Shifts in rhizosphere microbial communities and enzyme activity of Poa alpina across an alpine chronosequence

This study quantifies the influence of Poa alpina on the soil microbial community in primary succession of alpine ecosystems, and whether these effects are controlled by the successional stage. Four successional sites representative of four stages of grassland development (initial, 4 years (non-vegetated); pioneer, 20 years; transition, 75 years; mature, 9500 years old) on the Rotmoos glacier foreland, Austria, were sampled. The size, composition and activity of the microbial community in the rhizosphere and bulk soil were characterized using the chloroform-fumigation extraction procedure, phospholipid fatty acid (PLFA) analysis and measurements of the enzymes beta-glucosidase, beta-xylosidase, N-acetyl-beta-glucosaminidase, leucine aminopeptidase, acid phosphatase and sulfatase. The interplay between the host plant and the successional stage was quantified using principal component (PCA) and multidimensional scaling analyses. Correlation analyses were applied to evaluate the relationship between soil factors (C-org, N-t, C/N ratio, pH, ammonium, phosphorus, potassium) and microbial properties in the bulk soil. In the pioneer stage microbial colonization of the rhizosphere of P. alpina was dependent on the reservoir of microbial species in the bulk soil. As a consequence, the rhizosphere and bulk soil were similar in microbial biomass (ninhydrin-reactive nitrogen (NHR-N)), community composition (PLFA), and enzyme activity. In the transition and mature grassland stage, more benign soil conditions stimulated microbial growth (NHR-N, total amount of PLFA, bacterial PLFA, Gram-positive bacteria, Gram-negative bacteria), and microbial diversity (Shannon index H) in the rhizosphere either directly or indirectly through enhanced carbon allocation. In the same period, the rhizosphere microflora shifted from a G(-) to a more G(+), and from a fungal to a more bacteria-dominated community. Rhizosphere beta-xylosidase, N-acetyl-beta-glucosaminidase, and sulfatase activity peaked in the mature grassland soil, whereas rhizosphere leucine aminopeptidase, beta-glucosidase, and phosphatase activity were highest in the transition stage, probably because of enhanced carbon and nutrient allocation into the rhizosphere due to better growth conditions. Soil organic matter appeared to be the most important driver of microbial colonization in the bulk soil. The decrease in soil pH and soil C/N ratio mediated the shifts in the soil microbial community composition (bacPLFA, bacPLFA/fungPLFA, G(-), G(+)/G(-)). The activities of beta-glucosidase, beta-xylosidase and phosphatase were related to soil ammonium and phosphorus, indicating that higher decomposition rates enhanced the nutrient availability in the bulk soil. We conclude that the major determinants of the microllora vary along the successional gradient: in the pioneer stage the rhizosphere microflora was primarily determined by the harsh soil environment; under more favourable environmental conditions, however, the host plant selected for a specific microbial community that was related to the dynamic interplay between soil properties and carbon supply. (C) 2004 Elsevier Ltd. All rights reserved.

Shifts in rhizosphere microbial communities and enzyme activity of Poa alpina across an alpine chronosequence

