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PubMed2000

Spatial frequency tuned covariance channels for red-green and luminance-modulated gratings: psychophysical data from human adults.

Both chromatic and luminance-modulated stimuli are served by multiple spatial-frequency-tuned channels. This experiment investigated the independence versus interdependence of spatial frequency channels that serve the detection of red-green chromatic versus yellow-black luminance-modulated stimuli at low spatial frequencies. Contrast thresholds for both chromatic and luminance-modulated gratings were measured within 12 individual subjects using a repeated-measures design. Spatial frequencies ranged from 0.27 to 2.16 c/deg. A covariance structure analysis of individual differences was applied to the data. We computed statistical sources of individual variability, used them to define covariance channels, and determined the number and frequency tuning of these channels. For luminance-modulated gratings, two covariance channels were found, including one above and one below 1 c/deg [cf. Peterzell, & Teller (1996). Individual differences in contrast sensitivity functions: the coarsest spatial pattern analyzer. Vision Research, 36, 3077-3085]. For chromatic gratings, correlations between thresholds for most spatial frequencies were uniformly high, yielding a single covariance channel covering all but the highest spatial frequency tested. A combined analysis of both data sets recovered the same three covariance channels, and showed that detection thresholds for low-frequency red-green chromatic and luminance-modulated stimuli are served by separate, statistically independent processes.

Adult↗
PubMed1993

wingless expression mediates determination of peripheral nervous system elements in late stages of Drosophila wing disc development.

We have used conditional wingless genotypes to dissect the role of this gene in late stages of wing disc development. One of these genotypes (wgIL/wg-lacZ) is simultaneously a reporter of wingless transcription and temperature-sensitive for wingless function, and has allowed us to define its pattern of transcription in the absence of wingless activity. The primordia of a subset of the bristles of the notum, which develop in or immediately adjacent to wingless-expressing cells, depend upon wingless activity. The time-course of this contribution and the effect on proneural gene expression together suggest that wingless may regulate the activity of products of the achaete-scute complex in proneural clusters. wingless activity is also required at the presumptive wing margin and is a necessary precondition for the change in proliferation pattern in this region. The involvement of wingless in transducing or mediating positional signals for spatial patterning in imaginal disc development is discussed.

Animals↗
PubMed2002

Reciprocal functions of the Drosophila yellow and ebony proteins in the development and evolution of pigment patterns.

Body coloration affects how animals interact with the environment. In insects, the rapid evolution of black and brown melanin patterns suggests that these are adaptive traits. The developmental and molecular mechanisms that generate these pigment patterns are largely unknown. We demonstrate that the regulation and function of the yellow and ebony genes in Drosophila melanogaster play crucial roles in this process. The Yellow protein is required to produce black melanin, and is expressed in a pattern that correlates with the distribution of this pigment. Conversely, Ebony is required to suppress some melanin formation, and is expressed in cells that will produce both melanized and non-melanized cuticle. Ectopic expression of Ebony inhibits melanin formation, but increasing Yellow expression can overcome this effect. In addition, ectopic expression of Yellow is sufficient to induce melanin formation, but only in the absence of Ebony. These results suggest that the patterns and levels of Yellow and Ebony expression together determine the pattern and intensity of melanization. Based on their functions in Drosophila melanogaster, we propose that changes in the expression of Yellow and/or Ebony may have evolved with melanin patterns. Consistent with our hypothesis, we find that Yellow and Ebony are expressed in complementary spatial patterns that correlate with the formation of an evolutionary novel, male-specific pigment pattern in Drosophila biarmipes wings. These findings provide a developmental and genetic framework for understanding the evolution of melanin patterns.

Animals↗
PubMed2026

Ten quick tips for spatial transcriptomics analysis.

