In vitro DNA-based predator-prey system with oscillatory kinetics

A coupled system of two isothermal in vitro DNA/RNA amplification reactions using different primers is modeled kinetically with realistic rate parameters and shown to exhibit oscillatory behavior in a flow reactor. One of the two isothermal amplification reactions acts as a predator of the other, the prey. The mechanism of the oscillatory behavior is analyzed in terms of a hierarchy of kinetic models. The work provides an insight into the choice of parameters for experiments. The latter are important in providing detailed insight into the complex processes of ecological interactions and their evolution.     

社会-经济-自然复合生态系统有效物质(能量、货币)平衡模型的建立及其应用

根据质量守恒定律和有效物质（能量、货币）在系统内外部转化关系建立了社会、神经-自然复合生态系统有效物质（能量、货币）平衡模型,定义了模型特征参数。将模型应用于3个不同的研究领域,获得了相应研究领域的平衡模型,结果表明所建立的平衡模型具有通用性,它对于研究复合生态系统有效物质、能量和货币平衡具有重要的理论和实践意义。     

A critical assessment of two species distribution models: a case study of the vervet monkey (Cercopithecus aethiops)

Aim Species distribution models are invaluable tools in biogeographical, ecological and applied biological research, but specific concerns have been raised in relation to different modelling techniques in terms of their validity. Here we compare two fundamentally different approaches to species distribution modelling, one based on simple occurrence data where the lack of an ecological framework has been criticized, and the other firmly based in socio‐ecological theory but requiring highly detailed behavioural information that is often limited in availability. Location (Sub‐Saharan) Africa. Methods We used two distinct techniques to predict the realized distribution of a model species, the vervet monkey (Cercopithecus aethiops Linnaeus, 1758). A maximum entropy model was produced taking 13 environmental variables and presence‐only data from 174 sites throughout Africa as input, with an additional 58 sites retained to test the model. A time‐budget model considering the same environmental variables was constructed from detailed behavioural data on 20 groups representing 14 populations, with presence‐only data from the remaining 218 sites reserved to test model predictions on vervet monkey occurrence. Both models were further validated against a reference species distribution map as drawn up by the African Mammals Databank. Results Both models performed well, with the time budget and maximum entropy algorithms correctly predicting vervet monkey presence at 78.4% and 91.4% of their respective test sites. Similarly, the time‐budget model correctly predicted presence and absence at 87.4% of map pixels against the reference distribution map, and the maximum entropy model achieved a success rate of 81.8%. Finally, there was a high level of agreement (81.6%) between the presence–absence maps produced by the two models, and the environmental variables identified as most strongly driving vervet monkey distribution were the same in both models. Main conclusions The time‐budget and maximum entropy models produced accurate and remarkably similar species distribution maps, despite fundamental differences in their conceptual and methodological approaches. Such strong convergence not only provides support for the credibility of current results, but also relieves concerns about the validity of the two modelling approaches.     

Plugging space into predator-prey models: an empirical approach

Extrapolating ecological processes from small-scale experimental systems to scales of natural populations usually entails a considerable increase in spatial heterogeneity, which may affect process rates and, ultimately, population dynamics. We demonstrate how information on the heterogeneity of natural populations can be taken into account when scaling up laboratory-derived process functions, using the technique of moment approximation. We apply moment approximation to a benthic crustacean predator-prey system, where a laboratory-derived functional response is made spatial by including correction terms for the variance in prey density and the covariance between prey and predator densities observed in the field. We also show how moment approximation may be used to incorporate spatial information into a dynamic model of the system. While the nonspatial model predicts stable dynamics, its spatial equivalent also produces bounded fluctuations, in agreement with observed dynamics. A detailed analysis shows that predator-prey covariance, but not prey variance, destabilizes the dynamics. We conclude that second-order moment approximation may provide a useful technique for including spatial information in population models. The main advantage of the method is its conceptual value: by providing explicit estimates of variance and covariance effects, it offers the possibility of understanding how heterogeneity affects ecological processes.     

