A probabilistic model of mosaicism based on the histological analysis of chimaeric rat liver

The analysis of pattern development in mosaic and chimaeric animals has provided insight into a number of developmental problems. In order to aid the understanding of the dynamics of the development of mosaic tissues, a computer simulation of the generation of a mosaic tissue was created using simple probabilistic decisions. Results of quantitative analysis of the simulated mosaicism were compared with chimaeric liver. Chimaeric animals were produced by morula aggregation between histologically distinguishable strains of congenic rats. The livers of these animals revealed a pattern of patchy mosaicism unrelated to either acinar or lobular architecture of the organ. Independent quantifiable parameters were correlated and compared between the simulation and chimaeric liver tissue. This analysis showed that extensive cell migration is not required to develop finely variegated mosaic tissue and that the patterns of mosaicism observed could have resulted from tissue development in which as few as three reiterated decisions were required. First, the simulation established anlagen of two cell types of various specified proportions with randomly chosen placement. Second, in each generation of the simulation the order in which the cells divided was established randomly. Third, there was a random choice of the direction of placement of the daughter cell. The quantitative relationships between the proportion of cell types, the area of patches and the number of patches per unit area was consistent between the simulation and the chimaeric tissue.     

Corals and starfish devastation of the great barrier reef: Aggregation methods

Aggregation methods allow one to replace a large scale dynamical system (micro-system) by a reduced dynamical system (macro-system) governing a small number of global variables. This aggregation of variables can be performed when two time scales exist, a fast time scale and a slow time scale. Perturbation theory allows to obtain an approximated aggregated dynamical system which describes the behaviour of a few number of slow time varying variables which are constants of motion of the fast part of the micro-system. Aggregation methods are applied to the case of the devastation of the great barrier reef by the starfishes. We recall the Antonelli/Kazarinoff model which implies a stable limit cycle for the corals and starfish populations. This prey-predator model describes the interactions between two species of corals and the starfish. Then, we generalize the Antonelli/Kazarinoff model to the case of two spatial patches with a fast part describing the starfish migration on the patches and the human manipulation of the communities by divers and, a slow part describing the growth and the interactions between the populations. We obtain an aggregated model governing the total coral densities on the patches and the total starfish population. This model can exhibit stable limit cycle oscillations and a Hopf bifurcation. The critical value of the bifurcation parameter is expressed in terms of the proportions of coral species and starfish on the two patches. This implies for example that rather than random killing of starfish by the Australian military, it may be better to send teams of divers to outbreaking reefs when they first occur who will then manipulate the community structure to increase protection.     

The effect of landscape pattern on Mediterranean vegetation dynamics: A modelling approach using functional types

Abstract. In the framework of land use changes in the Mediterranean area, I asked to what extent different landscape structures might determine long‐term dynamics in Mediterranean ecosystems. To answer this question, a spatially explicit model was developed (the Melca model), incorporating two functional types of woody species dominant in Mediterranean ecosystems: a resprouter (R) and a non‐resprouter fire‐recruiter (seeders, S). The model was used as a tool for generating hypotheses on the possible consequences of different landscape scenarios. Thus, five different hierarchically structured random landscapes were generated, all having the same cover for the two functional types but different landscape structure (ranging from highly heterogeneous to homogeneous landscapes). After a 100‐yr simulation, plant cover and spatial pattern had changed and the changes were different for the different initial spatial configurations, suggesting that long‐term vegetation dynamics is spatially dependent (the resultant dynamics are sensitive to the initial spatial structure). In the landscapes where R‐type species had a low number of large patches and S‐species had a large number of small patches, the number of R‐patches increased and their size decreased, while the number of S‐patches decreased. In these cases, the final cover of the two types changed little from the initial cover. Landscapes with a large number of small R‐patches interspersed with S‐patches had a decrease in the number of R‐patches, an increase in the number of S‐patches and a decrease in the size of S‐patches. In these landscapes, final cover was significantly changed, increasing in R‐type and decreasing in S‐type species. These results suggest that low spatial autocorrelation (low aggregation) favours R‐type species. Implications for land management are also discussed.     

