Scaling sun and shade photosynthetic acclimation of Alocasia macrorrhiza to whole-plant performance – II. Simulation of carbon balance and growth at different photon flux densities

A whole-plant carbon balance model incorporating a light acclimation response was developed for Alocasia macrorrhiza based on empirical data and the current understanding of light acclimation in this species. The model was used to predict the relative growth rate (RGR) for plants that acclimated to photon flux density (PFD) by changing their leaf type, and for plants that produced only sun or shade leaves regardless of PFD. The predicted RGR was substantially higher for plants with shade leaves than for those with sun leaves at low PFD. However, the predicted RGR was not higher, and in fact was slightly lower, for plants with sun leaves than for those with shade leaves at high PFD. The decreased leaf area ratios (LARs) of the plants with sun leaves counteracted their higher photosynthetic capacities per unit leaf area (A_max). The model was manipulated by changing parameters to examine the sensitivity of RGR to variation in single factors. Overall, RGR was most sensitive to LAR and showed relatively little sensitivity to variation in A_max or maintenance respiration. Similarly, RGR was relatively insensitive to increases in leaf life-span beyond those observed. Respiration affected RGR only at low PFD, whereas A_max was moderately important only at high PFD.     

Conformational properties of topoisomerase II inhibitors and sequence specificity of DNA cleavage

The sequence specificity of topoisomerase-II-mediated DNA cleavage, stimulated by 2-methyl-9-hydroxy ellipticinium and 4′, 5′,7-trihydroyflavone (genistein) was investigated by sequencing analysis of DNA cleavage sites and molecular modeling techniques. The former drug exhibits a marked preference for a T base at the position immediately preceding the cleavage site (?1). The latter shares the preference for the same base, with an additional preference for a thymine at position +1. The cleavage intensity patterns for the two drugs differ considerably. From a conformational point of view, ellipticinium and genistein exhibit similar overall shape and dimensions. However, the fused ring system in the former generates a planar structure whereas the single bond, connecting the two aromatic portions in the latter, allows internal rotation. The most stable conformation of genistein corresponds to a deviation of about 40° from planarity. A computer-assisted analysis was carried out to compare the steric and electrostatic properties of the two compounds. Two types of preferred (energetically almost degenerate) alignment for the two molecules were found. One corresponds to overlapping of the 9-hydroxyl containing ring of ellipticinium with the 4′-hydroxyphenyl moiety of genistein, the other envisages the same moiety of ellipticine superimposed to the hydroxyl-benzopyrone portion of genistein. The structural similarities of the test drugs might account for the common preference for stimulation of DNA cleavage at position +1, whereas the different possible arrangements of genistein in the cleavable complex could explain both the additional +1 specificity exhibited by this compound and the differences in cleavage intensity patterns observed in comparison to ellipticinium.     

Ion channel formation by zervamicin-IIB

Zervamicin-IIB (Zrv-IIB) is a 16 residue peptaibol which forms voltage-activated, multiple conductance level channels in planar lipid bilayers. A molecular model of Zrv-IIB channels is presented. The structure of monomerc Zrv-II3 is based upon the crystal structure of Zervamicin-Leu. The helical backbone is kinked by a hydroxyproline residue at position 10. Zrv-IIB channels are modelled as helix bundles of from 4 to 8 parallel helices surrounding a central pore. The monomers are packed with their C-terminal helical segments in close contact, and the bundles are stabilized by hydrogen bonds between glutamine 11 and hydroxyproline 10 of adjacent helices. Interaction energy profiles for movement of three different probes species (K⁺, Cl^– and water) through the central pore are analyzed. The conformations of: (a) the sidechain of glutamine 3; (b) the hydroxyl group of hydroxyproline 10; and (c) the C-terminal hydroxyl group are optimized in order to maximize favourable interactions between the channel and the probes, resulting in favourable interaction energy profiles for all three. This suggests that conformational flexibility of polar sidechains enables the channel lining to mimic an aqueous environment.     

