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PubMed2006

Surface orientation, modulation frequency and the detection and perception of depth defined by binocular disparity and motion parallax.

Binocular disparity and motion parallax provide information about the spatial structure and layout of the world. Descriptive similarities between the two cues have often been noted which have been taken as evidence of a close relationship between them. Here, we report two experiments which investigate the effect of surface orientation and modulation frequency on (i) a threshold detection task and (ii) a supra-threshold depth-matching task using sinusoidally corrugated surfaces defined by binocular disparity or motion parallax. For low frequency corrugations, an orientation anisotropy was observed in both domains, with sensitivity decreasing as surface orientation was varied from horizontal to vertical. In the depth-matching task, for surfaces defined by binocular disparity the greatest depth was seen for oblique orientations. For surfaces defined by motion parallax, perceived depth was found to increase as surface orientation was varied from horizontal to vertical. In neither case was perceived depth for supra-threshold surfaces related to threshold performance in any simple manner. These results reveal clear differences between the perception of depth from binocular disparity or motion parallax, and between perception at threshold and supra-threshold levels of performance.

Cues↗
PubMed2004

Genetic differentiation of relictual populations of Alsophila spinulosa in southern China inferred from cpDNA trnL-F noncoding sequences.

The genetic differentiation and phylogeographical pattern of 11 relictual populations of Alsophila spinulosa distributed across Hainan, Guangdong, and Guangxi in southern China were inferred from sequence variations of trnL-F noncoding regions of chloroplast DNA (cpDNA). The length of trnL-F noncoding sequences varied from 863 to 940 bp. The A + T content was 62.23-63.36%. Sequences were neutral in terms of evolution (Tajima's criterion D=-0.62417, P>0.10 and Fu and Li's test D*=-1.45455, P>0.10; F*=-1.32798, P>0.10). Thirty-four haplotypes were identified based on nucleotide variation. Relatively high levels of haplotype diversity (h=0.929) and nucleotide diversity (Dij=0.022263) were detected in A. spinulosa, probably associated with its long evolutionary history which allowed the accumulation of genetic variation within lineages. Both the minimum spanning network and the strict consensus tree of the most parsimonious trees generated for haplotypes demonstrated that the investigated populations of A. spinulosa were subdivided into two geographical groups: Hainan and Guangdong-Guangxi. An analysis of molecular variance (AMOVA) indicated that most of the genetic variation (87.48%, P<0.001) was partitioned among regions. Spatial structure measurements revealed that population genetic structure was not related to geographical distance. This research suggests that blocked gene flow by Qiongzhou strait and an inbreeding system might result in the geographical subdivision between Hainan and Guangdong-Guangxi (F(ST)=0.92, Nm=0.09). Within each region, the "star like" pattern of phylogeography of haplotypes implied a population expansion process during evolutionary history. Gene genealogies together with coalescent theory were useful tools for uncovering the phylogeography of A. spinulosa.

China↗
PubMed1999

The influence of spatial reference frames on imagined object- and viewer rotations.

The human visual system can represent an object's spatial structure with respect to multiple frames of reference. It can also utilize multiple reference frames to mentally transform such representations. Recent studies have shown that performance on some mental transformations is not equivalent: Imagined object rotations tend to be more difficult than imagined viewer rotations. We reviewed several related research domains to understand this discrepancy in terms of the different reference frames associated with each imagined movement. An examination of the mental rotation literature revealed that observers' difficulties in predicting an object's rotational outcome may stem from a general deficit with imagining the cohesive rotation of the object's intrinsic frame. Such judgments are thus more reliant on supplementary information provided by other frames, such as the environmental frame. In contrast, as assessed in motor imagery and other studies, imagined rotations of the viewer's relative frame are performed cohesively and are thus mostly immune to effects of other frames.

Attention↗
PubMed2000

Effects of medium polarization and pre-existing field on activation energy of enzymatic charge-transfer reactions.

