In situ marker‐based assessment of leaf trait evolutionary potential in a marginal European beech population

Evolutionary processes are expected to be crucial for the adaptation of natural populations to environmental changes. In particular, the capacity of rear edge populations to evolve in response to the species limiting conditions remains a major issue that requires to address their evolutionary potential. In situ quantitative genetic studies based on molecular markers offer the possibility to estimate evolutionary potentials manipulating neither the environment nor the individuals on which phenotypes are measured. The goal of this study was to estimate heritability and genetic correlations of a suite of leaf functional traits involved in climate adaptation for a natural population of the tree Fagus sylvatica, growing at the rear edge of the species range. Using two marker‐based quantitative genetics approaches, we obtained consistent and significant estimates of heritability for leaf phenological (phenology of leaf flush), morphological (mass, area, ratio mass/area) and physiological (δ¹³C, nitrogen content) traits. Moreover, we found only one significant positive genetic correlation between leaf area and leaf mass, which likely reflected mechanical constraints. We conclude first that the studied population has considerable genetic diversity for important ecophysiological traits regarding drought adaptation and, second, that genetic correlations are not likely to impose strong genetic constraints to future population evolution. Our results bring important insights into the question of the capacity of rear edge populations to evolve.     

Identification of vegetation and soil carbon pools out of equilibrium in a process model via eddy covariance and biometric constraints

Assumptions of steady‐state conditions in biogeochemical modelling are often invoked because knowledge on the development status of the modelling domain is generally unavailable. Here, we investigate the role of vegetation pool sizes on nonequilibrium conditions through model‐data integration approaches for a set of sites using eddy covariance CO₂ flux data. The study is based on the Carnegie–Ames–Stanford Approach (CASA) model, modified (CASA_G) in order to evaluate the sensitivity of simulated net ecosystem production (NEP) fluxes to vegetation pool sizes. The experimental design is based on the inverse model optimization of different parameter vectors performed at the measurement site level. Each parameter vector prescribes different simulation dynamics that embody different model structural assumptions concerning (non)steady‐state conditions in vegetation and soil carbon pools. We further explore the potential of assimilating biometric constraints through the cost function for sites where in situ information on aboveground biomass or wood pools is available. The integration of biometric data yields marked improvements in the simulation of vegetation C pools compared to single constraints with eddy flux data. Overall, it is necessary to relax both vegetation and soil carbon pools for consistency with the observed data streams. Multiple constraints approaches also leads to variable model performance among the different experimental setups and model structures. We identify and assess the limitations of various model structures and the role of multiple constraints approaches for tackling issues of equifinality. These studies emphasize the need for establishing consistent data sets of fluxes and biometric data for successful model‐data fusion.     

Cross‐scale effects of structural and functional connectivity in pond networks on amphibian distribution in agricultural landscapes

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MapMaker and PathTracer for tracking carbon in genome‐scale metabolic models

Constraint‐based reconstruction and analysis (COBRA) modeling results can be difficult to interpret given the large numbers of reactions in genome‐scale models. While paths in metabolic networks can be found, existing methods are not easily combined with constraint‐based approaches. To address this limitation, two tools (MapMaker and PathTracer) were developed to find paths (including cycles) between metabolites, where each step transfers carbon from reactant to product. MapMaker predicts carbon transfer maps (CTMs) between metabolites using only information on molecular formulae and reaction stoichiometry, effectively determining which reactants and products share carbon atoms. MapMaker correctly assigned CTMs for over 97% of the 2,251 reactions in an Escherichia coli metabolic model (iJO1366). Using CTMs as inputs, PathTracer finds paths between two metabolites. PathTracer was applied to iJO1366 to investigate the importance of using CTMs and COBRA constraints when enumerating paths, to find active and high flux paths in flux balance analysis (FBA) solutions, to identify paths for putrescine utilization, and to elucidate a potential CO₂ fixation pathway in E. coli. These results illustrate how MapMaker and PathTracer can be used in combination with constraint‐based models to identify feasible, active, and high flux paths between metabolites.     

