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PubMed1999

Age-related differences in spatial memory: effects of structural and organizational context.

The authors examined effects of structural and organizational spatial context on younger and older adults' memory for an arrangement of dollhouse furniture pieces. For half of the participants, landmark objects (Experiment 1) and a floor plan beneath the array (Experiment 2) served as structural context during study and replacement. Organizational context was varied by grouping items randomly or as 6 rooms in a prototypical house. Two study and replacement trials were given. In Experiment 1, landmark structural cues improved younger adults' performance, whereas both age groups benefited from the floor plan in Experiment 2. In both experiments, positive effects of organizational context and trial occurred. Higher order interactions further revealed that structural and organizational context effects varied in size across trials, suggesting that both age groups used spatial contextual cues more effectively with practice. Implications of these results for current views on cognitive compensation in adulthood are discussed.

Adult↗
PubMed1999

Population differentiation in mediterranean plants: insights into colonization history and the evolution and conservation of endemic species

Colonization and isolation are critical events in the evolutionary dynamics of plant populations. In this paper I review how spatial population structure of genetic markers provides insights into the evolutionary significance of episodes of colonization and isolation in the Mediterranean flora. I use as themes to structure my review the following topics: spatial structure induced by historical associations among populations of widespread species; population differentiation in relation to the evolution of closely related species with disjunct distributions; the potential effect of founder events during colonization on character evolution; and the conservation implications of spatial population structure. My review illustrates that the Mediterranean flora is full of examples that provide key insights into such evolutionary and conservation issues.

Journal Article↗
PubMed2001

Spatial and temporal co-structure analyses between ichthyofauna and environment: an example in the tropics.

Ichthyofauna distribution and habitat characteristics of Thalassia beds in the Grand Cul-de-Sac marin lagoon in Guadeloupe were studied during a one-year survey. Environmental variables (9) were measured monthly in ten sites along with collection of fish communities. The environmental data set, analysed alone through between-within group 'principal component analysis' (PCA), exhibited a significant spatial and temporal variability. The fish data set, however, presented only a significant spatial structure, stable over the year. Given the lack of temporal variability in fish distribution, a 'between-site co-structure analysis' (BSCA) was used to compare the faunistic and environmental structures in space. The co-inertia structure was reduced to one axis representing a strong coast-reef gradient, the major common phenomena to both data sets. Environment and fish distribution allowed to distinguish sites directly under mangrove influence (characterised by high seagrasses, high concentration of chlorophyll a and high densities of zooplankton), to sites under reef influence (with short but dense seagrasses, clear water, and poor nutriments). For that purposes, the BSCA summarised efficiently what in common the fauna spatial structure and the environment spatial structure may present.

Animals↗
PubMed1995

Comparison of spatial arrangements of secondary structural elements in proteins.

We have developed a new method of protein structure comparison based on spatial arrangements of secondary structural elements (SSEs). Each SSE is represented by a single vector, and common spatial arrangements of vectors in a pair of proteins are detected. The method allows not only insertions and deletions of SSEs, but also topological permutations. It has a flexible target function that can be adjusted depending upon particular levels or definitions of structural similarity, and it is fast enough to allow structural comparisons for many pairs of proteins. The parameters for the target function are determined based on distributions of the geometrical variables for the spatial arrangements of the equivalent SSEs in well-known structural motifs. The obtained parameter set is tuned for detecting relatively strong structural similarity. We report several tests on examples including comparisons of known structural similarity and database searches for a target structure, and examine the results when this parameter set is used for the comparison of distantly related structures.

Alcohol Dehydrogenase↗
PubMed2004

Gene flow, historical population dynamics and genetic diversity within French Guianan populations of a rainforest tree species, Vouacapoua americana.

Both gene flow and historical events influence the genetic diversity of natural populations. One way to understand their respective impact is to analyze population genetic structure at large spatial scales. We studied the distribution of genetic diversity of 17 populations of Vouacapoua americana (Caesalpiniaceae) in French Guiana, using nine microsatellite loci. Low genetic diversity was observed within populations, with a mean allelic richness and gene diversity of 4.1 and 0.506, respectively, which could be due to low effective population size and/or past bottlenecks. Using the regression between Fst/(1-Fst), estimated between pairs of populations, and the logarithm of the geographical distance, the spatial genetic structure can partly be explained by isolation-by-distance and limited gene flow among populations. This result is in agreement with the species' biology, including seed and pollen dispersal by rodents and insects, respectively. In contrast, no clear genetic signal of historical events was found when examining genetic differentiation among populations in relation to biogeographical hypotheses or by testing for bottlenecks within populations. Our conclusion is that nuclear spatial genetic structure of V. americana, at the geographic scale of French Guiana, is better explained by gene flow rather than by historical events.

