Measuring the structural similarity of two communities composed of the same species

Summary The primary purpose of this paper is to propose empirical measures of the structural differences between two communities of plants or animals composed of the same species. Structure is defined to consist of; 1) the species in the community, 2) the pattern of interactions as represented by the covariance or correlation matrix of successive observations on each species, and 3) the mean abundances of each species in each of the two communities. Statistical tests are proposed for testing whether the covariance matrices and the vectors of mean densities for each community are equal and empirical measures of the differences between the covariance matrices and mean vectors are proposed. Given unequal covariance or correlation matrices the factor analysis model is used to derive empirical measures of the degree to which each variable of the ecosystem is responsible for the observed defferences in the pattern of interactions in each community. These tests and measures were applied to data gathered byHunter (1966) on the abundances of six species ofDrosophila censused monthly over a period of approximately two and a half years in two adjacent, but different habitats near Bogota, colombia. The two covariance matrices were significantly different indicating different patterns of interactions in the twoDrosophila communities.     

Do pollination syndromes cause modularity and predict interactions in a pollination network in tropical high‐altitude grasslands?

The concept of pollination syndromes has been widely questioned, since plant–pollinator interactions have proved to be more generalist than was previously thought. We examined whether the network of a tropical high‐altitude grassland contained groups of plants and pollinators that interact preferentially with each other. A general binary matrix was created. To assess the robustness of myophily, in all analyses we considered: 1) the whole network, 2) the network after the wasps were removed, and 3) the network after the flies were removed. For each network we evaluated whether: 1) the observed interactions were more related to syndromes than expected by chance, compared to an expected matrix; 2) there was a modular structure; 3) the modules found were more related to syndromes than expected by chance, compared to another expected matrix; 4) the syndromes were equally robust. For this analysis, the general matrix was subdivided into smaller matrices that included each pollination syndrome separately. To test the influence of the functional groups of pollinators and the phylogeny of plants, in addition to the general matrix, we also considered the first expected matrix, a quantitative functional group and a plant phylogeny matrix. The pollination syndromes determined the pattern of interactions in the network: 69% of the total interactions resulted from the functional group of pollinators predicted by the plant syndrome. The network showed greater modularity (13 modules) than expected by chance, mostly consisting of the expected functional groups of pollinators and plant syndromes. The modules were associated with pollination syndromes more than was predicted by chance. Most of the variation in interactions was explained by functional groups of pollinators or by plant syndromes. Plant phylogeny did not account for a significant amount of variation in the interactions. Our findings support the concept of pollination syndromes. However, the interactions were not equally predicted by different pollination syndromes, and the accuracy of the prediction was strongest for ornithophily and melittophily.     

Effects of complex extracellular matrices on 5-azacytidine-induced myogenesis

Culture dishes coated with extracellular matrix material synthesized by bovine endothelial cells, rat smooth muscle cells or human fibroblasts were used to study proliferation and myogenesis in C3H/10T1/2 C18 (10T1/2) cells primed to differentiate with 5-azacytidine (5-aza-CR). Endothelial and smooth muscle matrices were permissive for growth and myogenic differentiation of treated 10T1/2 cells, whereas the fibroblast matrix was inhibitory. All three types of matrix-coated dishes were refractory for myogenesis after brief exposure to trypsin. Analysis of the matrix glycosaminoglycans showed that high chondroitin sulfate relative to hyaluronic acid (HA) levels were favorable for the myogenic response. The ratio between these two glycosaminoglycans therefore had a major influence on mesenchymal differentiation. These results using complex extracellular matrices produced in vitro may be useful in understanding cell-matrix interactions during embryogenesis.     

Constraints and missing reactions in the urea cycle.

