Sensory evaluation of fruit quality and nutritional composition of 20 breadfruit (Artocarpus, Moraceae) cultivars

Twenty breadfruit cultivars growing in afield genebank at Kahanu Garden, National Tropical Botanical Garden, Hana, Maui, Hawaii, were evaluated for sensory attributes and nutrient composition. A taste panel scored eight flavor/aroma attributes, five textural attributes, and color. There were significant differences (P ≤ 0.01) in aroma, visual texture, flavor intensity, sweetness, starchiness, moistness, stringiness, firmness, and color. The greatest differences were in color and texture. Nutrient analyses showed significant differences (P ≤ 0.05) for energy, carbohydrates, ash, crude protein, potassium, magnesium, sodium, iron, copper, and zinc. Considering the versatility of breadfruit as a food, its ease of production, and its nutritional value, the numerous good quality flavorful cultivars available should be more widely grown for sustainable agriculture and food security.     

Functional diversity: back to basics and looking forward

Functional diversity is a component of biodiversity that generally concerns the range of things that organisms do in communities and ecosystems. Here, we review how functional diversity can explain and predict the impact of organisms on ecosystems and thereby provide a mechanistic link between the two. Critical points in developing predictive measures of functional diversity are the choice of functional traits with which organisms are distinguished, how the diversity of that trait information is summarized into a measure of functional diversity, and that the measures of functional diversity are validated through quantitative analyses and experimental tests. There is a vast amount of trait information available for plant species and a substantial amount for animals. Choosing which traits to include in a particular measure of functional diversity will depend on the specific aims of a particular study. Quantitative methods for choosing traits and for assigning weighting to traits are being developed, but need much more work before we can be confident about trait choice. The number of ways of measuring functional diversity is growing rapidly. We divide them into four main groups. The first, the number of functional groups or types, has significant problems and researchers are more frequently using measures that do not require species to be grouped. Of these, some measure diversity by summarizing distances between species in trait space, some by estimating the size of the dendrogram required to describe the difference, and some include information about species' abundances. We show some new and important differences between these, as well as what they indicate about the responses of assemblages to loss of individuals. There is good experimental and analytical evidence that functional diversity can provide a link between organisms and ecosystems but greater validation of measures is required. We suggest that non-significant results have a range of alternate explanations that do not necessarily contradict positive effects of functional diversity. Finally, we suggest areas for development of techniques used to measure functional diversity, highlight some exciting questions that are being addressed using ideas about functional diversity, and suggest some directions for novel research.     

A residue in helical conformation in the native state adopts a β-strand conformation in the folding transition state despite its high and canonical Φ-value

Delineating structures of the transition states in protein folding reactions has provided great insight into the mechanisms by which proteins fold. The most common method for obtaining this information is Φ-value analysis, which is carried out by measuring the changes in the folding and unfolding rates caused by single amino acid substitutions at various positions within a given protein. Canonical Φ-values range between 0 and 1, and residues displaying high values within this range are interpreted to be important in stabilizing the transition state structure, and to elicit this stabilization through native-like interactions. Although very successful in defining the general features of transition state structures, Φ-value analysis can be confounded when non-native interactions stabilize this state. In addition, direct information on backbone conformation within the transition state is not provided. In the work described here, we have investigated structure formation at a conserved β-bulge (with helical conformation) in the Fyn SH3 domain by characterizing the effects of substituting all natural amino acids at one position within this structural motif. By comparing the effects on folding rates of these substitutions with database-derived local structure propensity values, we have determined that this position adopts a non-native backbone conformation in the folding transition state. This result is surprising because this position displays a high and canonical Φ-value of 0.7. This work emphasizes the potential role of non-native conformations in folding pathways and demonstrates that even positions displaying high and canonical Φ-values may, nevertheless, adopt a non-native conformation in the transition state.     

