Plant trait responses to grazing – a global synthesis

Herbivory by domestic and wild ungulates is a major driver of global vegetation dynamics. However, grazing is not considered in dynamic global vegetation models, or more generally in studies of the effects of environmental change on ecosystems at regional to global scale. An obstacle to this is a lack of empirical tests of several hypotheses linking plant traits with grazing. We, therefore, set out to test whether some widely recognized trait responses to grazing are consistent at the global level. We conducted a meta‐analysis of plant trait responses to grazing, based on 197 studies from all major regions of the world, and using six major conceptual models of trait response to grazing as a framework. Data were available for seven plant traits: life history, canopy height, habit, architecture, growth form (forb, graminoid, herbaceous legume, woody), palatability, and geographic origin. Covariates were precipitation and evolutionary history of herbivory. Overall, grazing favoured annual over perennial plants, short plants over tall plants, prostrate over erect plants, and stoloniferous and rosette architecture over tussock architecture. There was no consistent effect of grazing on growth form. Some response patterns were modified by particular combinations of precipitation and history of herbivory. Climatic and historical contexts are therefore essential for understanding plant trait responses to grazing. Our study identifies some key traits to be incorporated into plant functional classifications for the explicit consideration of grazing into global vegetation models used in global change research. Importantly, our results suggest that plant functional type classifications and response rules need to be specific to regions with different climate and herbivory history.     

Large-scale production of mouse phenotypes: the search for animal models for inherited diseases in humans

This paper is aimed principally at bioinformaticians and biologists as an introduction to recent advances in mouse mutagenesis, concentrating on genome-wide screens utilising the powerful mutagen N-ethyl-N-nitroso-urea (ENU). It contains a brief background to the underlying genetics as well as details of the practical aspects of organisation and data capture for such projects.     

Using functional traits to predict species growth trajectories,and cross‐validation to evaluate these models for ecological prediction

Modeling plant growth using functional traits is important for understanding the mechanisms that underpin growth and for predicting new situations. We use three data sets on plant height over time and two validation methods—in‐sample model fit and leave‐one‐species‐out cross‐validation—to evaluate non‐linear growth model predictive performance based on functional traits. In‐sample measures of model fit differed substantially from out‐of‐sample model predictive performance; the best fitting models were rarely the best predictive models. Careful selection of predictor variables reduced the bias in parameter estimates, and there was no single best model across our three data sets. Testing and comparing multiple model forms is important. We developed an R package with a formula interface for straightforward fitting and validation of hierarchical, non‐linear growth models. Our intent is to encourage thorough testing of multiple growth model forms and an increased emphasis on assessing model fit relative to a model's purpose.     

Using niche-based modelling to assess the impact of climate change on tree functional diversity in Europe

Rapid anthropogenic climate change is already affecting species distributions and ecosystem functioning worldwide. We applied niche-based models to analyse the impact of climate change on tree species and functional diversity in Europe. Present-day climate was used to predict the distributions of 122 tree species from different functional types (FT). We then explored projections of future distributions under one climate scenario for 2080, considering two alternative dispersal assumptions: no dispersal and unlimited dispersal. The species-rich broadleaved deciduous group appeared to play a key role in the future of different European regions. Temperate areas were projected to lose both species richness and functional diversity due to the loss of broadleaved deciduous trees. These were projected to migrate to boreal forests, thereby increasing their species richness and functional diversity. Atlantic areas provided an intermediate case, with a predicted reduction in the numbers of species and occasional predicted gains in functional diversity. This resulted from a loss in species within the broadleaved deciduous FT, but overall maintenance of the group. Our results illustrate the fact that both species-specific predictions and functional patterns should be examined separately in order to assess the impacts of climate change on biodiversity and gain insights into future ecosystem functioning.     

Rates of Development, Survival and Predation of Immature Stages of Phytoseiulus Longipes (Acari: Mesostigmata: Phytoseiidae)

Larvae of Phytoseiulus longipes do not feed. Thus, the purpose of this research was to determine the functional response as well as developmental and survival rates of the nymphal stages of this predator on the egg stage of the prey Tetranychus pacificus. The egg consumption for both immature stages increased smoothly with a negative rate reaching a plateau (type II response). To complete their development, the protonymphs and deutonymphs consumed mean minimums of 3.15 and 3.56 eggs, respectively, at a prey density of 20 per excised leaf arena. The mean daily developmental and survival rates also showed a curvilinear rise to a plateau. These plateaus for both developmental (71%) and survival rates (100%) were obtained at a prey egg density of 20 for both nymphal stages. Attack coefficients and handling times for both predator stages were estimated using several curve fitting models. All these models indicated a higher value of attack coefficient and a lower value of handling time for deutonymphs as compared to protonymphs. These findings, combined with the knowledge of adults' predation response, foraging behaviour and prey preference, indicate this predator's overall potential as a biological control agent against web-spinning spider mites such as the Pacific spider mite.     

