A multiscale model for eccentric and concentric cardiac growth through sarcomerogenesis

We present a novel computational model for maladaptive cardiac growth in which kinematic changes of the cardiac chambers are attributed to alterations in cytoskeletal architecture and in cellular morphology. We adopt the concept of finite volume growth characterized through the multiplicative decomposition of the deformation gradient into an elastic part and a growth part. The functional form of its growth tensor is correlated to sarcomerogenesis, the creation and deposition of new sarcomere units. In response to chronic volume-overload, an increased diastolic wall strain leads to the addition of sarcomeres in series, resulting in a relative increase in cardiomyocyte length, associated with eccentric hypertrophy and ventricular dilation. In response to chronic pressure-overload, an increased systolic wall stress leads to the addition of sacromeres in parallel, resulting in a relative increase in myocyte cross sectional area, associated with concentric hypertrophy and ventricular wall thickening. The continuum equations for both forms of maladaptive growth are discretized in space using a nonlinear finite element approach, and discretized in time using the implicit Euler backward scheme. We explore a generic bi-ventricular heart model in response to volume- and pressure-overload to demonstrate how local changes in cellular morphology translate into global alterations in cardiac form and function.     

Diversity- and density-mediated allelopathic effects of resident plant communities on invasion by an exotic plant

Plant and Soil - Resident plants can exert allelopathic effects on introduced exotic plants, and resistance to exotic plant invasions usually increases with diversity and density of the resident...     

Insect herbivory stimulates allelopathic exudation by an invasive plant and the suppression of natives

Exotic invasive plants are often subjected to attack from imported insects as a method of biological control. A fundamental, but rarely explicitly tested, assumption of biological control is that damaged plants are less fit and compete poorly. In contrast, we find that one of the most destructive invasive plants in North America, Centaurea maculosa, exudes far higher amounts of (±)‐catechin, an allelopathic chemical known to have deleterious effects on native plants, when attacked by larvae of two different root boring biocontrol insects and a parasitic fungus. We also demonstrate that C. maculosa plants experimentally attacked by one of these biocontrols exhibit more intense negative effects on natives.     

A multiscale model for avascular tumor growth

The desire to understand tumor complexity has given rise to mathematical models to describe the tumor microenvironment. We present a new mathematical model for avascular tumor growth and development that spans three distinct scales. At the cellular level, a lattice Monte Carlo model describes cellular dynamics (proliferation, adhesion, and viability). At the subcellular level, a Boolean network regulates the expression of proteins that control the cell cycle. At the extracellular level, reaction-diffusion equations describe the chemical dynamics (nutrient, waste, growth promoter, and inhibitor concentrations). Data from experiments with multicellular spheroids were used to determine the parameters of the simulations. Starting with a single tumor cell, this model produces an avascular tumor that quantitatively mimics experimental measurements in multicellular spheroids. Based on the simulations, we predict: 1), the microenvironmental conditions required for tumor cell survival; and 2), growth promoters and inhibitors have diffusion coefficients in the range between 10(-6) and 10(-7) cm2/h, corresponding to molecules of size 80-90 kDa. Using the same parameters, the model also accurately predicts spheroid growth curves under different external nutrient supply conditions.     

A multiscale model for red blood cell mechanics

The objective of this article is the derivation of a continuum model for mechanics of red blood cells via multiscale analysis. On the microscopic level, we consider realistic discrete models in terms of energy functionals defined on networks/lattices. Using concepts of Γ-convergence, convergence results as well as explicit homogenisation formulae are derived. Based on a characterisation via energy functionals, appropriate macroscopic stress–strain relationships (constitutive equations) can be determined. Further, mechanical moduli of the derived macroscopic continuum model are directly related to microscopic moduli. As a test case we consider optical tweezers experiments, one of the most common experiments to study mechanical properties of cells. Our simulations of the derived continuum model are based on finite element methods and account explicitly for membrane mechanics and its coupling with bulk mechanics. Since the discretisation of the continuum model can be chosen freely, rather than it is given by the topology of the microscopic cytoskeletal network, the approach allows a significant reduction of computational efforts. Our approach is highly flexible and can be generalised to many other cell models, also including biochemical control.     

