代谢异速生长理论及其在微生物生态学领域的应用

新陈代谢是生物的基本生理过程,影响生物在不同环境中参与物质循环和能量转化的过程.代谢速率作为生物体重要的生命过程指标,几乎影响所有的生物活性速率,且在很多研究中均表现出异速生长现象.所谓代谢异速是指生物体代谢速率与其个体大小(或质量)之间存在的幂函数关系.代谢异速生长理论的提出,从机制模型角度解释了代谢异速关系这一普遍存在的生命现象.该理论利用分形几何学及流体动力学等原理,从生物能量学角度阐释了异速生长规律的机理,证实了3/4权度指数的存在;但同时有研究表明,权度指数因环境因素等影响处于2/3-1范围之间而非定值.随着研究工作的深入,代谢异速生长理论研究从起初的宏观动植物领域拓展到了微生物领域,在研究微生物的代谢异速生长理论时,可将微生物的可操作分类单元(Operational taxonomic unit,OTU)或具有特定功能的功能群视为一个微生物个体,基于其遗传多样性和功能多样性特征进行表征,以便于将微生物群落多样性与其生态功能性联系起来,使该理论在微生物生态学领域得到有效的补充和完善.尽管细菌具有独特的生物学特性,但与宏观生物系统中观测到的现象表现出明显的一致性.有研究表明,3个农田土壤细菌基于遗传多样性的OTU数的平均周转率分别为0.71、0.80和0.84,介于2/3与1之间,可能与生物代谢异速指数有一定关联,为微生物代谢异速指数的研究提出了一个参考解决方案.鉴于微生物个体特征和生物学特性,在分析代谢速率与个体大小关系中,从微生物单位个体的定义、个体大小表征到计量单位的统一,仍需更多的理论支持.分析了代谢异速生长理论在微生物与生态系统功能关系研究中的可能应用,延伸了该理论的应用范围,并对尚待加强的研究问题进行了评述和展望.     

DNA序列的多重分形Hurst分析

为了深入研究基因组序列的多重分形性质,首先选取12条较长的DNA序列,并根据此12条DNA序列的编码／非编码片段将DNA序列转换成相应的12条时间序列,其次对这12个时间序列进行多重分形Hurst分析,计算它们的Hurst指数,并且利用Hurst指数分析序列的自相似性,进一步将得到的Hurst指数与DNA一维游走模型相比较,发现12条序列均具有长程相关性,这说明DNA序列中确实存在着长程相关现象。     

Scaling in biochemical kinetics: dissection of a relaxation oscillator

In a case study of a class of biochemical models, methods of scaling are employed to determine the expected limits of validity of singular perturbation approaches to a relaxation oscillator. This work complements earlier analysis of the use of the quasi-steady-state approximation for the Michaelis-Menten approximation. These studies present an advantage over more conventional approaches in which attention is concentrated on a single parameter, in that the range of convergence is delineated more precisely in the full parameter space of the problem.     

Leaf phosphorus influences the photosynthesis–nitrogen relation: a cross-biome analysis of 314 species

The ecophysiological linkage of leaf phosphorus (P) to photosynthetic capacity (A _max) and to the A _max–nitrogen relation remains poorly understood. To address this issue we compiled published and unpublished field data for mass-based A _max, nitrogen (N) and P (n = 517 observations) from 314 species at 42 sites in 14 countries. Data were from four biomes: arctic, cold temperate, subtropical (including Mediterranean), and tropical. We asked whether plants with low P levels have low A _max, a shallower slope of the A _max–N relationship, and whether these patterns have a geographic signature. On average, leaf P was substantially lower in the two warmer than in the two colder biomes, with the reverse true for N:P ratios. The evidence indicates that the response of A _max to leaf N is constrained by low leaf P. Using a full factorial model for all data, A _max was related to leaf N, but not to leaf P on its own, with a significant leaf N ×  leaf P interaction indicating that the response of A _max to N increased with increasing leaf P. This was also found in analyses using one value per species per site, or by comparing only angiosperms or only woody plants. Additionally, the slope of the A _max–N relationship was higher in the colder arctic and temperate than warmer tropical and subtropical biomes. Sorting data into low, medium, and high leaf P groupings also showed that the A _max–N slope increases with leaf P. These analyses support claims that in P-limited ecosystems the A _max–N relationship may be constrained by low P, and are consistent with laboratory studies that show P-deficient plants have limited ribulose-1,5-bisphosphate regeneration, a likely mechanism for the P influence upon the A _max–N relation. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Density-dependence as a size-independent regulatory mechanism

The growth function of populations is central in biomathematics. The main dogma is the existence of density-dependence mechanisms, which can be modelled with distinct functional forms that depend on the size of the population. One important class of regulatory functions is the theta-logistic, which generalizes the logistic equation. Using this model as a motivation, this paper introduces a simple dynamical reformulation that generalizes many growth functions. The reformulation consists of two equations, one for population size, and one for the growth rate. Furthermore, the model shows that although population is density-dependent, the dynamics of the growth rate does not depend either on population size, nor on the carrying capacity. Actually, the growth equation is uncoupled from the population size equation, and the model has only two parameters, a Malthusian parameter rho and a competition coefficient theta. Distinct sign combinations of these parameters reproduce not only the family of theta-logistics, but also the van Bertalanffy, Gompertz and Potential Growth equations, among other possibilities. It is also shown that, except for two critical points, there is a general size-scaling relation that includes those appearing in the most important allometric theories, including the recently proposed Metabolic Theory of Ecology. With this model, several issues of general interest are discussed such as the growth of animal population, extinctions, cell growth and allometry, and the effect of environment over a population.     

