On resemblance measures for ecological studies, including taxonomic dissimilarities and a zero-adjusted Bray-Curtis coefficient for denuded assemblages

Bray-Curtis similarity is widely employed in multivariate analysis of assemblage data, for sound biological reasons. This paper discusses two problems, however, with its practical application: its behaviour is erratic (or even undefined) for the vanishingly sparse samples that may be found as an end-point to a severe impact gradient, or a start-point in colonisation studies; and, in common with all similarity measures on species-level data, it is sensitive to inconsistency of taxonomic identification through time. It is shown that the latter problem is ameliorated by application of ‘taxonomic dissimilarity’ coefficients, a natural extension of the concept of taxonomic distinctness indices. Two previous suggestions for use with presence/absence data, denoted here by Γ⁺ and Θ⁺, are noted to be simple generalisations of the Bray-Curtis and Kulczynski measures, respectively. Also seen is their ability to permit ordinations of assemblages from wide geographic scales, with no species in common, and for which Bray-Curtis would return zero similarity for all pairs of samples.The primary problem addressed, however, is that of denuded or entirely blank samples. Where it can be convincingly argued that impoverished samples are near-blank from the same cause, rather than by random occurrences from inadequate sample sizes (tow length, core diameter, transect or quadrat size etc.), a simple adjustment to the form of the Bray-Curtis coefficient can generate meaningful MDS displays which would otherwise collapse, and can improve values of the ANOSIM R statistic (increased separation of groups in multivariate space). It is also shown to have no effect at all on the normal functioning of a Bray-Curtis analysis when at least a modest amount of data is present for all samples.Examination of the properties of this ‘zero-adjusted’ Bray-Curtis measure goes hand-in-hand with a wider discussion of the efficacy of competing similarity, distance or dissimilarity coefficients (collectively: resemblance measures) in community ecology. The inherent biological guidelines underlying the ‘Bray-Curtis family’ of measures (including Kulczynski, Sorenson, Ochiai and Canberra dissimilarity) are made explicit. These and other commonly employed measures (e.g. Euclidean, Manhattan, Gower and chi-squared distances) are calculated for several ‘classic’ data sets of impact events or gradients in space and time. Behaviour of particular coefficients is judged against the interpretability of the resulting ordination plots and an objective measure of the ability to discriminate between a priori defined hypotheses, representing impact conditions. A second-stage MDS plot of a set of resemblance coefficients, based on the respective similarities of the multivariate patterns each generates (an MDS of MDS plots, in effect), is seen to be useful in determining which coefficients are extracting essentially different information from the same assemblage matrix. This suggests a mechanism for practical classification of the plethora of resemblance measures defined in the literature. Similarity-based ANOSIM R statistics and Spearman ρ correlations, whose non-parametric structure make them absolutely comparable across different resemblance measures, answer questions about whether the different information extracted by some coefficients is more, or less, helpful to the final biological interpretation.     

Structural characteristics of hydration sites in lysozyme

A new method is presented for determining the hydration site of proteins, where the effect of structural fluctuations in both protein and hydration water is explicitly considered by using molecular dynamics simulation (MDS). The whole hydration sites (HS) of lysozyme are composed of 195 single HSs and 38 clustered ones (CHS), and divided into 231 external HSs (EHS) and 2 internal ones (IHS). The largest CHSs, ‘Hg’ and ‘Lβ’, are the IHSs having 2.54 and 1.35 mean internal hydration waters respectively. The largest EHS, ‘Clft’, is located in the cleft region. The real hydration structure of a CHS is an ensemble of multiple structures. The transition between two structures occurs through recombinations of some H-bonds. The number of the experimental X-ray crystal waters is nearly the same as that of the estimated MDS hydration waters for 70% of the HSs, but significantly different for the rest of HSs.     

