酶动力学的极值原理假说

平衡态假说和稳态假说是酶动力学的基础。本文提出极值原理假说,用于完善平衡态假说和稳态假说的不足之处,扩大了酶动力学的应用范围,并以Michaelis-Menten方程为例进行了说明。     

Use of the Score Statistic for Testing Goodness-of-Fit of Some Generalised Distributions

The use of the score statistic to test whether a generalised distribution gives an improved fit over a non-generalised distribution is recommended. The score statistic for a generalised exponential family is derived. Several specific examples are given.     

Autosomal STRs Provide Genetic Evidence for the Hypothesis That Tai People Originate from Southern China

Tai people are widely distributed in Thailand, Laos and southwestern China and are a large population of Southeast Asia. Although most anthropologists and historians agree that modern Tai people are from southwestern China and northern Thailand, the place from which they historically migrated remains controversial. Three popular hypotheses have been proposed: northern origin hypothesis, southern origin hypothesis or an indigenous origin. We compared the genetic relationships between the Tai in China and their “siblings” to test different hypotheses by analyzing 10 autosomal microsatellites. The genetic data of 916 samples from 19 populations were analyzed in this survey. The autosomal STR data from 15 of the 19 populations came from our previous study (Lin et al., 2010). 194 samples from four additional populations were genotyped in this study: Han (Yunnan), Dai (Dehong), Dai (Yuxi) and Mongolian. The results of genetic distance comparisons, genetic structure analyses and admixture analyses all indicate that populations from northern origin hypothesis have large genetic distances and are clearly differentiated from the Tai. The simulation-based ABC analysis also indicates this. The posterior probability of the northern origin hypothesis is just 0.04 [95%CI: (0.01–0.06)]. Conversely, genetic relationships were very close between the Tai and populations from southern origin or an indigenous origin hypothesis. Simulation-based ABC analyses were also used to distinguish the southern origin hypothesis from the indigenous origin hypothesis. The results indicate that the posterior probability of the southern origin hypothesis [0.640, 95%CI: (0.524–0.757)] is greater than that of the indigenous origin hypothesis [0.324, 95%CI: (0.211–0.438)]. Therefore, we propose that the genetic evidence does not support the hypothesis of northern origin. Our genetic data indicate that the southern origin hypothesis has higher probability than the other two hypotheses statistically, suggesting that the Tai people most likely originated from southern China.     

Distributions of Cranial Pathologies Provide Evidence for Head-Butting in Dome-Headed Dinosaurs (Pachycephalosauridae)

Pachycephalosaurids are small, herbivorous dinosaurs with domed skulls formed by massive thickening of the cranial roof. The function of the dome has been a focus of debate: the dome has variously been interpreted as the product of sexual selection, as an adaptation for species recognition, or as a weapon employed in intraspecific combat, where it was used in butting matches as in extant ungulates. This last hypothesis is supported by the recent identification of cranial pathologies in pachycephalosaurids, which appear to represent infections resulting from trauma. However, the frequency and distribution of pathologies have not been studied in a systematic fashion. Here, we show that pachycephalosaurids are characterized by a remarkably high incidence of cranial injury, where 22% of specimens have lesions on the dome. Frequency of injury shows no significant difference between different genera, but flat-headed morphs (here interpreted as juveniles or females) lack lesions. Mapping of injuries onto a digitial pachycephalosaurid skull shows that although lesions are distributed across the dome, they cluster near the apex, which is consistent with the hypothesis that the dome functioned for intraspecific butting matches.     

A Maximum Likelihood Estimator for Shape Parameters of S‐Distributions

The S‐distribution is a four‐parameter distribution that is defined in terms of a differential equation, in which the cumulative is represented as the dependent variable: The article proposes a maximum likelihood estimator for the shape parameters of this distribution.     

