A Bayesian A-optimal and model robust design criterion

Summary . Suppose that the true model underlying a set of data is one of a finite set of candidate models, and that parameter estimation for this model is of primary interest. With this goal, optimal design must depend on a loss function across all possible models. A common method that accounts for model uncertainty is to average the loss over all models; this is the basis of what is known as Läuter's criterion. We generalize Läuter's criterion and show that it can be placed in a Bayesian decision theoretic framework, by extending the definition of Bayesian A‐optimality. We use this generalized A‐optimality to find optimal design points in an environmental safety setting. In estimating the smallest detectable trace limit in a water contamination problem, we obtain optimal designs that are quite different from those suggested by standard A‐optimality.     

Empirical evidence for an optimal body size in snakes

Abstract The concept of optimal size has been invoked to explain patterns in body size of terrestrial mammals. However, the generality of this phenomenon has not been tested with similarly complete data from other taxonomic groups. In this study we describe three statistical patterns of body size in snakes, all of which indicate an optimal length of 1.0 m. First, a distribution of largest body lengths of 618 snake species had a single mode at 1.0 m. Second, we found a positive relationship between the size of the largest member of an island snake assemblage and island area and a negative relationship between the size of the smallest member of an island snake assemblage and island area. Best-fit lines through these data cross at a point corresponding to 1.0 m in body length, the presumed optimal size for a one-species island. Third, mainland snake species smaller than 1.0 m become larger on islands whereas those larger than 1.0 m become smaller on islands. The observation that all three analyses converge on a common body size is concordant with patterns observed in mammals and partial analyses of four other disparate animal clades. Because snakes differ so strikingly from mammals (ectotherms, gape-limited predators, elongate body shape) the concordant patterns of these two groups provide strong evidence for the evolution of an optimal body size within independent monophyletic groups. However, snakes differ from other taxonomic groups that have been studied in exhibiting a body size distribution that is not obviously skewed in either direction. We suggest that idiosyncratic features of the natural history of ectotherms allow relatively unconstrained distributions of body size whereas physiological limitations of endotherms constrain distributions of body size to a right skew.     

Foraging efficiency of juvenile bluegill, Lepomis macrochirus, among different vegetated habitats

Optimal foraging theory is devoted to understanding how organisms maximize net energy gain. However, both the theory and empirical studies lack critical components, such as effects of environmental variables across habitats. We addressed the hypothesis that energetic returns of juvenile bluegill are affected by environmental variables characteristic of the vegetated habitats. Predicted optimal diet breadths were calculated and compared to prey items eaten by juvenile bluegill to determine if bluegill were foraging to maximize energetic gain. Differences in habitat profitability among vegetated sites were determined by comparing predictions of maximized energetic return rates (cals^-1) with prey contents of bluegill stomachs. Sizes of most prey items eaten by juvenile bluegill throughout the vegetated sites were smaller than the predicted optimal diet breadths. However, inclusion of smaller prey items in the diet did not seem to affect rate of energetic gain. Energetic return rates were maximized at the 1.5 and 2mm prey size classes and declined only slightly with inclusion of smaller prey sizes. Predicted energetic return rates and average mass in bluegill stomachs were related negatively. Average mass in bluegill stomachs also was associated negatively with Elodea canadensis stem densities and percent of light transfer, suggesting that foraging efficiency of bluegill decreased as plant density and percent of light increased. Results of our research indicate that maximization of energetic return rates is dependent upon availability of prey sizes that contribute to optimal foraging. Thus, determination of those habitats that provide the highest availability of benthic invertebrate prey with the least interference by stems is critical. Enhanced foraging capabilities can promote recruitment, faster growth, better body condition and survival.     

Comprehensive sequence analysis of translation termination sites in various eukaryotes

Recent investigations into the translation termination sites of various organisms have revealed that not only stop codons but also sequences around stop codons have an effect on translation termination. To investigate the relationship between these sequence patterns and translation as well as its termination efficiency, we analysed the correlation between strength of consensus and translation efficiency, as predicted according to Codon Adaptation Index (CAI) value. We used RIKEN full-length mouse cDNA sequences and ten other eukaryotic UniGene datasets from NCBI for the analyses. First, we conducted sequence profile analyses following translation termination sites. We found base G and A at position +1 as a strong consensus for mouse cDNA. A similar consensus was found for other mammals, such as Homo sapiens, Rattus norvegicus and Bos taurus. However, some plants had different consensus sequences. We then analysed the correlation between the strength of consensus at each position and the codon biases of whole coding regions, using information content and CAI value. The results showed that in mouse cDNA, CAI value had a positive correlation with information content at positions +1. We also found that, for positions with strong consensus, the strength of the consensus is likely to have a positive correlation with CAI value in some other eukaryotes. Along with these observations, biological insights into the relationship between gene expression level, codon biases and consensus sequence around stop codons will be discussed.     