The highly organized spatial structure of proteins' polar groups results in the existence of a permanent intraprotein electric field and in protein's weak dielectric response, i.e. its low dielectric constant. The first factor affects equilibrium free energy gap of a charge-transfer reaction, the second (medium polarization effect) influences both equilibrium and non-equilibrium (reorganization) energies, decreasing the latter substantially. In the framework of the rigorous 'fixed-charge-density' formalism, the medium polarization component of the reaction activation energy has been calculated, both for the activation energy of the elementary act proper, and the effective activation energy accounting for the charges' transfer from water into a low-dielectric structureless medium. In all typical cases of reactions, the energy spent for charge transfer from water into structureless 'protein' is larger than the gain in activation energy due to the protein's low reorganization energy. Therefore, the low dielectric constant of proteins is not sufficient to ensure their high catalytic activity, and an additional effect of the pre-existing intraprotein electric field, compensating for an excessive charging energy, is necessary. Only a combined action of low reorganization energy and pre-existing electric field provides proteins with their high catalytic activity. The dependence of activation energy on the globule geometry has been analyzed. It is shown that, for each reaction, an optimum set of geometric parameters exists. For five hydrolytic enzymes, the optimum globule radii have been calculated using the experimental geometry of their active sites. The calculated radii agree satisfactorily with the real sizes of these macromolecules, both by absolute and by relative values.

Carboxypeptidases↗
PubMed2002

Sequence-dependent motions of DNA: a normal mode analysis at the base-pair level.

Computer simulation of the dynamic structure of DNA can be carried out at various levels of resolution. Detailed high resolution information about the motions of DNA is typically collected for the atoms in a few turns of double helix. At low resolution, by contrast, the sequence-dependence features of DNA are usually neglected and molecules with thousands of base pairs are treated as ideal elastic rods. The present normal mode analysis of DNA in terms of six base-pair "step" parameters per chain residue addresses the dynamic structure of the double helix at intermediate resolution, i.e., the mesoscopic level of a few hundred base pairs. Sequence-dependent effects are incorporated into the calculations by taking advantage of "knowledge-based" harmonic energy functions deduced from the mean values and dispersion of the base-pair "step" parameters in high-resolution DNA crystal structures. Spatial arrangements sampled along the dominant low frequency modes have end-to-end distances comparable to those of exact polymer models which incorporate all possible chain configurations. The normal mode analysis accounts for the overall bending, i.e., persistence length, of the double helix and shows how known discrepancies in the measured twisting constants of long DNA molecules could originate in the deformability of neighboring base-pair steps. The calculations also reveal how the natural coupling of local conformational variables affects the global motions of DNA. Successful correspondence of the computed stretching modulus with experimental data requires that the DNA base pairs be inclined with respect to the direction of stretching, with chain extension effected by low energy transverse motions that preserve the strong van der Waals' attractions of neighboring base-pair planes. The calculations further show how one can "engineer" the macroscopic properties of DNA in terms of dimer deformability so that polymers which are intrinsically straight in the equilibrium state exhibit the mesoscopic bending anisotropy essential to DNA curvature and loop formation.

Anisotropy↗
PubMed2002

Interaction of cardiotoxins with membranes: a molecular modeling study.

Incorporation of beta-sheet proteins into membrane is studied theoretically for the first time, and the results are validated by the direct experimental data. Using Monte Carlo simulations with implicit membrane, we explore spatial structure, energetics, polarity, and mode of insertion of two cardiotoxins with different membrane-destabilizing activity. Both proteins, classified as P- and S-type cardiotoxins, are found to retain the overall "three-finger" fold interacting with membrane core and lipid/water interface by the tips of the "fingers" (loops). The insertion critically depends upon the structure, hydrophobicity, and electrostatics of certain regions. The simulations reveal apparently distinct binding modes for S- and P-type cardiotoxins via the first loop or through all three loops, respectively. This rationalizes an earlier empirical classification of cardiotoxins into S- and P-type, and provides a basis for the analysis of experimental data on their membrane affinities. Accomplished with our previous simulations of membrane alpha-helices, the computational method may be used to study partitioning of proteins with diverse folds into lipid bilayers.