Predicting Plant Diversity Response to Disturbance: Applicability of the Intermediate Disturbance Hypothesis and Mass Ratio Hypothesis

Predicting the relationships between disturbance, biodiversity and productivity of ecosystems continue to preoccupy ecologists and resource managers. Two hypotheses underpin many of the discussions. The Intermediate Disturbance Hypothesis (IDH), which proposes that biodiversity peaks at intermediate levels of disturbance, is often extended to predict that productivity follows the same response pattern. The Mass Ratio Hypothesis (MRH) proposes that the biological traits of the dominant species are the critical drivers of ecosystem function (e.g., productivity) and that these species increase in biomass rapidly after disturbance then stabilize. As a consequence, species diversity first peaks then declines after disturbance as a few species dominate the site. Both provide a conceptual link among disturbance, species diversity and productivity (an index of ecosystem function). We assessed the current state of empirical support for these two hypotheses with a literature survey and determined if their conformance is related to ecosystem type or site productivity. Conformance of IDH reported in past reviews (considering all ecosystems) ranged from 16 to 21%. This contrasts with our finding that in terrestrial ecosystems conformance to IDH was 46% (22 of 48 studies), 17% studies reported non-compliance, and 23% reported inconclusive results. Most studies explained their results with respect to IDH or MRH. Only two studies were specifically designed to test the validity of IDH or MRH. We conclude that (i) the IDH is mostly applicable to predict species diversity response to disturbance in upland sites of medium to high productivity and the MRH is applicable to organic sites of low productivity; (ii) there is a critical need for more studies specifically designed to test these hypotheses in natural ecosystems using common protocols; and (iii) enhanced understanding of these models will add value in refining management policies and in the selection of meaningful diversity indicators of sustainability.     

Extreme Variation of mtDNA Neutral Substitution Rate across Mammalian Species - the Longevity Hypothesis

Mol. Biol. Evol. 25:120–130. 2008. doi:10.1093/molbev/msm248 Numerical values in     

Seed Set and Natural Regeneration of Dendrocalamus membranaceus Munro after Mass and Sporadic Flowering in Yunnan,China

The flowering periods of woody bamboos, seed set, natural regeneration and death after flowering have been rarely observed and evaluated in the field. Dendrocalamus membranaceus Munro, a tropical woody bamboo mainly distributed in the Yunnan, displayed both sporadic as well as gregarious (mass) flowering and fruited from 2006 to 2013 following severe droughts. The aim of this study is to examine potential differences in seed set and natural regeneration between the two flowering patterns in natural D. membranaceus forests. We investigated and analyzed seed set, seed germination, seedling growth and mortality in both mass and sporadic flowering populations. Observations were made over a period of three years to record changes in bamboo seedling density, height and culm diameter. We observed a low natural seed set ranging from 1.76% to 7.49%, and a relatively high seed germination rate in the nursery from 59.6% to 71.0% for both types of flowering populations. Seeds germinated in 5–7 days after sowing and the germination period lasted 10–15 days. Seed set and germination rates in mass-flowering populations were significantly higher than those of sporadically flowering stands. The seedlings within sporadically flowering populations died within two years. In comparison, seedling mortality in the mass flowering population increased over two periods of observation from 64.92% to 98.89%, yet there was good seedling establishment left over, which showed mean height and mean culm diameter increasing by 1053.25% and 410.71%, respectively, in the second year of observations, and 137.10%, and 217.48%, respectively, in the third year. There are significant differences in seed set, natural regeneration ability and sustainability of bamboo populations between the mass flowering and sporadically flowering populations of D. membranaceus. Sporadic flowering populations failed to produce effective regeneration, while mass flowering populations were able to regenerate successfully. This study provides useful insights for conservation and natural forest management of D. membranaceus. We consider the merits of introducing other genetic provenances towards long-term maintenance of the stand features at sporadically flowering sites; meanwhile, the most economic option for mass flowering stands is to allow natural regeneration to take place through protecting such sites from further disturbance.     

