Enzyme/non-enzyme discrimination and prediction of enzyme active site location using charge-based methods

Calculations of charge interactions complement analysis of a characterised active site, rationalising pH-dependence of activity and transition state stabilisation. Prediction of active site location through large DeltapK(a)s or electrostatic strain is relevant for structural genomics. We report a study of ionisable groups in a set of 20 enzymes, finding that false positives obscure predictive potential. In a larger set of 156 enzymes, peaks in solvent-space electrostatic properties are calculated. Both electric field and potential match well to active site location. The best correlation is found with electrostatic potential calculated from uniform charge density over enzyme volume, rather than from assignment of a standard atom-specific charge set. Studying a shell around each molecule, for 77% of enzymes the potential peak is within that 5% of the shell closest to the active site centre, and 86% within 10%. Active site identification by largest cleft, also with projection onto a shell, gives 58% of enzymes for which the centre of the largest cleft lies within 5% of the active site, and 70% within 10%. Dielectric boundary conditions emphasise clefts in the uniform charge density method, which is suited to recognition of binding pockets embedded within larger clefts. The variation of peak potential with distance from active site, and comparison between enzyme and non-enzyme sets, gives an optimal threshold distinguishing enzyme from non-enzyme. We find that 87% of the enzyme set exceeds the threshold as compared to 29% of the non-enzyme set. Enzyme/non-enzyme homologues, "structural genomics" annotated proteins and catalytic/non-catalytic RNAs are studied in this context.     

Continuum heterogeneous biofilm model--a simple and accurate method for effectiveness factor determination

We present a novel analytical approach to describe biofilm processes considering continuum variation of both biofilm density and substrate effective diffusivity. A simple perturbation and matching technique was used to quantify biofilm activity using the steady-state diffusion-reaction equation with continuum variable substrate effective diffusivity and biofilm density, along the coordinate normal to the biofilm surface. The procedure allows prediction of an effectiveness factor, η, defined as the ratio between the observed rate of substrate utilization (reaction rate with diffusion resistance) and the rate of substrate utilization without diffusion limitation. Main assumptions are that (i) the biofilm is a continuum, (ii) substrate is transferred by diffusion only and is consumed only by microorganisms at a rate according to Monod kinetics, (iii) biofilm density and substrate effective diffusivity change in the x direction, (iv) the substrate concentration above the biofilm surface is known, and (v) the substratum is impermeable. With this approach one can evaluate, in a fast and efficient way, the effect of different parameters that characterize a heterogeneous biofilm and the kinetics of the rate of substrate consumption on the behavior of the biological system. Based on a comparison of η profiles the activity of a homogeneous biofilm could be as much as 47.8% higher than that of a heterogeneous biofilm, under the given conditions. A comparison of η values estimated for first order kinetics and η values obtained by numerical techniques showed a maximum deviation of 1.75% in a narrow range of modified Thiele modulus values. When external mass transfer resistance, is also considered, a global effectiveness factor, η(0) , can be calculated. The main advantage of the approach lies in the analytical expression for the calculation of the intrinsic effectiveness factor η and its implementation in a computer program. For the test cases studied convergence was achieved quickly after four or five iterations. Therefore, the simulation and scale-up of heterogeneous biofilm reactors can be easily carried out.     

Rate of loop formation in peptides: a simulation study

Experimental techniques with high temporal and spatial resolution extend our knowledge of how biological macromolecules self-organise and function. Here, we provide an illustration of the convergence between simulation and experiment made possible by techniques such as triplet-triplet energy transfer and fluorescence quenching with long-lifetime and fast-quenching fluorescent probes. These techniques have recently been used to determine the average time needed for two residues in a peptide or protein segment to form a contact. The timescale of this process is accessible to computer simulation, providing a microscopic interpretation of the data and yielding new insight into the disordered state of proteins. Conversely, such experimental data also provide a test of the validity of alternative choices for the molecular models used in simulations, indicating their possible deficiencies. We carried out simulations of peptides of various composition and length using several models. End-to-end contact formation rates and their dependence on peptide length agree with experimental estimates for some sequences and some force fields but not for others. The deviations are due to artefactual structuring of some peptides, which is not observed when an atomistic model for the solvation water is used. Simulations show that the observed experimental rates are compatible with considerably different distributions of the end-to-end distance; for realistic models, these are never Gaussian but indicative of a rugged energy landscape.     

Seasonal and spatial variation in the diet of brown trout (Salmo trutta L.) in the subarctic River Laxá, north-east Iceland

This study examines seasonal and spatial patterns in the diet composition, stomach fullness and condition of a landlocked population of brown trout (2.5–61.3 cm) in the lake-fed River Laxá in NE-Iceland. The stomach contents consisted predominantly of benthic invertebrates, such as blackfly larvae Simulium vittatum (58%), chironomids (24%) and the freshwater snail Radix peregra (7%). The seasonal and spatial patterns of S. vittatum in the stomach contents were consistent with published studies on the life cycle and production of S. vittatum in the River Laxá. Close to the Lake Myvatn outlet (0–16 km), S. vittatum constituted 63% of the stomach content volume, and exhibited two peaks (i.e., generations) in its seasonal contribution to the stomach contents, whereas further downstream (16–35 km) S. vittatum constituted 45% of the volume and showed only clear evidence of one generation. Seasonal fluctuations in S. vittatum availability appear to affect the stomach fullness and the condition factor of the trout, especially close to the lake outlet where the fluctuations are pronounced.     