DNA, Plant↗
PubMed1997

Protein chains in hair and epidermal keratin IF: structural features and spatial arrangements.

Over the past decade the progress made in characterising the structural hierarchy of both the hard and the epidermal keratin intermediate filaments has exceeded all expectations. The origin of much of this progress can be traced back to the quantity of amino acid sequence data that became available in the early/mid 1980s, and their interpretation in terms of a heterodimeric molecular structure. Subdomains were subsequently identified in both the rod and terminal domains, and now the roles of most of these have been determined in principle, if not yet fully in detail. TEM and STEM, together with very revealing crosslinking analyses have also allowed details to be determined of the mechanism by which molecules assemble into oligomers and oligomers into IF. It remains for the three-dimensional packing of keratin molecules in the IF to be elucidated, but even here progress is being made. A particularly exciting development over the last two or three years has been the establishment of the link between keratinopathies and single point nucleotide mutations in keratin genes. Furthermore, the clustering of mutation sites in regions involved in a key structural mode of molecular aggregation has provided, for the first time, an understanding of keratin diseases at the molecular level.

Amino Acid Sequence↗
PubMed2004

Complex dynamics of the formation of spatially localized standing structures in the vicinity of saddle-node bifurcations of waves in the reaction-diffusion model of blood clotting.

Local activation in a one-dimensional three-component reaction-diffusion model of blood clotting may lead to a formation of spatially localized standing structures (peaks) via several complex scenarios. In the first scenario, two concentration pulses first propagate from the site of activation, then stop and transform into peaks [Zarnitsina et al., Chaos 11, 57 (2001)]. Here, we examine this scenario, and also describe a different scenario of peak formation. In this scenario, two trigger waves propagate initially in opposite directions away from the site of activation. Then they stop and change direction of propagation toward each other to the activation site, where they interact and form a peak. Both of these scenarios of stable peak formation are observed in the vicinity of saddle-node bifurcation and may be viewed as a memory of the extinct wave modes.

Animals↗
PubMed1999

Is attentional selection to different levels of hierarchical structure based on spatial frequency?

Target identification is faster when the target level (global or local) is the same as that on the previous trial, presumably because attention is directed to the appropriate level. L. C. Robertson (1996) found that eliminating low spatial frequencies by contrast balancing eliminated this level repetition effect and concluded that attentional selection between different levels of structure is based on spatial frequency. In contrast, M. R. Lamb and E. W. Yund (1996a) found no effect of contrast balancing on the level repetition effect and thus concluded that attentional selection is not based on spatial frequency. In this study, the authors identified the procedural difference between the 2 studies responsible for this difference in results and replicated both findings. The data show that spatial frequency is not a necessary basis for attentional selection between global and local forms. Although it remains possible that spatial frequency is the basis of attentional selection under some circumstances, the data supporting this proposition are not yet compelling.

Adult↗
PubMed2006

Dinitrosyl-iron complexes with thiol-containing ligands: spatial and electronic structures.

Parameters of the EPR signals of monomeric dinitrosyl-iron complexes with 1H-1,2,4-triazole-3-thiol (DNIC-MT), obtained by treating MT+ferrous iron in DMSO solution with gaseous NO, have been compared with those of the crystalline monomeric DNIC-MT with tetrahedral structure. Dissolved DNIC-MT were characterized by the isotropic EPR signal centered at g=2.03 with half-width of 0.7 mT and quintet hyperfine structure when recorded at ambient temperature or the anisotropic EPR signal with g( perpendicular)=2.045, g( parallel)=2.014 from frozen solution at 77 kappa, Cyrillic. DNIC-MT in crystalline state showed the structure-less symmetrical singlet EPR signal centered at g=2.03 and half-width of 1.7 mT at both room and liquid nitrogen temperature. The Lorentz shape of this signal indicates the strong exchange interaction between these complexes in the DNIC-MT crystal. Being dissolved in DMSO the crystalline sample of DNIC-MT demonstrated the EPR signal typical for DNIC-MT, obtained by treating MT+ferrous iron in DMSO solution with gaseous NO. Low spin (S=1/2) d(9) electron configuration of DNIC-MT with tetrahedral structure (formula [(MT-S(.))(2)Fe(-1)(NO(+))(2)](+)) was suggested to be responsible for the signal of DNIC-MT in crystalline state. Dissolving of the crystals of DNIC-MT may result in the change of their spatial and electronic structure, namely, tetrahedral structure of the complexes characterized by low spin d(9) electronic configuration transforms into a plane-square structure with d(7) electronic configuration and low spin S=1/2 state (formula [(MT- S(-))(2)Fe(+)(NO(+))(2)](+)). The latter was suggested to be characteristic of other DNICs with various thiol-containing ligands in the solutions. The proposed mechanism of these DNICs formation from ferrous iron, thiol and NO shows that the process could be accompanied by the ionization of NO molecules to NO(+) and NO(-) ions in the complexes. Detailed analysis of the shape of the EPR signals of these complexes provided additional information about the exchange interaction typical for DNIC-MT in crystals.