Variables Aggregation in Time Varying Discrete Systems

In this work we extend approximate aggregation methods in time discrete linear models to the case of time varying environments. Approximate aggregation consists in describing some features of the dynamics of a general system involving many coupled variables in terms of the dynamics of a reduced system with a few number of variables. We present a time discrete time varying model in which we distinguish two time scales. By using perturbation methods we transform the system to make the global variables appear and build up the aggregated system. The asymptotic relationships between the general and aggregated systems are explored in the cases of a cyclically varying environment and a changing environment in process of stabilization. We show that under quite general conditions the knowledge of the behavior of the aggregated system characterizes that of the general system. The general method is also applied to aggregate a multiregional time dependent Leslie model showing that the aggregated model has demographic rates depending on the equilibrium proportions of individuals in the different patches.     

Fine-scale clonal structure and diversity within patches of a clone-forming dioecious shrub, Ilex leucoclada (Aquifoliaceae)

BACKGROUND AND AIMS: The mode of reproduction (sexual vs. asexual) is likely to have important effects on genetic variation and its spatial distribution within plant populations. An investigation was undertaken of fine-scale clonal structure and diversity within patches of Ilex leucoclada (a clone-forming dioecious shrub). METHODS: Six patches were selected in a 1-ha plot previously established in an old-growth beech forest. Two of the selected patches were composed predominantly of stems with male flowers (male patch), and two contained stems with predominantly female flowers (female patch). The remaining two patches contained stems with male flowers and stems with female flowers in more or less equal proportions (mixed patch). Different genets were distinguished using random amplified polymorphic DNA (RAPD) markers. KEY RESULTS: One hundred and fifty-six genets with different RAPD phenotypes were identified among 1928 stems from the six patches. Among the six patches, the male patches had the lowest clonal diversity, and the mixed patches had the highest. Distribution maps of the genets showed that they extended downhill, reflecting natural layering that occurred when stems were pressed to the ground by heavy snow. In every patch, there were a few large genets with many stems and many small genets with a few stems. CONCLUSION: The differences in clonal diversity among patches may be due to differences in seedling recruitment frequencies. The skewed distribution of genet size (defined as the number of stems per genet) within patches may be due to differences in the timing of germination, or age (with early-establishing genets having clear advantages for acquiring resources) and/or intraspecific competition.     

尺度变换的正确率分析

采用优势规则和随机规则为基础的尺度分析方法．对分类的TM数据(景观类型图,包含8类型)进行了尺度变换分析。随着尺度的增加。优势规则分析方法使景观中优势景观类型的面积增加,相反．面积较小的非优势景观类型的面积减少。随机规则使各景观类型的面积基本上保持不变。随着尺度的增加．随机Kappa指数、位置Kappa指数和标准Kappa指数减少。在优势规则分析法中数量Kappa指数减少,但在随机规则为基础的处理中它保持100％。优势规则处理中的正确率大于随机规则处理的。由景观类型的面积百分比引起的数量正确率在优势规则处理中增加．但在随机规则处理中保持9．64％不变;相反数量错误在优势规则处理中明显增加。但在随机规则处理中少量增加。偶然正确率保持12．50％不变。位置正确率减少,相反位置错误明显增加。层和亚层水平上的位置正确率和错误的变化不明显．而网格水平上的位置正确率和错误大幅度减少。网格水平上的位置正确率和错误率决定了整个位置正确率和错误率．同时位置正确率和错误率基本上决定了整个正确率和错误率。标准Kappa指数大于等于70％作为选择依据．认为210m是优势规则处理法的尺度阈值,150m是随机规则处理法的尺度阈值。欲提高尺度阈值,必须改变研究范围或分类系统。     