Shoot and compound leaf comparisons in eudicots: dynamic morphology as an alternative approach

Recent developmental studies suggest that the compound leaf is a more or less incompletely developed shoot. Instead of treating compound leaves and shoots as non-homologous, this interpretation draws a continuum between them. The present work considers the plant as a hierarchical series of units on which similar developmental processes are at work, and where each level (shoot, compound leaf, leaflet) is 'repeated' by the next higher level. Measurements related to the expression of developmental processes operating on leaves at the shoot level and on leaflets at the compound leaf level were used to determine if similar processes are at work at these different levels during early stages of organogenesis. Plants with compound leaves showing acropetal leaflet inception, representing a total of 16 species from ten eudicot families, were studied. Based on several types of quantitative analyses, there appears to be a continuum between so-called shoots, compound leaves and leaflets in the species studied. This perspective, qualified as dynamic morphology, both parallels and complements the classical interpretation.  © 2003 The Linnean Society of London, Botanical Journal of the Linnean Society, 2003, 143, 219−230.     

Gradients of life-history variation: an intercontinental comparison of fishes

Multivariate analysis identified atwo-dimensional continuum of life-historyvariation among 301 fish species from Europe,North America, South America and the Atlanticand Pacific coasts of North America. The firstaxis was associated with larger body size,higher fecundity, delayed maturation, fewerreproductive events, and shorter breedingseason on one end and small size, lowfecundity, early maturity, multiplereproductive events per year, and prolongedbreeding season on the other. The second axiscontrasted fishes having larger eggs and moreparental care against fishes with the oppositesuite of traits.Phylogenetic affiliations of species wereapparent in the general patterns of ordinationof species within orders, indicatingevolutionary divergences in life-historypatterns. In fact, partitioning the variance oflife-history traits showed that taxonomic orderand latitude were the most important factorsand geographic region and habitat the least.Despite phylogenetic constraints, basiclife-history patterns showed consistencybetween distantly geographical regions,latitudinal ranges and basic adult habitats,indicating convergences in life-historypatterns. Although the basic life-historypatterns seemed repeatable among distantlyrelated taxa, geographical and latitudinalaffiliations were apparent. Species from SouthAmerica are skewed toward the opportunisticendpoint, whereas North American marine speciesare skewed toward the periodic endpoint of thetrilateral continuum model. Most of the fishspecies from South American data set came fromfluctuating environments, so an opportunisticstrategy of early maturation and continuousspawning permits efficient recolonization ofhabitats over small spatial scales. Incontrast, most species in the North Americanand European data sets came from seasonalhabitats that are nonetheless more hydrologicalstable, so a periodic strategy of delayingmaturation to attain large clutches enhancesadult survivorship during suboptimalenvironmental conditions and recruitment whenearly life stages encounter suitableenvironmental conditions. Similarly,latitudinal affiliations were also observed:opportunistic strategists more common intropical latitudes and periodic strategistsmore common in temperate and Arctic latitudes.     

The SER Standards: a globally relevant and inclusive tool for improving restoration practice—a reply to Higgs et al.

In response to a critique by Higgs et al., this article clarifies the content and intent of the Society for Ecological Restoration's (SER) International Standards for the Practice of Ecological Restoration. Higgs et al. expressed concern that the SER Standards are not sufficiently underpinned by principles and risk disenfranchising some practitioners by narrowing what qualifies as ecological restoration. To demonstrate that these concerns are unfounded, we discuss the policy context and principles on which the Standards are based, its organizational structure, the innovative and inclusive approach used for development, and highlight significant errata by Higgs et al.     

Perceptions of Equid Well Being Well-Being in South Dakota

In South Dakota, the status of equid well being is relatively unknown. This study sought to (a) gain understanding about the current perceptions of nonhuman animal well being in South Dakota, with an emphasis on horses and other equids; (b) determine the level of care equids are reportedly receiving and the perceived challenges to equine well being in South Dakota, and (c) determine if people from diverse geographical locations (east or west of the Missouri River) have similar views on the well being of equids in South Dakota. Respondents indicated the current level of equid well being in South Dakota is sufficient, but there is room for improvement. Current challenges for the equid population of South Dakota were the high annual cost of horse care, poor horsemanship, dental problems, and whether caregivers understand basic equine care. Several significant associations arose between where a respondent lives (Western or Eastern South Dakota) and their level of agreement with various statements. The results provide a benchmark to gauge well being and help give direction for future educational needs that can continue to improve equid care.     

Analysis and understanding of butterfly community composition based on multivariate approaches and the concept of generalist/specialist strategies

We analyzed butterfly community composition using multivariate analyses. The results of principal components analysis showed that the butterfly community was composed mainly of two species groups. This species grouping was also supported by the results of the cluster analysis (unweighted pair‐group method using arithmetic average). Comparing the present results with species classification based on the generalist/specialist concept, the butterfly community was found to be composed of five species groups differing from each other in their ecological characteristics: a specialist group, two intermediate groups and two generalist groups. By comparison of their characteristics, it was suggested that, in the butterfly community, the positions of the specialist group and one of the generalist groups are the endpoints on the generalist/specialist selection spectrum, and the three other groups are positioned between these two extremes. The multivariate analyses showed that the species grouping with the generalist/specialist concept based only on voltinism and larval diet breadth was not sufficient to classify both intermediate and generalist groups, and also succeeded in extracting a typical generalist group from the butterfly community. From these results, we propose and recommend the synergetic application of the generalist/specialist concept and multivariate approaches to the detailed analysis and deeper understanding of community structure and composition.