Alternate Binding Modes for a Ubiquitin-SH3 Domain Interaction Studied by NMR Spectroscopy

Surfaces of many binding domains are plastic, enabling them to interact with multiple targets. An understanding of how they bind and recognize their partners is therefore predicated on characterizing such dynamic interfaces. Yet, these interfaces are difficult to study by standard biophysical techniques that often ‘freeze’ out conformations or that produce data averaged over an ensemble of conformers. In this study, we used NMR spectroscopy to study the interaction between the C-terminal SH3 domain of CIN85 and ubiquitin that involves the ‘classical’ binding sites of these proteins. Notably, chemical shift titration data of one target with another and relaxation dispersion data that report on millisecond time scale exchange processes are both well fit to a simple binding model in which free protein is in equilibrium with a single bound conformation. However, dissociation constants and chemical shift differences between free and bound states measured from both classes of experiment are in disagreement. It is shown that the data can be reconciled by considering three-state binding models involving two distinct bound conformations. By combining titration and dispersion data, kinetic and thermodynamic parameters of the three-state binding reaction are obtained along with chemical shifts for each state. A picture emerges in which one bound conformer has increased entropy and enthalpy relative to the second and chemical shifts similar to that of the free state, suggesting a less packed interface. This study provides an example of the interplay between entropy and enthalpy to fine-tune molecular interactions involving the same binding surfaces.     

Structure in plant–animal interaction assemblages

We present a comprehensive approach to detect pattern in assemblages of plant and animal species linked by interactions such as pollination, frugivory or herbivory. Simple structural models produce gradient, compartmented or nested patterns of interaction; intermediate patterns between a gradient and compartments are possible, and nesting within compartments produces a combined model. Interaction patterns can be visualized and analyzed either as matrices, as bipartite networks or as multivariate sets through correspondence analysis. We argue that differences among patterns represent outcomes of distinct evolutionary and ecological processes in these highly diversified assemblages. Instead of choosing one model a priori, assemblages should be probed for a suite of patterns. A plant–pollinator assemblage exemplifies a simple nested pattern, whereas a plant–herbivore assemblage illustrates a compound pattern with nested structures within compartments. Compartmentation should reflect coevolutionary histories and constraints, whereas differences in species abundance or dispersal may generate nestedness.     

Patterns of univariate and multivariate plasticity to elevated carbon dioxide in six European populations of Arabidopsis thaliana

The impact of elevated carbon dioxide on plants is a growing concern in evolutionary ecology and global change biology. Characterizing patterns of phenotypic integration and multivariate plasticity to elevated carbon dioxide can provide insights into ecological and evolutionary dynamics in future human‐altered environments. Here, we examined univariate and multivariate responses to carbon enrichment in six functional traits among six European accessions of Arabidopsis thaliana. We detected phenotypic plasticity in both univariate and multivariate phenotypes, but did not find significant variation in plasticity (genotype by environment interactions) within or among accessions. Eigenvector, eigenvalue variance, and common principal components analyses showed that elevated carbon dioxide altered patterns of trait covariance, reduced the strength of phenotypic integration, and decreased population‐level differentiation in the multivariate phenotype. Our data suggest that future carbon dioxide conditions may influence evolutionary dynamics in natural populations of A. thaliana.     

MENT: Methylation and expression database of normal and tumor tissues

Integrated analysis of DNA methylation and gene expression can reveal specific epigenetic patterns that are important during carcinogenesis. We built an integrated database of DNA methylation and gene expression termed MENT (Methylation and Expression database of Normal and Tumor tissues) to provide researchers information on both DNA methylation and gene expression in diverse cancers. It contains integrated data of DNA methylation, gene expression, correlation of DNA methylation and gene expression in paired samples, and clinicopathological conditions gathered from the GEO (Gene Expression Omnibus) and TCGA (The Cancer Genome Atlas). A user-friendly interface allows users to search for differential DNA methylation by either ‘gene search’ or ‘dataset search’. The ‘gene search’ returns which conditions are differentially methylated in a gene of interest, while ‘dataset search’ returns which genes are differentially methylated in a condition of interest based on filtering options such as direction, DM (differential methylation value), and p-value. MENT is the first database which provides both DNA methylation and gene expression information in diverse normal and tumor tissues. Its user-friendly interface allows users to easily search and view both DNA methylation and gene expression patterns. MENT is freely available at http://mgrc.kribb.re.kr:8080/MENT/.     