Specially Constructed Growth Cabinets for Simulation of the Spectral Photon Distributions Found Under Natural Vegetation Canopies

This report describes specially constructed cabinets in whichthe spectral photon distributions found in nature and undervegetation canopies were simulated. Simulation was achievedby the use of various combinations of incandescent and fluorescentlight sources. Undesirable wavelengths, especially those inthe infrared region of the spectrum, were effectively filteredout before reaching the growing area, without using refrigeration.It was possible to grow plants under various conditions of temperature,day/night temperatures, photoperiod, light quality and quantity,end-of-day light, and night-breaks.     

Natural Selection and the Frequency Distributions of ``silent' DNA Polymorphism in Drosophila

In Escherichia coli, Saccharomyces cerevisiae, and Drosophila melanogaster, codon bias may be maintained by a balance among mutation pressure, genetic drift, and natural selection favoring translationally superior codons. Under such an evolutionary model, silent mutations fall into two fitness categories: preferred mutations that increase codon bias and unpreferred changes in the opposite direction. This prediction can be tested by comparing the frequency spectra of synonymous changes segregating within populations; natural selection will elevate the frequencies of advantageous mutations relative to that of deleterious changes. The frequency distributions of preferred and unpreferred mutations differ in the predicted direction among 99 alleles of two D. pseudoobscura genes and five alleles of eight D. simulans genes. This result confirms the existence of fitness classes of silent mutations. Maximum likelihood estimates suggest that selection intensity at silent sites is, on average, very weak in both D. pseudoobscura and D. simulans (|N(e)s| & 1). Inference of evolutionary processes from within-species sequence variation is often hindered by the assumption of a stationary frequency distribution. This assumption can be avoided when identifying the action of selection and tested when estimating selection intensity.     

Contribution for the Derivation of a Soil Screening Value (SSV) for Uranium,Using a Natural Reference Soil

In order to regulate the management of contaminated land, many countries have been deriving soil screening values (SSV). However, the ecotoxicological data available for uranium is still insufficient and incapable to generate SSVs for European soils. In this sense, and so as to make up for this shortcoming, a battery of ecotoxicological assays focusing on soil functions and organisms, and a wide range of endpoints was carried out, using a natural soil artificially spiked with uranium. In terrestrial ecotoxicology, it is widely recognized that soils have different properties that can influence the bioavailability and the toxicity of chemicals. In this context, SSVs derived for artificial soils or for other types of natural soils, may lead to unfeasible environmental risk assessment. Hence, the use of natural regional representative soils is of great importance in the derivation of SSVs. A Portuguese natural reference soil PTRS1, from a granitic region, was thereby applied as test substrate. This study allowed the determination of NOEC, LOEC, EC₂₀ and EC₅₀ values for uranium. Dehydrogenase and urease enzymes displayed the lowest values (34.9 and <134.5 mg U Kg, respectively). Eisenia andrei and Enchytraeus crypticus revealed to be more sensitive to uranium than Folsomia candida. EC₅₀ values of 631.00, 518.65 and 851.64 mg U Kg were recorded for the three species, respectively. Concerning plants, only Lactuca sativa was affected by U at concentrations up to 1000 mg U kg¹. The outcomes of the study may in part be constrained by physical and chemical characteristics of soils, hence contributing to the discrepancy between the toxicity data generated in this study and that available in the literature. Following the assessment factor method, a predicted no effect concentration (PNEC) value of 15.5 mg kg⁻¹_dw was obtained for U. This PNEC value is proposed as a SSV for soils similar to the PTRS1.     

Ecological Interactions Shape the Dynamics of Seed Predation in Acrocomia aculeata (Arecaceae)

Background

The complex network of direct and indirect relationships determines not only the species abundances but also the community characteristics such as diversity and stability. In this context, seed predation is a direct interaction that affects the reproductive success of the plant. For Acrocomia aculeata, the seed predation by Pachymerus cardo and Speciomerus revoili in post-dispersal may destroy more than 70% of the propagules and is influenced by the herbivory of the fruits during pre-dispersal. Fruits of plants with a higher level of herbivory during pre-dispersal are less attacked by predators in post-dispersal. We proposed a hypothesis that describes this interaction as an indirect defense mediated by fungi in a multitrophic interaction. As explanations, we proposed the predictions: i) injuries caused by herbivores in the fruits of A. aculeata favor fungal colonization and ii) the colonization of A. acuelata fruit by decomposing fungi reduces the selection of the egg-laying site by predator.