Amino Acid Sequence↗
PubMed1980

Correlations between internal mobility and stability of globular proteins.

The recent work is surveyed which leads to the suggestions that the conformation of globular proteins in solution corresponds to a dynamic ensemble of rapidly interconverting spatial structures, that clusters of hydrophobic amino acid side chains have an important role in the architecture of protein molecules, and that mechanistic aspects of protein denaturation can be correlated with internal mobility seen in the native conformation. These conclusions resulted originally from high resolution 1H nuclear magnetic resonance (NMR) studies of aromatic ring mobility, exchange of interior amide protons and thermal denaturation of the basic pancreatic trypsin inhibitor and a group of related proteins. Various new approaches to further characterize proteins in solution have now been taken and preliminary data are presented. These include computer graphics to outline hydrophobic clusters in globular protein structures, high resolution 1H-NMR experiments at variable hydrostatic pressure and 13C-NMR relaxation measurements. At the present early stage of these new investigations it appears that the hydrophobic cluster model for globular proteins is compatible with the data obtained.

Amino Acids↗
PubMed2001

Transformation of acridone synthase to chalcone synthase.

Acridone synthase (ACS) and chalcone synthase (CHS) catalyse the pivotal reactions in the formation of acridone alkaloids or flavonoids. While acridone alkaloids are confined almost exclusively to the Rutaceae, flavonoids occur abundantly in all seed-bearing plants. ACSs and CHSs had been cloned from Ruta graveolens and shown to be closely related polyketide synthases which use N-methylanthraniloyl-CoA and 4-coumaroyl-CoA, respectively, as the starter substrate to produce the acridone or naringenin chalcone. As proposed for the related 2-pyrone synthase from Gerbera, the differential substrate specificities of ACS and CHS might be attributed to the relative volume of the active site cavities. The primary sequences as well as the immunological cross reactivities and molecular modeling studies suggested an almost identical spatial structure for ACS and CHS. Based on the Ruta ACS2 model the residues Ser132, Ala133 and Val265 were assumed to play a critical role in substrate specificity. Exchange of a single amino acid (Val265Phe) reduced the catalytic activity by about 75% but grossly shifted the specificity towards CHS activity, and site-directed mutagenesis replacing all three residues by the corresponding amino acids present in CHS (Ser132Thr, Ala133Ser and Val265Phe) fully transformed the enzyme to a functional CHS with comparatively marginal ACS activity. The results suggested that ACS divergently has evolved from CHS by very few amino acid exchanges, and it remains to be established why this route of functional diversity has developed in the Rutaceae only.

Acyltransferases↗
PubMed2003

A model of animal movements in a bounded space.

Most studies describing animal movements have been developed in the framework of population dispersion or population dynamics, and have mainly focused on movements in open spaces. During their trips, however, animals are likely to encounter physical heterogeneities that guide their movements and, as a result, influence their spatial distribution. In this paper, we develop a statistical model of individual movement in a bounded space. We introduced cockroaches in a circular arena and quantified accurately the behaviors underlying their movement in a finite space. Close to the edges, we considered that the animals exhibit a linear movement mode with a constant probability per unit time to leave the edge and enter the central zone of the arena. Far from the walls cockroaches were assumed to move according to a diffusive random walk which enabled us to overcome the inherent problem of the quantification of the turning angle distribution. A numerical model implementing the behavioral rules derived from our experiments, confirms that the pattern of the spatial distribution of animals observed can be reliably accounted for by wall-following behaviors combined with a diffusive random walk. The approach developed in this study can be applied to model the movements of animals in various environment under consideration of spatial structure.

Animals↗
PubMed2004

Periodic local disturbance in host-parasitoid metapopulations: host suppression and parasitoid persistence.