ULTRASTRUCTURAL DISTRIBUTION OF CELL SURFACE ANTIGENS IN AVIAN TUMOR VIRUS-INFECTED CHICK EMBRYO FIBROBLASTS

The distribution of neoantigens in the surface membrane of avian tumor virus-infected chicken embryo fibroblasts was examined on carbon replicas of cell cultures using hemocyanin-labeled antibody. New determinants appearing on the cell surface of virally infected but not transformed cells are thought to be common with components of the viral envelope. These antigens were found to exist in a diffuse, random array on the dorsal cell surface, with a denser accumulation along the cell processes. In living cells, surface antigens are capable of several types of redistribution when activated by reaction with antibody. Leukosis virus-infected (non-transformed) cells showed two apparently independent modes of redistribution: a relocation of some antibody-related sites to the cell margin; or an involvement of essentially all sites in randomly dispersed aggregates. Viral antigenic sites on sarcoma virus-infected (transformed) cells, reacted with antibody, were able to produce weak marginal relocation; but revealed a more striking tendency to migrate to some central location. The centripetal coalescence thus formed resembles the "cap" noted in other systems. Prior aggregation into "patches" may not be a prerequisite for such cap formation. Tumor-specific surface antigen detection and mapping was attempted by this technique, but results were equivocal. An antigen possibly characteristic of rapidly dividing cells occurred in a sparse, diffuse fashion over the surface of morphologically distinct "round" cells.     

Cell lineage analysis of Schwann cells in the PNS determined by shiverer-normal mouse chimeras

The myelin of the peripheral nervous system from the shiverer mutant mice is characterized by the absence of myelin basic protein, while the other myelin protein components are present at normal levels. Myelin lamella formation is normal in the shiverer mutant. Therefore, by using antiserum against myelin basic protein, we can distinguish the shiverer from the wild-type control myelin immunohistochemically. To study the cell lineage of Schwann cells, chimeras produced by the aggregation of eight-cell embryos from wild-type mice and shiverer mice have been used. Using myelin basic protein as a marker, it was observed that Schwann cells in the sciatic nerve existed as patches of cells with like-genotype. The patches occurred in a linear array along the axons with some intermingling of Schwann cells. Complete randomization by intermingling of Schwann cells was not observed and clones of Schwann cells may persist as contiguous groups throughout peripheral nerve development.     

Using n-alkanes to estimate diet composition of herbivores: a novel mathematical approach

N-alkanes are long-chain saturated hydrocarbons occurring in plant cuticles that can be used as chemical markers for estimating the diet composition of herbivores. An important constraint of using n-alkanes to estimate diet composition with currently employed mathematical procedures is that the number of markers must be equal or larger than the number of diet components. This is a considerable limitation when dealing with free-ranging herbivores feeding on complex plant communities. We present a novel approach for the estimation of diet composition using n-alkanes which applies equally to cases where the number of markers is lower, equal or greater than the number of plant species in the diet. The model uses linear programming to estimate the minimum and maximum proportions of each plant in the diet, and avoids the need for grouping species in order to reduce the number of estimated dietary components. We illustrate the model with two data sets of n-alkane content of plants and faeces obtained from a sheep grazing experiment conducted in Australia and a red deer study in Portugal. Our results are consistent with previous studies on those data sets and provide additional information on the proportions of individual species in the diet. Results show that sheep included in the diet high proportions of white clover (from 0.25 to 0.37), and relatively high proportions of grasses (e.g. brome from 0.14 to 0.26) but tended to avoid Lotus spp. (always less than 0.04 of the diet). For red deer we found high proportions of legumes (e.g. Trifolium angustifolium and Vicia sativa reaching maximum proportions of 0.42 and 0.30 of the diet, respectively) with grasses being less important and Cistus ladanifer, a browse, also having relevance (from 0.21 to 0.42 of the diet).     

Local movement and edge effects on competition and coexistence in ephemeral-patch models

For insects exploiting spatially structured arrays of resource patches (host plants, fungi, carrion, etc.), the distribution of individuals among patches can have important consequences for the coexistence of competitors. In general, intraspecific aggregation of consumer individuals over the landscape of patches stabilizes competition. Oviposition behavior of individual females can generate aggregation of larvae across patches and, therefore, strongly influences the outcome of competition between co-occurring species. We used simulation models to evaluate the consequences (for the coexistence of competitors) of different movement behaviors by females before and between oviposition events. Coexistence times increase when females are more likely to travel among neighboring patches than among distant ones. Coexistence times are also longer when females begin egg laying near the site of their emergence. Preoviposition dispersal is, therefore, destabilizing. We also considered responses by females to edges of resource arrays. Edge effects are generally stabilizing, delaying competitive exclusion by increasing larval aggregation, but different responses to edges have dramatically different effects on coexistence. The longest coexistence times occur when edges are "sticky", such that females encountering an edge tend to remain there.     

