too fine to be resolved cannot be distinguished from a uniform field. However, our experiments using peripheral vision demonstrate that reliable pattern detection is possible for images far beyond the resolution limit. The visual percept which arises in this case is an illusion called aliasing in which the apparent spatial structure of the stimulus is quite different from that actually present. Aliasing begins at spatial frequencies just above the classical resolution limit, which is taken as evidence that peripheral resolution is limited by the coarse spacing of visual neurons rather than by increased size of their receptive fields. At a given eccentricity, the very finest pattern which produces aliasing has a spatial period which approaches the smallest anatomical dimension: the diameter of a single cone photoreceptor.

Form Perception↗

PubMed1990

Knowledge-based prediction of protein structures.

We propose a knowledge-based approach to the prediction of protein structures in cases where there is no sequence-homology to proteins with known spatial structure. Using methods from Artificial Intelligence we attempt to take into account long-range interactions within the prediction process. This allows not only the assignment of secondary but also of supersecondary structure elements. In particular, the patterns used as conditions of prediction rules are generated by learning methods from information contained in the Protein Data Base. Patterns on higher levels of the protein structure hierarchy are used as constraints to reduce the combinatorial search space. These patterns may also be used to search for specified structure motifs by interactive retrieval.

Artificial Intelligence↗

PubMed1999

Genetic structure, reproductive biology and ecology of isolated populations of asplenium csikii (Aspleniaceae, pteridophyta)

The potential for environmental heterogeneity to generate spatial structuring of genotypes in seed-plant populations that occupy patchy habitats has been demonstrated by several studies, but little is known about the population structure of pteridophytes occupying patchy environments. In this study we have examined the genetic structure of isolated populations of the rock fern Asplenium csikii, an ecological specialist, growing almost exclusively on perpendicular walls of natural rock outcrops. All genetic variation observed in this taxon was partitioned between localities; no allozyme variation was found within a site and each site was colonized by a single multilocus phenotype (MLP). In total, five different MLPs were recorded from the nine localities, with two MLPs present at more than one site. Previous examination of population structure and genetic diversity in another rock fern, A. ruta-muraria, showed that the genetic diversity increases through multiple colonization over time. However, we cannot find any such correlation for A. csikii. All populations are genetically uniform, despite the probably considerable age of the populations and sites. Earlier studies concluded that the ample production of wind-borne propagules would lead to multiple colonization of sites and that reproductive features, such as single-spore colonization and subsequent intragametophytic selfing, would lead to very little genetic structuring of fern populations. In contrast to this prediction, it appears that ecological specialization and the scarcity of the narrowly defined niche contribute strongly to the pronounced partitioning of genetic variability observed in populations of A. csikii.

Journal Article↗

PubMed2000

Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy.

Lateral resolution that exceeds the classical diffraction limit by a factor of two is achieved by using spatially structured illumination in a wide-field fluorescence microscope. The sample is illuminated with a series of excitation light patterns, which cause normally inaccessible high-resolution information to be encoded into the observed image. The recorded images are linearly processed to extract the new information and produce a reconstruction with twice the normal resolution. Unlike confocal microscopy, the resolution improvement is achieved with no need to discard any of the emission light. The method produces images of strikingly increased clarity compared to both conventional and confocal microscopes.

Actins↗

PubMed2000

Full capacity of recombinant Escherichia coli heat-stable enterotoxin fusion proteins for extracellular secretion, antigenicity, disulfide bond formation, and activity.