Within many agricultural systems, insect pests and their natural enemies are forced to persist as a metapopulation, continuously recolonizing patches following disturbance through harvesting or spraying with insecticides. Despite the need to understand factors influencing biocontrol success, few theoretical studies of host-parasitoid interactions have examined the potential impact of local disturbance within a metapopulation framework. Here, we add periodic local mortality to series of classical host-parasitoid models to examine its effect on host suppression and parasitoid persistence. Using a deterministic lattice model, we show that despite the wide range of complex dynamics generated at the patch level, the region wide pattern of disturbance is the key factor influencing host suppression. The level of host suppression achieved can be understood in terms of both the strength of density dependent parasitism, and the relative amounts of host and parasitoid mixing amongst patches of different ages. Local dispersal among patches is sufficient to ensure coexistence of the host and parasitoid, though persistence is not necessarily associated with the formation of self-organized spatial structures reported in previous studies. Finally, a stochastic version of the model is developed, in order to highlight how the effects of demographic stochasticity may influence biocontrol success in highly disturbed agricultural systems.

Animals↗
PubMed1987

A purine-pyrimidine motif verifying an identical presence in almost all gene taxonomic groups.

A statistical parameter identifies, with a high degree of significance, a motif which is present in protein-coding sequences of eukaryotes, prokaryotes, chloroplasts, mitochondria, viral introns, ribosomal RNA genes, and transfer RNA genes. The random probability of occurrence of such a situation is 10(-12). This motif has the following properties: (i) its significant presence in almost all present-day genes explains why it can be considered as primitive oligonucleotide, (ii) its nucleotide order is: YRY (N)6YRY, R being a purine base, Y a pyrimidine one and N any base, (iii) its length and its terminal trinucleotides YRY suggest a primordial function related to the spatial structure of the DNA sequences. This motif is found in some viral protein-coding genes, but not in eukaryotic introns.

Base Sequence↗
PubMed2000

Mutational spectra for polycyclic aromatic hydrocarbons in the supF target gene.

An SV40-based shuttle vector system was used to identify the types of mutational changes and the sites of mutation within the supF DNA sequence generated by the four stereoisomers of benzo[c]phenanthrene 3,4-dihydrodiol 1,2-epoxide (B[c]PhDE), by racemic mixtures of bay or fjord region dihydrodiol epoxides (DE) of 5-methylchrysene, of 5, 6-dimethylchrysene, of benzo[g]chrysene and of 7-methylbenz[a]anthracene and by two direct acting polycyclic aromatic hydrocarbon carcinogens, 7-bromomethylbenz[a]anthracene (7-BrMeBA) and 7-bromomethyl-12-methylbenz[a]anthracene (7-BrMe-12-MeBA). The results of these studies demonstrated that the predominant type of mutation induced by these compounds is the base substitution. The chemical preference for reaction at deoxyadenosine (dAdo) or deoxyguanosine (dGuo) residues in DNA, which is in general correlated with the spatial structure (planar or non-planar) of the reactive polycyclic aromatic hydrocarbon, is reflected in the preference for mutation at A&z.ccirf;T or G&z.ccirf;C pairs. In addition, if the ability to react with DNA in vivo is taken into account, the relative mutagenic potencies of the B[c]PhDE stereoisomers are consistent with the higher tumorigenic activity associated with non-planar polycyclic aromatic hydrocarbons and their extensive reaction with dAdo residues in DNA. Comparison of the types of mutations generated by polycyclic aromatic hydrocarbons and other bulky carcinogens in this shuttle vector system suggests that all bulky lesions may be processed by a similar mechanism related to that involved in replication past apurinic sites. However, inspection of the distribution of mutations over the target gene induced by the different compounds demonstrated that individual polycyclic aromatic hydrocarbons induce unique patterns of mutational hotspots within the target gene. A polymerase arrest assay was used to determine the sequence specificity of the interaction of reactive polycyclic aromatic hydrocarbons with the shuttle vector DNA. The results of these assays revealed a divergence between mutational hotspots and polymerase arrest sites for all compounds investigated, i.e., sites of mutational hotspots do not correspond to sites where high levels of adduct formation occur, and suggested that some association between specific adducts and sequence context may be required to constitute a premutagenic lesion. A site-specific mutagenesis system employing a single-stranded vector (M13mp7L2) was used to investigate the mutational events a single benzo[a]pyrene or benzo[c]phenanthrene dihydrodiol epoxide-DNA adduct elicits within specific sequence contexts. These studies showed that sequence context can cause striking differences in mutagenic frequencies for given adducts. In addition, these sequence context effects do not originate only from nucleotides immediately adjacent to the adduct, but are also modulated by more distal nucleotides. The implications of these results for mechanisms of polycyclic aromatic hydrocarbon-induced mutagenesis and carcinogenesis are discussed.