Hijacking the translation apparatus by RNA viruses

As invading viruses do not harbor functional ribosomes in their virions, successful amplification of the viral genomes requires that viral mRNAs compete with cellular mRNAs for the host cell translation apparatus. Several RNA viruses have evolved remarkable strategies to recruit the host translation initiation factors required for the first steps in translation initiation by host cell mRNAs. This review describes the ways that three families of RNA viruses effectively usurp limiting translation initiation factors from the host.     

Fine root growth and element concentrations of Norway spruce as affected by wood ash and liquid fertilisation

A field experiment to test various management practices of sustainable forestry was conducted in a Swiss spruce forest for two growing seasons. Treatments were a control (C), yearly application of 4000 kg ha^–1 wood ash (A), daily irrigation with a steady state fertilisation as `optimal nutrition` (F) and irrigation with a water control (W). Samples were taken on a 5 × 5 m grid once a year with a soil corer to determine fine root biomass ( 2 mm) and soil pH of the topsoil. A subset of the fine root samples was further analysed for its nutrient composition by CN and ICP-AES analyses. The dynamics of root growth were observed with the aid of ingrowth-cores after 1, 1.5, and 2 years of treatment and the growth pattern was analysed in terms of biomass, tips, forks, length and root diameter of the samples. The A, F and also the W treatment resulted in a significant increase of soil pH in the topsoil. The fine root density increased over the two growing seasons, irrespective of the treatment. The root growth was only slightly different between the treatments with a initially faster growth under the A treatment. The W treatment reduced the number of root tips and forks, and the root length, while the A treatment increased the number of root tips, forks and the root length, but reduced the diameter. The differences between the three harvesting times (March 1999, October 1999, March 2000) of the ingrowth-cores stressed seasonal differences in root growth and the development of quasi `steady state' root dynamics. The root turnover was not changed by the treatments. The elements in the fine roots were strongly affected by the treatments A and F and sometimes by W. Fine root N increased with the F treatment, while C concentrations decreased under the A, F and W treatments. The Ca and Mg concentrations were strongly enhanced by A but also by the F treatment. The K and P concentrations in the fine roots were improved by all three applications. Due to the pH increase Al, Fe and Mn concentrations in the fine roots were decreased by the A and F treatments. S and Zn concentrations showed inconsistent changes over the growing seasons. The results of this study were comparable with those of other studies in Europe and confirm the abilities of the fine roots as indicators of forest nutrition, to some extent more sensitive than the commonly used foliar analysis.     

A vector with the downstream box of the initiation codon can highly enhance protein expression in Escherichia coli

An expression vector, pET-DB, with a perfectly matching downstream box of the initiation codon has been constructed on the basis of the pET system. Any gene of interest can then be inserted into the vector. Four genes were used to test the expression efficiency of the vector. The results show that the vector pET-DB can further increase protein expression level at least up to 35–70% as compared with the initial T7 expression system, indicating that the downstream box can enhance protein expression in Escherichia coli.     

Statistical methods for detecting molecular adaptation

The past few years have seen the development of powerful statistical methods for detecting adaptive molecular evolution. These methods compare synonymous and nonsynonymous substitution rates in protein-coding genes, and regard a nonsynonymous rate elevated above the synonymous rate as evidence for darwinian selection. Numerous cases of molecular adaptation are being identified in various systems from viruses to humans. Although previous analyses averaging rates over sites and time have little power, recent methods designed to detect positive selection at individual sites and lineages have been successful. Here, we summarize recent statistical methods for detecting molecular adaptation, and discuss their limitations and possible improvements.     

A mechanistic model for partial preferences

Classic prey optimal foraging model assumes that individual predators are globally omniscient; that is, they have exact knowledge of prey population densities in the environment. This study examines a spatially explicit individual-based model of a one-predator two-prey system where individual predators are assumed to be omniscient only locally, i.e., to know prey population densities only in the range of their perception. Due to local variations in prey numbers, the probability of acceptance of less profitable prey shifts from the zero-one rule to a gradually decreasing function, for which an explicit formula is derived, giving way to partial preferences. A corresponding predator functional response to more profitable prey is shown to have a sigmoid-like form.