Requirements for comparing the performance of finite element models of biological structures

The widespread availability of three-dimensional imaging and computational power has fostered a rapid increase in the number of biologists using finite element analysis (FEA) to investigate the mechanical function of living and extinct organisms. The inevitable rise of studies that compare finite element models brings to the fore two critical questions about how such comparative analyses can and should be conducted: (1) what metrics are appropriate for assessing the performance of biological structures using finite element modeling? and, (2) how can performance be compared such that the effects of size and shape are disentangled? With respect to performance, we argue that energy efficiency is a reasonable optimality criterion for biological structures and we show that the total strain energy (a measure of work expended deforming a structure) is a robust metric for comparing the mechanical efficiency of structures modeled with finite elements. Results of finite element analyses can be interpreted with confidence when model input parameters (muscle forces, detailed material properties) and/or output parameters (reaction forces, strains) are well-documented by studies of living animals. However, many researchers wish to compare species for which these input and validation data are difficult or impossible to acquire. In these cases, researchers can still compare the performance of structures that differ in shape if variation in size is controlled. We offer a theoretical framework and empirical data demonstrating that scaling finite element models to equal force: surface area ratios removes the effects of model size and provides a comparison of stress-strength performance based solely on shape. Further, models scaled to have equal applied force:volume ratios provide the basis for strain energy comparison. Thus, although finite element analyses of biological structures should be validated experimentally whenever possible, this study demonstrates that the relative performance of un-validated models can be compared so long as they are scaled properly.     

Predicting the buoyancy, equilibrium and potential swimming ability of giraffes by computational analysis

Giraffes (Giraffa camelopardalis) are often stated to be unable to swim, and while few observations supporting this have ever been offered, we sought to test the hypothesis that giraffes exhibited a body shape or density unsuited for locomotion in water. We assessed the floating capability of giraffes by simulating their buoyancy with a three-dimensional mathematical/computational model. A similar model of a horse (Equus caballus) was used as a control, and its floating behaviour replicates the observed orientations of immersed horses. The floating giraffe model has its neck sub-horizontal, and the animal would struggle to keep its head clear of the water surface. Using an isometrically scaled-down giraffe model with a total mass equal to that of the horse, the giraffe's proportionally larger limbs have much higher rotational inertias than do those of horses, and their wetted surface areas are 13.5% greater relative to that of the horse, thus making rapid swimming motions more strenuous. The mean density of the giraffe model (960 gm/l) is also higher than that of the horse (930 gm/l), and closer to that causing negative buoyancy (1000 gm/l). A swimming giraffe - forced into a posture where the neck is sub-horizontal and with a thorax that is pulled downwards by the large fore limbs - would not be able to move the neck and limbs synchronously as giraffes do when moving on land, possibly further hampering the animal's ability to move its limbs effectively underwater. We found that a full-sized, adult giraffe will become buoyant in water deeper than 2.8 m. While it is not impossible for giraffes to swim, we speculate that they would perform poorly compared to other mammals and are hence likely to avoid swimming if possible.     

Euclidean geometry explains why lengths allow precise body mass estimates in terrestrial invertebrates: the case of oribatid mites

Indirect measures of soil invertebrate body mass M based on equations relating the latter to body length (l) are becoming increasingly used due to the required painstaking laboratory work and the technical difficulties involved in obtaining some thousands of reliable weight estimates for animals that can be very small. The implicit assumption of such equations is that dM/dV=δ, where V is body volume and δ is a constant density value. Classical Euclidean scaling implies that V∝l³∝M. One may thus derive M from l when the latter can provide a good estimate of V and the assumption of a constant δ is respected. In invertebrates, equations relating weight to length indicate that the power model always provides the best fit. However, authors only focused on the empirical estimation of slopes linking the body mass to the length measure variables, sometimes fitting exponential and linear models that are not theoretically grounded. This paper explicates how power laws derive from fundamental Euclidean scaling and describes the expected allometric exponents under the above assumptions. Based on the classical Euclidean scaling theory, an equivalent sphere is defined as a theoretical sphere with a volume equal to that of the organism whose body mass must be estimated. The illustrated application to a data set on soil oribatid mites helps clarify all these issues. Lastly, a general procedure for more precise estimation of M from V and δ is suggested.     

The role of down-slope water and nutrient fluxes in the response of Arctic hill slopes to climate change

The down-slope movement of water and nutrients should link plant and soil processes along hill slopes. This linkage ought to be particularly strong in Arctic ecosystems where permafrost confines flowing water near the surface. We examined whether these hill-slope processes are important in assessments of the responses of Arctic tundra to changes in CO₂ and climate using the Marine Biological Laboratory–General Ecosystem Model. Because higher rates of water flow decrease the distance over which nutrients must diffuse to the roots, down-slope vegetation is more productive under current conditions. In response to elevated CO₂ and a warmer, wetter climate, the relative increase in carbon stored in vegetation and soils was higher uphill, but the absolute increase was higher downhill. Very little of the increase in carbon anywhere on the hill slope resulted from an increase in total ecosystem nitrogen. Instead, the increases were associated with increases in vegetation C:N ratio (woodiness) and with the redistribution of nitrogen from soils (low C:N) to vegetation (high C:N). Because these changes are fueled by nitrogen already in place, the down-slope movement of nitrogen does not appear to be a major determinant of the responses of Arctic tundra to changes in CO₂ and climate.