Plant physiology in theory and practice: An analysis of the WBE model for vascular plants

The theoretical model of West, Brown and Enquist (hereafter WBE) proposed the fractal geometry of the transport system as the origin of the allometric scaling laws observed in nature. The WBE model has either been criticized for some restrictive and biologically unrealistic constraints or its reliability debated on the evidence of empirical tests. In this work, we revised the structure of the WBE model for vascular plants, highlighting some critical assumptions and simplifications and discuss them with regard to empirical evidence from plant anatomy and physiology. We conclude that the WBE model had the distinct merit of shedding light on some important features such as conduit tapering. Nonetheless, it is over-simplistic and a revised model would be desirable with an ontogenetic perspective that takes some important phenomena into account, such as the transformation of the inner sapwood into heartwood and the effect of hydraulic constraints in limiting the growth in height.     

WBE 模型及其在生态学中的应用：研究概述

介绍了WBE模型,综述了该模型在生态学中的应用进展。WBE模型,以及以该模型为基础的MTE模型,假设生物体为自相似分形网络结构,提出代谢速率和个体大小之间存在3/4指数关系,分别预测了从个体到生物圈多个尺度上的生物属性之间的异速生长关系,而且部分得到了验证。WBE模型的应用涵盖了个体组织生物量、年生长率,种群密度和生态系统单位面积产量、能量流动率等多个方面;即使在生物圈大尺度上,WBE模型也可用来预测试验中无法直接测量的特征变量的属性,如全球碳储量的估算等。至今,关于WBE和MTE模型仍然存在各种褒贬争论,讨论焦点主要集中于模型建立的前提假设以及权度指数的预测。今后的研究工作应规范试验技术和方法,考虑物种多样性和环境等因素的影响,提出符合各类生物的模型结构体系,使其具有更广泛的应用性和预测性。     

Metabolic scaling in insects supports the predictions of the WBE model

The functional association between body size and metabolic rate (BS-MR) is one of the most intriguing issues in ecological physiology. An average scaling exponent of 3/4 is broadly observed across animal and plant taxa. The numerical value of 3/4 is theoretically predicted under the optimized version of West, Brown, and Enquist's vascular resource supply network model. Insects, however, have recently been proposed to express a numerically different scaling exponent and thus application of the WBE network model to insects has been rejected. Here, we re-analyze whether such variation is indeed supported by a global deviation across all insect taxa at the order and family levels to assess if specific taxa influence insect metabolic scaling. We show that a previous reported deviation is largely due to the effect of a single insect family (Termitidae). We conclude that the BS-MR relationship in insects broadly supports the core predictions of the WBE model. We suggest that the deviation observed within the termites warrants further investigation and may be due to either difficulty in accurately measuring termite metabolism and/or particularities of their life history. Future work on allometric scaling should assess the nature of variation around the central tendencies in scaling exponents in order to test if this variation is consistent with core assumptions and predictions of the WBE model that stem by relaxing its secondary optimizing assumptions that lead to the 3/4 exponent.     

The generality of the island rule reexamined

Aim  M.V. Lomolino and colleagues have recently reviewed the island rule in mammals and other vertebrates, claiming it is a general pattern. They have portrayed our recent analysis as weakly supporting the island rule, seeing weakness in our use of what they considered to be inadequate size indices (skulls and teeth, rather than mass or body length) and in our use of large islands. They argue that size evolution on islands points to a bauplan-specific fundamental size. We aim to test the generality of the rule and the adequacy of some of the data used to support it.
Location  Insular environments world-wide.
Methods  We collate and analyse data on skull sizes of carnivores and body masses of mammals in general to see whether there is a graded trend from dwarfism in large species to gigantism in smaller ones.
Results  The island rule is not supported with either the carnivore or the mammal data sets. Island area does not influence size change.
Main conclusions  Our results suggest that data recently advanced in support of the island rule are inadequate and that the island rule is not a general pattern for all mammals.     

On the generality of the latitudinal diversity gradient

The decline of biodiversity with latitude has received great attention, but both the concise pattern and the causes of the gradient are under strong debate. Most studies of the latitudinal gradient comprise only one or few organism types and are often restricted to certain region or habitat types. To test for significant variation in the gradient between organisms, habitats, or regions, a meta-analysis was conducted on nearly 600 latitudinal gradients assembled from the literature. Each gradient was characterized by two effect sizes, strength (correlation coefficient) and slope, and additionally by 14 variables describing organisms, habitats, and regions. The analysis corroborated the high generality of the latitudinal diversity decline. Gradients on regional scales were significantly stronger and steeper than on local scales, and slopes also varied with sampling grain. Both strength and slope increased with organism body mass, and strength increased with trophic level. The body mass-effect size relation varied for ecto- versus homeotherm organisms and for different dispersal types, suggesting allometric effects on energy use and dispersal ability as possible mechanisms for the body mass effect. Latitudinal gradients were weaker and less steep in freshwater than in marine or terrestrial environments and differed significantly between continents and habitat types. The gradient parameters were not affected by hemisphere or the latitudinal range covered. This analysis is the first to describe these general and significant patterns, which have important consequences for models aiming to explain the latitudinal gradient.     

