A periodic table for ecology? A chemist's view of plant functional types

Abstract. A functional type approach, in which the complexity found in nature is reduced by grouping organisms that are functionally similar into a single classification, is being promoted in global change research. This paper examines a proposed analogy between this functional type approach in global change ecology and the periodic table of the elements in chemistry. When applied to a ‘bottom-up’ approach for defining functional types in ecology, in which large numbers of organisms are classified into smaller groups based on similarity of certain functions, the analogy fails. Ecological functions are not simple attributes of a biological entity, as electronic structure is for a chemical element, but are themselves complex chemical and physical systems that often interact strongly with the environment. The analogy to the periodic table may be of some use as an organizing tool in a ‘top-down’ approach in which a modelling context is used to define the number of ‘elements’ and their properties. This will be elaborated for plant functional types. Each PFT is assigned characteristics that allow its response to the driving forces of change, e.g. temperature, precipitation, soil nutrients, disturbance, to be predicted. ‘Rules of combination’ determine how the mix of PFTs in a particular ecosystem changes to form different ecosystems, which would correspond in the analogy to chemical compounds. However, these requirements present significant challenges to the usefulness of the analogy, even as an organizing tool in the ‘top-down’ approach.     

A functional�Cstructural modelling approach to autoregulation of nodulation

Background and Aims

Autoregulation of nodulation is a long-distance shoot–root signalling regulatory system that regulates nodule meristem proliferation in legume plants. However, due to the intricacy and subtleness of the signalling nature in plants, molecular and biochemical details underlying mechanisms of autoregulation of nodulation remain largely unknown. The purpose of this study is to use functional–structural plant modelling to investigate the complexity of this signalling system. There are two major challenges to be met: modelling the 3D architecture of legume roots with nodulation and co-ordinating signalling-developmental processes with various rates.

Methods

Soybean (Glycine max) was chosen as the target legume. Its root system was observed to capture lateral root branching and nodule distribution patterns. L-studio, a software tool supporting context-sensitive L-system modelling, was used for the construction of the architectural model and integration with the internal signalling.

Key Results

A branching pattern with regular radial angles was found between soybean lateral roots, from which a root mapping method was developed to characterize the laterals. Nodules were mapped based on ‘nodulation section’ to reveal nodule distribution. A root elongation algorithm was then developed for simulation of root development. Based on the use of standard sub-modules, a synchronization algorithm was developed to co-ordinate multi-rate signalling and developmental processes.

Conclusions

The modelling methods developed here not only allow recreation of legume root architecture with lateral branching and nodulation details, but also enable parameterization of internal signalling to produce different regulation results. This provides the basis for using virtual experiments to help in investigating the signalling mechanisms at work.     

How similar are nut-cracking and stone-flaking? A functional approach to percussive technology

Various authors have suggested similarities between tool use in early hominins and chimpanzees. This has been particularly evident in studies of nut-cracking which is considered to be the most complex skill exhibited by wild apes, and has also been interpreted as a precursor of more complex stone-flaking abilities. It has been argued that there is no major qualitative difference between what the chimpanzee does when he cracks a nut and what early hominins did when they detached a flake from a core. In this paper, similarities and differences between skills involved in stone-flaking and nut-cracking are explored through an experimental protocol with human subjects performing both tasks. We suggest that a ‘functional’ approach to percussive action, based on the distinction between functional parameters that characterize each task and parameters that characterize the agent''s actions and movements, is a fruitful method for understanding those constraints which need to be mastered to perform each task successfully, and subsequently, the nature of skill involved in both tasks.     

A dimeric structure of PD-L1: functional units or evolutionary relics?

PD-L1 is a member of the B7 protein family, most of whose members so far were identified as dimers in a solution and crystalline state, either complexed or uncomplexed with their ligand(s). The binding of PD-L1 with its receptor PD-1 (CD279) delivers an inhibitory signal regulating the T cell function. Simultaneously with the Garboczi group, we successfully solved another structure of human PD-L1 (hPD-L1). Our protein crystallized in the space group of C222₁ with two hPD-L1 molecules per asymmetric unit. After comparison of reported B7 structures, we have found some intrinsic factors involved in the interaction of these two molecules. Based on these results, we tend to believe this uncomplexed hPD-L1 structure demonstrated its potential dimeric state in solution, although it could just be an evolutionary relic, too weak to be detected under present technology, or still a functional unit deserved our attentions.     