Global stability of an SIR epidemic model with time delays

An SIR disease transmission model is formulated under the assumption that the force of infection at the present time depends on the number of infectives at the past. It is shown that a disease free equilibrium point is globally stable if no endemic equilibrium point exists. Further the endemic point (if it exists) is globally stable with respect to the whole state space except the neighborhood of the disease free state.Research partly supported by the Ministry of Education, Science and Culture, Japan, Grant 05640256     

Persistence of Native C4 Grasses under High-Intensity, Short-Duration Summer Bison Grazing in the Eastern Tallgrass Prairie

Disturbances such as burning or grazing maintain the herbaceous nature of eastern tallgrass prairie. These disturbances are also known to affect the relative abundance of warm-season (C4) and cool-season (C3) grasses in native prairie. Although burning is a commonly used tool, the utility of livestock grazing to manage restored prairie is less understood. We established five monocultures and one mixture of C4 grass species of the eastern tallgrass prairie in southern Wisconsin. To examine their persistence under high-intensity, short-duration summer grazing, we estimated cover of several functional groups and C4 species over a 6-year period (2000 through 2006) in a randomized complete block design. After a 2-year establishment phase (1998–1999), bison were rotated through paddocks two or three times annually during late June, July, or early August. All C4 grasses declined over time but at different rates depending on the species. Switchgrass ( Panicum virgatum ) decreased at the lowest rate, whereas Little bluestem ( Schizachyrium scoparium ) cover declined faster than Big bluestem ( Andropogon gerardii ), Indiangrass ( Sorghastrum nutans ), and Sideoats grama ( Bouteloua curtipendula ), whose rates of decline were not significantly different from each other. Succession followed a predictable trajectory with annual grasses initially colonizing interstitial space among C4 grasses, followed by legumes, which ultimately gave way to exotic C3 forage grasses. The focal C4 grasses remained the dominant functional group 8 years postseeding, but recolonization by non-native C3 grasses increased over the study period.     

The zinc complex catalyzed hydration of alkyl isothiocyanates

Based upon our preceding studies of the hydration of CO₂, COS and CS₂, accelerated by the carbonic anhydrase (CA) using simplified [ZnL₃OH]⁺ complexes as model catalysts, we calculated the hydration mechanisms of both the uncatalyzed and the [ZnL₃OH]⁺-catalyzed reactions (L = NH₃) of isothiocyanates RNCS on the B3LYP/6-311+G(d,p) level of theory. Interestingly, the transition state for the favored metal mediated reaction with the lowest Gibbs free energy is only slightly higher than in the case of CO₂ (depending on the attacking atom (N or S). Calculations under inclusion of solvent corrections show a reduction of the selectivity and a slight decrease of the Gibbs free energy in the rate-determining steps. The most plausible pathway prefers the mechanism via a Lindskog proton-shift transition state leading to the thermodynamically most stable product, the carbamatic-S-acid. Furthermore, powerful electron withdrawing substituents R of the cumulenic substrates influence the selectivity of the reaction to a significant extent. Especially the CF₃-group in trifluoromethylisothiocyanate reverses the selectivity. This investigation demonstrates that reaction principles developed by nature can be translated to develop efficient catalytic methods, in this case presumably for the transformation of a wide variety of heterocumulenes aside from CO₂, COS and CS₂. Figure Competing transition structures for the [ZnL₃OH]⁺-mediated activation of isothiocyanates Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Dynamic prediction of time to a clinical event with sparse and irregularly measured longitudinal biomarkers