We have successfully used the major subunit ClpG of Escherichia coli CS31A fimbriae as an antigenic and immunogenic exposure-delivery vector for various heterologous peptides varying in nature and length. However, the ability of ClpG as a carrier to maintain in vitro and in vivo the native biological properties of passenger peptide has not yet been reported. To address this possibility, we genetically fused peptides containing all or part of the E. coli human heat-stable enterotoxin (STh) sequence to the amino or carboxyl ends of ClpG. Using antibodies to the ClpG and STh portions for detecting the hybrids; AMS (4-acetamido-4'-maleimidylstilbene-2, 2'-disulfonate), a potent free thiol-trapping reagent, for determining the redox state of STh in the fusion; and the suckling mouse assay for enterotoxicity, we demonstrated that all ClpG-STh proteins were secreted in vitro and in vivo outside the E. coli cells in a heat-stable active oxidized (disulfide-bonded) form. Indeed, in contrast to many earlier studies, blocking the natural NH(2) or COOH extremities of STh had, in all cases, no drastic effect on cell release and toxin activity. Only antigenicity of STh C-terminally extended with ClpG was strongly affected in a conformation-dependent manner. These results suggest that the STh activity was not altered by the chimeric structure, and therefore that, like the natural toxin, STh in the fusion had a spatial structure flexible enough to be compatible with secretion and enterotoxicity (folding and STh receptor recognition). Our study also indicates that disulfide bonds were essential for enterotoxicity but not for release, that spontaneous oxidation by molecular oxygen occurred in vitro in the medium, and that the E. coli cell-bound toxin activity in vivo resulted from an effective export processing of hybrids and not cell lysis. None of the ClpG-STh subunits formed hybrid CS31A-STh fimbriae at the cell surface of E. coli, and a strong decrease in the toxin activity was observed in the absence of CS31A helper proteins. In fact, chimeras translocated across the outer membrane as a free folded monomer once they were guided into the periplasm by the ClpG leader peptide through the CS31A-dependent secretory pathway. In summary, ClpG appears highly attractive as a carrier reporter protein for basic and applied research through the engineering of E. coli for culture supernatant delivery of an active cysteine-containing protein, such as the heat-stable enterotoxin.

Adhesins, Escherichia coli↗

PubMed2002

Functional maps of the junctions between interglobular contacts and active sites in glycolytic enzymes -- a comparative analysis of the biochemical and structural data.

BACKGROUND: Oligomers and separate subunits of the glycolytic enzymes often have different catalytic properties. However, spectral data show an apparent lack of significant conformational changes during oligomerization. Since the conformation of an enzyme determines its catalytic properties, the structural mechanism(s) influencing the activity is of considerable interest. MATERIAL/METHODS: Analysis of the spatial structures of the junctions between interglobular contacts and binding sites may give a clue to the mechanism(s) of the activation. In this work, the problem was studied using available structural and biochemical data for the oligomeric enzymes of glycolysis. RESULTS: Computational analysis of the structures of the junctions has identified three structurally distinct types of junctions: 1. interglobular binding site (2 of 8 enzymes); 2. domain-domain stabilization (5 of 8); and 3. 'sequence overlap' or a local conformational change (all enzymes). Thus the catalytic activity may be influenced through the shifts of the modules of protein structure (types 1, 2) and/or due to a slight change in the local structure (type 3). The more common junctions of types 2 and 3 are well conserved among eukaryotic enzymes, which suggests their biological importance. CONCLUSIONS: The results suggest that a profound and a complex change in conformation in subunits of an oligomeric enzyme may not be necessary for a significant change in the catalytic properties. The analysis maps the residues important for the junctions and thus for the link between the catalytic activity and the oligomeric state of the enzymes.

Animals↗

PubMed2001

Fronts, Waves, and Stationary Patterns in Electrochemical Systems In the appendix we list the minimal equations (prototype equations) that describe the phenomena of self-organization discussed in the individual sections.

Oscillatory behavior has been observed for almost all electrochemical reactions in a certain, although sometimes small, range of external parameters. Only in the past ten years has it been possible, however, to find a common explanation for the occurrence of these temporal self-organization phenomena of chemically completely different electrochemical reactions. The breakthrough was achieved because new methods and concepts, which had been developed in nonlinear dynamics to describe the spontaneous formation of order in various disciplines, could be applied. This development in turn was only possible because the underlying laws are universal at a certain abstract level. Oscillations are only one possible manifestation of nonlinear behavior. Examples of other features that are often closely associated with temporal instabilities are spatial structures and waves. Initiated by the theoretical progress and the development of new experimental techniques, spatial pattern formation in electrochemical systems has been targeted for investigations in the past few years. Based on these investigations, it can be predicted under which conditions temporal or spatial pattern formation can be expected. Furthermore, the possibility of predicting the occurrence of instabilities indicates that it might be feasible to exploit nonlinear effects to increase, for example, the yield of electrocatalytic reactions. Here we discuss physicochemical mechanisms that lead to pattern formation in electrochemical systems. At the same time, we stress the generic principles that are responsible for self-structuring processes in many chemical and biological systems.

Journal Article↗

PubMed2005

Genetic differentiation and gene flow among populations of the alpine butterfly, Parnassius smintheus, vary with landscape connectivity.