A functional link between Polo-like kinase 1 and the mammalian Target-Of-Rapamycin pathway?

Polo like kinase-1 is a key effector of cell division and its over-expression in several cancers is often linked with negative prognostic. We recently described that Plk1 is over-expressed in acute myeloid leukemia, and that its inhibition selectively reduces the proliferation of leukemic cells. Here, we report that Plk1 inhibition or depletion using pharmacological and siRNA approaches decreased the phosphorylation of two mTOR substrates in AML cells. In HCT116 cells, inducible expression of a constitutively active form of Plk1 leads to activation of mTOR, as shown by increased phosphorylation of its 4E-BP1 and RPS6 down-stream targets. In addition, HCT116 cells over-expressing the active form of Plk1 were characterized by abnormal growth that could be reversed by rapamycin, a specific inhibitor of the TORC1 complex. Altogether these data suggest the existence of a molecular and functional link between the Plk1 mitotic kinase and the mTOR pathway. Given the different established functions of Plk1 and mTOR during the cell cycle, we will discuss the possible meaning of this functional relationship.     

How functional is functional? Ecological groupings in terrestrial animal ecology: towards an animal functional type approach

Understanding mechanisms to predict changes in plant and animal communities is a key challenge in ecology. The need to transfer knowledge gained from single species to a more generalized approach has led to the development of categorization systems where species’ similarities in life strategies and traits are classified into ecological groups (EGs) like functional groups/types or guilds. While approaches in plant ecology undergo a steady improvement and refinement of methodologies, progression in animal ecology is lagging behind. With this review, we aim to initiate a further development of functional classification systems in animal ecology, comparable to recent developments in plant ecology. We here (i) give an overview of terms and definitions of EGs in animal ecology, (ii) discuss existing classification systems, methods and application areas of EGs (focusing on terrestrial vertebrates), and (iii) provide a “roadmap towards an animal functional type approach” for improving the application of EGs and classifications in animal ecology. We found that an animal functional type approach requires: (i) the identification of core traits describing species’ dependency on their habitat and life history traits, (ii) an optimization of trait selection by clustering traits into hierarchies, (iii) the assessment of “soft traits” as substitute for hardly measurable traits, e.g. body size for dispersal ability, and (iv) testing of delineated groups for validation including experiments.     

Is it functional?

This report describes the first scientific meeting of the British Society for Proteome Research (BSPR), which was organised jointly with the European Bioinformatics Institute (EBI) and held in July 2004. The focus of the conference was functional proteomics with an emphasis on possible clinical application. The main subjects described here are: the need to simplify samples, the use of biological fluids versus tissue, consideration of biological and experimental variation and the creation of databases to achieve meaningful functional analysis.     

A modelling framework to simulate foliar fungal epidemics using functional–structural plant models

Background and Aims

Sustainable agriculture requires the identification of new, environmentally responsible strategies of crop protection. Modelling of pathosystems can allow a better understanding of the major interactions inside these dynamic systems and may lead to innovative protection strategies. In particular, functional–structural plant models (FSPMs) have been identified as a means to optimize the use of architecture-related traits. A current limitation lies in the inherent complexity of this type of modelling, and thus the purpose of this paper is to provide a framework to both extend and simplify the modelling of pathosystems using FSPMs.

Methods

Different entities and interactions occurring in pathosystems were formalized in a conceptual model. A framework based on these concepts was then implemented within the open-source OpenAlea modelling platform, using the platform''s general strategy of modelling plant–environment interactions and extending it to handle plant interactions with pathogens. New developments include a generic data structure for representing lesions and dispersal units, and a series of generic protocols to communicate with objects representing the canopy and its microenvironment in the OpenAlea platform. Another development is the addition of a library of elementary models involved in pathosystem modelling. Several plant and physical models are already available in OpenAlea and can be combined in models of pathosystems using this framework approach.

Key Results

Two contrasting pathosystems are implemented using the framework and illustrate its generic utility. Simulations demonstrate the framework''s ability to simulate multiscaled interactions within pathosystems, and also show that models are modular components within the framework and can be extended. This is illustrated by testing the impact of canopy architectural traits on fungal dispersal.

Conclusions

This study provides a framework for modelling a large number of pathosystems using FSPMs. This structure can accommodate both previously developed models for individual aspects of pathosystems and new ones. Complex models are deconstructed into separate ‘knowledge sources’ originating from different specialist areas of expertise and these can be shared and reassembled into multidisciplinary models. The framework thus provides a beneficial tool for a potential diverse and dynamic research community.     