Organization of macroalgal assemblages in the Northeast Pacific: the assumption of homogeneity and the illusion of generality

Evidence for the geographic generality of the causes of intertidal zonation and the indirect effects of a keystone predator, the sea otter, on subtidal kelp assemblages was examined. Most research on intertidal algal assemblages has been done at a few protected sites where zonation is distinct. Surveys of wave-exposed intertidal sites in central and northern California show that assemblage structure is highly variable. This indicates that our present understanding of assemblage organization, including the effects of mussel-algal interactions, may not be widely applicable. Surveys of kelp forest habitat along the entire coast of California suggest that deforestation by sea urchins is uncommon in the absence of sea otters. These examples indicate that the generality of commonly accepted causes of algal assemblage structure in the Northeast Pacific may be an illusion based on assumptions of environmental homogeneity.     

Comparing strategies to preserve evolutionary diversity

The likely future extinction of various species will result in a decline of two quantities: species richness and phylogenetic diversity (PD, or ‘evolutionary history’). Under a simple stochastic model of extinction, we can estimate the expected loss of these quantities under two conservation strategies: An ‘egalitarian’ approach, which reduces the extinction risk of all species, and a ‘targeted’ approach that concentrates conservation effort on the most endangered taxa. For two such strategies that are constrained to experience the same expected loss of species richness, we ask which strategy results in a greater expected loss of PD. Using mathematical analysis and simulation, we describe how the strategy (egalitarian versus targeted) that minimizes the expected loss of PD depends on the distribution of endangered status across the tips of the tree, and the interaction of this status with the branch lengths. For a particular data set consisting of a phylogenetic tree of 62 lemur species, with extinction risks estimated from the IUCN ‘Red List’, we show that both strategies are virtually equivalent, though randomizing these extinction risks across the tip taxa can cause either strategy to outperform the other. In the second part of the paper, we describe an algorithm to determine how extreme the loss of PD for a given decline in species richness can be. We illustrate the use of this algorithm on the lemur tree.     

Successively-responsive drug-carrier vesicles assembled by 'supramolecular amphiphiles'

Novel vesicles assembled by ‘supramolecular amphiphiles’ based on the inclusion complexes between 1 and β-CDs (β-CD and HP-β-CD) were found to carry drugs and be successively-responsive to external stimuli for the first time. These vesicles were observed by TEM and SEM and confirmed by DLS. The formation patterns of ‘supramolecular amphiphiles’ characterized by UV and NMR can be controlled by choosing different hosts. Unlike traditional drug delivery and releasing systems, the ‘useless’ inclusion complexes 1·β-CDs in thinking formula can assemble into vesicles to carry both cytotoxic 1 and drugs (piroxicam and ampicillin) at one time, confirmed by TEM, UV, and NMR data. Also the vesicles assembled by 1·β-CDs can be successively-responsive to acidifying and oxidizing, and release drugs and cytotoxic compounds in order.     

Composition and spatio temporal variability of the epiphytic macroalgal assemblage of Fucus vesiculosus Linnaeus at Clare Island, Mayo, western Ireland

The composition and the patterns of spatial and temporal variability of the epiphytic assemblages of Fucus vesiculosus of Clare Island, on the western coast of Ireland, were investigated for an annual cycle. Specimens of Fucus were collected on seven sampling dates from three sites of the island (Portlea, Kinnacorra and Portnakilly). Data of cover of the most common epiphytic species were collected and analysed by multivariate and univariate techniques. Elachista fucicola, Polysiphonia lanosa, Porphyra umbilicalis, Spongonema tomentosum and Ulva compressa were the most common species. Spatial and temporal variation was detected both for the whole assemblage and for the most abundant species. In general, the assemblage was quantitatively more abundant and diverse in spring-summer than in autumn-winter. In spring-summer, there was a clear differentiation among the assemblage of Portnakilly and the assemblages of the other two sites. Individual species were also generally more abundant in spring-summer and their distribution at the three sites was often not consistent in time; P. lanosa was the only epiphyte for which a consistent effect of site was found. Spatial variation on a scale of meters to tens of meters was the most striking pattern of distribution of the epiphytic assemblage; significant effects related to this spatial scale were detected both for the whole assemblage and for individual species. Phenological patterns of the epiphytic species determining availability of propagules and limited dispersal, leading to aggregated patterns of distribution, are considered the main factors responsible of such patchiness. The importance of the incorporation of small spatial scales in sampling designs analysing the distributional patterns of epiphytic assemblages is discussed.     