Spatial transcriptomics (ST) enables genome-wide gene expression profiling while retaining spatial context within tissue sections. Since the foundational work by Ståhl et al. in 2016, the field has expanded rapidly, with diverse platforms now spanning sequencing-based (e.g., Visium, Visium HD, Slide-seq, Stereo-seq, and Seq-Scope) and imaging-based (e.g., MERFISH, Xenium, and CosMx SMI) approaches. The breadth of platforms, data structures, and computational tools, however, can be daunting for newcomers. Here, we present ten quick tips spanning the entire ST research workflow: whether ST suits a given biological question, how to select a platform aligned with study objectives, how to understand and process ST data, and which software tools to employ for analysis and visualization. We further discuss interpreting spatial patterns in biological context, integrating complementary modalities such as single-cell RNA sequencing and spatial proteomics, and leveraging public datasets and sharing results. Finally, we highlight current limitations of ST, particularly the challenge of reconstructing three-dimensional tissue architecture from serial tissue sections. This review provides biologists, bioinformaticians, and clinician-scientists with a concise, platform-neutral roadmap for incorporating ST into research, from experimental design to biological discovery.

Spatial Transcriptomics↗
PubMed2002

[Analysis on competition and coexistence patterns of Aneurolepidium chinense and its main companion species].

In this study, transects were set in areas where Aneurolepidium chinense and its companion species grew together. Competition and coexistence patterns of these species in the ecotone were analyzed using the following measures:frequency distribution, spatial pattern, and pattern intensity. Patterns of A. chinense and its main companion species were diverse. Aggregation was the tactics for A. chinense to defend the foreign species' invading or disperse itself. There existed competition and coexistence between A. chinense and its main companion species. A. chinense and Phragmite communis competed and coexisted through suppression. A. chinense and Kalimeris interifolia coexisted through competition. Hierochloe glabra and Puccinellia tenuiflora competed with A. chinense through clonal growth. Calamagrostis epigeios was suppressed by A. chinense.

China↗
PubMed1996

Soil-transmitted helminthiases in China: a spatial statistical analysis.

The prevalence of the soil-transmitted helminthiases is extremely high in some rural areas in China. The endemic foci of these human parasites constitute one of the most neglected public health problems. A large scale survey on human parasites (1988-1992) was conducted in China. The prevalences of the soil-transmitted helminthiases in the 30 provinces, autonomous regions and municipalities were reported and correlated with ecological factors (Yu et al, 1994; Xu et al, 1995). In this paper, we re-examined and analyzed the reported results with a spatial pattern test statistic, the D statistic. The values of the D statistic indicated that the spatial correlation of the prevalence of the soil-transmitted helminthiases in China was significant. We also found that the spatial correlation of the prevalence could largely be explained by the paddy field area per capita. The correlation of the prevalence of the soil-transmitted helminthiases and the paddy field area per capita was higher than the correlation of the prevalence with the factors found previously by Xu et al (1995).

China↗
PubMed2003

Spatio-temporal patterns of soil available nutrients following experimental disturbance in a pine forest.

Although disturbance is known to alter soil nutrient heterogeneity, it remains unclear whether spatial patterns in soil nutrients after disturbance follow predictable temporal changes that reflect underlying processes. This study examined the effects of tree harvesting and girdling on overall variability, geostatistical patterns, and resource congruence of soil available nutrients in a mature Pinus elliottii Engelm. forest. The two disturbances led to different patterns of vegetation removal, forest floor redistribution, and revegetation, but showed similar post-disturbance changes in overall soil nutrient variability. Soil nutrient variability increased after both disturbances by more than 5-fold, and then decreased, returning to the undisturbed level in 4 years. Spatial structures assessed using geostatistics did not show predictable temporal trends. However, girdled plots showed more persistent spatial structures in soil nutrients than harvested plots, and had semivariogram ranges mostly equal to or less than 10 m, reflecting effects of persistent and spatially stable patches of undisturbed hardwoods that had an average patch size of 10 m. Resource congruence examined with Spearman rank correlations was nil before disturbance, increased after disturbance and then became nil again by the 4th year post-disturbance. The timing of the increase was related to treatment, occurring in the 1st year after disturbance in the girdled plots, but not until the 2nd year in the harvested plots. These two patterns of congruence were potentially caused by different rates of nutrient patch formation and resource uptake by plants during early succession. Although temporal changes in soil heterogeneity have been documented previously, the present study indicates that temporal trends in nutrient variability after disturbance may be predictable, and that the marked changes in spatio-temporal patterns of soil nutrients as a result of disturbance are ephemeral.