Evaluating prognostic accuracy of biomarkers under competing risk

To develop more targeted intervention strategies, an important research goal is to identify markers predictive of clinical events. A crucial step toward this goal is to characterize the clinical performance of a marker for predicting different types of events. In this article, we present statistical methods for evaluating the performance of a prognostic marker in predicting multiple competing events. To capture the potential time-varying predictive performance of the marker and incorporate competing risks, we define time- and cause-specific accuracy summaries by stratifying cases based on causes of failure. Such definition would allow one to evaluate the predictive accuracy of a marker for each type of event and compare its predictiveness across event types. Extending the nonparametric crude cause-specific receiver operating characteristics curve estimators by Saha and Heagerty (2010), we develop inference procedures for a range of cause-specific accuracy summaries. To estimate the accuracy measures and assess how covariates may affect the accuracy of a marker under the competing risk setting, we consider two forms of semiparametric models through the cause-specific hazard framework. These approaches enable a flexible modeling of the relationships between the marker and failure times for each cause, while efficiently accommodating additional covariates. We investigate the asymptotic property of the proposed accuracy estimators and demonstrate the finite sample performance of these estimators through simulation studies. The proposed procedures are illustrated with data from a prostate cancer prognostic study.     

Meta-analysis for surrogacy: accelerated failure time models and semicompeting risks modeling

There has been great recent interest in the medical and statistical literature in the assessment and validation of surrogate endpoints as proxies for clinical endpoints in medical studies. More recently, authors have focused on using metaanalytical methods for quantification of surrogacy. In this article, we extend existing procedures for analysis based on the accelerated failure time model to this setting. An advantage of this approach relative to proportional hazards model is that it allows for analysis in the semicompeting risks setting, where we model the region where the surrogate endpoint occurs before the true endpoint. Several estimation methods and attendant inferential procedures are presented. In addition, between- and within-trial methods for evaluating surrogacy are developed; a novel principal components procedure is developed for quantifying trial-level surrogacy. The methods are illustrated by application to data from several studies in colorectal cancer.     

Development of an optimal formulation for oxidative stability of walnut-beverage emulsions based on gum arabic and xanthan gum using response surface methodology

The susceptibility of lipids to oxidation is one of the most fundamental problems in oil-in-water emulsions. A response surface methodology 5-level-3-factor central-composite rotatable design was applied to study the effects of key formula ingredients including walnut oil (WO, 3-6%, w/w), gum arabic (GA, 5-10%, w/w) and xanthan gum (XG, 0.05-0.15%, w/w) on lipid oxidation in walnut-beverage emulsions. During 30 days’ storage, the oxidation process was monitored by evaluating the peroxide value, anisidine value and total oxidation (Totox) value in different emulsion formulations. Use of XG as a stabilizer at high concentrations considerably inhibited the oxidation of WO in the prepared emulsions. The experimental data were satisfactorily fitted to quadratic models using multiple regression analysis. The optimum conditions to obtain the minimum peroxide (0.923 mequiv. O₂/kg oil), anisidine (0.500) and Totox (2.347) values are met when a walnut-beverage emulsion is formulated with 3% WO, 10% GA and 0.12% XG.     

The value of coordinated management of interacting ecosystem services

Coordinating decisions and actions among interacting sectors is a critical component of ecosystem-based management, but uncertainty about coordinated management's effects is compromising its perceived value and use. We constructed an analytical framework for explicitly calculating how coordination affects management decisions, ecosystem state and the provision of ecosystem services in relation to ecosystem dynamics and socio-economic objectives. The central insight is that the appropriate comparison strategy to optimal coordinated management is optimal uncoordinated management, which can be identified at the game theoretic Nash equilibrium. Using this insight we can calculate coordination's effects in relation to uncoordinated management and other reference scenarios. To illustrate how this framework can help identify ecosystem and socio-economic conditions under which coordination is most influential and valuable, we applied it to a heuristic case study and a simulation model for the California Current Marine Ecosystem. Results indicate that coordinated management can more than double an ecosystem's societal value, especially when sectors can effectively manipulate resources that interact strongly. However, societal gains from coordination will need to be reconciled with observations that it also leads to strategic simplification of the ecological food web, and generates both positive and negative impacts on individual sectors and non-target species.     