The effects of social context on the hormonal and behavioral responsiveness of human fathers

We tested first-time fathers with their 22-month old toddlers to determine whether social context variables such as pre-test absence from the child and presence of the mother affected physiological measures associated with paternal responsiveness. Heart rate and blood pressure readings as well as blood samples to determine prolactin, testosterone and cortisol levels were taken before and after the 30-min father–toddler interactions. Fathers were tested on a day when they were away from their child for several hours before testing (‘without-child’ day) and on another day where they remained with their child throughout the day (‘with-child’ day). Most measures decreased over the 30-min test period but relative decreases were context-dependent. Men maintained higher prolactin levels when they were away from their children longer before testing on the ‘without-child’ day. Cortisol levels decreased during both tests and they decreased more on the ‘with-child’ day for men who had spent more time alone with their toddler before the test. Heart-rate and diastolic (but not systolic) blood pressure decreased more on the ‘with-child’ day than on the ‘without-child’ day. Fathers' testosterone levels decreased when their partners were less involved in the interactions. Compared to men with high responsiveness ratings on both days, men whose responsiveness increased after being away from their child on the ‘without-child’ day maintained higher systolic blood pressure and had a greater decrease in testosterone levels. We conclude that context may be more important in determining fathers' physiological responses to child contact than has previously been appreciated, particularly for some individuals.     

Quantifying assemblage distinctness with time: an example using temperate epibenthos

Artificial substrata are an often-used tool in assessing community development; here we quantify the changing presence of functional groups of benthos with replicate, depth, site, and time in order to explain differences in the structure of the surrounding mature communities. We placed replicate, machined slate panels (15×15×1 cm) in the intertidal, 6 and 12 m at two sites of differing flow rates at Lough Hyne, SW Ireland. They were placed at the same time of year and removed after 2, 6, 12, and 24 months from 1999 to 2001, to compare with a similar experiment run from 1997 to 1999. Furthermore, to examine trends of local assemblages older than 24 months, we examined boulders from each depth/site combination. Percentage cover of 13 functional groups, selected in relation to their competitive abilities, was measured using point intercept analysis of high-resolution digital images of the panels. These data were then quantified using our derived measure of distinctness. Replicates became more similar, and sites and depths both became more distinct with time from 2 to 24 months, although there was less distinctness at the high flow site throughout all stages of the study. Principal components analysis (PCA) of data suggested that all site/depth panel combinations only became truly distinct at the 24-month stage of the study. From 2 to 24 months, ‘good’ competitors increased in space, ‘intermediate’ competitors peaked after ≈12 months, and ‘poor’ competitors reduced in their space occupation with increasing time. Both in similarity and space occupation of functional groups, the 1997-1999 and 1999-2001 data showed high levels of pattern convergence. That there was little difference between assemblages at 12 and 24 months validated our upper time limit of period of study, but at 24 months, assemblages still differed from natural substrata and we suggest that many years would have been necessary to eliminate this difference.     

The neural basis of colour vision in the butterfly, Heliconius erato

Single unit recordings from visual interneurons in the protocerbrum of the neotropical butterfly Heliconius erato, revealed a variety of fibre types with wavelength specific patterns of activity. These ‘colour fibres’ were divided into four broad categories based upon the nature of their response to a flash of monochromatic light: (1) ‘simple’ colour fibres, which respond with excitation, when the eye is stimulated with some specific, narrow portion of the visible spectrum; (2) ‘on-off’ fibres, which produce ‘on’ bursts in response to certain portions of the spectrum, and ‘off’ effects when stimulated with other wavelengths; (3) ‘variable latency’ units which demonstrate dramatic shifts in latency, with comparatively small changes in the stimulating wavelength; and (4) ‘red-blue movement’ units which demonstrate bursts of activity when stimulated with flashes of red or blue light, and also serve as a non-directional movement detector. The wide variety of colour fibres appears to be correlated with the great behavioural significance of colour to this species.     

