The rank of data matrices in a spectrophotometric study of a ligand-biopolymer complex formation

The dependences of concentrations of ligand-linear polymer complex species vs. the concentration of free ligand were calculated. The analysis of the data suggests that the variance of the property studied considerably depends on the parameters of ligand-polymer complex formation (cooperativity and the average number of monomers occupied by the ligand). The rank of the matrix of concentration fractions of species was estimated using the singular value decomposition by the method of principal component analysis. As the cooperativity increases, the rank matrix decreases from 4 to 2. An increase in the average number of monomers occupied by the ligand at high cooperativity leads to an increase in the matrix rank from 2 to 3.     

Resolution of independently titrating spectral components in the ultraviolet circular dichroism of subtilisin enzymes by matrix rank analysis.

The ultraviolet circular dichroism of di-isopropylphophoryl-subtilisins Carlsberg and Novo (EC 3.4.21.14) has been examined as a function of pH. The CD of these enzymes below 260 nm is invariant over the pH interval 4 to 12, below or above which spectral changes occur suggesting a transition to a random coil form. Above pH 8 contributions due to the ionization of tyrosyl residues appear in the CD above 260 nm as bands shifted to longer wavelengths. Three independently titratable components, obtained by matrix rank analysis, account for the observed CD spectral changes above 260 nm of Dip-subtilisin Carlsberg in the pH interval 8 to 12. By contrast, two components were derived for the Novo enzyme. The identities of the matrix rank components were surmised from their apparent pKa values. One component of both subtilisin enzymes corresponds to the CD of the "buried" or irreversibly titratable tyrosyl residues of the enzyme. The other matrix rank components correspond to the CD of the "exposed" or freely ionizable tyrosyl residues. These residues are optically active only in the ionized state. Two types of "exposed" tyrosyl residues, arising because of differing sensitivity to the ionization of the "partially buried" or abnormally titrating tyrosyl residues, are evident in Dip-subtilisin Carlsberg. A pH-induced local conformational change in this enzyme is proposed to account for this behavior. The "partially buried" tyrosyl residues of both subtilisins appear to be devoid of optical activity in either the tyrosyl or tyrosylate form.     

Nestedness and niche‐based species loss in moorland plant communities

Communities in isolated habitat patches surrounded by inhospitable matrices often form a nested subset pattern. However, the underlying causal mechanisms and conservation implications of nestedness in regional communities remain controversial. The nested ranks of species in a nested species‐by‐site matrix may reflect a gradient of species vulnerability to extinction or of colonization ability. However, nestedness analysis has rarely been used to explore determinants of species rank; consequently, little is known of underpinning mechanisms. In this study, we examined nestedness in moorland plant communities widely interspersed within the subalpine zone of northern Japan. Moorland sites differed in area (1000–160 000 m²) and were naturally isolated from one another to various extents within an inhospitable forest matrix. We also determined whether site characteristics (physical and morphometric measures) and species characteristics (niche position and breadth, based on species’ traits) are related to nestedness. Moorland plant communities in the study area were significantly nested. The pH and moorland kernel density (proxy for spatial clustering of moorlands around the focal site) were the most important predictors of moorland site nested rank in a nestedness matrix. Niche breadths of species (measured as variation in leaf mass area and height) predicted species’ nested ranks. Selective environmental tolerances imposed by environmental harshness and selective extinction caused by declines in site carrying capacities probably account for the nested subset pattern in moorland plant communities. The nested rank of species in the nestedness matrix can therefore be translated into the potential order of species loss explainable by species niche breadths (based on variation in functional traits). Complementary understanding of the determinants of site ranking and species ranking in the nestedness matrix provides powerful insight into ecological processes underlying nestedness and into the ways by which communities are assembled or disassembled by such processes.     

Modification of the theory of dual radiation action for attenuated fields. II. Application to the analysis of soft X-ray results

A formalism developed in the first paper in this series, based on the generalized Theory of Dual Radiation Action, is applied to survival data for cells exposed to soft X rays. It is shown that, in contrast to previous published analyses, this formalism--modified to account for the attenuation of dose across the sensitive matrix of the cell--is fully consistent with the experimental results. The reasons for previous disagreements are discussed.     