The effect of close approaches for tagging activities by small research vessels on the behavior of humpback whales (Megaptera novaeangliae)

Small research vessels are often used as platforms for tagging activities to collect behavioral data on cetaceans and they have the potential to disturb that group or individual. If this disturbance is ignored, results and conclusions produced by that study could be inaccurate. Here land‐based behavioral data of migrating humpback whales (Megaptera novaeangliae) (n = 29) were used to determine the effect of close approaches for tagging by research vessels on their diving, movement and surface behaviors. Groups of whales were tagged, using digital recording tags, by small research vessels, as part of a behavioral response study. In groups that were approached for tagging, temporary changes in movement behaviors during close approaches were found, with subsequent recovery to “pre‐approach” levels. In female‐calf groups more long‐term changes in travel speed were found. Results suggest that, although close approaches for tagging by small vessels may cause behavioral changes in humpback whales, this change may be small and temporary. However, in female‐calf groups, the behavioral change may be greater and longer lasting. This study shows that when using small vessels for behavioral research, disturbance, and recovery should be measured to ensure integrity of data used for other analyses.     

Ecologically based definition of seasons clarifies predator–prey interactions

Species interactions within food webs are driven by multiple constraints, including those imposed by seasonal changes in the environment. Ecologically sound definitions of seasons may therefore be a prerequisite for clarifying predator prey interactions. Most studies define biological seasons based on fixed schedules or on temporal changes in a single movement measurement. We used a novel clustering approach based on homogeneous space‐use patterns of GPS‐collared animals to reveal 7 biological seasons for caribou Rangifer tarandus caribou, and 5 for both moose Alces alces and grey wolves Canis lupus interacting in a boreal ecosystem. Subsequent evaluation of niche overlap showed that, as predicted, wolves had a stronger spatio‐temporal connection with moose, its main prey, than with caribou. Movement constraints and limiting resource distributions similarly affected all species in some instances, but also caused temporal changes in the extent of niche overlap between wolves and its two prey. The risk that caribou faced was not only linked to the niche overlap with wolves, but also to the extent of wolf‐moose niche overlap during the same period. Food‐web properties emerged from the analysis, with temporal changes in relative niche overlap reflecting the strength of trophic interactions during the year. Our study demonstrates how the study of trophic interactions can benefit from comprehensive definitions of biological seasons.     

Analyzing self‐controlled case series data when case confirmation rates are estimated from an internal validation sample

Vaccine safety studies are often electronic health record (EHR)‐based observational studies. These studies often face significant methodological challenges, including confounding and misclassification of adverse event. Vaccine safety researchers use self‐controlled case series (SCCS) study design to handle confounding effect and employ medical chart review to ascertain cases that are identified using EHR data. However, for common adverse events, limited resources often make it impossible to adjudicate all adverse events observed in electronic data. In this paper, we considered four approaches for analyzing SCCS data with confirmation rates estimated from an internal validation sample: (1) observed cases, (2) confirmed cases only, (3) known confirmation rate, and (4) multiple imputation (MI). We conducted a simulation study to evaluate these four approaches using type I error rates, percent bias, and empirical power. Our simulation results suggest that when misclassification of adverse events is present, approaches such as observed cases, confirmed case only, and known confirmation rate may inflate the type I error, yield biased point estimates, and affect statistical power. The multiple imputation approach considers the uncertainty of estimated confirmation rates from an internal validation sample, yields a proper type I error rate, largely unbiased point estimate, proper variance estimate, and statistical power.     

Influence of geographical extent on typology- and model-based assessments of taxonomic completeness of river macroinvertebrates