The stoichiometric relations in a series of biochemical reactions are summarized by a stoichiometric number matrix (with a column for each reaction) and a conservation matrix (with a row for each constraint). These two matrices for a series or cycle of biochemical reactions are related because the columns of the stoichiometric number matrix are in the null space of the conservation matrix, and the rows of the transpose of the conservation matrix are in the null space of the transpose of the stoichiometric number matrix. The conservation matrix for a system of biochemical reactions is of interest because it shows the nature of the constraints in addition to the conservation of atoms and groups. Constraints beyond those for the conservation of atoms and groups indicate "missing reactions" that do not occur because the enzymes involved couple reactions that could occur and still conserve atoms and groups. The interpretation of conservation matrices and stoichiometric matrices for a reaction system is complicated by the fact that they are not unique. However, their row-reduced forms are unique, as are their dimensions, which represent the number of reactants and number of independent reactions. Two matrices that look different contain the same information if they have the same row-reduced form. The urea cycle, which involves five enzyme-catalyzed reactions, and its net reaction are discussed in terms of the linear constraints produced by enzyme catalysis. A procedure to obtain a set of conservation equations that will yield the correct net reaction is described.     

Matrix analyses of interaction among fingers in static force production tasks

The fingers on a hand show interactions in force production tasks. The interfinger connection matrices (IFMs) quantify these interactions (Li et al. 2002; Zatsiorsky et al. 2002b; Danion et al. 2003). The goal of the present study was to explore the differences in the IFMs of individual subjects and, in particular, to establish a procedure that may be used in the future for diagnostic purposes. Subjects (n=20) pressed downward maximally with ten different combinations of the four fingers, index (I), middle (M), ring (R), and little (L): I, M, R, L, IM, MR, RL, IMR, MRL, and IMRL. Voluntary activation of a subset of the four fingers was accompanied by an involuntary force production by fingers that were not intentionally activated (enslaving). Interfinger connection matrices were computed for each subject by the artificial neural network. The similarities/dissimilarities (proximities) between the individual matrices were determined. This procedure was performed twice: (a) for nonnormalized IFMs whose elements represented the amount of force (in newtons) exerted by a finger i in response to a unit command to a finger j; and (b) for normalized IFMs, after dividing the elements of each IFM by the total force produced by the four fingers acting together (the elements of the matrix are in percents). The 20×20 matrix of the proximities was subjected to multidimensional scaling (MDS) to reduce the number of dimensions and identify the major ones. To interpret the meaning of the computed dimensions, they were regressed on a set of finger force parameters described in the text. For the nonnormalized IFMs an interpretable dimension was the strength of the subjects. For the normalized IFMs two dimensions were interpreted: (a) the location of the point of resultant force application along the mediolateral axis that is defined by the pattern of force sharing among the fingers and (b) the total contribution of the enslaved forces into the total finger force. We speculate that the similarity of typical everyday tasks across the population promotes the similarity of the IMFs reflecting optimal hand functioning over these tasks. AcknowledgementsThis study was partly supported by NIH grants NS-35032, AR-048563 and AG-18751. The support from the Whittaker Foundation to Dr. Z.M. Li is also acknowledged.     

Quantitative analysis of the effect of cancer invasiveness and collagen concentration on 3D matrix remodeling

Extracellular matrix (ECM) remodeling is a key component of cell migration and tumor metastasis, and has been associated with cancer progression. Despite the importance of matrix remodeling, systematic and quantitative studies on the process have largely been lacking. Furthermore, it remains unclear if the disrupted tensional homeostasis characteristic of malignancy is due to initially altered ECM and tissue properties, or to the alteration of the tissue by tumor cells. To explore these questions, we studied matrix remodeling by two different prostate cancer cell lines in a three-dimensional collagen system. Over one week, we monitored structural changes in gels of varying collagen content using confocal reflection microscopy and quantitative image analysis, tracking metrics of fibril fraction, pore size, and fiber length and diameter. Gels that were seeded with no cells (control), LNCaP cells, and DU-145 cells were quantitatively compared. Gels with higher collagen content initially had smaller pore sizes and higher fibril fractions, as expected. However, over time, LNCaP- and DU-145-populated matrices showed different structural properties compared both to each other and to the control gels, with LNCaP cells appearing to favor microenvironments with lower collagen fiber fractions and larger pores than DU-145 cells. We posit that the DU-145 cells' preference for denser matrices is due to their higher invasiveness and proteolytic capabilities. Inhibition of matrix proteases resulted in reduced fibril fractions for high concentration gels seeded with either cell type, supporting our hypothesis. Our novel quantitative results probe the dynamics of gel remodeling in three dimensions and suggest that prostate cancer cells remodel their ECM in a synergistic manner that is dependent on both initial matrix properties as well as their invasiveness.     