Molecular Phylogeny of Microsporidians with Particular Reference to Species that Infect the Muscles of Fish

Ribosomal DNA from eight species of microsporidians infecting fish have been sequenced. Seven of these species infect the skeletal muscle of fish ( Pleistophora spp.) and one species infects migratory mesenchyma cells ( Glugea anomala ). These sequences, in addition to other available microsporidian rDNA sequences from a broad range of host taxa, have been used in phylogenetic analysis. This analysis revealed that muscle-infecting microsporidians from fish are a polyphyletic group, indicating that characters supposed to be important in the classification of the genus Pleistophora have to be re-evaluated. One character that probably has a polyphyletic origin is the amorphous coat, which has been extensively used in the definition of this genus. Furthermore, our results showed that the insect parasitizing Pleistophora spp. are not related to the true pleistophorans parasitic in skeletal muscle of fish. Phylogenetic analysis of small subunit rDNA sequences revealed disagreements between the molecular phylogeny and classifications based upon ultrastruclure. Many of the morphological characters claimed to be important in microsporidian classifications appeared to have arisen several times during evolution: for example, the diplokaryon and sporophorous vesicles.     

DALI and the persistence of protein shape

DALI is a popular resource for comparing protein structures. The software is based on distance‐matrix alignment. The associated web server provides tools to navigate, integrate and organize some data pushed out by genomics and structural genomics. The server has been running continuously for the past 25 years. Structural biologists routinely use DALI to compare a new structure against previously known protein structures. If significant similarities are discovered, it may indicate a distant homology, that is, that the structures are of shared origin. This may be significant in determining the molecular mechanisms, as these may remain very similar from a distant predecessor to the present day, for example, from the last common ancestor of humans and bacteria. Meta‐analysis of independent reference‐based evaluations of alignment accuracy and fold discrimination shows DALI at top rank in six out of 12 studies. The web server and standalone software are available from http://ekhidna2.biocenter.helsinki.fi/dali .     

Sensitivity, principal component and flux analysis applied to signal transduction: the case of epidermal growth factor mediated signaling

MOTIVATION: Novel high-throughput genomic and proteomic tools are allowing the integration of information from a range of biological assays into a single conceptual framework. This framework is often described as a network of biochemical reactions. We present strategies for the analysis of such networks. RESULTS: The direct differential method is described for the systematic evaluation of scaled sensitivity coefficients in reaction networks. Principal component analysis, based on an eigenvalue-eigenvector analysis of the scaled sensitivity coefficient matrix, is applied to rank individual reactions in the network based on their effect on system output. When combined with flux analysis, sensitivity analysis allows model reduction or simplification. Using epidermal growth factor (EGF) mediated signaling and trafficking as an example of signal transduction, we demonstrate that sensitivity analysis quantitatively reveals the dependence of dual-phosphorylated extracellular signal-regulated kinase (ERK) concentration on individual reaction rate constants. It predicts that EGF mediated reactions proceed primarily via an Shc-dependent pathway. Further, it suggests that receptor internalization and endosomal signaling are important features regulating signal output only at low EGF dosages and at later times.     

C et style: La chronologie de l’art pariétal à l’heure actuelle

The chronology of the Paleolithic art proposed by A. Leroi-Gourhan had a strong installation among the specialists until his death, in the years 1980s of the last century. After that the system SMA of direct dating began to be applied producing some disagreements and a supposed revolution against the chronological-stylistic procedure that has been overvalued. There are not so many disagreements and when they appear, they can tinge the French author's procedure and to improve it partly. If we take it with enough flexibility and aperture, it continues being a non perfect model, but useful and valid to organize the graphs of the Upper Paleolithic whose systematic should continue based on the material documentation, in the represented forms and in all the technical procedures that allow to specify and to improve our chronological arguments.     

Measuring Evolutionary Constraints Through the Dimensionality of the Phenotype: Adjusted Bootstrap Method to Estimate Rank of Phenotypic Covariance Matrices

The potential and direction of phenotypic evolution is constrained by the distribution of genetic variation for the traits as described by the phenotypic (P) and genetic covariance matrices (G). The rank of the covariance matrix reflects the number of independent variational dimensions of the phenotype. Covariance matrices with less than full rank indicate lack of variation in some directions of the phenotype space and thus are an indication of absolute evolutionary constraints. Because selection acts upon phenotypic variation, the rank of P represents the upper limit of the dimensionality in G, relevant for selection response. The limitations of current methods to estimate matrix rank motivated us to analyze and adjust a bootstrap method and evaluate its performance by simulation. The results show that the modified bootstrap method (ABRE) gives reliable and rather conservative rank estimates when the sample size is sufficient for the number of variables studied (the sample size is at least five-fold the number of variables). Applying the method to various datasets suggests high phenotypic dimensionality in all cases. The analysis thus provides no evidence for absolute evolutionary constraints. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Estimation in a multiplicative mixed model involving a genetic relationship matrix

Genetic models partitioning additive and non-additive genetic effects for populations tested in replicated multi-environment trials (METs) in a plant breeding program have recently been presented in the literature. For these data, the variance model involves the direct product of a large numerator relationship matrix A, and a complex structure for the genotype by environment interaction effects, generally of a factor analytic (FA) form. With MET data, we expect a high correlation in genotype rankings between environments, leading to non-positive definite covariance matrices. Estimation methods for reduced rank models have been derived for the FA formulation with independent genotypes, and we employ these estimation methods for the more complex case involving the numerator relationship matrix. We examine the performance of differing genetic models for MET data with an embedded pedigree structure, and consider the magnitude of the non-additive variance. The capacity of existing software packages to fit these complex models is largely due to the use of the sparse matrix methodology and the average information algorithm. Here, we present an extension to the standard formulation necessary for estimation with a factor analytic structure across multiple environments.     