Modelling of phytoplankton allelopathy with Monod–Haldane-type functional response—A mathematical study

In this paper, a three-tier model of phytoplankton, zooplankton and nutrient is considered and stability of different equilibrium points is analyzed along with Hopf-bifurcation around coexisting equilibrium point. Here, we have assumed toxication process as the guiding factor for bloom formation as well as its termination and this process is incorporated into our model by choosing the zooplankton grazing function as a Monod–Haldane function due to the phytoplankton toxicity. Extensive numerical simulations have been performed to validate the analytical findings and these simulation work reveal the chaotic oscillation exhibited by the model system for certain choice of the parameter values.     

Does environmental heterogeneity drive functional trait variation? A test in montane and alpine meadows

While community‐weighted means of plant traits have been linked to mean environmental conditions at large scales, the drivers of trait variation within communities are not well understood. Local environmental heterogeneity (such as microclimate variability), in addition to mean environmental conditions, may decrease the strength of environmental filtering and explain why communities support different amounts of trait variation. Here, we assess two hypotheses: first, that more heterogeneous local environments and second, that less extreme environments, should support a broader range of plant strategies and thus higher trait variation. We quantified drivers of trait variation across a range of environmental conditions and spatial scales ranging from sub‐meter to tens of kilometers in montane and alpine plant communities. We found that, within communities, both environmental heterogeneity and environmental means are drivers of trait variation. However, the importance of each environmental factor varied depending on the trait. Our results indicate that larger‐scale trait–climate linkages that hold across communities also apply at small spatial scales, suggesting that microclimate variation within communities is a key driver of community functional diversity. Microclimatic variation provides a potential mechanism for helping to maintain diversity in local communities and also suggests that small‐scale environmental heterogeneity should be measured as a better predictor of functional diversity.     

Does functional redundancy exist?

Functional redundancy has often been assumed as an intuitive null hypothesis in biodiversity experiments, but theory based on the classical Lotka-Volterra competition model shows that functional redundancy sensu stricto is incompatible with stable coexistence. Stable coexistence requires differences between species which lead to functional complementarity and differences between the yields of mixtures and monocultures. Only a weaker version of functional redundancy, i.e. that mixture yields lie within the range of variation of monoculture yields, is compatible with stable coexistence in Lotka-Volterra systems. Spatial and temporal environmental variability may provide room for functional redundancy at small spatial and temporal scales, but is not expected to do so at the larger scales at which environmental variations help maintain coexistence. Neutral coexistence of equivalent competitors, non-linear per capita growth rates, and lack of correlation between functional impact and biomass may provide the basis for the existence of functional redundancy in natural ecosystems. Overall, there is a striking parallel between the conditions that allow stable coexistence and those that allow overyielding.     

Meprin A and meprin α generate biologically functional IL-1β from pro-IL-1β

The present study demonstrates that both oligomeric metalloendopeptidase meprin A purified from kidney cortex and recombinant meprin α are capable of generating biologically active IL-1β from its precursor pro-IL-1β. Amino-acid sequencing analysis reveals that meprin A and meprin α cleave pro-IL-1β at the His¹¹⁵-Asp¹¹⁶ bond, which is one amino acid N-terminal to the caspase-1 cleavage site and five amino acids C-terminal to the meprin β site. The biological activity of the pro-IL-1β cleaved product produced by meprin A, determined by proliferative response of helper T-cells, was 3-fold higher to that of the IL-1β product produced by meprin β or caspase-1. In a mouse model of sepsis induced by cecal ligation puncture that results in elevated levels of serum IL-1β, meprin inhibitor actinonin significantly reduces levels of serum IL-1β. Meprin A and meprin α may therefore play a critical role in the production of active IL-1β during inflammation and tissue injury.     

Which functional groups of the molybdopterin ligand should be considered when modeling the active sites of the molybdenum and tungsten cofactors? A density functional theory study

A density functional theory study of the influence of the various functional groups of the molybdopterin ligand on electronic and geometric properties of active-site models for the molybdenum and tungsten cofactors has been undertaken. We used analogous molybdenum and tungsten complexes with increasingly accurate representation of the molybdopterin ligands and compared bond lengths, angles, charge distribution, composition of the binding orbitals, as well as the redox potentials in relation to each other. On the basis of our findings, we suggest using ligand systems including the pyrane and the pyrazine rings, besides the dithiolene function, to obtain sufficiently reliable computational, but also synthetic, models for the molybdenum and tungsten cofactors, whereas the second ring of the pterin might be neglected for efficiency reasons.     