Analysis of non-Newtonian effects within an aorta-iliac bifurcation region

The geometry of the arteries at or near arterial bifurcation influences the blood flow field, which is an important factor affecting arteriogenesis. The blood can act sometimes as a non-Newtonian fluid. However, many studies have argued that for large and medium arteries, the blood flow can be considered to be Newtonian. In this work a comprehensive investigation of non-Newtonian effects on the blood fluid dynamic behavior in an aorta-iliac bifurcation is presented. The aorta-iliac geometry is reconstructed with references to the values reported in Shah et al. (1978); the 3D geometrical model consists of three filleted cylinders of different diameters. Governing equations with the appropriate boundary conditions are solved with a finite-element code. Different rheological models are used for the blood flow through the lumen and detailed comparisons are presented for the aorta-iliac bifurcation. Results are presented in terms of the velocity profiles in the bifurcation zone and Wall Shear Stress (WSS) for different sides of the bifurcation both for male and female geometries, showing that the Newtonian fluid assumption can be made without any particular loss in terms of accuracy with respect to the other more complex rheological models.     

Power-law models of signal transduction pathways

The mathematical modelling of signal transduction pathways has become a valuable aid to understanding the complex interactions involved in intracellular signalling mechanisms. An important aspect of the mathematical modelling process is the selection of the model type and structure. Until recently, the convention has been to use a standard kinetic model, often with the Michaelis-Menten steady state assumption. However this model form, although valuable, is only one of a number of choices, and the aim of this article is to consider the mathematical structure and essential features of an alternative model form--the power-law model. Specifically, we analyse how power-law models can be applied to increase our understanding of signal transduction pathways when there may be limited prior information. We distinguish between two kinds of power law models: a) Detailed power-law models, as a tool for investigating pathways when the structure of protein-protein interactions is completely known, and; b) Simplified power-law models, for the analysis of systems with incomplete structural information or insufficient quantitative data for generating detailed models. If sufficient data of high quality are available, the advantage of detailed power-law models is that they are more realistic representations of non-homogenous or crowded cellular environments. The advantages of the simplified power-law model formulation are illustrated using some case studies in cell signalling. In particular, the investigation on the effects of signal inhibition and feedback loops and the validation of structural hypotheses are discussed.     

An ecologist's guide to the animal model

1. Efforts to understand the links between evolutionary and ecological dynamics hinge on our ability to measure and understand how genes influence phenotypes, fitness and population dynamics. Quantitative genetics provides a range of theoretical and empirical tools with which to achieve this when the relatedness between individuals within a population is known.
2. A number of recent studies have used a type of mixed-effects model, known as the animal model, to estimate the genetic component of phenotypic variation using data collected in the field. Here, we provide a practical guide for ecologists interested in exploring the potential to apply this quantitative genetic method in their research.
3. We begin by outlining, in simple terms, key concepts in quantitative genetics and how an animal model estimates relevant quantitative genetic parameters, such as heritabilities or genetic correlations.
4. We then provide three detailed example tutorials, for implementation in a variety of software packages, for some basic applications of the animal model. We discuss several important statistical issues relating to best practice when fitting different kinds of mixed models.
5. We conclude by briefly summarizing more complex applications of the animal model, and by highlighting key pitfalls and dangers for the researcher wanting to begin using quantitative genetic tools to address ecological and evolutionary questions.     

鄂尔多斯高原植物群落季节生长格局模拟

影响大尺度空间生态模型模拟结果与资源管理整合的因素主要有两种:一是一些模型生态学意义不明确,二是一些模型所需要的生态输入信息过于复杂。建立一个基于基本的生态学公理且输入较为简单的生态学模型,便于更加有效地服务于资源环境管理。该模型用于模拟发生严重荒漠化的鄂尔多斯高原植物群落的季节及年生长、叶片投影盖度、蒸发系数。模型首先基于降雨、蒸散、渗漏及土壤水分特性与蒸发系数(k)的关系,采用迭代的计算方法,模拟植物群落蒸散与土壤可利用水分达到平衡状态时的k值,进而采用得到广泛验证的经验公式计算植物群落的其它参数。野外N PP观察数据对模型的验证表明:模拟结果与观察值相符较好。模拟结果表明:蒸发系数小于0 .35×10 - 2 ,显示鄂尔多斯高原气候较为干燥;叶片投影盖度低于5 0 % ;除东部的准格尔旗外,植物群落净第一性生产力均低于1t/(hm2·a) ,近90 %的N PP累积集中于5至8月份。根据该文的模拟结果,在进行植被恢复时,恢复植被密度必须低于5 0 % ,放牧密度以0 .8～2 .0个/hm2 羊单位为宜     