Methodology/Principal Findings

For prediction (i), differences in the fungal colonization in fruits with an intact or damaged epicarp were evaluated in fruits exposed in the field. For prediction (ii), we performed fruit observations in the field to determine the number of eggs of P. cardo and/or S. revoili per fruit and the amount of fungal colonization in the fruits. In another experiment, in the laboratory, we use P. cardo females in a triple-choice protocol. Each insect to choose one of the three options: healthy fruits, fruits with fungus, or an empty pot. The proposed hypothesis was corroborated. Fruits with injuries in the epicarp had a higher fungal colonization, and fruits colonized by fungi were less attractive for egg-laying by seed predators.

Conclusion/Significance

This study emphasizes the importance of exploring the networks of interactions between multitrophic systems to understand the dynamics and maintenance of natural populations.     

On the Importance of Countergradients for the Development of Retinotopy: Insights from a Generalised Gierer Model

During the development of the topographic map from vertebrate retina to superior colliculus (SC), EphA receptors are expressed in a gradient along the nasotemporal retinal axis. Their ligands, ephrin-As, are expressed in a gradient along the rostrocaudal axis of the SC. Countergradients of ephrin-As in the retina and EphAs in the SC are also expressed. Disruption of any of these gradients leads to mapping errors. Gierer''s (1981) model, which uses well-matched pairs of gradients and countergradients to establish the mapping, can account for the formation of wild type maps, but not the double maps found in EphA knock-in experiments. I show that these maps can be explained by models, such as Gierer''s (1983), which have gradients and no countergradients, together with a powerful compensatory mechanism that helps to distribute connections evenly over the target region. However, this type of model cannot explain mapping errors found when the countergradients are knocked out partially. I examine the relative importance of countergradients as against compensatory mechanisms by generalising Gierer''s (1983) model so that the strength of compensation is adjustable. Either matching gradients and countergradients alone or poorly matching gradients and countergradients together with a strong compensatory mechanism are sufficient to establish an ordered mapping. With a weaker compensatory mechanism, gradients without countergradients lead to a poorer map, but the addition of countergradients improves the mapping. This model produces the double maps in simulated EphA knock-in experiments and a map consistent with the Math5 knock-out phenotype. Simulations of a set of phenotypes from the literature substantiate the finding that countergradients and compensation can be traded off against each other to give similar maps. I conclude that a successful model of retinotopy should contain countergradients and some form of compensation mechanism, but not in the strong form put forward by Gierer.     

Seed Mass and Germination Behaviour in Populations of the Dune-building Grass Leymus arenarius

The individual mean seed (caryopsis) mass of 34 natural populationsof Leymus arenarius widely distributed in Iceland and one eachfrom Scotland and England showed a six-fold variation. Phenotypicplasticity was a factor in the variation between populationsin different environments but there was also likely to havebeen genetic differentiation. Heavy-seeded populations tendedto come from early successional sites, where they also producedlonger spikes and more seeds per spike. Individual seed masswas also very variable on spikes within populations and withinspikes; lighter seeds were found consistently in the lower thirdof the spike and in the florets distal to the rachis in thespikelets. Germination was examined using the powerful methods of SurvivalAnalysis. There were striking asymptotic relationships betweenseed mass and germination: an inverse relationship between mediangermination time and seed mass and a positive relationship betweentotal germination percentage and seed mass. Samples from small-seededpopulations typically achieved half the total germination oflarge-seeded ones, with up to ten-fold longer median germinationtimes. Similar trends emerged from analysis of large- and small-seededspikes within populations and large- and small-seeded floretswithin spikelets. Natural stands of Leymus arenarius are harvested on a largescale in Iceland for sowing in reclamation programmes to combatunstable and eroding sands. The harvest period is short andsusceptible to autumn gales and grazing. Mean individual seedmass would provide a rapid and reliable measure of seed quality,in terms of rapid germination and high germination rate. Standsshould not be selected for harvest unless the individual seedmass averaged for whole spikes is at least 5 mg and such standsare most likely to be found in early-successional dune sites.Copyright1995, 1999 Academic Press Leymus arenarius, lymegrass, seed mass, germination, population differentiation, sand stabilization, dune succession, Survival Analysis     