黑曲霉S4生淀粉糖化酶纯化组分的性质及其动力学常数

生淀粉糖化酶是可以水解生淀粉的葡萄糖糖化酶(Ec3.2.1.3,α-1.4-糖苷酶),它是近代工业中极为重要的酶类之一。虽然对生淀粉糖化酶可水解淀粉中所有的D-糖苷键已经清楚,由单糖逆合成寡糖的动力学研究也比较深入,但有关它对各种常用生淀粉材料的水解动力学以及各生淀粉糖化酶组分之间的相互关系的研究却很少。本研究通过在不同温度和pH下,生淀粉糖化酶的三个组分对寡糖和各种生淀粉作用的动力学常数,以及在不同pH值下它们对各生淀粉     

Modelling the effects of alternative nutrient control policies — the example of Slapton Ley,Devon, UK

In the period since 1945, Slapton Ley, a small, coastal lake in Southwest England, has been eutrophccated by nutrient inputs generated both by the intensification of agriculture, and the discharge of sewage effluent. Two simple models have been used to identify the main sources of catchment outputs, and to evaluate historical changes in land use, and their likely effect on lake trophic status.Restoration strategies may also be evaluated using the same models. They suggest that in order to reduce loads upon the Ley to within OECD permissible limits, not only will all sewage and phosphate detergent inputs need to be prevented, but also losses from agricultural land must be reduced. This could take the form of the zoning of the catchment so that riparian zones are used, not as at present, for the grazing of livestock, but are converted to woodland, and more particularly eg to buffer strips sensu Mander (1985, 1992).This policy, if implemented comprehensively, would reduce external phosphorus loads to within permissible limits. Eventually, however, some kind of internal control, such as manipulation of the fish populations, may also have to be attempted, in order to remove the memory of five decades of eutrophication.     

Environmental DNA reveals a mismatch between diversity facets of Amazonian fishes in response to contrasting geographical,environmental and anthropogenic effects

Freshwater ecosystems are among the most endangered ecosystem in the world. Understanding how human activities affect these ecosystems requires disentangling and quantifying the contribution of the factors driving community assembly. While it has been largely studied in temperate freshwaters, tropical ecosystems remain challenging to study due to the high species richness and the lack of knowledge on species distribution. Here, the use of eDNA-based fish inventories combined to a community-level modelling approach allowed depicting of assembly rules and quantifying the relative contribution of geographic, environmental and anthropic factors to fish assembly. We then used the model predictions to map spatial biodiversity and assess the representativity of sites surveyed in French Guiana within the EU Water Framework Directive (WFD) and highlighted areas that should host unique freshwater fish assemblages. We demonstrated a mismatch between the taxonomic and functional diversity. Taxonomic assemblages between but also within basins were mainly the results of dispersal limitation resulting from basin isolation and natural river barriers. Contrastingly, functional assemblages were ruled by environmental and anthropic factors. The regional mapping of fish diversity indicated that the sites surveyed within the EU WFD had a better representativity of the regional functional diversity than taxonomic diversity. Importantly, we also showed that the assemblages expected to be the most altered by anthropic factors were the most poorly represented in terms of functional diversity in the surveyed sites. The predictions of unique functional and taxonomic assemblages could, therefore, guide the establishment of new survey sites to increase fish diversity representativity and improve this monitoring program.     