Domains of the human androgen receptor and glucocorticoid receptor involved in binding to the nuclear matrix

Steroid receptors have been reported to bind to the nuclear matrix. The nuclear matrix is operationally defined as the residual nuclear structure that remains after extraction of most of the chromatin and all soluble and loosely bound componnets. To obtain insight in the molecular mechanism of the interaction of steroid receptors with the nuclear matrix, we studied the binding of several deletion mutants of the human androgen receptor (hAR) and the human glucocorticoid receptor (hGR) to the nuclear matrix. Receptor binding was tested for two different nuclear matrix preparations: complete matrices, in which most matrix proteins are retained during the isolation procedure, and depleted matrices, which consist of only a subset of these proteins. The results show that the C-terminal domain of the hAR binds tightly to both depleted and complete matrices. In addition, at least one other domain of the hAR binds to complete matrices but not to depleted matrices. In contrast to the hAR, the hGR binds only to complete matrices. For this interaction both the DNA-binding domain and the C-terminal domain of the hGR are required, whereas the N-terminal domain is not. We conclude that specific protein domains of the hAR and the hGR are involved in binding to the nuclear matrix. In addition, our results indicate that the hAR and the hGR are attached to the nuclear matrix through different molecular interactions.     

定量评估豢养长江江豚个体间的优势关系

2000年1—4月和2000年4月—2002年4月,分别连续3个月和2年观察了中国科学院水生生物研究所白鱀豚馆6头长江江豚（3雌3雄,8个不同组合群）个体间发生的3种交互关系,即接近—逃开、接近—接触和接近—尾鳍击打。在累计8,162min的观察时间内,共观察到这些交互关系1,685次。本研究将江豚个体间发生的这3种交互关系作为个体间优势关系的指示,并分别给交互双方赋予不同的分值,采用优势比分矩阵方法定量分析了江豚个体之间的优势关系。结果表明江豚群体内存在优势关系。同性别个体之间,优势关系与年龄和饲养时间有关,年龄大的个体比年龄小的个体具有优势,饲养时间短的个体比饲养时间长的个体具有优势。但是,异性成年个体之间,优势关系通常是可变的。     

A theory of natural selection incorporating interaction among individuals. IV. Use of related groups of inbred individuals

The present series of papers attempts to accommodate interaction among individuals in evolutionary theory. The interaction phenomenon is genetically characterized by two dimensions (direct and associate) of gene activity. For optimal selection results, a balance between the two dimensions must occur. In the first paper of the series, it was shown that random interactions resulted in an unbalanced selection response in that the direct, but not associate, effects were included in the expression for gene frequency change. The next three papers of the series (II, III and IV) were designed to determine whether or not selection with life-history models that involved non-random interactions would be useful in ameliorating the problem of selection balance.In the present study, two kinds of non-random gene association are analyzed jointly by restricting interactions to related individuals that are derived from inbred base populations. The analyses are generalized to accommodate heterogeneous as well as homogeneous groups of interacting individuals. The joint contributions of inbreeding and consanguinity to selection response are analysed by use of the nine gene-identity parameters devised by Harris.It is demonstrated that consanguinity alone or in conjunction with inbreeding does improve selection balance. However, inbreeding alone does not. Also, the influence of inbreeding is not dependent on group size, whereas the influence of consanguinity is conditioned by the size of the group. Thus, by introducing associate effects into the selection process, the use of related groups can provide the genetical bases for the evolution of social behavior phenomena such as altruism.     