Study of the inclusion of the (R)- and (S)-camphor enantiomers in α-cyclodextrin by X-ray crystallography and molecular dynamics

The inclusion of (R)- and (S)-camphor compounds in α-cyclodextrin has been studied by X-ray crystallography. The crystal structures of the complexes reveal that one guest molecule is accommodated inside the cavity formed by a head-to-head cyclodextrin dimer. In the crystal lattice, the dimers form layers which are successively shifted by half a dimer. In both (R)- and (S)-cases, the camphor molecule exhibits disorder and occupies three major sites with orientations that can be described as either ‘polar’ or ‘equatorial’. Molecular dynamics simulations performed for the observed complexes indicate that although the carbonyl oxygen of both (R)- and (S)-camphor switches between different hydrogen bonding partners, it maintains the observed mode of ‘polar’ or ‘equatorial’ alignment.     

Phenology and seed setting success of snowbed plant species in contrasting snowmelt regimes in the Central Pyrenees

Plant growth and performance in snowbed communities are strongly influenced by the length of the growing period remaining after the snowmelt date. Under the scenario of climate change, studying the phenological responses of snowbed species to variations in snowmelt date might be crucial to understand their ability to adapt and survive under changing conditions. We studied 13 plant species from contrasting biological and ecological groups (i.e. ‘snowbed specialists’, ‘preferential species’ and ‘generalist species’) growing in four snowbed plots with siliceous substrates in the Central Pyrenees. These species were monitored for two consecutive years and in two different microsites, namely the central part and the peripheral part of each snowbed plot. We characterised their phenological cycle and length and their success in seed setting, measured as the number of individuals succeeding in dispersing their seeds.     

Kinetics of the Multistep Rupture of Fibrin ‘A-a’ Polymerization Interactions Measured Using Atomic Force Microscopy

Fibrin, the structural scaffold of blood clots, spontaneously polymerizes through the formation of ‘A-a’ knob-hole bonds. When subjected to external force, the dissociation of this bond is accompanied by two to four abrupt changes in molecular dimension observable as rupture events in a force curve. Herein, the configuration, molecular extension, and kinetic parameters of each rupture event are examined. The increases in contour length indicate that the D region of fibrinogen can lengthen by ∼50% of the length of a fibrin monomer before rupture of the ‘A-a’ interaction. The dependence of the dissociation rate on applied force was obtained using probability distributions of rupture forces collected at different pull-off velocities. These distributions were fit using a model in which the effects of the shape of the binding potential are used to quantify the kinetic parameters of forced dissociation. We found that the weak initial rupture (i.e., event 1) was not well approximated by these models. The ruptured bonds comprising the strongest ruptures, events 2 and 3, had kinetic parameters similar to those commonly found for the mechanical unfolding of globular proteins. The bonds ruptured in event 4 were well described by these analyses, but were more loosely bound than the bonds in events 2 and 3. We propose that the first event represents the rupture of an unknown interaction parallel to the ‘A-a’ bond, events 2 and 3 represent unfolding of structures in the D region of fibrinogen, and event 4 is the rupture of the ‘A-a’ knob-hole bond weakened by prior structural unfolding. Comparison of the activation energy obtained via force spectroscopy measurements with the thermodynamic free energy of ‘A-a’ bond dissociation indicates that the ‘A-a’ bond may be more resistant to rupture by applied force than to rupture by thermal dissociation.     

Mapping of protein-protein interaction sites by the 'absence of interference' approach

Protein-protein interactions are critical to most biological processes, and locating protein-protein interfaces on protein structures is an important task in molecular biology. We developed a new experimental strategy called the ‘absence of interference’ approach to determine surface residues involved in protein-protein interaction of established yeast two-hybrid pairs of interacting proteins. One of the proteins is subjected to high-level randomization by error-prone PCR. The resulting library is selected by yeast two-hybrid system for interacting clones that are isolated and sequenced. The interaction region can be identified by an absence or depletion of mutations. For data analysis and presentation, we developed a Web interface that analyzes the mutational spectrum and displays the mutational frequency on the surface of the structure (or a structural model) of the randomized protein†. Additionally, this interface might be of use for the display of mutational distributions determined by other types of random mutagenesis experiments. We applied the approach to map the interface of the catalytic domain of the DNA methyltransferase Dnmt3a with its regulatory factor Dnmt3L. Dnmt3a was randomized with high mutational load. A total of 76 interacting clones were isolated and sequenced, and 648 mutations were identified. The mutational pattern allowed to identify a unique interaction region on the surface of Dnmt3a, which comprises about 500-600 Å². The results were confirmed by site-directed mutagenesis and structural analysis. The absence-of-interference approach will allow high-throughput mapping of protein interaction sites suitable for functional studies and protein docking.     