1. River InVertebrate Prediction and Classification System (RIVPACS)‐type predictive models are increasingly used to assess the biological condition of freshwaters, but management schemes may also be based on a priori groupings of similar water bodies (typologies) to control for natural variation in biota. The two approaches may lead to disagreements of the biological status of a site, depending on, for example, the spatial scale at which assessments are conducted. 2. We used data from 96 reference and 134 potentially impacted sites from Western and Central Finland to compare RIVPACS‐type models and a simple size‐based typology of rivers for the assessment of taxonomic completeness (the quotient of the Observed‐to‐Expected number of predicted taxa, O / E) of riffle macroinvertebrates. We specifically examined how geographical extent influences bioassessment performance (accuracy, precision and sensitivity to detect impact) of the two approaches. To fully examine the behaviour of the O / E‐index with the two approaches at differing spatial scales, we performed all assessments with a full range of thresholds for predicted taxa occurrence probabilities (p_t from 0+ to 0.9). 3. Both approaches performed consistently better than the corresponding null models. At the larger extent (i.e. assessment encompassing the whole study area), the RIVPACS‐approach performed in all aspects better than the typology‐approach. However, at the smaller extent (i.e. regional assessments) the RIVPACS‐type models and the typologies showed similar accuracy to predict the actual fauna (mean E), similar precision (SD) of cross‐validated O / E and similar sensitivity to detect sites with human impairment. 4. SD(O / E) decreased (i.e. precision increased) consistently with increasing p_t. However, both approaches were most sensitive at intermediate p_t:s (c. 0.2–0.6) when taxa with low predicted occurrence probabilities were excluded. 5. Our results show that RIVPACS‐type predictive models are less susceptible to variations in spatial scale, whereas the performance of a priori typologies increases with decreasing spatial extent. Thus, RIVPACS‐type models are more efficient for large‐scale bioassessments, but at restricted spatial scales, or with an otherwise biologically meaningful stratification, simple a priori classifications can be equally useful for the assessment of taxonomic completeness of river macroinvertebrates.     

Wise Mind project: a school-based environmental approach for preventing weight gain in children

Objective: The Wise Mind pilot study compared the efficacy of an environmental approach for prevention of inappropriate weight gain in children with an active control condition that used an environmental approach for modifying expectancies related to the use of alcohol, tobacco, and drugs. Research Methods and Procedures: A total of 670 second to sixth grade students from four schools were enrolled in the study. The study spanned 2 academic years, and 586 students were available for evaluation at the end of the study. Two schools were randomly assigned to each treatment arm. The environmental approach for weight gain prevention focused on modification of eating habits and physical activity, and the active control group focused on modification of expectancies related to substance use. Results: Using an intention to treat design, the study found no differences in weight gain prevention between the two interventions. The weight gain prevention program was associated with reduction of total caloric intake, reduction of dietary fat intake, reduction of protein intake, and increased physical activity in comparison with the active control group and relative to baseline. These changes in food intake were attributed to changes in food selections that resulted from modification of school cafeteria menus and food preparation. Discussion: The Wise Mind school‐based weight gain prevention program induced behavioral changes in healthy eating and physical activity but did not induce significant changes in body weight in comparison with the control arm. Recommendations for future research are provided.     

Development of a high-performance affinity chromatography-based method to study the biological interaction between whole micro-organisms and target proteins

Aims: The bacteria–host molecular cross‐talk is the matter of primary importance both in pathogenesis and in commensalism. Principally based on immunological methods, the methodologies commonly utilized for these studies are laborious and require specific antibodies. Here, we developed a new high‐performance affinity chromatography (HPAC)‐based approach that allows a direct measure of the interaction between whole bacterial cells and host molecules. Methods and Results: Bifidobacterium lactis BI07 cells immobilized on amino‐derivatized silica beads were utilized as stationary phase in a high‐performance affinity chromatography approach. The analytes plasminogen, collagen I and collagen IV were injected, and interactions were evaluated by the insertion in an HPLC system with UV detection. According to our data, Bif. lactis BI07 is capable of interacting with plasminogen, while it does not exhibit any binding activity to collagen I and IV. Conclusions: In this study, we implemented a high‐performance affinity chromatography‐based method to characterize the biological interaction between whole micro‐organisms and target proteins. Significance and Impact of the Study: With respect to the approaches commonly utilized to study the interaction between bacteria and host proteins, this HPAC‐based approach is fast and cheaper than other methods and allows a direct measure of the interaction between bacterial cells and target molecules.     

Floral scent evolution in the section Pseudophrys: pollinator‐mediated selection or phylogenetic constraints?