This study quantifies the influence of Poa alpina on the soil microbial community in primary succession of alpine ecosystems, and whether these effects are controlled by the successional stage. Four successional sites representative of four stages of grassland development (initial, 4 years (non-vegetated); pioneer, 20 years; transition, 75 years; mature, 9500 years old) on the Rotmoos glacier foreland, Austria, were sampled. The size, composition and activity of the microbial community in the rhizosphere and bulk soil were characterized using the chloroform-fumigation extraction procedure, phospholipid fatty acid (PLFA) analysis and measurements of the enzymes beta-glucosidase, beta-xylosidase, N-acetyl-beta-glucosaminidase, leucine aminopeptidase, acid phosphatase and sulfatase. The interplay between the host plant and the successional stage was quantified using principal component (PCA) and multidimensional scaling analyses. Correlation analyses were applied to evaluate the relationship between soil factors (C-org, N-t, C/N ratio, pH, ammonium, phosphorus, potassium) and microbial properties in the bulk soil. In the pioneer stage microbial colonization of the rhizosphere of P. alpina was dependent on the reservoir of microbial species in the bulk soil. As a consequence, the rhizosphere and bulk soil were similar in microbial biomass (ninhydrin-reactive nitrogen (NHR-N)), community composition (PLFA), and enzyme activity. In the transition and mature grassland stage, more benign soil conditions stimulated microbial growth (NHR-N, total amount of PLFA, bacterial PLFA, Gram-positive bacteria, Gram-negative bacteria), and microbial diversity (Shannon index H) in the rhizosphere either directly or indirectly through enhanced carbon allocation. In the same period, the rhizosphere microflora shifted from a G(-) to a more G(+), and from a fungal to a more bacteria-dominated community. Rhizosphere beta-xylosidase, N-acetyl-beta-glucosaminidase, and sulfatase activity peaked in the mature grassland soil, whereas rhizosphere leucine aminopeptidase, beta-glucosidase, and phosphatase activity were highest in the transition stage, probably because of enhanced carbon and nutrient allocation into the rhizosphere due to better growth conditions. Soil organic matter appeared to be the most important driver of microbial colonization in the bulk soil. The decrease in soil pH and soil C/N ratio mediated the shifts in the soil microbial community composition (bacPLFA, bacPLFA/fungPLFA, G(-), G(+)/G(-)). The activities of beta-glucosidase, beta-xylosidase and phosphatase were related to soil ammonium and phosphorus, indicating that higher decomposition rates enhanced the nutrient availability in the bulk soil. We conclude that the major determinants of the microllora vary along the successional gradient: in the pioneer stage the rhizosphere microflora was primarily determined by the harsh soil environment; under more favourable environmental conditions, however, the host plant selected for a specific microbial community that was related to the dynamic interplay between soil properties and carbon supply. (C) 2004 Elsevier Ltd. All rights reserved.

Multivariate relationships between groundwater chemistry and toxicity in an urban aquifer

Multivariate statistical methods were used to investigate file Causes of toxicity and controls on groundwater chemistry from 274 boreholes in an Urban area (London) of the United Kingdom. The groundwater was alkaline to neutral, and chemistry was dominated by calcium, sodium, and Sulfate. Contaminants included fuels, solvents, and organic compounds derived from landfill material. The presence of organic material in the aquifer caused decreases in dissolved oxygen, sulfate and nitrate concentrations. and increases in ferrous iron and ammoniacal nitrogen concentrations. Pearson correlations between toxicity results and the concentration of individual analytes indicated that concentrations of ammoinacal nitrogen, dissolved oxygen, ferrous iron, and hydrocarbons were important where present. However, principal component and regression analysis suggested no significant correlation between toxicity and chemistry over the whole area. Multidimensional Scaling was used to investigate differences in sites caused by historical use, landfill gas status, or position within the sample area. Significant differences were observed between sites with different historical land use and those with different gas status. Examination of the principal component matrix revealed that these differences are related to changes in the importance of reduced chemical species.

Virtual landmarking for locality aware peer IDs

In Peer-to-Peer (P2P) networks, it is often desirable to assign node IDs which preserve locality relationships in the underlying topology. Node locality can be embedded into node IDs by utilizing a one dimensional mapping by a Hilbert space filling curve on a vector of network distances from each node to a subset of reference landmark nodes within the network. However this approach is fundamentally limited because while robustness and accuracy might be expected to improve with the number of landmarks, the effectiveness of 1 dimensional Hilbert Curve mapping falls for the curse of dimensionality. This work proposes an approach to solve this issue using Landmark Multidimensional Scaling (LMDS) to reduce a large set of landmarks to a smaller set of virtual landmarks. This smaller set of landmarks has been postulated to represent the intrinsic dimensionality of the network space and therefore a space filling curve applied to these virtual landmarks is expected to produce a better mapping of the node ID space. The proposed approach, the Virtual Landmarks Hilbert Curve (VLHC), is particularly suitable for decentralised systems like P2P networks. In the experimental simulations the effectiveness of the methods is measured by means of the locality preservation derived from node IDs in terms of latency to nearest neighbours. A variety of realistic network topologies are simulated and this work provides strong evidence to suggest that VLHC performs better than either Hilbert Curves or LMDS use independently of each other.