Electron Spin Resonance Spectroscopy↗
PubMed2003

Spatial representation of odorant structure in the moth antennal lobe: a study of structure-response relationships at low doses.

How odorant structure and concentration are spatially represented within the primary olfactory integration center, the antennal lobe (AL) or olfactory bulb (OB) in invertebrates and vertebrates, respectively, is currently a topic of high interest. Here, we show the spatial representation of odorant structure in the antennal lobe of the moth Spodoptera littoralis by imaging calcium activity evoked by straight chain aliphatic alcohols and aldehydes at low doses. Activity patterns of a given odor were most similar to compounds with the same functional group, differing in chain length by only one carbon atom. A chain length dependency was present as the most activated glomerulus in the lobe shifted from a medial to a lateral position with increasing chain length of the molecule. Statistical analysis revealed that in both classes of chemicals the chain length of the molecule was represented in a similar way. No topographically fixed domains were observed for any of the classes. However, activity patterns evoked by lower chain length molecules were spatially more distinct than patterns evoked by higher chain length molecules. The number of activated glomeruli for both classes of chemicals increased with increasing chain length to reach a maximum at eight or nine C atoms followed by a decrease as the chain length further increased.

Alcohols↗
PubMed1989

Aiming error under transformed spatial mappings suggests a structure for visual-motor maps.

Transformed spatial mappings were used to perturb normal visual-motor processes and reveal the structure of internal spatial representations used by the motor control system. In a 2-D discrete aiming task performed under rotated visual-motor mappings, the pattern of spatial movement error was the same for all Ss: peak error between 90 degrees and 135 degrees of rotation and low error for 180 degrees rotation. A two-component spatial representation, based on oriented bidirectional movement axes plus direction of travel along such axes, is hypothesized. Observed reversals of movement direction under rotations greater than 90 degrees are consistent with the hypothesized structure. Aiming error under reflections, unlike rotations, depended on direction of movement relative to the axis of reflection (see Cunningham & Pavel, in press). Reaction time and movement time effects were observed, but a speed-accuracy tradeoff was found only for rotations for which the direction-reversal strategy could be used. Finally, adaptation to rotation operates at all target locations equally but does not alter the relative difficulty of different rotations. Structural properties of the representation are invariant under learning.

Adult↗
PubMed2004

Spatial integration in structure from motion.

In three experiments we investigated whether the perception of 3D structure from the optic-flow involves a process of spatial integration. The observer's task was to judge the 3D orientation of local velocity field patches. In two conditions, the patches were presented either in isolation, or as part of a global optic-flow. In Experiment 1, the global optic-flow was a linear velocity field. In Experiment 2, the patches were embedded in a randomly perturbed linear velocity field. In Experiment 3, the local patches belonged to a smoothly curved surface. The results of these three experiments lead to two main conclusions: (1) a process linking spatially separated patches into global entities does affect the perception of local surface orientation induced by the optic-flow, and (2) linearity or smoothness of the global velocity field are not necessary conditions for spatial integration.

Adult↗
PubMed1994

Detecting clinical and balanced selection using spatial autocorrelation analysis under kin-structured migration.

Recently spatial autocorrelation has been employed to infer microevolutionary processes from patterns of genetic variation. In theory, different processes should show characteristic signature correlograms; e.g., clinal selection should produce correlograms decreasing from positive to negative autocorrelation, whereas uniform balanced selection should lead to no spatial autocorrelation. The ability of a statistical method such as spatial autocorrelation analysis to distinguish between these selective regimes or even to detect departures from neutrality is dependent on the strength of the evolutionary force and the population structure. Weak selection or migration will not be apparent against the expected background of stochastic noise. Moreover, the population structure may generate sufficient stochastic variation such that even strong evolutionary forces may fail to be detected. This study uses computer simulation to examine the effects of kin-structured migration and three different selective regimes on the shape of spatial correlograms to assess the ability of this technique to detect different microevolutionary processes. Genetic variation among 8 loci is simulated in a linear set of 25 artificial populations. Kin-structured stepping-stone migration among adjacent populations is modeled; directional, balanced, and clinal selection, as well as neutral loci are considered. These experiments show that strong selection produces correlograms of the predicted shape. However, with an anthropologically reasonable population structure, considerable stochastic variation among correlograms for different alleles may still exist. This suggests the need for caution in inferring genetic process from spatial patterns.