The generality of kinase-catalyzed biotinylation

Kinase-catalyzed protein phosphorylation is involved in a wide variety of cellular events. Development of methods to monitor phosphoproteins in normal and diseased states is critical to fully characterize cell signaling. Towards phosphoprotein analysis tools, our lab reported kinase-catalyzed labeling where γ-phosphate modified ATP analogs are utilized by kinases to label peptides or protein substrates with a functional tag. In particular, the ATP-biotin analog was developed for kinase-catalyzed biotinylation. However, kinase-catalyzed labeling has been tested rigorously with only a few kinases, preventing use of ATP-biotin as a general tool. Here, biotinylation experiments, gel or HPLC-based quantification, and kinetic measurements indicated that twenty-five kinases throughout the kinome tree accepted ATP-biotin as a cosubstrate. With this rigorous characterization of ATP-biotin compatibility, kinase-catalyzed labeling is now immediately useful for studying phosphoproteins and characterizing the role of phosphorylation in various biological events.     

Interaction generality, a measurement to assess the reliability of a protein-protein interaction

Here we introduce the ‘interaction generality’ measure, a new method for computationally assessing the reliability of protein–protein interactions obtained in biological experiments. This measure is basically the number of proteins involved in a given interaction and also adopts the idea that interactions observed in a complicated interaction network are likely to be true positives. Using a group of yeast protein–protein interactions identified in various biological experiments, we show that interactions with low generalities are more likely to be reproducible in other independent assays. We constructed more reliable networks by eliminating interactions whose generalities were above a particular threshold. The rate of interactions with common cellular roles increased from 63% in the unadjusted estimates to 79% in the refined networks. As a result, the rate of cross-talk between proteins with different cellular roles decreased, enabling very clear predictions of the functions of some unknown proteins. The results suggest that the interaction generality measure will make interaction data more useful in all organisms and may yield insights into the biological roles of the proteins studied.     

Assessing the generality of global leaf trait relationships

Global-scale quantification of relationships between plant traits gives insight into the evolution of the world's vegetation, and is crucial for parameterizing vegetation-climate models. A database was compiled, comprising data for hundreds to thousands of species for the core 'leaf economics' traits leaf lifespan, leaf mass per area, photosynthetic capacity, dark respiration, and leaf nitrogen and phosphorus concentrations, as well as leaf potassium, photosynthetic N-use efficiency (PNUE), and leaf N : P ratio. While mean trait values differed between plant functional types, the range found within groups was often larger than differences among them. Future vegetation-climate models could incorporate this knowledge. The core leaf traits were intercorrelated, both globally and within plant functional types, forming a 'leaf economics spectrum'. While these relationships are very general, they are not universal, as significant heterogeneity exists between relationships fitted to individual sites. Much, but not all, heterogeneity can be explained by variation in sample size alone. PNUE can also be considered as part of this trait spectrum, whereas leaf K and N : P ratios are only loosely related.     

The generality of Constructive Neutral Evolution

Constructive Neutral Evolution (CNE) is an evolutionary mechanism that can explain much molecular inter-dependence and organismal complexity without assuming positive selection favoring such dependency or complexity, either directly or as a byproduct of adaptation. It differs from but complements other non-selective explanations for complexity, such as genetic drift and the Zero Force Evolutionary Law, by being ratchet-like in character. With CNE, purifying selection maintains dependencies or complexities that were neutrally evolved. Preliminary treatments use it to explain specific genetic and molecular structures or processes, such as retained gene duplications, the spliceosome, and RNA editing. Here we aim to expand the scope of such explanation beyond the molecular level, integrating CNE with Multi-Level Selection theory, and arguing that several popular higher-level selection scenarios are in fact instances of CNE. Suitably contextualized, CNE occurs at any level in the biological hierarchy at which natural selection as normally construed occurs. As examples, we focus on modularity in protein–protein interaction networks or “interactomes,” the origin of eukaryotic cells and the evolution of co-dependence in microbial communities—a variant of the “Black Queen Hypothesis” which we call the “Gray Queen Hypothesis”.     