Statistical comparison of proximity matrices: applications in animal behaviour

Animal behaviour studies often require the diagnosis and statistical evaluation of patterns among individuals of a group. However, association values derived for all pairs of individuals are mathematically interrelated and, hence, difficult to evaluate. A general method of matrix comparison, called the Mantel test, is described which accounts for such interdependencies. In this test, two square difference matrices are compared to determine whether a statistical association exists between corresponding elements. For example, distances in one of the matrices might represent differences in songs for each pair of a group of birds, while distances in the other matrix could be the geographic distances between each of the same bird pairs; the test would assess whether or not birds close to one another have songs that are more similar than those pairs that are located further apart geographically. Distances in the matrices can be of a variety of sorts (depending on the application), including for instance geographic distances, morphological differences, or behavioural differences. The test has wide applicability in studies of animal behaviour, and we present three examples. First, dialects of splendid sunbirds (Nectarinia coccinigaster) were investigated to determine whether local or regional patterns of geographic variation in song were present, and whether birds with similar dialects were concentrated within the same habitat. Second, dominance hierarchies of white-throated sparrows (Zonotrichia albicollis) and dark-eyed juncos (Junco hyemalis oreganus) were analysed by constructing appropriate hypothesis matrices that were contrasted against a matrix summarizing behavioural interrelationships of flock members. In the third application, involving progressions of yellow baboons (Papio cynocephalus), an approach was developed to assess whether members of a given sex occur adjacent (or at least closer) to one another in progression order more often than expected by chance, and also whether individuals of a given sex tend to be found at or near the end of a progression more frequently than predicted. Other possible applications of the Mantel test are discussed, and a detailed computational example is included.     

Matrix dimensions bias demographic inferences: implications for comparative plant demography

While the wealth of projection matrices in plant demography permits comparative studies, variation in matrix dimensions complicates interspecific comparisons. Collapsing matrices to a common dimension may facilitate such comparisons but may also bias the inferred demographic parameters. Here we examine how matrix dimension affects inferred demographic elasticities and how different collapsing criteria perform. We analyzed 13 x 13 matrices representing nine plant species, collapsing these matrices (i) into even 7 x 7, 5 x 5, 4 x 4, and 3 x 3 matrices and (ii) into 5 x 5 matrices using different criteria. Stasis and fecundity elasticities increased when matrix dimension was reduced, whereas those of progression and retrogression decreased. We suggest a collapsing criterion that minimizes dissimilarities between the original- and collapsed-matrix elasticities and apply it to 66 plant species to study how life span and growth form influence the relationship between matrix dimension and elasticities. Our analysis demonstrates that (i) projection matrix dimension has significant effects on inferred demographic parameters, (ii) there are better-performing methods than previously suggested for standardizing matrix dimension, and (iii) herbaceous perennial projection matrices are particularly sensitive to changes in matrix dimensionality. For comparative demographic studies, we recommend normalizing matrices to a common dimension by collapsing higher classes and leaving the first few classes unaltered.     

The donation game with roles played between relatives

We consider a social game with two choices, played between two relatives, where roles are assigned to individuals so that the interaction is asymmetric. Behaviour in each of the two roles is determined by a separate genetic locus. Such asymmetric interactions between relatives, in which individuals occupy different behavioural contexts, may occur in nature, for example between adult parents and juvenile offspring. The social game considered is known to be equivalent to a donation game with non-additive payoffs, and has previously been analysed for the single locus case, both for discrete and continuous strategy traits. We present an inclusive fitness analysis of the discrete trait game with roles and recover equilibrium conditions including fixation of selfish or altruistic behaviour under both behavioural contexts, or fixation of selfish behaviour under one context and altruistic behaviour under the other context. These equilibrium solutions assume that the payoff matrices under each behavioural context are identical. The equilibria possible do depend crucially, however, on the deviation from payoff additivity that occurs when both interacting individuals act altruistically.     