Male rank and reproductive activity in Savanna baboons

Access to sexually receptive baboon females has been linked to male dominance rank. An intensive 19-month field study of mate choice and mate competition among savanna baboons was undertaken in order to elucidate those factors influencing mating success. During this study, male agonistic rank was not correlated with male mating success among adult males. However, the inclusion of adolescent males into the analysis yielded significant correlations between rank and mating success. Examination of prior fieldwork revealed that no baboon field study has conclusively demonstrated a significant correlation between male rank and reproduction among adult males. Most studies reporting a correlation between male rank and reproduction have included subadult males in the analysis. It is concluded that male rank is an unreliable predictor of male reproductive activity among adult male baboons. A low agonistic rank need not reduce male mating success because adult male baboons utilize a variety of reproductive tactics in gaining access to consort females.     

False Correlates of Nested Patterns: A Case Study Using Temporary Pond Microcrustaceans

Nestedness analysis is a popular tool for inferring spatial species distributions, and therefore has management and conservation relevance. Ecologists frequently compute nestedness and subsequently use Spearman rank correlations for inferring relationships between the observed nested ranks of sites with biogeographic and environmental variables. Using temporary pond microcrustaceans hatched from microcosms as a case study, this paper shows that the application of this method can be problematic. While the overall degree and significance of nestedness was robust against a statistical error, the results obtained from randomly generated matrices, in which community structure from the original microcrustacean incidence matrix was maintained (fixed rows –fixed columns constraints), showed that rank correlations of observed nested patterns can be vulnerable to a Type 1 error (detecting an effect when there is none). Using expected nestedness patterns derived from rarefied original matrices to control for sample size effects did not change this result. This problem may have arisen as a result of a quantitative bias related to the disproportionate impact of rank positions of individual ponds in the analysis. Future extensive simulations studies, involving different community structures, should help identify the general reliability of rank correlation results in nestedness analyses. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Estimating sampling error of evolutionary statistics based on genetic covariance matrices using maximum likelihood

We explore the estimation of uncertainty in evolutionary parameters using a recently devised approach for resampling entire additive genetic variance–covariance matrices ( G ). Large‐sample theory shows that maximum‐likelihood estimates (including restricted maximum likelihood, REML) asymptotically have a multivariate normal distribution, with covariance matrix derived from the inverse of the information matrix, and mean equal to the estimated G . This suggests that sampling estimates of G from this distribution can be used to assess the variability of estimates of G , and of functions of G . We refer to this as the REML‐MVN method. This has been implemented in the mixed‐model program WOMBAT. Estimates of sampling variances from REML‐MVN were compared to those from the parametric bootstrap and from a Bayesian Markov chain Monte Carlo (MCMC) approach (implemented in the R package MCMCglmm). We apply each approach to evolvability statistics previously estimated for a large, 20‐dimensional data set for Drosophila wings. REML‐MVN and MCMC sampling variances are close to those estimated with the parametric bootstrap. Both slightly underestimate the error in the best‐estimated aspects of the G matrix. REML analysis supports the previous conclusion that the G matrix for this population is full rank. REML‐MVN is computationally very efficient, making it an attractive alternative to both data resampling and MCMC approaches to assessing confidence in parameters of evolutionary interest.     

Surface proteome analysis identifies platelet derived growth factor receptor-alpha as a critical mediator of transforming growth factor-beta-induced collagen secretion