Mapping the complexity of ecological models

We propose to define the complexity of an ecological model as the statistical complexity of the output it produces. This allows for a direct comparison between data and model complexity. Working with univariate time series, we show that this measure ‘blindly’ discriminates among the different dynamical behaviours a model can exhibit. We then search a model parameter space in order to segment it into areas of different dynamical behaviour and calculate the maximum complexity a model can generate. Given a time series, and the problem of choosing among a number of ecological models to study it, we suggest that models whose maximum complexity is lower than the time series complexity should be disregarded because they are unable to reconstruct some of the structures contained in the data. Similar reasoning could be used to disregard models’ subdomains as well as areas of unnecessary high complexity. We suggest that model complexity so defined better captures the difficulty faced by a user in managing and understanding the behaviour of an ecological model than measures based on a model ‘size’.     

Application of classification-tree models to characterize the mycobiota of grapes on the basis of origin

Classification-tree (CT) models are a simple and robust exploratory data analysis technique that can be used in classification, regressions and summaries of data. They distill complex ecological relationships into simplified rules and identify the species necessary for sample classification on the basis of detailed ecological inventories. The usefulness of this technique to characterize and represent differences in the grape mycobiota of distinct origins was evaluated. Grapes from four Portuguese winemaking regions were selected for a 3-year study: Alentejo, Douro, Ribatejo and Vinhos Verdes. The mycobiota of grapes was assessed with plating methods and the frequencies of isolations of the fungal taxa identified in 32 samples were used as a training dataset. The CT algorithm selected the fungal taxa and respective frequencies to classify grapes according to its region of origin. The ten-fold cross-validation technique was used for model evaluation. The success rate of the model was quantified and expressed in the number of correctly classified samples overall and into region. Furthermore, model refinement was performed using attribute selection algorithms and class redefinition. A simple tree model was generated that classified grapes into three regional origins: Douro, South (Alentejo and Ribatejo classes together) and Vinhos Verdes, on the basis of the incidence of Aspergillus niger aggregate and Penicillium thomii in samples with an accuracy of 82%. The merits and demerits of these models are discussed.     

Comparison of a Homology Built Model of Angiogenin to its Crystal Structure

The comparison of our homology built model of human angiogenin with the recently determined x-ray structure of the same is reported. The basic details of the structure in terms of alpha -helices and beta sheets were found to be common. The main differences between the model and the x-ray data lie in a C-terminal rearrangement in the x-ray structure that causes the C-terminus to end in a 3₁₀ helix which puts the residue GLN-117 (ALA-122 in bovine pancreatic ribonuclease A, RNaseA) into the active site. The homology model was updated by producing a new sequence alignment using the information from the x-ray data which improved the r.m.s. by 0.5Å. This new alignment is also reported here. A check for systematic bias was carried out using the RNaseA structures from which the x-ray and homology models were derived. A detailed comparison of torsion angles and hydrogen bonding between all the structures have been compared and the model displays several hydrogen bonds that are not present in the parent RNaseA structures but are present in the x-ray structure of angiogenin.Electronic Supplementary Material available.     

The ecological role of cephalopods and their representation in ecosystem models

Cephalopods, especially squids, are believed to have a structuring role in marine ecosystems as a link between different trophic levels, primarily due to their voracious prey consumption and high production rate. Cephalopod ecology, however, is still poorly understood as observational studies often give highly uncertain and variable results due to the peculiarities of cephalopod behaviour and biology, and their responsiveness to external drivers. This review evaluates our representation of cephalopods in ecosystem models and the insights given by these models on the role of cephalopods in our oceans. We examined ecosystem models from 13 regions to analyse the representation of cephalopods and compared their results to local trophic studies. Our analysis indicated that most ecosystem models inadequately include cephalopods in terms of model structure and parametrization; although some models still have the capacity to draw valuable conclusions regarding the impact and role of cephalopods within the system. Oceanic squid species have a major role linking trophic levels and food webs from different habitats. The importance of neritic species varies locally, but generally cephalopods have a substantial impact via their consumer role. To better understand the ecological role of cephalopods, improved representation of these species in ecosystem models is a critical requirement and could be achieved relatively easily to more accurately articulate the mechanisms regulating the ecological role of cephalopods.