A model for estimating the extent of variegation in mosaic tissues

A method is described which allows the size of patches of like cells in mosaic tissues to be estimated from the frequency with which small samples taken from the tissue contain both of the mosaic cell types. The mosaic patches are represented as close-packed geometric figures arranged in twoor three-dimensional tissues. Small samples drawn at random from these tissues will include portions of one or more patches; only those samples which include portions of two or more dissimilar patches (mixed samples) will contain both cell types. The expected frequency of mixed samples is calculated as a function of the shape of the mosaic patches, the frequency of the two mosaic cell types and the sample to patch size ratio. This expected frequency is not strongly dependent on patch shape for triangular, square and hexagonal patches in two dimensions or for cubic and orthotetrakaidekahedral patches in three dimensions. Elongation of square patches along one axis or of cubic patches along one or two axes results in slight increases in the expected frequency of mixed samples for given sample to patch size ratio.     

Usage of monophonic and biphonic calls by free-ranging resident killer whales (Orcinus orca) in Kamchatka, Russian Far East

Killer whale discrete calls include types containing an overlapping high-frequency component (biphonic calls) and types without an overlapping high-frequency component (monophonic calls). In the resident killer whales of the Northeast Pacific, biphonic discrete calls exhibit higher source levels than monophonic calls, which suggests different active space and consequently different functions for monophonic and biphonic call types. In this study we investigate the potential communicative functions of monophonic and biphonic discrete calls produced by killer whales from Kamchatka (Northwest Pacific). We analyze how the usage of these calls depends on the number of pods present in the area and type of activity. Our results show that the usage of monophonic and biphonic calls in Kamchatkan killer whales depends on the number of pods in the area and is less dependent on the type of activity. Biphonic calls are more common when more than one pod is present in the area and could therefore function as markers of pod and matriline affiliation, serving mainly as cohesion signals. Monophonic calls dominated the vocalizations when a single pod was present, while in the presence of more than one pod both categories were used in equal proportions.     

Nestedness,SLOSS and conservation networks of boreal herb‐rich forests

Question: Herb‐rich patches are biodiversity hotspots for vascular plants in boreal forests. We ask: Do species occurrences on herb‐rich patches show a non‐random, nested structure?; Does patch size relate to richness of edaphically demanding and red‐listed species?; Does a set of small patches support more edaphically demanding and red‐listed species than a few large patches of the equal area? Location: Eastern Finland (63°04′N, 29°52′E), boreal vegetation zone. Data: Vegetation mapping of 90 herb‐rich sites, varying from 0.05 to 6.93 ha in size and belonging to six different, predetermined forest site types. Results: Using the RANDNEST procedure, only one site type showed a significantly nested pattern, and patch area was not related to “nestedness” in any of the site types. The number of edaphically demanding and red‐listed plant species was positively correlated with a patch size in three forest site types. In all site types, a set of small patches had more edaphically demanding and red‐listed species than did a few large patches of the equal total area. Conclusions: For conservation, it is essential to protect representative sets of different herb‐rich forest site types because flora varies between the site types. Within herb‐rich forest site types, several small areas may support representative species composition. However, successful conservation requires thorough species inventories, because of the high level of heterogeneity between the herb‐rich patches.     

Biodiversity and ecological forest-cover domains in boreal landscapes

Studies of spatial forest patterns have traditionally focused on habitat remnants within a landscape, but few have explicitly accounted for natural habitat patterns inherent to those landscapes. At broader scales, all cover types are to some degree subdivided. In boreal forest landscapes, forests, peat lands and water bodies form a variety of different spatial structures depending on their proportions and arrangement. To assess the spatial arrangement of forest patches relevant to organisms and ecological processes, we systematically sampled and analysed 57 boreal forest landscapes (10,000 ha in size) in central Finland. Our results show that even though forest is spatially very subdivided into discrete patches in boreal landscapes it becomes generally well-connected if narrow non-forested gaps are ignored. The proportion of forest cover varied from 17.8 to 75.3% and the number of discrete forest patches from 37 to 213. The average percolation threshold for forest cover was 46.8%. If ≤100 m wide non-forested gaps were ignored and forest patches were joined, the percolation threshold dropped to 33.3%. There were on average 13 discrete clusters of forest patches if forest patches within 200 m distance were combined. These results suggest that if a boreal forest species is able to cross even relatively narrow non-forested gaps, it is likely to perceive these boreal forest landscapes as continuous. Even though our present analysis was based on static forest cover patterns, it is important to consider landscape pattern domains when assessing habitat fragmentation and its consequences to populations of organisms.     