Error, reproducibility and sensitivity: a pipeline for data processing of Agilent oligonucleotide expression arrays

Background: Expression microarrays are increasingly used to obtain large scale transcriptomic information on a wide range of biological samples. Nevertheless, there is still much debate on the best ways to process data, to design experiments and analyse the output. Furthermore, many of the more sophisticated mathematical approaches to data analysis in the literature remain inaccessible to much of the biological research community. In this study we examine ways of extracting and analysing a large data set obtained using the Agilent long oligonucleotide transcriptomics platform, applied to a set of human macrophage and dendritic cell samples. Results: We describe and validate a series of data extraction, transformation and normalisation steps which are implemented via a new R function. Analysis of replicate normalised reference data demonstrate that intrarray variability is small (only around 2 of the mean log signal), while interarray variability from replicate array measurements has a standard deviation (SD) of around 0.5 log(2) units (6 of mean). The common practise of working with ratios of Cy5/Cy3 signal offers little further improvement in terms of reducing error. Comparison to expression data obtained using Arabidopsis samples demonstrates that the large number of genes in each sample showing a low level of transcription reflect the real complexity of the cellular transcriptome. Multidimensional scaling is used to show that the processed data identifies an underlying structure which reflect some of the key biological variables which define the data set. This structure is robust, allowing reliable comparison of samples collected over a number of years and collected by a variety of operators. Conclusions: This study outlines a robust and easily implemented pipeline for extracting, transforming normalising and visualising transcriptomic array data from Agilent expression platform. The analysis is used to obtain quantitative estimates of the SD arising from experimental (non biological) intra- and interarray variability, and for a lower threshold for determining whether an individual gene is expressed. The study provides a reliable basis for further more extensive studies of the systems biology of eukaryotic cells.

Age and microenvironment outweigh genetic influence on the Zucker rat microbiome

Animal models are invaluable tools which allow us to investigate the microbiome-host dialogue. However, experimental design introduces biases in the data that we collect, also potentially leading to biased conclusions. With obesity at pandemic levels animal models of this disease have been developed; we investigated the role of experimental design on one such rodent model. We used 454 pyrosequencing to profile the faecal bacteria of obese (n = 6) and lean (homozygous n = 6; heterozygous n = 6) Zucker rats over a 10 week period, maintained in mixed-genotype cages, to further understand the relationships between the composition of the intestinal bacteria and age, obesity progression, genetic background and cage environment. Phylogenetic and taxon-based univariate and multivariate analyses (non-metric multidimensional scaling, principal component analysis) showed that age was the most significant source of variation in the composition of the faecal microbiota. Second to this, cage environment was found to clearly impact the composition of the faecal microbiota, with samples from animals from within the same cage showing high community structure concordance, but large differences seen between cages. Importantly, the genetically induced obese phenotype was not found to impact the faecal bacterial profiles. These findings demonstrate that the age and local environmental cage variables were driving the composition of the faecal bacteria and were more deterministically important than the host genotype. These findings have major implications for understanding the significance of functional metagenomic data in experimental studies and beg the question; what is being measured in animal experiments in which different strains are housed separately, nature or nurture?

Interpreters’ perception of linguistic and non linguistic factors affecting quality: a survey through the World Wide Web

This paper will present and discuss the results of an empirical study on perception of quality in interpretation carried out on a sample of 286 interpreters across five continents. Since the 1980’s the field of Interpreting Studies has been witnessing an ever growing interest in the issue of quality in interpretation both in academia and in professional circles, but research undertaken so far is surprisingly lacking in methodological rigour. This survey is an attempt to revise previous studies on interpreters’ perception of quality through the implementation of new Information Technology which allowed us to administer a traditional research tool such as a questionnaire, in a highly innovative way; i.e., through the World Wide Web. Using multidimensional scaling, a perceptual map based upon the results of the manner in which interpreters ranked a list of linguistic and nonlinguistic criteria according to their perception of importance in the interpretative process,was devised.