Animals↗
PubMed2001

A motion aftereffect seen more strongly by the non-adapted eye: evidence of multistage adaptation in visual motion processing.

We found that the motion aftereffect measured using a directionally ambiguous counterphase grating (flicker MAE) can be stronger when it is measured for the non-adapted eye than when measured for the adapted eye. The monocularly viewed adaptation stimulus was the movement of a missing-fundamental grating (2f+3f motion), for which the movement of the higher-order spatial structure was dominantly perceived, while the first-order structure was physically moving in the opposite direction. For observers who perceived the MAE consistently in the direction opposite to the movement of the higher-order structures, the MAE was larger for the non-adapted eye than for the adapted eye. This finding of 'over-100% transfer' invalidates the standard view that the IOT is a direct measure of the binocularity of the adapted neurones. In addition, the finding provides convincing support for the hypothesis that the flicker MAE reflects adaptation at multiple processing stages

Adaptation, Physiological↗
PubMed2002

A comparative study of stimulus-specific pupil responses in the domestic fowl (Gallus gallus domesticus) and the human.

Pupil responses triggered by specific stimulus attributes such as spatial structure, colour and light flux changes were measured in eight domestic fowl. Comparative experiments were also carried out in human subjects. The results were unexpected in that large increments in light flux caused only small constrictions of the pupil. A red stimulus, on the other hand, caused a relatively large pupil response, but a green stimulus was less effective. This finding suggests that the size of the pupil, apart from being controlled by well-described pretectal pathways that mediate luminance responses, is also subject to other inputs. The pupil response in the domestic fowl may therefore make an effective quantitative indicator of things of significance to the animal. In some ways these observations are similar to other findings in primates in that the processing of stimulus attributes such as colour and structure that are not normally associated with the light reflex pathway can cause a pupil response. The fowl pupil does however respond very fast when large light flux changes or red stimuli are involved. Results obtained with sinusoidally modulated light flux changes reveal a short response latency of 105 ms (SD=8.3). In contrast, human responses measured for similar stimulus conditions reveal a latency of 434 ms (SD=36). The speed of pupil response in the fowl is significantly higher than in humans, but the response amplitude is usually small. Another interesting observation is the lack of sustained response to changes in ambient illumination. These findings suggest that the input to the pupilloconstrictor neurones in the fowl consists largely of transient neurones with little sustained component.

Adult↗
PubMed2002

Failure of direction identification for briefly presented second-order motion stimuli: evidence for weak direction selectivity of the mechanisms encoding motion.