Climate–ecosystem modelling made easy: The Land Sites Platform

Dynamic Global Vegetation Models (DGVMs) provide a state-of-the-art process-based approach to study the complex interplay between vegetation and its physical environment. For example, they help to predict how terrestrial plants interact with climate, soils, disturbance and competition for resources. We argue that there is untapped potential for the use of DGVMs in ecological and ecophysiological research. One fundamental barrier to realize this potential is that many researchers with relevant expertize (ecology, plant physiology, soil science, etc.) lack access to the technical resources or awareness of the research potential of DGVMs. Here we present the Land Sites Platform (LSP): new software that facilitates single-site simulations with the Functionally Assembled Terrestrial Ecosystem Simulator, an advanced DGVM coupled with the Community Land Model. The LSP includes a Graphical User Interface and an Application Programming Interface, which improve the user experience and lower the technical thresholds for installing these model architectures and setting up model experiments. The software is distributed via version-controlled containers; researchers and students can run simulations directly on their personal computers or servers, with relatively low hardware requirements, and on different operating systems. Version 1.0 of the LSP supports site-level simulations. We provide input data for 20 established geo-ecological observation sites in Norway and workflows to add generic sites from public global datasets. The LSP makes standard model experiments with default data easily achievable (e.g., for educational or introductory purposes) while retaining flexibility for more advanced scientific uses. We further provide tools to visualize the model input and output, including simple examples to relate predictions to local observations. The LSP improves access to land surface and DGVM modelling as a building block of community cyberinfrastructure that may inspire new avenues for mechanistic ecosystem research across disciplines.     

Causal inference and large-scale expert validation shed light on the drivers of SDM accuracy and variance

Aim

To develop a causal understanding of the drivers of Species distribution model (SDM) performance.

Location

United Kingdom (UK).

Methods

We measured the accuracy and variance of SDMs fitted for 518 species of invertebrate and plant in the UK. Our measure of variance reflects variation among replicate model fits, and taxon experts assessed model accuracy. Using directed acyclic graphs, we developed a causal model depicting plausible effects of explanatory variables (e.g. species' prevalence, sample size) on SDM accuracy and variance and quantified those effects using a multilevel piecewise path model.

Results

According to our model, sample size and niche completeness (proportion of a species' niche covered by sampling) directly affect SDM accuracy and variance. Prevalence and range completeness have indirect effects mediated by sample size. Challenging conventional wisdom, we found that the effect of prevalence on SDM accuracy is positive. This reflects the facts that sample size has a positive effect on accuracy and larger sample sizes are possible for widespread species. It is possible, however, that the omission of an unobserved confounder biased this effect. Previous studies, which reported negative correlations between prevalence and SDM accuracy, conditioned on sample size.

Main conclusions

Our model explicates the causal basis of previously reported correlations between SDM performance and species/data characteristics. It also suggests that niche completeness has similarly large effects on SDM accuracy and variance as sample size. Analysts should consider niche completeness, or proxies thereof, in addition to sample size when deciding whether modelling is worthwhile.     

Phase shifts of the adult locomotor activity rhythm in Calliphora vicina induced by non-steroidal ecdysteroid agonist RH 5849

RH 5849, a non-steroidal ecdysteroid mimic, was found to cause consistent phase shifts in the circadian rhythm of locomotor activity of the blowfly, Calliphora vicina. This compound causes phase advances in the early subjective night and phase delays in the late subjective night. This effect is the opposite, but not the mirror image of the phase response curve obtained for 1 h light pulses. This suggests that ecdysteroids might act as entraining agents via the output pathway by feedback to clock neurons in the brain. A computer model based on 12 pacemaker neurons with circadian periods ( values) from short to long without simulated feedback from the ecdysteroid system becomes arrhythmic; with feedback, the oscillators become synchronized to a common period. The possible role of ecdysteroids as endogenous synchronizing agents in the insect circadian system is discussed.     

氯化镧对玉米根切段钾离子外渗影响的动力学研究

研究了氯化镧对玉米(Zea mays L.)“京早8号”根切段细胞膜透性及质子分泌的影响,并用动力学方法研究了钾离子外渗过程的变化。氯化镧处理可降低外渗液的电导率及K~ 和糖的外渗量,使质子分泌活动增强。用动力学方法分析玉米根切段K~ 外渗过程的结果表明:(1)应用于K~ 吸收研究的数学模型也能适应于K~ 外渗的研究;(2)在LaCl_3和(或)CaCl_2存在的条件下,最大吸收速度(V_(max))升高,而米氏常数(K_m)没有变化;(3)在LaCl_3和(或)CaCl_2存在的条件下,K~ 外渗量降低是由于最大吸收速度(V_(max))升高所致。