Ecosystem↗
PubMed2004

Metapopulation genetic structure of two coexisting parasitoids of the Glanville fritillary butterfly.

We investigated the metapopulation genetic structure of two specialist parasitoids, Cotesia melitaearum and Hyposoter horticola, attacking the Glanville fritillary butterfly (Melitaea cinxia) in the Aland Islands south-western Finland. The host butterfly persists as a classic metapopulation in a network of 4,000 small habitat patches within an area of 50 by 70 km . The two parasitoids are known to differ greatly in their population dynamics and spatial pattern of occupancy in local host populations. Analysis of genetic population structure using F(ST) and clustering of multilocus genotypes revealed a distinct large-scale spatial structure in C. melitaearum but a very weak pattern in H. horticola. This result is consistent with the known difference in the dispersal range (much longer in H. horticola) and population size (much greater in H. horticola) of the two parasitoids.

Animals↗
PubMed1998

Integrated FGF and BMP signaling controls the progression of progenitor cell differentiation and the emergence of pattern in the embryonic anterior pituitary.

The mechanisms by which inductive signals control the identity, proliferation and timing of differentiation of progenitor cells in establishing spatial pattern in developing vertebrate tissues remain poorly understood. We have addressed this issue in the embryonic anterior pituitary, an organ in which distinct hormone cell types are generated in a precise temporal and spatial order from an apparently homogenous ectodermal primordium. We provide evidence that in this tissue the coordinate control of progenitor cell identity, proliferation and differentiation is imposed by spatial and temporal restrictions in FGF- and BMP-mediated signals. These signals derive from adjacent neural and mesenchymal signaling centers: the infundibulum and ventral juxtapituitary mesenchyme. The infundibulum appears to have a dual signaling function, serving initially as a source of BMP4 and subsequently of FGF8. The ventral juxtapituitary mesenchyme appears to serve as a later source of BMP2 and BMP7. In vitro, FGFs promote the proliferation of progenitor cells, prevent their exit from the cell cycle and contribute to the specification of progenitor cell identity. BMPs, in contrast, have no apparent effect on cell proliferation but instead appear to act with FGFs to control the initial selection of thyrotroph and corticotroph progenitor identity.

Animals↗
PubMed2004

Phase transition of traveling waves in bacterial colony pattern.

Depending on the growth condition, bacterial colonies can exhibit different morphologies. Many previous studies have used reaction diffusion equations to reproduce spatial patterns. They have revealed that nonlinear reaction term can produce diverse patterns as well as nonlinear diffusion coefficient. Typical reaction term consists of nutrient consumption, bacterial reproduction, and sporulation. Among them, the functional form of sporulation rate has not been biologically investigated. Here we report experimentally measured sporulation rate. Then, based on the result, a reaction diffusion model is proposed. One-dimensional simulation showed the existence of traveling wave solution. We study the wave form as a function of the initial nutrient concentration and find two distinct types of solution. Moreover, transition between them is very sharp, which is analogous to phase transition. The velocity of traveling wave also shows sharp transition in nonlinear diffusion model, which is consistent with the previous experimental result. The phenomenon can be explained by separatrix in reaction term dynamics. Results of two-dimensional simulation are also shown and discussed.

Bacillus↗
PubMed1998

Spatially restricted expression of pipe in the Drosophila egg chamber defines embryonic dorsal-ventral polarity.

Expression of pipe in the somatic tissue of the Drosophila ovary is required for the formation of embryonic dorsal-ventral polarity. pipe, which encodes an enzyme similar to the glycosaminoglycan-modifying enzyme heparan sulfate 2-O-sulfotransferase, is expressed in a spatially restricted domain of follicle cells on the ventral side of the egg chamber. Mutations that affect follicular polarity correspondingly alter the spatial pattern of pipe expression. Directed expression of pipe in otherwise pipe mutant females restores embryonic lateral and ventral pattern elements and can orient the dorsal-ventral axis of the embryo. Thus, the localized expression of pipe and the spatially restricted modification of carbohydrate chains play pivotal roles in the mechanisms that establish embryonic pattern and integrate follicular and embryonic polarity.