We sought to investigate why the direction of second-order motion, unlike first-order motion, cannot be identified when the stimulus exposure duration is brief (<200 ms). In a series of experiments observers identified both the orientation (vertical or horizontal) and the direction (left, right, down or up) of a drifting sinusoidal modulation (0.93 c/ degrees ) in either the luminance (first order) or the contrast (second order) of a two-dimensional noise carrier. All motion stimuli were equated for visibility, and the duration was varied using the method of constant stimuli. Performance was measured for second-order motion over a range of drift temporal frequencies (0.63-5.04 Hz) and for first-order motion stimuli composed of two, opposite drifting modulations in luminance of unequal modulation depth. Orientation-identification performance was nearly 100% correct for both first-order and second-order motion stimuli, even at the briefest stimulus duration tested (26.49 ms). Direction identification for first-order motion was also typically good with brief presentations, but was poor for second-order motion when the exposure duration was < approximately 200 ms. Importantly increasing either the drift temporal frequency of second-order motion or the bidirectional nature of the first-order motion patterns produced comparable levels of performance for the two varieties of motion (i.e. the minimum duration required for reliable direction identification could be equated). As orientation-identification performance for the first-order and second-order motion stimuli was comparably good and minimally affected by duration, the marked differences on the direction-identification task must be specific to mechanisms that encode drift direction, rather than spatial structure. We propose that second-order motion detectors are much less selective for stimulus direction than first-order motion sensors, and thus are more susceptible to the deleterious effects of limiting stimulus duration (which introduces spurious motion in the opposite direction, particularly at low drift rates). Alternative explanations based on the delayed propagation of second-order motion signals or the temporal characteristics of the underlying motion mechanisms are not supported by our findings.

Humans↗
PubMed1999

Integration and segregation of local motion signals: the role of contrast polarity.

In the initial stages of visual processing in primates, more or less separated ON and OFF pathways have been shown to exist. There is ample evidence, that this separation includes the initial stages of motion processing. In the present study, experiments were conducted to investigate whether this ON versus OFF distinction persists into the integration stage of local motion information. We constructed stimuli that consisted of clusters of checks with equal contrast polarity, which could be varied in size, and compared them to stimuli with a random polarity distribution. We found that the ON versus OFF distinction remains partly intact, while interactions between the two systems are also apparent. These interactions prove to be highly correlated with the spatial structure of the stimulus. We propose a mechanism of contrast-sign specific integration of local motion signals, after which these separate ON and OFF pools engage in mutually inhibitory interactions.

Computer Graphics↗
PubMed1999

How does noise influence the estimation of speed?

Local motion signals have to be combined in space and time, to yield a coherent motion percept as it is involved in a variety of visual tasks. This combination necessarily means to trade-off between loosing spatio-temporal resolution by pooling local signals and maintaining perceptually significant segmentation between them. When signals are pooled to detect the presence of coherent motion in large amounts of random noise, the question raised is how the noise affects the perceived quality, in particular speed, of the coherent motion. Is there an analogy to the well-known reduction in the perceived speed of moving gratings at low contrast? Using a two-interval forced-choice procedure, we have investigated the assessment of speed in random-dot kinematograms containing different proportions of noise. Under the conditions investigated, there is no strong reduction of perceived speed with increasing noise, as long as coherence levels remain well above the thresholds for directional judgements. This basic result, which could suggest considerable but not perfect segregation of signal and noise motion components in the pooling process leading to speed estimation, is discussed in relation to a model that is designed to decode speed from a population of elementary motion detectors (EMDs) of the correlation type. A strategy to estimate speed from a set of EMDs with a variety of spatio-temporal tuning does not only provide a velocity predictor unambiguous with the spatial structure of the stimulus, but also is largely independent of noise.

Adult↗
PubMed2001

Linking population-level risk assessment with landscape and habitat models.

Ecological risk assessment at the population level often involves predicting the effects of a particular change in the land-use patterns on the viability of native species. A common method of addressing such questions is modeling the metapopulation dynamics of the species in the landscape. However, the landscape and, as a result, the spatial structure of the metapopulation usually do not remain unchanged, thus the assessment of viability must incorporate the dynamic nature of the landscape. A new link being developed between a metapopulation modeling program (RAMAS) and a landscape dynamics program (LANDIS) will allow the transitional dynamics of the landscape to be incorporated into assessment of viability and threat. This approach combines methods of landscape prediction with those of metapopulation simulation. The link between the landscape model and metapopulation model is provided by statistical models of habitat suitability for the species in focus.

Animals↗