Patterns of Cross-Continental Variation in Tree Seed Mass in the Canadian Boreal Forest

Seed mass is an adaptive trait affecting species distribution, population dynamics and community structure. In widely distributed species, variation in seed mass may reflect both genetic adaptation to local environments and adaptive phenotypic plasticity. Acknowledging the difficulty in separating these two aspects, we examined the causal relationships determining seed mass variation to better understand adaptability and/or plasticity of selected tree species to spatial/climatic variation. A total of 504, 481 and 454 seed collections of black spruce (Picea mariana (Mill.) B.S.P.), white spruce (Picea glauca (Moench) Voss) and jack pine (Pinus banksiana Lamb) across the Canadian Boreal Forest, respectively, were selected. Correlation analyses were used to determine how seed mass vary with latitude, longitude, and altitude. Structural Equation Modeling was used to examine how geographic and climatic variables influence seed mass. Climatic factors explained a large portion of the variation in seed mass (34, 14 and 29%, for black spruce, white spruce and jack pine, respectively), indicating species-specific adaptation to long term climate conditions. Higher annual mean temperature and winter precipitation caused greater seed mass in black spruce, but annual precipitation was the controlling factor for white spruce. The combination of factors such as growing season temperature and evapotranspiration, temperature seasonality and annual precipitation together determined seed mass of jack pine. Overall, sites with higher winter temperatures were correlated with larger seeds. Thus, long-term climatic conditions, at least in part, determined spatial variation in seed mass. Black spruce and Jack pine, species with relatively more specific habitat requirements and less plasticity, had more variation in seed mass explained by climate than did the more plastic species white spruce. As traits such as seed mass are related to seedling growth and survival, they potentially influence forest species composition in a changing climate and should be included in future modeling of vegetation shifts.     

Gene Network Polymorphism Is the Raw Material of Natural Selection: The Selfish Gene Network Hypothesis

Population genetics, the mathematical theory of modern evolutionary biology, defines evolution as the alteration of the frequency of distinct gene variants (alleles) differing in fitness over the time. The major problem with this view is that in gene and protein sequences we can find little evidence concerning the molecular basis of phenotypic variance, especially those that would confer adaptive benefit to the bearers. Some novel data, however, suggest that a large amount of genetic variation exists in the regulatory region of genes within populations. In addition, comparison of homologous DNA sequences of various species shows that evolution appears to depend more strongly on gene expression than on the genes themselves. Furthermore, it has been demonstrated in several systems that genes form functional networks, whose products exhibit interrelated expression profiles. Finally, it has been found that regulatory circuits of development behave as evolutionary units. These data demonstrate that our view of evolution calls for a new synthesis. In this article I propose a novel concept, termed the selfish gene network hypothesis, which is based on an overall consideration of the above findings. The major statements of this hypothesis are as follows. (1) Instead of individual genes, gene networks (GNs) are responsible for the determination of traits and behaviors. (2) The primary source of microevolution is the intraspecific polymorphism in GNs and not the allelic variation in either the coding or the regulatory sequences of individual genes. (3) GN polymorphism is generated by the variation in the regulatory regions of the component genes and not by the variance in their coding sequences. (4) Evolution proceeds through continuous restructuring of the composition of GNs rather than fixing of specific alleles or GN variants.