Categorizing Australian landscapes as an aid to assessing the generality of landscape management guidelines

Aim A key question in ecology and ecological management is the extent to which management guidelines developed in one location can be generalized to other areas. Landscapes differ in their biophysical characteristics and the degree of human alteration imposed on them. Our aim was to develop a conceptual framework of Australian landscapes, on the basis of a few simple indicators, that can be used to enhance the communication of information in planning and managing landscapes, particularly for biodiversity conservation. Location The project considered landscapes across the continent of Australia. Methods The project was a desktop exercise and the approach was to identify the minimum set of variables, and levels within variables, that are most meaningful from the perspective of Australian landscapes and their management. This involved the identification of the key environmental axes and development of a proposed set of matrices involving various combinations of the axes, which was revised following consultation with stakeholders. Results We developed a framework based on the primary variables of climate and vegetation. For climate, we used an agro‐climatic classification incorporating a moisture index, growth index and seasonality, with climate classes aligned to existing bioregions. Vegetation was broadly classified on the presence or absence of a tree layer and whether the understorey was grassy or shrub‐dominated. Secondary variables were the degree of landscape alteration and modification. The sensitivity of broad categories to ecosystem dysfunction was assessed, and the relative abundance of different categories across Australia was determined. Not all categories need to be considered since not all combinations of variables occur. Main conclusions The framework provides a set of broad categories of landscapes with differing characteristics. We can then assess the importance of different types of threat in the different categories. By pulling together the potential threats in a systematic way across categories, we can start to consider what appropriate management responses might be in each case. Further, by providing a convenient way to compare landscapes in different categories, it becomes possible to see where generalizations among different landscapes may be possible and where they are definitely not likely to be helpful.     

Challenges to the common dogma

Some 15 years ago, Gane (now Dr. Gane Ka-Shu Wong,Professor and iCORE Chair in Biosystems Informatics,University of Alberta, Canada) and I were staring at a set of plots and scratching our heads,     

On the generality of stability-complexity relationships in Lotka-Volterra ecosystems

Understanding how complexity persists in nature is a long-standing goal of ecologists. In theoretical ecology, local stability is a widely used measure of ecosystem persistence and has made a major contribution to the ecosystem stability-complexity debate over the last few decades. However, permanence is coming to be regarded as a more satisfactory definition of ecosystem persistence and has relatively recently become available as a tool for assessing the global stability of Lotka-Volterra communities. Here we document positive relationships between permanence and Lotka-Volterra food web complexity and report a positive correlation between the probability of local stability and permanence. We investigate further the frequency of discrepancy (attributed to fragile systems that are locally stable but not permanent or locally unstable systems that are permanent and have cyclic or chaotic dynamics), associate non-permanence with the local stability or instability of equilibria on the boundary of the state-space, and investigate how these vary with aspects of ecosystem complexity. We find that locally stable interior equilibria tend to have all locally unstable boundary equilibria. Since a locally stable boundary is inconsistent with permanent dynamics, this can explain the observed positive correlation between local interior stability and permanence. Our key finding is that, at least in Lotka-Volterra model ecosystems, local stability may be a better measure of persistence than previously thought.     

Challenges to therapy in the future

Quadruple therapy (with a proton pump inhibitor (PPI), metronidazole, tetracycline and bismuth) is generally reserved for second-line treatment; however, studies using this regimen for 7 days have found it to be effective even in metronidazole-resistant strains. Resistance is an ongoing problem with antimicrobial therapy but considerable progress has now been made into understanding the underlying genetic mechanisms of this process. Metronidazole resistance in Europe is usually in the range of 20-30% of strains but may be as high as 70% in some countries. One genetic mechanism involved is thought to be a mutation of the rdxA gene. Macrolide resistance appears to be on the increase in Europe, varying from 1% in some countries to 13% in others. The genetic mechanism involved has been shown to be a point mutation of a ribosomal RNA. Amoxicillin resistance is an emerging problem that has an adverse effect on eradication rates in clinical practice. Resistance has been shown to be caused by the absence of one of the four binding proteins in the cell wall. Few novel antibiotics have been developed for use in eradication therapy, although rifabutin, secnidazole and furazolidone have shown some success as part of combination therapy. Alternative therapies that have been tested include mucosal protective agents which have been used in place of a PPI in some eradication regimens with some success, and the somatostatin analog, octreotide, that has been used as part of quadruple therapy in place of a PPI and produced eradication rates of approximately 88%. The ultimate challenge is still to develop a safe and effective vaccine against Helicobacter pylori. Current and future research will also focus on identifying genetic targets for therapy, adhesion molecule analogs to prevent binding of the bacterium, and urease inhibitors. The current triple therapy treatment options available for the eradication of Helicobacter pylori infection are over 90% effective in susceptible organisms and there are very few medical conditions to which we can offer such efficacious treatment. Unfortunately, the recommendations made at consensus conferences are not always put into practice and physicians in primary care may be unaware of the true efficacy of eradication therapy. Treatment is very simple: three drugs, twice a day for 1 week. The main focus for both primary care physicians and gastroenterologists should be to reinforce the need for patient compliance, otherwise we will see an increase in antibiotic resistance. Patients should be prewarned that they may experience some mild side effects and should be encouraged to complete the course of treatment. The real challenge for the future will be the management of patients who do not respond to first-line treatment. This paper will focus on potential problems with therapy, such as antibiotic resistance, and possible future solutions, such as novel antibiotics and vaccines.