Interaction with functional membrane proteins—A common mechanism of toxicity for lipophilic environmental chemicals?

• 1.1. The effects of several phenols, anilines and aliphatic alcohols on yeast plasma membrane H⁺-ATPase and purine transport system as well as on Na⁺, K⁺-ATPase and adenosine uptake by Chinese hamster ovary cells (CHO) were investigated.
• 2.2. In all cases an inhibition was observed, which could be correlated with the octanol/water partition coefficients of the substances tested, thus making quantitative structure-activity predictions possible.
• 3.3. The observed effects correlated well with the influence of the chemicals on cell growth.
• 4.4. The results suggest a common mechanism of toxicity by the action of hydrophobic xenobiotics on biomembranes.

     

What can venom phospholipases A(2) tell us about the functional diversity of mammalian secreted phospholipases A(2)?

Most venomous animals including snakes, bees and scorpions contain a variety of venom phospholipases A(2) (vPLA(2)s) which participate in both digestion of prey and venom toxicity. So far, more than 150 vPLA(2)s have been characterized. They all have a conserved fold with several disulfide bridges, can be catalytically active or not, and several of them can display a tremendous array of toxic effects including neurotoxicity and myotoxicity. Furthermore, the molecular diversity of vPLA(2)s found within a single snake venom can result from positive Darwinian selection. Over the last decade, receptors and binding proteins for vPLA(2)s have been identified in mammals, suggesting that vPLA(2)s can exert their toxicities through specific protein-protein interactions, besides their catalytic activity. The brain N-type receptors are involved in the neurotoxicity of vPLA(2)s, but are not yet cloned. The M-type receptor has been cloned from skeletal muscle, belongs to the superfamily of C-type lectins, and interestingly, has homology with vPLA(2) inhibitors purified from snake blood. The molecular diversity of vPLA(2)s and the presence of receptors for vPLA(2)s in mammals raises the possibility that there is also a diversity of mammalian secreted PLA(2)s (msPLA(2)s) which are the normal endogenous ligands of the vPLA(2) receptors. This view led us to clone five novel msPLA(2)s (IID, IIE, IIF, III, and X msPLA(2)s), which together with the previously cloned msPLA(2)s (IB, IIA, IIC, and V), indicate that mammals also express a large diversity of sPLA(2)s. M-type receptors can have IB and IIA msPLA(2)s as natural endogenous ligands, suggesting that msPLA(2)s, like vPLA(2)s, can function as both enzymes and ligands. msPLA(2)s were first implicated in lipid digestion, and more recently in host defense mechanisms including inflammation and antibacterial defense. The growing molecular diversity of msPLA(2)s, which all have a specific tissue distribution, and the presence of receptors suggest that msPLA(2)s, like vPLA(2)s, are endowed with a wide array of biological effects which remain to be discovered.     

How does habitat complexity affect ant foraging success? A test using functional measures on three continents

Habitat complexity can mediate key processes that structure local assemblages through effects on factors such as competition, predation and foraging behaviour. While most studies address assemblage responses to habitat complexity within one locality, a more global approach allows conclusions with greater independence from the phylogenetic constraints of the target assemblages, thus allowing greater generality. We tested the effects of natural and manipulated habitat complexities on ant assemblages from South Africa, Australia and Sweden, in order to determine if there were globally consistent responses in how functional measures of foraging success are regulated by habitat complexity. Specifically, we considered how habitat complexity affected ant foraging rates including the speed of discovery and rate of monopolisation. We also tested if habitat complexity affected the body size index, a size-related morphological trait, of ants discovering resources and occupying and monopolising the resources after 180 min. Ants were significantly slower to discover baits in the more complex treatments, consistent with predictions that they would move more slowly through more complex environments. The monopolisation index was also lower in the more complex treatments, suggesting that resources were more difficult to defend. Our index of ant body size showed trends in the predicted direction for complexity treatments. In addition, ants discovering, occupying and monopolising resources were smaller in simple than in complex natural habitats. Responses of discovering ants to resources in natural habitats were clear in only one of three regions. Consistent with our predictions, habitat complexity thus affected functional measures of the foraging success of ants in terms of measures of discovery and monopolisation rates and body size traits of successful ants. However, patterns were not always equally clear in manipulative and mensurative components of the study.