Bias↗
PubMed2025

soFusion: facilitating tissue structure identification via spatial multi-omics data fusion.

The rapid advancement of spatial multi-omics technologies has opened new avenues for dissecting tissue architecture with unprecedented resolution. However, inherent disparities across omics modalities, such as differences in biological hierarchy and resolution, pose significant challenges for integrative analysis. To address this, we present soFusion, a method for representation learning on spatial multi-omics data that enables automated identification of tissue compartmentalization. soFusion employs a graph convolutional network (GCN) to extract latent embeddings from spatial omics profiles. To simultaneously capture both cross-modality relationships and modality-specific features, we introduce a novel strategy for intra- and inter-omics feature learning. Moreover, modality-specific decoders are designed to preserve the unique information embedded in each omics type. We evaluated soFusion on multiple datasets including gene expression, protein expression, and epigenetic features. Across all benchmarks, soFusion consistently outperformed existing methods in delineating anatomical structures and identifying spatial domains with improved continuity and reduced noise. Collectively, soFusion offers an effective solution for spatial multi-omics integration, substantially enhancing the robustness of spatial domain identification.

Humans↗
PubMed2004

Analysis of baculovirus IE1 in living cells: dynamics and spatial relationships to viral structural proteins.

IE1, a principal transcriptional activator of the baculovirus Bombyx mori nucleopolyhedrovirus (BmNPV), is an essential factor for viral DNA replication. During viral infection, IE1 accumulates in discrete subnuclear structures where viral DNA replication occurs. To analyse the dynamic properties of IE1, we monitored green fluorescent protein-tagged IE1 (IE1-GFP) in BmNPV-infected B. mori cells by live-cell microscopy. Time-lapse imaging showed that IE1-associated structures gradually expanded and occasionally fused with one another, while photobleaching experiments revealed that IE1-GFP was relatively immobile inside the IE1-associated structures. To investigate the spatial relationships between IE1 and viral structural proteins in infected cells, three GFP-tagged viral components were expressed together with DsRed-tagged IE1. Two structural proteins that constitute the occlusion-derived virus (ODV), P91-GFP and GFP-ODV-E25, localized to the periphery of the IE1-associated structures. While local accumulations of these proteins were often in contact with the IE1-associated structures, they did not extend beyond the boundaries of the structures. In contrast, the major capsid protein VP39-GFP predominantly accumulated within the IE1-associated structures. These data indicated, in conjunction with the finding of a high DNA content in the structures, that IE1 localizes to the virogenic stroma and therefore support the prediction previously proposed that the virogenic stroma is a site for viral DNA replication as well as for the assembly of nucleocapsids.

Animals↗
PubMed2003

Spatial ecological and genetic structure of a mixed population of sexual diploid and apomictic triploid dandelions.

Ecological differentiation is widely seen as an important factor enabling the stable coexistence of closely related plants of different ploidy levels. We studied ecological and genetic differentiation between co-occurring sexual diploid and apomictic triploid Taraxacum section Ruderalia by analysing spatial patterns both in the distribution of cytotypes and in the distribution of genetic variation within and between the cytotypes. A significant relationship between ploidy level and elevation was found. This mode of ecological differentiation however, was not sufficient to explain the significant spatial structure in the distribution of diploids and triploids within the population. Strong congruence was found between the spatial genetic patterns within the diploids and within the triploids. We argue that this congruence is an indication of gene flow between neighbouring plants of different ploidy levels.

Demography↗
PubMed1995

Visuo-spatial working memory: structures and variables affecting a capacity measure.

The present paper examines the issue of the capacity of visuo-spatial working memory. A series of experiments test the hypothesis that two different components are critical in visuo-spatial working memory (passive store and active imagery operations), and, thereafter, attempt to specify the variables that affect the capacity of the passive store component. In the experiments, congenitally blind and sighted participants were asked to remember the spatial positions of target objects in two-dimensional matrices, with or without simultaneously performing a sequence of spatially-based imagery operations. We considered both the positions recall performance (the passive storage component) and the sequential imagery processing performance (the active processing component). We suggest that the two components of visuo-spatial working memory are independent. We also propose that both the number of relevant matrices and the number of target objects within each matrix affect the capacity of visuo-spatial working memory, with the latter factor possibly playing a greater role than the former one.

Adult↗