5' Untranslated Regions↗
PubMed2001

Interrelations of myogenic response, progressive atrophy of muscle fibers, and cell death in denervated skeletal muscle.

Little is known concerning the time-course and structural dynamics of reactivation of compensatory myogenesis in denervated muscle, its initiating cellular mechanisms, and the relationship between this process and the progression of postdenervation atrophy. The purpose of this study was to investigate the interrelations between temporal and spatial patterns of the myogenic response in denervated muscle and progressive atrophy of muscle fibers. Another objective was to study whether reactivation of myogenesis correlates with destabilization of the differentiated state and death of denervated muscle cells. It has remained unclear whether muscle fiber atrophy was the primary factor activating the myogenic response, what levels of cellular atrophy were associated with its activation, and whether the initiation and intensity of myogenesis depended on the local and individual heterogeneity of atrophic changes among fibers. For this reason, our objective was also to identify the levels of atrophic and degenerative changes in denervated muscle fibers that are correlated with activation of the myogenic response. We found that the reactivation of myogenesis in the tibialis anterior and extensor digitorum longus muscles of the rat starts between days 10-21 following nerve transection, before atrophy has attained advanced level, long before dead cells are found in the tissue. Formation of new muscle fibers reaches its maximum between 2 and 4 months following denervation and gradually decreases with progressive postdenervation atrophy. The myogenic response is biphasic and includes two distinct processes. The first process resembles the formation of secondary and tertiary generations of myotubes during normal muscle development and dominates during the first 2 months of denervation. During this period, activated satellite cells form new myotubes on live differentiated muscle fibers. Most of the daughter myotubes in 1- and 2-month denervated muscle develop on the surface of fast type parent muscle fibers, and some of the newly formed muscle fibers express slow myosin. Some fast type parent fibers are weakly or, more rarely, moderately immunopositive for embryonic isomyosin. This indicates that reactivation of myogenesis may also depend on the fiber type. The level of atrophy, destabilization of the differentiated myofiber phenotype, and degenerative changes of individual fibers in denervated muscle are very heterogeneous. The myogenic response of the first type is associated predominantly with fibers of average and higher than average levels of atrophy. Muscle cells that undergo a lesser degree of atrophy also form daughter fibers, although with a lower incidence. We did not find any correlation between the size of newly formed fibers and the level of atrophy of parent fibers. The topographical distribution of new myotubes both in the peripheral and central areas of the mid-belly equatorial sections at the early stages following nerve transection indicates that myogenesis of the first type represents a systemic reaction of muscle to the loss of neural control. These data indicate that activation of the myogenic response does not depend on cell death and degenerative processes per se. The second type of myogenesis is a typical regenerative reaction that occurs mainly within the spaces surrounded by the basal laminae of dead muscle fibers. Myocytes of different sizes are susceptible to degeneration and death, which indicates that cell death in denervated muscle does not correlate with levels of muscle cell atrophy. The regenerative process frequently results in development of abnormal muscle cells that branch or form small clusters. Replacement of lost fibers becomes activated between 2 and 4 months following nerve transection, i.e., mainly at advanced stages of postdenervation atrophy, when cell death becomes a contributing factor of the atrophic process. In long-term denervated muscle, the first and second types of myogenesisoccur concurrently, and the topographical distribution of the myogenic response becomes more heterogeneous than during the first weeks following denervation. Thus, our data demonstrate differential temporal and spatial expression of two patterns of myogenesis in denervated muscle that appear to be controlled by different regulatory mechanisms during the postdenervation period. (c) 2001 Wiley-Liss, Inc.

Animals↗
PubMed1996

Differential temporal evolution of post-training changes in regional brain glucose metabolism induced by repeated spatial discrimination training in mice: visualization of the memory consolidation process?