A simple landscape-scale test of a spatially explicit population model: patch occupancy in fragmented south-eastern Australian forests

The results of a landscape‐scale test of ALEX, a widely used metapopulation model for Population Viability Analysis (PVA), are described. ALEX was used to predict patch occupancy by the laughing kookkaburra and the sacred kingfisher in patches of eucalypt forest in south‐eastern Australia. These predictions were compared to field surveys to determine the accuracy of the model. Predictions also were compared to a “naïve” null model assuming no fragmentation effects.
The naïve null model significantly over‐predicted the number of eucalypt patches occupied by the sacred kingfisher, but the observed patch occupancy was not significantly different from that predicted using ALEX. ALEX produced a better fit to the field data than the naïve null model for the number of patches occupied by the laughing kookaburra. Nevertheless, ALEX still significantly over‐predicted the number of occupied patches, particularly remnants dominated by certain forest types – ribbon gum and narrow‐leaved peppermint. The predictions remained significantly different from observations, even when the habitat quality of these patches was reduced to zero. Changing the rate of dispersal improved overall predicted patch occupancy, but occupancy rates for the different forest types remained significantly different from the field observations. The lack of congruence between field data and model predictions could have arisen because the laughing kookaburra may move between an array of patches to access spatially separated food and nesting resources in response to fragmentation. Alternatively, inter‐specific competition may be heightened in a fragmented habitat. These types of responses to fragmentation are not incorporated as part of traditionally applied metapopulation models. Assessments of predictions from PVA models are rare but important because they can reveal the types of species for which forecasts are accurate and those for which they are not. This can assist the collection of additional empirical data to identify important factors affecting population dynamics.     

Counterfactual links to the proportion of treatment effect explained by a surrogate marker

In a randomized clinical trial, a statistic that measures the proportion of treatment effect on the primary clinical outcome that is explained by the treatment effect on a surrogate outcome is a useful concept. We investigate whether a statistic proposed to estimate this proportion can be given a causal interpretation as defined by models of counterfactual variables. For the situation of binary surrogate and outcome variables, two counterfactual models are considered, both of which include the concept of the proportion of the treatment effect, which acts through the surrogate. In general, the statistic does not equal either of the two proportions from the counterfactual models, and can be substantially different. Conditions are given for which the statistic does equal the counterfactual model proportions. A randomized clinical trial with potential surrogate endpoints is undertaken in a scientific context; this context will naturally place constraints on the parameters of the counterfactual model. We conducted a simulation experiment to investigate what impact these constraints had on the relationship between the proportion explained (PE) statistic and the counterfactual model proportions. We found that observable constraints had very little impact on the agreement between the statistic and the counterfactual model proportions, whereas unobservable constraints could lead to more agreement.     

Diffusion-limited forward rate constants in two dimensions. Application to the trapping of cell surface receptors by coated pits.