A game-theoretic model for punctuated equilibrium: species invasion and stasis through coevolution

A general theory of coevolution is developed that combines the ecological effects of species' densities with the evolutionary effects of changing phenotypes. Our approach also treats the evolutionary changes between coevolving species with discreet traits after the appearance of a new species. We apply this approach to habitat selection models where new species first emerge through competitive selection in an isolated habitat. This successful invasion is quickly followed by evolutionary changes in behavior when this species discovers the other habitat, leading to punctuated equilibrium as the final outcome.     

Multiple anthropogenic changes cause biodiversity loss through plant invasion

Non‐native invasive plants are a widely acknowledged threat to global biodiversity. However, our understanding of the mechanisms underlying plant invasion, and the relative importance of multiple rather than single drivers, remains poor. Here, we provide a case study using time‐series data to reconstruct patterns of change, and field experiments to test for causality. We show how, over a 50‐year period, a series of unrelated human‐induced changes created highly favorable conditions for the non‐native tree mallow (Lavatera arborea) to turn invasive, causing loss of native vegetation and seabird breeding habitat. The combination of three drivers: human‐introduced disease, climate warming and a fisheries‐mediated increase in seabird populations, removed major constraints on plant population growth, (i.e. grazer control, climatic control, germination opportunity and nutrient limitation). Collectively, these changes created optimal conditions for the rapid expansion of tree mallow. The resulting dramatic impact on both the native vegetation and breeding seabirds, notably puffins (Fratercula arctica), exemplifies how non‐native invasive plant species can transform terrestrial ecosystems. While climate change is regarded as a key factor behind plant invasion, we highlight that multiple rather than single factors may be critical to biodiversity loss.     

Restoration through reassembly: plant traits and invasion resistance

One of the greatest challenges for ecological restoration is to create or reassemble plant communities that are resistant to invasion by exotic species. We examine how concepts pertaining to the assembly of plant communities can be used to strengthen resistance to invasion in restored communities. Community ecology theory predicts that an invasive species will be unlikely to establish if there is a species with similar traits present in the resident community or if available niches are filled. Therefore, successful restoration efforts should select native species with traits similar to likely invaders and include a diversity of functional traits. The success of trait-based approaches to restoration will depend largely on the diversity of invaders, on the strength of environmental factors and on dispersal dynamics of invasive and native species.     

A three-dimensional multiscale model for gas exchange in fruit

Respiration of bulky plant organs such as roots, tubers, stems, seeds, and fruit depends very much on oxygen (O2) availability and often follows a Michaelis-Menten-like response. A multiscale model is presented to calculate gas exchange in plants using the microscale geometry of the tissue, or vice versa, local concentrations in the cells from macroscopic gas concentration profiles. This approach provides a computationally feasible and accurate analysis of cell metabolism in any plant organ during hypoxia and anoxia. The predicted O2 and carbon dioxide (CO2) partial pressure profiles compared very well with experimental data, thereby validating the multiscale model. The important microscale geometrical features are the shape, size, and three-dimensional connectivity of cells and air spaces. It was demonstrated that the gas-exchange properties of the cell wall and cell membrane have little effect on the cellular gas exchange of apple (Malus×domestica) parenchyma tissue. The analysis clearly confirmed that cells are an additional route for CO2 transport, while for O2 the intercellular spaces are the main diffusion route. The simulation results also showed that the local gas concentration gradients were steeper in the cells than in the surrounding air spaces. Therefore, to analyze the cellular metabolism under hypoxic and anoxic conditions, the microscale model is required to calculate the correct intracellular concentrations. Understanding the O2 response of plants and plant organs thus not only requires knowledge of external conditions, dimensions, gas-exchange properties of the tissues, and cellular respiration kinetics but also of microstructure.     

A multiscale model for multiple platelet aggregation in shear flow

Biomechanics and Modeling in Mechanobiology - We developed a multiscale model for simulating aggregation of multiple, free-flowing platelets in low–intermediate shear viscous flow, in which...     