Estimates of heritability and correlations of morphometric traits in Clarkia (Onagraceae)

Summary Interspecific heritability values were estimated using parent-offspring regression analyses for 11 morphological traits differentiating Clarkia nitens and C. speciosa subsp. polyantha. Estimates ranged from near 0 for anther color and germination percentage, to 0.8 for calyx length and petal tip color. Phenotypic, genetic, and environmental correlation matrices were computed to determine the extent of interspecific correlations of traits. Cluster analyses of the genetic and environmental correlation matrices each resulted in three clusters of correlated traits; however, the clusters derived from the two matrices were different. The clusters produced by analysis of the environmental correlation matrix were similar to the factors obtained from principal component analysis of the phenotypic correlation matrix. Genetic correlations may result from strong linkage due to interspecific chromosomal differences.     

Essential role of the concentration of immobilized ligands in affinity chromatography:: Purification of guanidinobenzoatase on an ionized ligand

Guanidinobenzoatase, a plasma protein with possible application as a ‘tumor marker’, has been fully purified by one-step affinity chromatography. The affinity matrix was prepared by ‘controlled’ immobilization of an enzyme inhibitor (agmatine) onto commercial agarose gels containing carboxyl moieties activated as N-hydroxysuccinimide esters. In this way, agmatine becomes immobilized through an amido bond and preserves an ionized guanidino moiety. Different matrices with different concentration of ligands were prepared in order to evaluate their properties as affinity supports. Interestingly, matrices with a very low concentration of immobilized ligands (2 μmol/ml, corresponding to the modification of only 5% of active groups in the commercial resins) exhibited a low capacity for unspecific adsorption of proteins (as anion-exchange resins) and displayed also a high capacity for specific adsorption of our target protein. On the other hand, when affinity matrices possessed a moderate concentration of agmatine (10 μmol/ml of gel or higher), two undesirable phenomena were observed: (a) the matrix behaves as a very good anionic exchange support able to non-specifically adsorb most of plasma proteins and (b) the specific adsorption of our target protein becomes much lower. The latter phenomenon could be due to steric hindrances promoted by the interaction between each individual immobilized ligand and the corresponding binding pocket in the target protein. These hindrances could also be promoted by the presence of a fairly dense layer of immobilized ligands covering the support surface, thus preventing interactions between immobilized ligands and partially buried protein-binding pockets. In this way, a successful affinity purification (23.5% yield, ×220 purification factor, a unique electrophoretic band) could be achieved by combination of three approaches: (i) the use of affinity matrices possessing a very low density of immobilized ligands, (ii) performing affinity adsorption at high ionic strength and (iii) performing specific desorption with substrates or substrate analogues.     

New probability matrices for identification of Streptomyces

The character state data obtained for clusters defined in a previous phenetic classification were used to construct two probabilistic matrices for Streptomyces species. These superseded an original published identification matrix by exclusion of other genera and the inclusion of more Streptomyces species. Separate matrices were constructed for major and minor clusters. The minimum number of diagnostic characters for each matrix was selected by computer programs for determination of character separation indices (CHARSEP) and a selection of group diagnostic properties (DIACHAR). The resulting matrices consisted of 26 phena x 50 characters (major clusters) and 28 phena x 39 characters (minor clusters). Cluster overlap (OVERMAT program) was small in both matrices. Identification scores were used to evaluate both matrices. The theoretically best scores for the most typical example of each cluster (MOSTTYP program) were all satisfactory. Input of test data for randomly selected cluster representatives resulted in correct identification with high scores. The major cluster matrix was shown to be practically sound by its application to 35 unknown soil isolates, 77% of which were clearly identified. The minor cluster matrix provides tentative probabilistic identifications as the small number of strains in each cluster reduces its ability to withstand test variation. A diagnostic table for single-membered clusters, constructed using the CHARSEP and DIACHAR programs, was also produced.     