Evaluating perceptual separation in a pilot system for affective composition

Research evaluating perceptual responses to music has identified many structural features as correlates that might be incorporated in computer music systems for affectively charged algorithmic composition and/or expressive music performance. In order to investigate the possible integration of isolated musical features to such a system, a discrete feature known to correlate some with emotional responses – rhythmic density – was selected from a literature review and incorporated into a prototype system. This system produces variation in rhythm density via a transformative process. A stimulus set created using this system was then subjected to a perceptual evaluation. Pairwise comparisons were used to scale differences between 48 stimuli. Listener responses were analysed with Multidimensional scaling (MDS). The 2-Dimensional solution was then rotated to place the stimuli with the largest range of variation across the horizontal plane. Stimuli with variation in rhythmic density were placed further from the source material than stimuli that were generated by random permutation. This, combined with the striking similarity between the MDS scaling and that of the 2-dimensional emotional model used by some affective algorithmic composition systems, suggests that isolated musical feature manipulation can now be used to parametrically control affectively charged automated composition in a larger system.

An incremental space to visualize dynamic data sets

In Information Visualization, adding and removing data elements can strongly impact the underlying visual space. We have developed an inherently incremental technique (incBoard) that maintains a coherent disposition of elements from a dynamic multidimensional data set on a 2D grid as the set changes. Here, we introduce a novel layout that uses pairwise similarity from grid neighbors, as defined in incBoard, to reposition elements on the visual space, free from constraints imposed by the grid. The board continues to be updated and can be displayed alongside the new space. As similar items are placed together, while dissimilar neighbors are moved apart, it supports users in the identification of clusters and subsets of related elements. Densely populated areas identified in the incSpace can be efficiently explored with the corresponding incBoard visualization, which is not susceptible to occlusion. The solution remains inherently incremental and maintains a coherent disposition of elements, even for fully renewed sets. The algorithm considers relative positions for the initial placement of elements, and raw dissimilarity to fine tune the visualization. It has low computational cost, with complexity depending only on the size of the currently viewed subset, V. Thus, a data set of size N can be sequentially displayed in O(N) time, reaching O(N (2)) only if the complete set is simultaneously displayed.

Fast long-range connections in transportation networks

Multidimensional scaling is applied in order to visualize an analogue of the small-world effect implied by edges having different displacement velocities in transportation networks. Our findings are illustrated for two real-world systems, namely the London urban network (streets and underground) and the US highway network enhanced by some of the main US airlines routes. We also show that the travel time in these two networks is drastically changed by attacks targeting the edges with large displacement velocities. (C) 2011 Elsevier By. All rights reserved.

Data mining por meio de análise de redes, no contexto de filtro colaborativo

Tendo como motivação o desenvolvimento de uma representação gráfica de redes com grande número de vértices, útil para aplicações de filtro colaborativo, este trabalho propõe a utilização de superfícies de coesão sobre uma base temática multidimensionalmente escalonada. Para isso, utiliza uma combinação de escalonamento multidimensional clássico e análise de procrustes, em algoritmo iterativo que encaminha soluções parciais, depois combinadas numa solução global. Aplicado a um exemplo de transações de empréstimo de livros pela Biblioteca Karl A. Boedecker, o algoritmo proposto produz saídas interpretáveis e coerentes tematicamente, e apresenta um stress menor que a solução por escalonamento clássico.

Ant community richness and composition across a gradient from Eucalyptus plantations to secondary Atlantic Forest

As florestas secundárias e plantações de espécies exóticas estão se expandindo nas paisagens tropicais. No entanto, nossa compreensão sobre o valor destas florestas para a conservação da biodiversidade de invertebrados ainda é incipiente. Neste trabalho, usamos a fauna de formigas de serapilheira para avaliar a diversidade desses insetos entre três florestas de Eucalyptus, sendo uma comercial (quatro anos de idade) e duas abandonadas em diferentes idades de regeneração (16 e 31 anos) e uma área de Mata Atlântica secundária. A riqueza total foi mais alta na floresta secundária e nos plantios de Eucalyptus abandonados há mais tempo. A densidade de espécies na floresta secundária foi significativamente maior quando comparado as plantações de Eucalyptus, mas não difere entre eucaliptais; análise de ordenação revelou diferenças na composição de espécies entre as plantações de Eucalyptus com subbosque ausente e com subbosque desenvolvido ou em desenvolvimento. Ainda, foi constatada uma sobreposição acentuada entre amostras de serapilheira das florestas de eucaliptos abandonadas há mais tempo e a floresta secundária. em geral, plantações de eucalipto foram caracterizadas pela presença de espécies generalistas e de ampla distribuição. Nossos resultados indicam que embora o subbosque de plantações de eucaliptos com maior idade de regeneração suporte um conjunto relativamente alto de espécies generalistas de formigas, é improvável que eucaliptais conservem a maioria das espécies de florestas primárias, especialmente predadores especializados, Dacetini e espécies nômades.