Microenvironment driven invasion: a multiscale multimodel investigation

Cancer is a complex, multiscale process, in which genetic mutations occurring at a subcellular level manifest themselves as functional and morphological changes at the cellular and tissue scale. The importance of interactions between tumour cells and their microenvironment is currently of great interest in experimental as well as computational modelling. Both the immediate microenvironment (e.g. cell-cell signalling or cell-matrix interactions) and the extended microenvironment (e.g. nutrient supply or a host tissue structure) are thought to play crucial roles in both tumour progression and suppression. In this paper we focus on tumour invasion, as defined by the emergence of a fingering morphology, which has previously been shown to be dependent upon harsh microenvironmental conditions. Using three different modelling approaches at two different spatial scales we examine the impact of nutrient availability as a driving force for invasion. Specifically we investigate how cell metabolism (the intrinsic rate of nutrient consumption and cell resistance to starvation) influences the growing tumour. We also discuss how dynamical changes in genetic makeup and morphological characteristics, of the tumour population, are driven by extreme changes in nutrient supply during tumour development. The simulation results indicate that aggressive phenotypes produce tumour fingering in poor nutrient, but not rich, microenvironments. The implication of these results is that an invasive outcome appears to be co-dependent upon the evolutionary dynamics of the tumour population driven by the microenvironment.     

Propagule pressure and an invasion syndrome determine invasion success in a plant community model

The success of species invasions depends on multiple factors, including propagule pressure, disturbance, productivity, and the traits of native and non‐native species. While the importance of many of these determinants has already been investigated in relative isolation, they are rarely studied in combination. Here, we address this shortcoming by exploring the effect of the above‐listed factors on the success of invasions using an individual‐based mechanistic model. This approach enables us to explicitly control environmental factors (temperature as surrogate for productivity, disturbance, and propagule pressure) as well as to monitor whole‐community trait distributions of environmental adaptation, mass, and dispersal abilities. We simulated introductions of plant individuals to an oceanic island to assess which factors and species traits contribute to invasion success. We found that the most influential factors were higher propagule pressure and a particular set of traits. This invasion trait syndrome was characterized by a relative similarity in functional traits of invasive to native species, while invasive species had on average higher environmental adaptation, higher body mass, and increased dispersal distances, that is, had greater competitive and dispersive abilities. Our results highlight the importance in management practice of reducing the import of alien species, especially those that display this trait syndrome and come from similar habitats as those being managed.     

Some roles of allelopathic compounds in plant communities

Banzan Kumazawa reported some 300 years ago in Japan that rain or dew which washes the leaves of red pine (Pinus densiflora) is harmful to crops growing under the pine. De Candolle suggested also in 1832 that certain weeds secrete toxins which inhibit growth of crop plants. Despite these suggestions, it is only in the past 70 years that appreciable research has been done in the field of allelopathy and only in the past 15 years that much research has been directed toward elucidating some of the many roles of allelopathy in ecological processes. Some of the more notable ecological phenomena and processes in which allelopathy has been implicated are: succession, patterning of vegetation, prevention of seed decay prior to germination, inhibition of nitrification by climax ecosystems, dormancy of seeds, promotion of infection by pathogens, and resistance to infection.     

A simulation model of plant invasion: long-distance dispersal determines the pattern of spread

Mechanisms and consequences of biological invasions are a global issue. Yet, one of the key aspects, the initial phase of invasion, is rarely observed in detail. Data from aerial photographs covering the spread of Heracleum mantegazzianum (Apiaceae, native to Caucasus) on a local scale of hectares in the Czech Republic from the beginning of invasion were used as an input for an individual-based model (IBM), based on small-scale and short-time data. To capture the population development inferred from the photographs, long-distance seed dispersal, changes in landscape structures and suitability of landscape elements to invasion by H. mantegazzianum were implemented in the model. The model was used to address (1) the role of long-distance dispersal in regional invasion dynamics, and (2) the effect of land-use changes on the progress of the invasion. Simulations showed that already small fractions of seed subjected to long-distance dispersal, as determined by systematic comparison of field data and modelling results, had an over-proportional effect on the spread of this species. The effect of land-use changes on the simulated course of invasion depends on the actual level of habitat saturation; it is larger for populations covering a high proportion of available habitat area than for those in the initial phase of invasion. Our results indicate how empirical field data and model outputs can be linked more closely with each other to improve the understanding of invasion dynamics. The multi-level, but nevertheless simple structure of our model suggests that it can be used for studying the spread of similar species invading in comparable landscapes.     