In clinical research and practice, landmark models are commonly used to predict the risk of an adverse future event, using patients' longitudinal biomarker data as predictors. However, these data are often observable only at intermittent visits, making their measurement times irregularly spaced and unsynchronized across different subjects. This poses challenges to conducting dynamic prediction at any post-baseline time. A simple solution is the last-value-carry-forward method, but this may result in bias for the risk model estimation and prediction. Another option is to jointly model the longitudinal and survival processes with a shared random effects model. However, when dealing with multiple biomarkers, this approach often results in high-dimensional integrals without a closed-form solution, and thus the computational burden limits its software development and practical use. In this article, we propose to process the longitudinal data by functional principal component analysis techniques, and then use the processed information as predictors in a class of flexible linear transformation models to predict the distribution of residual time-to-event occurrence. The measurement schemes for multiple biomarkers are allowed to be different within subject and across subjects. Dynamic prediction can be performed in a real-time fashion. The advantages of our proposed method are demonstrated by simulation studies. We apply our approach to the African American Study of Kidney Disease and Hypertension, predicting patients' risk of kidney failure or death by using four important longitudinal biomarkers for renal functions.     

How does the push/pull effect of the axial ligand influence the catalytic properties of Compound I of catalase and cytochrome P450?

Density functional theory (DFT) calculations on the chemoselective epoxidation versus hydroxylation reactions of propene by oxoiron porphyrin models mimicking the active sites of catalase, cytochrome P450 (P450) and horseradish peroxidase Compound I (CpdI) are presented. The catalase reactions are concerted and proceed via two-state reactivity patterns on competing doublet and quartet spin state surfaces, but the lowest barrier is the one leading to epoxide products on the doublet spin surface. The results are compared with earlier DFT studies of models of cytochrome P450, horseradish peroxide (HRP), taurine/alpha-ketoglutarate dioxygenase and some synthetic oxoiron catalysts. The catalase barriers are midway in between those obtained for HRP and P450 models, so that tyrosinate ligated heme systems should be able to catalyze C-H hydroxylation and C=C epoxidation reactions. We show that for heme systems the barrier height of epoxidation linearly correlates with the electron affinity of Compound I as expected from the electron transfer mechanism of the rate determining step. Our studies show that the axial ligand does not influence the chemoselectivity of a reaction but that it does regulate the barrier heights and rate constants. Finally, we estimated the effect of the axial ligand on the oxoiron group and derived that it contributes from a field effect due to the charge of the ligand and a quantum mechanical effect as a result of orbital mixing. In catalase, the major component is the field effect, while the quantum mechanical effect is negligible. This is in contrast to P450 CpdI, where both effects are of similar order of magnitude.     

The axial ligand effect of oxo-iron porphyrin catalysts. How does chloride compare to thiolate?

We have performed density functional theory calculations on an oxo-iron porphyrin catalyst with chloride as an axial ligand and tested its reactivity toward propene. The reactions proceed via multistate reactivity on competing doublet and quartet spin surfaces. Close-lying epoxidation and hydroxylation mechanisms are identified, whereby in the gas phase the epoxidation reaction is dominant, while in environments with a large dielectric constant the hydroxylation pathways become competitive. By contrast to reactions with thiolate as an axial ligand all low-lying pathways have small ring-closure and rebound barriers, so it is expected that side products and rearrangements will be unlikely with Fe=O(porphyrin)Cl, whereas with Fe=O(porphyrin)SH some side products were predicted. The major differences in the electronic configurations of Fe=O(porphyrin)Cl and Fe=O(porphyrin)SH are due to strong mixing of thiolate orbitals with iron 3d orbitals, a mixing which is much less with chloride as an axial ligand. Predictions of the reactivity of ethylbenzene-h ₁₂ versus ethylbenzene-d ₁₂ are made. Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

Functional additive models for optimizing individualized treatment rules

A novel functional additive model is proposed, which is uniquely modified and constrained to model nonlinear interactions between a treatment indicator and a potentially large number of functional and/or scalar pretreatment covariates. The primary motivation for this approach is to optimize individualized treatment rules based on data from a randomized clinical trial. We generalize functional additive regression models by incorporating treatment-specific components into additive effect components. A structural constraint is imposed on the treatment-specific components in order to provide a class of additive models with main effects and interaction effects that are orthogonal to each other. If primary interest is in the interaction between treatment and the covariates, as is generally the case when optimizing individualized treatment rules, we can thereby circumvent the need to estimate the main effects of the covariates, obviating the need to specify their form and thus avoiding the issue of model misspecification. The methods are illustrated with data from a depression clinical trial with electroencephalogram functional data as patients' pretreatment covariates.     