     

Sexual differences in microhabitat selection of breeding little bustards Tetrax tetrax: Ecological segregation based on vegetation structure

We examined sexual differences in patterns of vegetation structure selection in the sexually dimorphic little bustard. Differences in vegetation structure between male, female and non-used locations during reproduction were examined and used to build a presence/absence model for each sex. Ten variables were measured in each location, extracting two PCA factors (PC1: a visibility-shelter gradient; PC2: a gradient in food availability) used as response variables in GLM explanatory models. Both factors significantly differed between female, male and control locations. Neither study site nor phenology was significant. Logistic regression was used to model male and female presence/absence. Female presence was positively associated to cover of ground by vegetation litter, as well as overall vegetation cover, and negatively to vegetation density over 30 cm above ground. Male presence was positively related to litter cover and short vegetation and negatively to vegetation density over 30 cm above ground. Models showed good global performance and robustness. Female microhabitat selection and distribution seems to be related to the balance between shelter and visibility for surveillance. Male microhabitat selection would be related mainly to the need of conspicuousness for courtship. Accessibility to food resources seems to be equally important for both sexes. Differences suggest ecological sexual segregation resulting from different ecological constraints. These are the first detailed results on vegetation structure selection in both male and female little bustards, and are useful in designing management measures addressing vegetation structure irrespective of landscape composition. Similar microhabitat approaches can be applied to manage the habitat of many declining farmland birds.     

Evaluation of the structural quality of modeled proteins by using globularity criteria

Background  

The knowledge of the three-dimensional structure of globular proteins is fundamental for a detailed investigation of their functional properties. Experimental methods are too slow for structure investigation on a large scale, while computational prediction methods offer alternatives that are continuously being improved. The international Comparative Assessment of Structure Prediction (CASP), an "a posteriori" evaluation of the quality of theoretical models when the experimental structure becomes available, demonstrates that predictions can be successful as well as unsuccessful, and this suggests the necessity for evaluations able to discard "a priori" the wrong models.     

Why do some species have geographically varying responses to fire history?

A capacity to predict the effects of fire on biota is critical for conservation in fire‐prone regions as it assists managers to anticipate the outcomes of different approaches to fire management. The task is complicated because species’ responses to fire can vary geographically. This poses challenges, both for conceptual understanding of post‐fire succession and fire management. We examine two hypotheses for why species may display geographically varying responses to fire. 1) Species’ post‐fire responses are driven by vegetation structure, but vegetation – fire relationships vary spatially (the ‘dynamic vegetation’ hypothesis). 2) Regional variation in ecological conditions leads species to select different post‐fire ages as habitat (the ‘dynamic habitat’ hypothesis). Our case study uses data on lizards at 280 sites in a ～ 100 000 km² region of south‐eastern Australia. We compared the predictive capacity of models based on 1) habitat associations, with models based on 2) fire history and vegetation type, and 3) fire history alone, for four species of lizards. Habitat association models generally out‐performed fire history models in terms of predictive capacity. For two species, habitat association models provided good discrimination capacity even though the species showed geographically varying post‐fire responses. Our results support the dynamic vegetation hypothesis, that spatial variation in relationships between fire and vegetation structure results in regional variation in fauna–fire relationships. These observations explain how the widely recognised ‘habitat accommodation’ model of animal succession can be conceptually accurate yet predictively weak.     

红树林湿地模型研究进展

红树林是位于海岸潮间带的森林湿地生态系统,具有抗风削浪、保护堤岸、封存CO2缓解全球气候变化等多种功能。然而,由于地理位置及生存环境特殊,红树林湿地模型的研究相对内陆湿地滞后。为了推动红树林湿地模型的研究,本文将目前常见红树林湿地模型按功能划分为植被生长生产模型、水文模型、物流能流模型三类,以阐述相关模型研究的进展,并对目前红树林湿地模型研究提出几点看法:(1)现有红树林湿地模型在不同区域、尺度下运行的有效性有待进一步验证;(2)国内对红树林生态系统服务及植被恢复工作相关模型研究较少,今后需加强该方面的研究。