Composição da fauna de formigas (Hymenoptera: Formicidae) de serapilheira em florestas semidecídua e de Eucalyptus spp., na região sudeste do Brasil

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Os efeitos da estrutura de habitat sobre as comunidades de aranhas em uma floresta de caatinga do nordeste brasileiro

The inherent complexity of natural communities is a challenge to our understanding about how the habitat influences the abundance, local distribution and species diversity. The habitat can influence community structure in multiple ways and elucidate these relationships has provoked a lot of debate in ecology. The habitat heterogeneity hypothesis states that an increase in habitat heterogeneity (number of habitats) leads to an increase in species diversity in the landscape due to an expansion in niche dimensions. This study aims to identify whether this hypothesis is valid for the spiders that inhabit a locality in the Caatinga of northeastern Brazil. Cursorial and arboreal spiders were sampled in 30 plots within an area of Caatinga together with measures of environmental complexity, habitat heterogeneity and environmental parameters related to multiple aspects of vegetation architecture and species composition of woody plants. Stepwise multiple regressions were used to define which local environmental parameters best explain the variation in arboreal and cursorial spiders richness. Then a NMDS (Nonmetric multidimensional scaling) was used to reduce the number of predictive variables to those who are the most important and best represent the variation in spiders richness associated with the environment they were sampled. The results show a clear segregation between the guilds of arboreal and cursorial spiders, both related to what kind of environmental variables best explain its variation as well as in relation to what part of the vegetation they occupy

Representação social do ensinar: a dimensão pedagógica do habitus professoral

Teaching is an activity inherent to the human condition. Historically, from the institutionalization of education, the key role to pursue that activity has been attributed to the teacher, who is required to adapt to the demands of each historical conjuncture. Currently, according to the new paradigmatic requirements, the teacher must possess various skills in order to handle the complex and challenging act of teaching. Assuming the existence of a gap between what the State and the scientific discourse recommend the teacher act upon in the classroom, a decision was made to identify the configuration and structure of social representation in the act of teaching, put forth by elementary school teachers in the public schools of Natal, RN, Brazil. Therefore, the research relied on the theoretical model developed by Domingos Sobrinho (1998, 2000, 2003), which articulates the praxeology of Pierre Bourdieu with the theory of social representations of Serge Moscovici (1978). It was intended to demonstrate how teachers habitus, in its due historical context, directs the construction of social representations in the act of teaching which guides the actions of the teacher, particularly in the classroom context. At the methodological level, the following methods and techniques were used: bibliographic and documentary review in order to identify the scientific discourse on the subject matter and the official parameters of educational regulation and the act of teaching; the Procedure of Multiple Classifications PMC in order to capture the configuration and structure of the representational content in focus, the direct observation of the classroom to identify in actual terms the social representation as "guide to action" as the theory preaches. From the standpoint of the analysis, quantitative data were analysed through Multidimensional Scaling MDS, covering in this study the Multidimensional Scale Analysis MSA and Smallest Space Analysis SSA; and non-parametric statiscal techniques. Additional data of qualitative value had to undergo categorical content analysis. It was then concluded that the teachers investigated guided themselves by social representation, the product of collectively constructed and shared assumptions about the act of teaching, forming a synthesis of different sources of information and knowledge acquirement, involving elements of common sense, religious habitus, pedagogic models considered outdated, the agencies responsible for teacher training and the hegemonic discourse about education today