Levels of gene flow among populations vary both inter- and intraspecifically, and understanding the ecological bases of variation in levels of gene flow represents an important link between the ecological and evolutionary dynamics of populations. The effects of habitat spatial structure on gene flow have received considerable attention; however, most studies have been conducted at a single spatial scale and without background data on how individual movement is affected by landscape features. We examined the influence of habitat connectivity on inferred levels of gene flow in a high-altitude, meadow-dwelling butterfly, Parnassius smintheus. For this species, we had background data on the effects of landscape structure on both individual movement and on small-scale population genetic differentiation. We compared genetic differentiation and patterns of isolation by distance, based on variation at seven microsatellite loci, among three regions representing two levels of connectivity of high-altitude, nonforested habitats. We found that reduced connectivity of habitats, resulting from more forest cover at high altitudes, was associated with greater genetic differentiation among populations (higher estimated FST), a breakdown of isolation by distance, and overall lower levels of inferred gene flow. These observed differences were consistent with expectations based on our knowledge of the movement behaviour of this species and on previous population genetic analyses conducted at the smaller spatial scale. Our results indicate that the role of gene flow may vary among groups of populations depending on the interplay between individual movement and the structure of the surrounding landscape.

Animals↗

PubMed1999

Structure activity studies on leaving group derivatives of [meso-1,2-bis-(2,6-dichloro-4-hydroxyphenyl)ethylenediamine] platinum(II).

The spatial structures of leaving group derivatives of [meso-1,2-bis(2,6-dichloro-4-hydroxyphenyl)ethylenediamine]platinum(II) (meso-1-PtL2; L2 = SO4, Cl2, I2, CBDC (cyclobutane-1,1-dicarboxylate)) were investigated by NMR methods and correlated with their reactivity against nucleophiles, their estrogenic potency, and their activity on the hormone dependent MCF-7 mammary carcinoma cell line. It was demonstrated that beside the non-leaving group meso-1 the PtL2 moiety of meso-PtL2 complexes is important for the estrogen receptor binding. Among the tested complexes meso-1-PtI2 possesses the highest affinity for the estrogen receptor (RBA = 2.6) and represents a strong estrogen on the MCF-7-2a cell line. The use of CBDC as leaving group decreases the effects. Meso-1-PtCBDC shows an RBA of 0.06 and has only half of the estrogenic activity. Both complexes are sufficiently stable under physiological conditions, so a transformation into the dichloroplatinum(II) complex prior to the binding to the estrogen receptor can be excluded. Due to their high stability meso-1-PtI2 and meso-1-PtCBDC were only marginally active on the human estrogen receptor positive MCF-7 cell line, while meso-1-PtSO4 and meso-1-PtCl2 reduced the cell growth to T/Cmax = 45% and 25%, respectively.

Animals↗

PubMed1983

Secondary structure of the lac repressor DNA-binding domain by two-dimensional 1H nuclear magnetic resonance in solution.

A recently proposed approach for spatial structure determination in noncrystalline proteins by nuclear magnetic resonance was applied to the lac repressor DNA-binding domain. On the basis of sequence-specific 1H NMR assignments, the location of alpha-helices in the amino acid sequence was determined from nuclear Overhauser enhancement data and from amide proton exchange studies. These investigations provide detailed experimental data on the structure of a noncrystalline DNA-binding protein. The results support the hypothesis advanced by others that sequence-specific interactions between lac repressor and DNA are mediated by a particular spatial arrangement of two alpha-helices common to various different DNA-binding proteins.

Amino Acid Sequence↗

PubMed2006

Model for intermittency of energy dissipation in turbulent flows.

Modeling the intermittent behavior of turbulent energy dissipation processes in both space and time is often a relevant problem when dealing with phenomena occurring in high-Reynolds-number flows, especially in astrophysical and space fluids. In this paper, a dynamical model is proposed to describe the intermittency of the energy dissipation rate in a turbulent system. This is done by using a shell model to simulate the time evolution of the turbulent cascade and introducing some heuristic rules, partly inspired by the well-known p model, to construct a spatial structure of the energy dissipation rate. In order to validate the model and to study its spatial intermittency properties, a series of numerical simulations have been performed. These show that the level of spatial intermittency of the system can be simply tuned by varying a single parameter of the model and that scaling laws in agreement with those obtained from experiments on fully turbulent hydrodynamic flows can be recovered. It is finally suggested that the model could represent a useful tool to simulate the intermittent structure of turbulent energy dissipation in those high-Reynolds-number astrophysical fluids where impulsive energy release processes can be associated with the dynamics of the turbulent cascade.

Journal Article↗