A functional trait perspective on plant invasion

Background and Aims

Global environmental change will affect non-native plant invasions, with profound potential impacts on native plant populations, communities and ecosystems. In this context, we review plant functional traits, particularly those that drive invader abundance (invasiveness) and impacts, as well as the integration of these traits across multiple ecological scales, and as a basis for restoration and management.

Scope

We review the concepts and terminology surrounding functional traits and how functional traits influence processes at the individual level. We explore how phenotypic plasticity may lead to rapid evolution of novel traits facilitating invasiveness in changing environments and then ‘scale up’ to evaluate the relative importance of demographic traits and their links to invasion rates. We then suggest a functional trait framework for assessing per capita effects and, ultimately, impacts of invasive plants on plant communities and ecosystems. Lastly, we focus on the role of functional trait-based approaches in invasive species management and restoration in the context of rapid, global environmental change.

Conclusions

To understand how the abundance and impacts of invasive plants will respond to rapid environmental changes it is essential to link trait-based responses of invaders to changes in community and ecosystem properties. To do so requires a comprehensive effort that considers dynamic environmental controls and a targeted approach to understand key functional traits driving both invader abundance and impacts. If we are to predict future invasions, manage those at hand and use restoration technology to mitigate invasive species impacts, future research must focus on functional traits that promote invasiveness and invader impacts under changing conditions, and integrate major factors driving invasions from individual to ecosystem levels.     

植物化感物质及化感潜力与土壤养分的相互影响

植物化感作用与许多生态因子有关.土壤养分缺乏,影响着许多植物化感物质的产生,从而影响植物的化感潜力;反过来,植物化感物质也通过络合、吸附、酸溶解、竞争、抑制等方式影响土壤的养分形态和水平.本文总结了植物化感物质及化感潜力与土壤养分的相互影响,并提出了今后该领域值得进一步研究的问题.包括以下几方面：加强植物化感研究与土壤 植物营养学研究的结合,以更深入地阐明植物化感物质、化感作用与土壤养分变化的关系;加强植物化感研究与生态系统养分循环研究的结合,以类似自然（nature-like）的方式模拟自然界植物所受的养分干,使养分干扰的化感研究结果更加逼真、可靠;加强对养分过量及受污染时植物化感作用的研究,为揭示农业和林业生产中植物的相互作用机制和生物量变化机制提供新的思路,为生态保护提供科学依据.     

A model for suppression and dominance in trees

A new differential equation model for the growth of trees, involving structure/storage partitioning, is set up. The model, which is relatively simple, is shown to exhibit suppression and dominance effects. It also suggests a possible mechanism for the bimodal distributions of tree size which are observed in even-aged monoculture stands.     

A multiscale theoretical model for diffusive mass transfer in cellular biological media

An integrated methodology is developed for the theoretical analysis of solute transport and reaction in cellular biological media, such as tissues, microbial flocs, and biofilms. First, the method of local spatial averaging with a weight function is used to establish the equation which describes solute conservation at the cellular biological medium scale, starting with a continuum-based formulation of solute transport at finer spatial scales. Second, an effective-medium model is developed for the self-consistent calculation of the local diffusion coefficient in the cellular biological medium, including the effects of the structural heterogeneity of the extra-cellular space and the reversible adsorption to extra-cellular polymers. The final expression for the local effective diffusion coefficient is: D(Abeta)=lambda(beta)D(Aupsilon), where D(Aupsilon) is the diffusion coefficient in water, and lambda(beta) is a function of the composition and fundamental geometric and physicochemical system properties, including the size of solute molecules, the size of extra-cellular polymer fibers, and the mass permeability of the cell membrane. Furthermore, the analysis sheds some light on the function of the extra-cellular hydrogel as a diffusive barrier to solute molecules approaching the cell membrane, and its implications on the transport of chemotherapeutic agents within a cellular biological medium. Finally, the model predicts the qualitative trend as well as the quantitative variability of a large number of published experimental data on the diffusion coefficient of oxygen in cell-entrapping gels, microbial flocs, biofilms, and mammalian tissues.