• Sexually deceptive orchid species from the Mediterranean genus Ophrys usually interact with one or a few pollinator species by means of specific floral scents. In this study, we investigated the respective role of pollinator‐mediated selection and phylogenetic constraints in the evolution of floral scents in the section Pseudophrys.
• We built a phylogenetic tree of 19 Pseudophrys species based on three nuclear loci; we gathered a dataset on their pollination interactions from the literature and from our own field data; and we extracted and analysed their floral scents using solid phase microextraction and gas chromatography‐mass spectrometry. We then quantified the phylogenetic signal carried by floral scents and investigated the link between plant–pollinator interactions and floral scent composition using phylogenetic comparative methods.
• We confirmed the monophyly of the section Pseudophrys and demonstrated the existence of three main clades within this section. We found that floral scent composition is affected by both phylogenetic relationships among Ophrys species and pollination interactions, with some compounds (especially fatty acid esters) carrying a significant phylogenetic signal and some (especially alkenes and alkadienes) generating dissimilarities between closely related Pseudophrys pollinated by different insects.
• Our results show that in the section Pseudophrys, floral scents are shaped both by pollinator‐mediated selection and by phylogenetic constraints, but that the relative importance of these two evolutionary forces differ among compound classes, probably reflecting distinct selective pressures imposed upon behaviourally active and non‐active compounds.

     

Structural characterization of a new N‐substituted pantothenamide bound to pantothenate kinases from Klebsiella pneumoniae and Staphylococcus aureus

Pantothenate kinase (PanK) is the rate‐limiting enzyme in Coenzyme A biosynthesis, catalyzing the ATP‐dependent phosphorylation of pantothenate. We solved the co‐crystal structures of PanKs from Staphylococcus aureus (SaPanK) and Klebsiella pneumonia (KpPanK) with N‐[2‐(1,3‐benzodioxol‐5‐yl)ethyl] pantothenamide (N354‐Pan). Two different N354‐Pan conformers interact with polar/nonpolar mixed residues in SaPanK and aromatic residues in KpPanK. Additionally, phosphorylated N354‐Pan is found at the closed active site of SaPanK but not at the open active site of KpPanK, suggesting an exchange of the phosphorylated product with a new N354‐Pan only in KpPanK. Together, pantothenamides conformational flexibility and binding pocket are two key considerations for selective compound design. Proteins 2014; 82:1542–1548. © 2014 Wiley Periodicals, Inc.     

Applying a continua landscape approach to evaluate plant response to fragmentation: Primula vulgaris in the Cantabrian mountains

Question: Continua landscape approaches conceptualize the effects of habitat fragmentation on the biota by considering fragmented landscapes as continuous gradients, departing from the view of habitat as either suitable (fragment) or unsuitable (matrix). They also consider the ecological gradients or the ‘Umwelt’ (species‐specific perception of the landscape) to represent the processes that ultimately limit organisms' ability to colonize and persist within habitat remnants. Are these approaches suitable for evaluating the response of plant species to fragmentation? Location: Fragmented mid‐elevation temperate forests, Cantabrian range, Spain. Methods: The presence, abundance and demographic structure of populations of the perennial herb Primula vulgaris were sampled across a continuous extent of 100 ha, subdivided into 400 50 m × 50 m sampling units. These variables were related to forest availability, forest subdivision and edge density, topography and the spatial clumpiness of populations (a measure of plant dispersal constraints and, hence, a major surrogate of plant Umwelt). Results: Fragmentation processes, especially habitat loss, negatively affect P. vulgaris, with a stronger effect on presence than on abundance and demography. Despite the importance of habitat availability, P. vulgaris does not occupy all potentially suitable forest habitat, mostly owing to dispersal constraints. A positive effect of slope on plant presence also suggests some effect of habitat quality in determining establishment and occupancy of forest landscape. Conclusions: Within‐habitat dispersal constraints are as important as forest fragmentation in determining the landscape‐scale distribution of P. vulgaris. By assessing the relative role of the diverse fragmentation processes, and of the species' landscape perception, a continua landscape approach proves to be a valuable tool for predicting plant response to landscape change.     