The present study analyses the effects of the stage of learning on the spatial patterns and time-course of [14C]glucose uptake in BALB/c mice brain regions produced by spatial discrimination training in an eight-arm radial maze. Our particular approach was designed to follow, during the post-training period, the level of functional activity in individual brain areas which may underlie the memory consolidation process. Regional mapping of relative [14C]glucose uptake was assessed at three post-training time intervals (5 min, 1 and 3 h) after either the first (Day 1), the fourth (Day 4) or the last (Day 9) daily training session of the discrimination task and compared with sham-conditioned animals placed in the same experimental environment. The results indicated that numerous subcortical and cortical brain regions exhibit metabolic alterations following the acquisition of the spatial discrimination task. These alterations, which were specifically related to learning since they did not appear in sham-conditioned animals, were functions both of the post-training interval studied and of the degree of mastery of the task. On Day 1, a progressive, time-dependent and sequential increase in labelling was found from subcortical (5 min post-training) to cortical regions (3 h post-training). On Day 4, a peak of cortical metabolic activation was identified at 1 h post-training. In contrast, on Day 9, maximum labelling was found 5 min post-training in all subcortical and cortical regions followed by a general monotonic decline at 1 and 3 h post-training. These findings, which show widely distributed changes of metabolic activity in the brain, are consistent with the hypothesis that learning involves distributed neural networks. The sequential activation from subcortical to cortical regions seems to indicate a general mechanism whose function would ultimately be to store cortical memory representations. The acquisition-dependent shifts in the patterns of post-training metabolic labelling observed as a function of task mastery may be taken to represent a visualization of the spatio-temporal evolution of the networks of brain structures actively engaged in the memory consolidation process. In particular, the present data suggest that the duration of post-acquisition memory processing is a function of the quantity of new information which has to be dealt with by the central nervous system.

Animals↗
PubMed2004

Role of shear forces and adhesion molecule distribution on P-selectin-mediated leukocyte rolling in postcapillary venules.

Rolling on the venular endothelium is a critical step in the recruitment of leukocytes during the inflammatory response. P-selectin is a key mediator of leukocyte rolling, which is an early event in the inflammatory cascade; this rolling is likely to be directly regulated by both local fluid shear forces and P-selectin site densities in the microvasculature. However, neither the spatial pattern of P-selectin expression in postcapillary venules nor the effect of local expression patterns on rolling behavior in intact functional venules is known. We investigated the influence of local shear forces and the spatial distribution of endothelial P-selectin in intact blood perfused post capillary venules in anesthetized mice using intravital confocal microscopy, high temporal resolution particle tracking, and immunofluorescent labeling. We demonstrated a shear-dependent increase in average leukocyte rolling velocity that was attributable to a shear-dependent increase in the occurrence of transient leukocyte detachments from the endothelial surface: translational velocity during leukocyte contact with the vessel wall remained constant. P-selectin expression was not different in venules with characteristically different shear rates or diameters but varied significantly within individual venules. In postcapillary venules, regions of high P-selectin expression correlated with regions of slow leukocyte rolling. Thus the characteristically variable leukocyte rolling in vivo is a function of the spatial heterogeneity in P-selectin expression. The study shows how the local hydrodynamic forces and the nonuniform pattern of P-selectin expression affect the behavior of interacting leukocytes, providing direct evidence for the local variation of adhesion molecule expression as a mechanism for the regulation of leukocyte recruitment.

Animals↗
PubMed2006

The role of the dorsal CA3 hippocampal subregion in spatial working memory and pattern separation.

A delayed-match-to-sample for spatial location task was used to measure spatial pattern separation and working memory. On each trial, an object covered a baited food well in one of 15 spatial locations along a row of food wells perpendicular to the start box. Once the rat exited the start box, displaced the object to receive a food reward and then returned to the startbox, the same food well was then quickly re-baited, an identical object was positioned to cover the food well and another identical object was positioned in a different location along the row of food wells covering a different unbaited food well. On the ensuing choice phase, the animal was allowed to choose between the two objects. The object that covered the same food well as the object in the sample phase was the correct choice and the second foil object was the incorrect choice. Five spatial separations (15-105 cm) were randomly used to separate the correct object from the foil object during the choice phase. Once a preoperative criterion was met, each rat received bilateral intracranial infusions of either ibotenic acid or the vehicle into the CA3 subregion of the dorsal hippocampus. Following surgery, rats with CA3 lesions were significantly impaired relative to controls across all spatial separations suggesting that CA3 lesions impaired working memory. Although the dorsal CA3 subregion of the hippocampus may play a role in pattern separation, the data suggest that this region is critically involved in spatial working memory.