Levene tests of homogeneity of variance for general block and treatment designs

This article develops a weighted least squares version of Levene's test of homogeneity of variance for a general design, available both for univariate and multivariate situations. When the design is balanced, the univariate and two common multivariate test statistics turn out to be proportional to the corresponding ordinary least squares test statistics obtained from an analysis of variance of the absolute values of the standardized mean-based residuals from the original analysis of the data. The constant of proportionality is simply a design-dependent multiplier (which does not necessarily tend to unity). Explicit results are presented for randomized block and Latin square designs and are illustrated for factorial treatment designs and split-plot experiments. The distribution of the univariate test statistic is close to a standard F-distribution, although it can be slightly underdispersed. For a complex design, the test assesses homogeneity of variance across blocks, treatments, or treatment factors and offers an objective interpretation of residual plots.     

Patterns of spatial and temporal variation of macrofauna under boulders in a sheltered boulder field

Abstract Spatial and temporal patterns of abundance of animals and plants must be quantified before models to explain distributions can be developed. These patterns also provide essential data for measuring potential effects of environmental disturbances. Studies in many different habitats have shown that most organisms, particularly invertebrates, have highly variable and interactive patterns of abundance, with much variability at the smallest temporal and spatial scales. Intertidal boulder fields in New South Wales, Australia, support a diverse fauna, many species of which are relatively rare. These habitats are commonly found near rock‐platforms and in sheltered estuaries and are subjected to many human disturbances. Although there have been a few studies on the fauna in boulder fields, none has documented variability of the assemblage using multivariate and univariate techniques and most studies have not incorporated different spatial and temporal scales. This study quantifies spatial variation at three scales (metres, tens of metres alongshore and tens of metres upshore) and temporal variation at two scales (3 months and 2 years) of the assemblage of molluscs and echinoderms in a sheltered boulder field subjected to little natural or human disturbance. Multivariate analyses revealed that each site contained a distinct assemblage, mainly due to the relative abundances of a few species. Most species, those generally only found under boulders and common, widespread species, had considerable spatial variability in abundances, with more than 90% measured at the smallest scale, that is metre to metre within a site. Changes in abundances over 3 months or 2 years varied among species and sites in unpredictable ways. These data show that sampling designs to measure impacts on these fauna will need to be complex and must incorporate a number of spatial and temporal scales if they are to be able to detect impact against such a variable background.     

Multivariate Dimensionality Reduction Approaches to Identify Gene-Gene and Gene-Environment Interactions Underlying Multiple Complex Traits

The elusive but ubiquitous multifactor interactions represent a stumbling block that urgently needs to be removed in searching for determinants involved in human complex diseases. The dimensionality reduction approaches are a promising tool for this task. Many complex diseases exhibit composite syndromes required to be measured in a cluster of clinical traits with varying correlations and/or are inherently longitudinal in nature (changing over time and measured dynamically at multiple time points). A multivariate approach for detecting interactions is thus greatly needed on the purposes of handling a multifaceted phenotype and longitudinal data, as well as improving statistical power for multiple significance testing via a two-stage testing procedure that involves a multivariate analysis for grouped phenotypes followed by univariate analysis for the phenotypes in the significant group(s). In this article, we propose a multivariate extension of generalized multifactor dimensionality reduction (GMDR) based on multivariate generalized linear, multivariate quasi-likelihood and generalized estimating equations models. Simulations and real data analysis for the cohort from the Study of Addiction: Genetics and Environment are performed to investigate the properties and performance of the proposed method, as compared with the univariate method. The results suggest that the proposed multivariate GMDR substantially boosts statistical power.