Mutational analysis of the stability of the H2A and H2B histone monomers

The eukaryotic histone heterodimer H2A-H2B folds through an obligatory dimeric intermediate that forms in a nearly diffusion-limited association reaction in the stopped-flow dead time. It is unclear whether there is partial folding of the isolated monomers before association. To address the possible contributions of structure in the monomers to the rapid association, we characterized H2A and H2B monomers in the absence of their heterodimeric partner. By far-UV circular dichroism, the H2A and H2B monomers are 15% and 31% helical, respectively—significantly less than observed in X-ray crystal structures. Acrylamide quenching of the intrinsic Tyr fluorescence was indicative of tertiary structure. The H2A and H2B monomers exhibit free energies of unfolding of 2.5 and 2.9 kcal mol^− 1, respectively; at 10 μM, the sum of the stability of the monomers is ∼ 60% of the stability of the native dimer. The helical content, stability, and m values indicate that H2B has a more stable, compact structure than H2A. The monomer m values are larger than expected for the extended histone fold motif, suggesting that the monomers adopt an overly collapsed structure. Stopped-flow refolding—initiated from urea-denatured monomers or the partially folded monomers populated at low denaturant concentrations—yielded essentially identical rates, indicating that monomer folding is productive in the rapid association and folding of the heterodimer. A series of Ala and Gly mutations were introduced into H2A and H2B to probe the importance of helix propensity on the structure and stability of the monomers. The mutational studies show that the central α-helix of the histone fold, which makes extensive intermonomer contacts, is structured in H2B but only partially folded in H2A.     

Evolutionarily distinctive species often capture more phylogenetic diversity than expected

Evolutionary distinctiveness measures of how evolutionarily isolated a species is relative to other members of its clade. Recently, distinctiveness metrics that explicitly incorporate time have been proposed for conservation prioritization. However, we found that such measures differ qualitatively in how well they capture the total amount of evolution (termed phylogenetic diversity, or PD) represented by a set of species. We used simulation and simple graph theory to explore this relationship with reference to phylogenetic tree shape. Overall, the distinctiveness measures capture more PD on more unbalanced trees and on trees with many splits near the present. The rank order of performance was robust across tree shapes, with apportioning measures performing best and node-based measures performing worst. A sample of 50 ultrametric trees from the literature showed the same patterns. Taken together, this suggests that distinctiveness metrics may be a useful addition to other measures of value for conservation prioritization of species. The simplest measure, the age of a species, performed surprisingly well, suggesting that new measures that focus on tree shape near the tips may provide a transparent alternative to more complicated full-tree approaches.     

Evolutionary and ecological implications of genome size in the North American endemic sagebrushes and allies (Artemisia, Asteraceae)

The genome size of 51 populations of 20 species of the North American endemic sagebrushes (subgenus Tridentatae ), related species, and some hybrid taxa were assessed by flow cytometry, and were analysed in a phylogenetic framework. Results were similar for most Tridentatae species, with the exception of three taxonomically conflictive species:  Artemisia bigelovii Gray,  Artemisia pygmaea Gray, and  Artemisia rigida Gray. Genome size homogeneity (together with the high morphological, chemical, and karyological affinities, as well as low DNA sequence divergence) could support a recent diversification process in this geographically restricted group, thought to be built upon a reticulate evolutionary framework. The Tridentatae and the other North American endemic Artemisia show a significantly higher genome size compared with the other subgenera. Our comparative analyses including genome size results, together with different kinds of ecological and morphological traits, suggest an evolutionary change in lifestyle strategy linked to genome expansion, in which junk or selfish DNA accumulation might be involved. Conversely, weed or invasive behaviour in Artemisia is coupled with lower genome sizes. Data for both homoploid and polyploid hybrids were also assessed. Genome sizes are close to the expected mean of parental species for homoploid hybrids, but are lower than expected in the allopolyploids, a phenomenon previously documented to be related with polyploidy.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 94 , 631–649.