Animals↗
PubMed1995

Patterns of bud-site selection in the yeast Saccharomyces cerevisiae.

Cells of the yeast Saccharomyces cerevisiae select bud sites in either of two distinct spatial patterns, known as axial (expressed by a and alpha cells) and bipolar (expressed by a/alpha cells). Fluorescence, time-lapse, and scanning electron microscopy have been used to obtain more precise descriptions of these patterns. From these descriptions, we conclude that in the axial pattern, the new bud forms directly adjacent to the division site in daughter cells and directly adjacent to the immediately preceding division site (bud site) in mother cells, with little influence from earlier sites. Thus, the division site appears to be marked by a spatial signal(s) that specifies the location of the new bud site and is transient in that it only lasts from one budding event to the next. Consistent with this conclusion, starvation and refeeding of axially budding cells results in the formation of new buds at nonaxial sites. In contrast, in bipolar budding cells, both poles are specified persistently as potential bud sites, as shown by the observations that a pole remains competent for budding even after several generations of nonuse and that the poles continue to be used for budding after starvation and refeeding. It appears that the specification of the two poles as potential bud sites occurs before a daughter cell forms its first bud, as a daughter can form this bud near either pole. However, there is a bias towards use of the pole distal to the division site. The strength of this bias varies from strain to strain, is affected by growth conditions, and diminishes in successive cell cycles. The first bud that forms near the distal pole appears to form at the very tip of the cell, whereas the first bud that forms near the pole proximal to the original division site (as marked by the birth scar) is generally somewhat offset from the tip and adjacent to (or overlapping) the birth scar. Subsequent buds can form near either pole and appear almost always to be adjacent either to the birth scar or to a previous bud site. These observations suggest that the distal tip of the cell and each division site carry persistent signals that can direct the selection of a bud site in any subsequent cell cycle.

Cell Division↗
PubMed2001

Stanniocalcin gene expression during mouse urogenital development: a possible role in mesenchymal-epithelial signalling.

Stanniocalcin (STC) is a polypeptide hormone first discovered in fish and more recently in mammals. In mammals, the STC gene is widely expressed and the hormone is involved in a variety of functions, but STC does not normally circulate in the blood. In both kidney and gut, STC regulates phosphate fluxes across the transporting epithelia, whereas in brain it protects neurons against cerebral ischemia and promotes neuronal cell differentiation. However, the gene is most highly expressed in ovary and expression is dramatically up-regulated by both pregnancy and nursing. STC mRNA levels are also high in the developing mouse embryo, but literally nothing is known of the tissue pattern of gene expression. Therefore, the aim of this study was to map the temporal and spatial patterns of gene expression during mouse embryologic development, starting with the urogenital system where the gene is so highly expressed in adults. STC mRNA was evident as early as E10.5 in both the mesonephros and genital ridge. Between E10.5 and 14.5 in developing kidney, STC was produced in undifferentiated mesenchyme cells and sequestered by ureteric bud epithelial cells that did not express the gene but nonetheless contained high levels of STC protein. Thereafter, the distribution pattern resembled that in adults such that gene expression predominated in collecting duct cells, whereas protein was present in most nephron segments. The pattern of gene expression during gonadal development was sexually dimorphic. In males, expression was first evident on E12.5 in interstitial mesenchyme cells surrounding the developing sex cords, whereas the protein accumulated in developing gonocytes within the sex cords that did not express the gene. This pattern became more pronounced over the course of gestation. In contrast, ovarian gene expression was only weakly evident during development. Collectively, the evidence suggests that in addition to its regulatory effects in adults, STC has novel and distinctive roles in the mesenchymal-epithelial interactions that are vital to normal organogenesis.

Animals↗