MOLECULAR AND MORPHOMETRIC DATA PINPOINT SPECIES BOUNDARIES IN HALIMEDA SECTION RHIPSALIS (BRYOPSIDALES,CHLOROPHYTA)1

Molecular systematic studies have changed the face of algal taxonomy. Particularly at the species level, molecular phylogenetic research has revealed the inaccuracy of morphology‐based taxonomy: Cryptic and pseudo‐cryptic species were shown to exist within many morphologically conceived species. This study focused on section Rhipsalis of the green algal genus Halimeda. This section was known to contain cryptic diversity and to comprise species with overlapping morphological boundaries. In the present study, species diversity within the section and identity of individual specimens were assessed using ITS1–5.8S–ITS2 (nrDNA) and rps3 (cpDNA) sequence data. The sequences grouped in a number of clear‐cut genotypic clusters that were considered species. The same specimens were subjected to morphometric analysis of external morphological and anatomical structures. Morphological differences between the genotypic cluster species were assessed using discriminant analysis. It was shown that significant morphological differences exist between genetically delineated species and that allocation of specimens to species on the basis of morphometric variables is nearly perfect. Anatomical characters yielded better results than external morphological characters. Two approaches were offered to allow future morphological identifications: a probabilistic approach based on classification functions of discriminant analyses and the classical approach of an identification key.     

Approaches to Selecting Native Plant Replacements for Fleshy-Fruited Invasive Species

Invasive plants are a serious threat to biodiversity. Yet, in some cases, they may play an important ecological role in heavily modified landscapes, such as where fleshy‐fruited invasive plants support populations of native frugivores. How can such conservation conflicts be managed? We advocate an approach in which native fleshy‐fruited plants are ranked on their ability to provide the fruit food resources for native frugivores currently being provided by invasive plants. If these native taxa are preferentially used, where ecologically appropriate, in plantings for restoration and in park and garden settings, they could help support native frugivore populations in the event of extensive invasive plant control. We develop and critically examine six approaches to selecting candidate native plant taxa: a multivariate approach based on the frugivore assemblage, a scoring model, and several multivariate approaches (including trait combinations having the greatest correlation with the diet of the native frugivore assemblage) based on the functional traits of fruit morphology, phenology, conspicuousness, and accessibility. To illustrate these approaches, we use a case study with Bitou bush (Chrysanthemoides monilifera subsp. rotundata) (Asteraceae), an Australian Weed of National Significance. The model using a dissimilarity value generated from all available traits identified a set of species used by the frugivores of C. monilifera more than null models. A replacement approach using species ranked by either all traits available or the frugivore community appears best suited to guide selection of plants in restoration practice.     

Identification and characterization of a brilliant yellow pigment produced by Bordetella pertussis

Culture supernatants of Bordetella pertussis are a brilliant yellow; however, the structure and biological role of the responsible pigment have not been investigated. In this study, a brilliant yellow‐colored fraction was extracted from culture supernatants of B. pertussis and analyzed by HPLC. UV–visible spectral analysis and mass spectrometry identified the brilliant yellow pigment as riboflavin. Riboflavin production was high in lag and early log phases and riboflavin was found to enhance growth of B. pertussis in low‐density cultures. Riboflavin production is not regulated by the BvgAS system. In addition, it was found that other Bordetella species, such as B. parapertussis , B. holmesii and B. bronchiseptica, also release riboflavin into their culture supernatants. This is the first report that B. pertussis secrets riboflavin to the extracellular space and that riboflavin may promote its growth. The mechanism may be associated with pathogenesis of B. pertussis .

     

Integration of biocatalyst and process engineering for sustainable and efficient n‐butanol production

Recent environmental economic developments generate a need for sustainable and cost‐effective (microbial) processes for the production of high‐volume, low‐priced bulk chemicals. As an example, n‐butanol has, as a second‐generation biofuel, beneficial characteristics compared to ethanol in liquid transportation fuel applications. The industrial revival of the classic n‐butanol (ABE) fermentation requires process and strain engineering solutions for overcoming the main process limitations: product toxicity and low space–time yield. Reaction intensification on the biocatalyst, fermentation, and bioprocess level can be based on economic and ecologic evaluations using quantifiable constraints. This review describes the means of process intensification for biotechnological processes. A quantitative approach is then used for the comparison of the massive literature on n‐butanol fermentation. A comprehensive literature study—including key fermentation performance parameters—is presented and the results are visualized using the window of operation methodology. The comparison allowed the identification of the key constraints, high cell densities, high strain stability, high specific production rate, cheap in situ product removal, high n‐butanol tolerance, to operate in situ product removal efficiently, and cheap carbon source. It can thus be used as a guideline for the bioengineer during the combined biocatalyst, fermentation, and bioprocess development and intensification.