Statistical analysis of functional response experiments

The aim of this paper is to highlight the benefits of a full data analysis of a functional response data set, compared to the usual one‐pass regression analysis. In a biological control setting where the choice of organism is often based on comparative studies of the functional responses, it is imperative to have both reliable estimates and a feeling of the degree of confidence one is willing to put on the figures. We analyzed a data set involving the freshwater predator Notonecta glauca (Hemiptera) preying on Asellus aquaticus during 24 h. The specific aim of the analysis was to test whether the functional response is of type II or type III. The different stages of a complete analysis are (1) a preliminary inspection of the data, (2) model building, (3) a model check and (4) a combination of the results with independent information. We argue that the analysis is best done with the predation rate as response and define a test for the location of its maximum. The existence of a maximum is typical for type III functional response. We explain why the binomial distribution is a natural error distribution, and how to implement the regression analysis within the family of generalized linear models using two competing link functions, the logit and the reciprocal. There is marked overdispersion which increases with increasing prey numbers. We use prior weights to take account of it. Using all available data, a type III functional response is warranted with the reciprocal link, but not with the logit link Model checks using Pearson residuals and regression diagnostics based on point deletions show that three points have a particularly strong influence on the parameter estimates. If these are deleted, the functional response type III is then warranted for both link functions. The complete analysis enables us to determine the various degrees of uncertainty and to draw biological conclusions with corresponding confidence. We are convinced that the data set shows a type III functional response, but we are less sure about which link function to choose. Furthermore, the marked overdispersion at high density, the regression diagnostics, as well as independent information on a change in the behaviour of the prey at high density, indicate that the experimental conditions may have changed as a function of the prey density.     

EMMA--the European mouse mutant archive.

The European Mouse Mutant Archive (EMMA) offers the worldwide scientific community a free archiving service for its mutant mouse lines and access to a wide range of disease models and other research tools. EMMA is currently comprised of seven partners who operate as the primary mouse repository in Europe. EMMA' s primary objectives are to establish and manage a unified repository for maintaining mouse mutations and to make them available to the scientific community. In addition to these core services, the consortium can generate germ-free (axenic) mice for its customers and also hosts courses in cryopreservation. EMMA is a founder member of the Federation of International Mouse Resources (FIMRe). The EMMA network is funded by the participating institutes, national research programmes and the European Commission Research Infrastructures Programme.     

热带森林植物功能群及其动态研究进展

热带森林极高的物种多样性和结构复杂性给生态学研究带来了很多挑战。植物功能群是对特定环境响应相似或对主要的生态过程具有相似作用的物种组合。应用植物功能群的方法是有效减少热带森林群落复杂性,并揭示其格局和过程的良好途径。在介绍植物功能群概念和划分途径的基础上,分析了热带森林植物功能群的时空动态规律。一般来讲,划分植物功能群通常有3种途径,并可通过5个步骤来完成。热带森林植物功能群的空间分布常受景观格局的制约,而环境异质性往往是影响不同植物功能群组配比例变化的直接原因。不同类型的植物功能群随演替过程发生显著的替代,而干扰体系和全球气候变化对功能群的动态过程具有重要的驱动作用。以功能群为基础的动态模型在模拟热带林群落动态和预测植被潜在分布等方面具有广阔的发展前景。探索有效的植物功能分类方法、构建完善的植物功能性状数据库、开发更为精确的功能群动态模型以及加强基于景观水平的植物功能群动态机制的认识等是未来热带森林植物功能群及其动态研究的重要方向。     

Patterns of plant functional traits in the biogeography of West African grasses (Poaceae)

Grasses (Poaceae) are the largest family of vascular plants in Burkina Faso with 254 species. In the savannahs they are the most important family in terms of abundance and species richness, in other habitats, such as gallery forests, there are only few species. On the country scale there is a change in growth form: while in the Sahelian north most grasses are small therophytes, the Sudanian south is characterized by tall, often perennial grasses. To analyse these patterns in detail, we compiled a database on grass occurrences and used it in an ecological niche modelling approach with the programme Maxent to obtain country‐wide distribution models. Secondly we used data on photosynthetic type, height, leaf width and growth form to aggregate the species distributions and quantified the relative importance of functional groups per grid cell. Pronounced latitudinal differences could be shown for life forms, photosynthesis and size: the drier north is characterized by smaller, mainly therophytic grasses with a high share of C4 NAD‐ME photosynthesis, while the more humid south is characterized by tall, often hemicryptophytic grasses with C4 NADP‐ME photosynthesis. For leaf width, no clear country‐wide patterns could be observed, but local differences with more broad‐leaved grasses in humid areas.