Fibroblasts are extracellular matrix-producing cells in the lung. Fibroblast activation by transforming growth factor-beta leads to myofibroblast-differentiation and increased extracellular matrix deposition, a hallmark of pulmonary fibrosis. While fibroblast function with respect to migration, invasion, and extracellular matrix deposition has been well-explored, little is known about the surface proteome of lung fibroblasts in general and its specific response to fibrogenic growth factors, in particular transforming growth factor-beta.We thus performed a cell-surface proteome analysis of primary human lung fibroblasts in presence/absence of transforming growth factor-beta, followed by characterization of our findings using FACS analysis, Western blot, and siRNA-mediated knockdown experiments.We identified 213 surface proteins significantly regulated by transforming growth factor-beta, platelet derived growth factor receptor-alpha being one of the top down-regulated proteins. Transforming growth factor beta-induced downregulation of platelet derived growth factor receptor-alpha induced upregulation of platelet derived growth factor receptor-beta expression and phosphorylation of Akt, a downstream target of platelet derived growth factor signaling. Importantly, collagen type V expression and secretion was strongly increased after forced knockdown of platelet derived growth factor receptor-alpha, an effect that was potentiated by transforming growth factor-beta. We therefore show previously underappreciated cross-talk of transforming growth factor-beta and platelet derived growth factor signaling in human lung fibroblasts, resulting in increased extracellular matrix deposition in a platelet derived growth factor receptor-alpha dependent manner. These findings are of particular importance for the treatment of lung fibrosis patients with high pulmonary transforming growth factor-beta activity.     

Inactive photosystem II centers: A resolution of discrepencies in photosystem II quantitation

The abundance of photosystem II in chloroplast thylakoid membranes has been a contentious issue because different techniques give quite different estimates of photosystem II titer. This discrepancy led in turn to disagreements regarding the stoichiometry of photosystem II to photosystem I in these membranes. We believe that the discrepancy in photosystem II quantitation is resolved by evidence which shows that a large population of photosystem II centers with negligible turnover rates are present in isolated thylakoid membranes as well as in normally developed leaves of healthy plants.     

Improved eigenanalysis of discrete subpopulations and admixture using the minimum average partial test

Principal components analysis of genetic data has benefited from advances in random matrix theory. The Tracy-Widom distribution has been identified as the limiting distribution of the lead eigenvalue, enabling formal hypothesis testing of population structure. Additionally, a phase change exists between small and large eigenvalues, such that population divergence below a threshold of F(ST) is impossible to detect and above which it is always detectable. I show that the plug-in estimate of the effective number of markers in the EIGENSOFT software often exceeds the rank of the sample covariance matrix, leading to a systematic overestimation of the number of significant principal components. I describe an alternative plug-in estimate that eliminates the problem. This improvement is not just an asymptotic result but is directly applicable to finite samples. The minimum average partial test, based on minimizing the average squared partial correlation between individuals, can detect population structure at smaller F(ST) values than the corrected test. The minimum average partial test is applicable to both unadmixed and admixed samples, with arbitrary numbers of discrete subpopulations or parental populations, respectively. Application of the minimum average partial test to the 11 HapMap Phase III samples, comprising 8 unadmixed samples and 3 admixed samples, revealed 13 significant principal components.     

Visualizing rank deficient models: a row equation geometry of rank deficient matrices and constrained-regression

Situations often arise in which the matrix of independent variables is not of full column rank. That is, there are one or more linear dependencies among the independent variables. This paper covers in detail the situation in which the rank is one less than full column rank and extends this coverage to include cases of even greater rank deficiency. The emphasis is on the row geometry of the solutions based on the normal equations. The author shows geometrically how constrained-regression/generalized-inverses work in this situation to provide a solution in the face of rank deficiency.     

Multivariate analysis of sexual dimorphism in two types of dermatoglyphic traits in five endogamous populations of West Bengal, India

Five different endogamous populations who encompass the main social rank in the caste hierarchy of West Bengal were analysed for this report. The present approach is to compare the pattern of sex differences/similarities exhibited by two different sets of dermatoglyphic traits. Cluster and discriminant analysis and Mantel test of matrix correlations were performed. The nature of variation between sexes within population groups and two types of variable sets has a good similarity in all five populations. These results strongly suggest that the two categories of dermatoglyphic variables provide similar possibilities to discriminate between the sexes in populations.     

Assignment of segments of the bacteriorhodopsin sequence to positions in the structural map.

Specific amino acid sequence segments have been assigned to locations in the structural map of bacteriorhodopsin using two-dimensional neutron diffraction data and a model building analysis. Models are constructed computationally by building specific regions of the amino acid sequence as alpha helices and then positioning the helices on axes indicated by the density map of Henderson and Unwin (Nature [Lond.]. 1975, 257:28-32). Neutron diffraction data were collected from samples of stacked, oriented "native" purple membranes as well as purple membranes containing different kinds of deuterated amino acids. Models differing in the assignments of helices to specific axes and in rotations of the helices about those axes were tested against the neutron data using a weighted residual factor to rank the models. This residual factor was calculated between observed and predicted intensity differences for pairs of data sets. Using this approach, a small set of related models has been found that predicts the observed intensity changes between five independent data sets. These models are inconsistent with the proposed locations of the retinal chromophore and the carboxyl terminus and with any of the previously proposed models for bacteriorhodopsin.