A variety of receptors are known to aggregate in specialized cell surface structures called coated pits, prior to being internalized when the coated pits close off. At 37 degrees C on human fibroblasts, as well as on other cell types, a recycling process maintains a constant number of coated pits on the cell surface. In this paper, we explore implications for receptor aggregation and internalization of the two types of recycling models that have been proposed for the maintenance of the coated pit concentration. In one model, coated pits alternate between accessible and inaccessible states at fixed locations on the cell surface, while in the other model, coated pits recycle to random locations on the cell surface. We consider receptors that are randomly inserted in the membrane, move by pure diffusion with diffusion coefficient D, and are instantly and irreversibly trapped when they reach a coated pit boundary (the diffusion limit). For such receptors, we calculate for each of the two models: the mean time tau to reach a coated pit, the forward rate constant k+ for the interaction of a receptor with a coated pit, and the fraction phi of receptors aggregated in coated pits. We show that for the parameters that characterize coated pits on human fibroblasts, the way in which coated pits return to the surface has a negligible effect on the values of tau, k+, and phi for mobile receptors, D greater than or equal to 1.0 X 10(-11) cm2/s, but has a substantial effect for "immobile" receptors, D much less than 1 X 10(-11) cm2/s. We present numerical examples to show that it may be possible to distinguish between these models if one can monitor slowly diffusing receptors (D less than 1 X 10(-11) cm2/s) on cells whose coated pits have relatively short lifetimes (less than or equal to 1 min). Finally, we show that for the low-density lipoprotein (LDL) receptor on human fibroblasts (D = 4.5 X 10(-11) cm2/s), the predicted and observed values of K+ and phi are in close agreement. Therefore, even for slowly diffusing LDL receptor, unaided diffusion as the transport mechanism of receptors to coated pits is consistent with measured rates of LDL internalization.     

Large-scale co-aggregation of fluorescent lipid probes with cell surface proteins

Large scale aggregation of fluorescein-labeled immunoglobulin E (IgE) receptor complexes on the surface of RBL cells results in the co- aggregation of a large fraction of the lipophilic fluorescent probe 3,3'-dihexadecylindocarbocyanine (diI) that labels the plasma membranes much more uniformly in the absence of receptor aggregation. Most of the diI molecules that are localized in patches of aggregated receptors have lost their lateral mobility as determined by fluorescence photobleaching recovery. The diI outside of patches is mobile, and its mobility is similar to that in control cells without receptor aggregates. It is unlikely that the co-aggregation of diI with IgE receptors is due to specific interactions between these components, as two other lipophilic probes of different structures are also observed to redistribute with aggregated IgE receptors, and aggregation of two other cell surface antigens also results in the coredistribution of diI at the RBL cell surface. Quantitative analysis of CCD images of labeled cells reveals some differences in the spatial distributions of co- aggregated diI and IgE receptors. The results indicate that cross- linking of specific cell surface antigens causes a substantial change in the organization of the plasma membrane by redistributing pre- existing membrane domains or causing their formation.     

Effects of asymmetric dispersal and environmental gradients on the stability of host–parasitoid systems

We consider host–parasitoid systems spatially distributed on a row of patches connected by dispersal. We analyze the effects of dispersal frequency, dispersal asymmetry, number of patches and environmental gradients on the stability of the host–parasitoid interactions. To take into account dispersal frequency, the hosts and parasitoids are allowed to move from one patch to a neighboring patch a certain number of times within a generation. When this number is high, aggregation methods can be used to simplify the proposed initial model into an aggregated model describing the dynamics of both the total host and parasitoid populations. We show that as the number of patches increases less asymmetric parasitoid dispersal rates are required for stability. We found that the 'CV²>1 rule' is a valid approximation for stability if host growth rate is low, otherwise the general condition of stability we establish should be preferred. Environmental variability along the row of patches is introduced as gradients on host growth rate and parasitoid searching efficiency. We show that stability is more likely when parasitoids move preferentially towards patches where they have high searching efficiency or when hosts go mainly to patches where they have a low growth rate.     

Ultrastructural and lectin binding changes during the formation of the animal dimple in oocytes of Discoglossus pictus (Anura)

The numbers of spores, stalk cells, and basal disk cells in fruiting bodies of Dictyostelium discoideum were estimated by direct cell counting. It was found that the ratios of differentiated cells varied with the number of cells in the fruiting body. Hence, this invalidates, in D. discoideum at least, an assumption used in many theories of differentiation that proportions do not vary with size. Simple statistical analysis showed that a semilogarithmic equation could describe the relationship of spore to stalk cell number and spore to basal disk cell number, whereas a double-logarithmic equation described the basal disk and stalk cell number relationship. Studies under different environmental conditions and with different strains suggest that the basic equations describing the relationships are conserved. However, quantitative differences in the proportioning of the cell types have been observed. Previous papers concerning the proportions of D. discoideum are reviewed, and the implications of the results, in regard to theories of differentiation, are analyzed.