Elasticity analysis in epidemiology: an application to tick-borne infections

The application of projection matrices in population biology to plant and animal populations has a parallel in infectious disease ecology when next-generation matrices (NGMs) are used to characterize growth in numbers of infected hosts ( R ₀). The NGM is appropriate for multi-host pathogens, where each matrix element represents the number of cases of one type of host arising from a single infected individual of another type. For projection matrices, calculations of the sensitivity and elasticity of the population growth rate to changes in the matrix elements has generated insight into plant and animal populations. These same perturbation analyses can be used for infectious disease systems. To illustrate this in detail we parameterized an NGM for seven tick-borne zoonoses and compared them in terms of the contributions to R ₀ from three different routes of transmission between ticks, and between ticks and vertebrate hosts. The definition of host type may be the species of the host or the route of infection, or, as was the case for the set of tick-borne pathogens, a combination of species and the life stage at infection. This freedom means that there is a broad range of disease systems and questions for which the methodology is appropriate.     

MALDI/MS peptide mass fingerprinting for proteome analysis: identification of hydrophobic proteins attached to eucaryote keratinocyte cytoplasmic membrane using different matrices in concert

BACKGROUND: MALDI-TOF-MS has become an important analytical tool in the identification of proteins and evaluation of their role in biological processes. A typical protocol consists of sample purification, separation of proteins by 2D-PAGE, enzymatic digestion and identification of proteins by peptide mass fingerprint. Unfortunately, this approach is not appropriate for the identification of membrane or low or high pI proteins. An alternative technique uses 1D-PAGE, which results in a mixture of proteins in each gel band. The direct analysis of the proteolytic digestion of this mixture is often problematic because of poor peptide detection and consequent poor sequence coverage in databases. Sequence coverage can be improved through the combination of several matrices. RESULTS: The aim of this study was to trust the MALDI analysis of complex biological samples, in order to identify proteins that interact with the membrane network of keratinocytes. Peptides obtained from protein trypsin digestions may have either hydrophobic or hydrophilic sections, in which case, the direct analysis of such a mixture by MALDI does not allow desorbing of all peptides. In this work, MALDI/MS experiments were thus performed using four different matrices in concert. The data were analysed with three algorithms in order to test each of them. We observed that the use of at least two matrices in concert leads to a twofold increase of the coverage of each protein. Considering data obtained in this study, we recommend the use of HCCA in concert with the SA matrix in order to obtain a good coverage of hydrophilic proteins, and DHB in concert with the SA matrix to obtain a good coverage of hydrophobic proteins. CONCLUSION: In this work, experiments were performed directly on complex biological samples, in order to see systematic comparison between different matrices for real-life samples and to show a correlation that will be applicable to similar studies. When 1D gel is needed, each band may contain a great number of proteins, each present in small amounts. To improve the proteins coverage, we have performed experiments with some matrices in concert. These experiments enabled reliable identification of proteins, without the use of Nanospray MS/MS experiments.     

An analysis of G matrix variation in two closely related cricket species,Gryllus firmus and G. pennsylvanicus

An important issue in evolutionary biology is understanding the pattern of G matrix variation in natural populations. We estimated four G matrices based on the morphological traits of two cricket species, Gryllus firmus and G. pennsylvanicus, each reared in two environments. We used three matrix comparison approaches, including the Flury hierarchy, to improve our ability to perceive all aspects of matrix variation. Our results demonstrate that different methods perceive different aspects of the matrices, which suggests that, until more is known about these methods, future studies should use several different statistical approaches. We also found that the differences in G matrices within a species can be larger than the differences between species. We conclude that the expression of the genetic architecture can vary with the environment and that future studies should compare G matrices across several environments. We also conclude that G matrices can be conserved at the level of closely related species.     

Long-term patterns of agonistic interactions in a captive group of wolves (Canis lupus)

Agonistic interactions were recorded in a captive group of wolves (Canis lupus) for a period of 21 months. Seventy-five per cent of all interactions were accounted for by only 4 or less of a possible 28 pairs during any given period of the study. Several animals were involved in very few agonistic interactions, and in many relationships such interactions were absent. Patterns of agonistic interaction alone did not suggest social relationships or an overall social structure applicable to all group members, although some evidence of a dominance hierarchy was found. Patterns of agonistic interactions were shown to involve several independent dimensions in different relationships. Further details of an underlying social organization are likely to emerge only from long-term studies which examine several dimensions of, and the interrelations between, a wide range of social interactions.