Habitat selection and density of couas in Madagascar: implication for their conservation

The forests in Madagascar are threatened by logging and burning. Because of their importance for biodiversity conservation, monitoring their animal populations is also important. We worked at two stations in the western dry forest where we studied three species of terrestrial couas in several forest plots, which differed in their degradation state. Some were burnt; others were logged. By measuring vegetation characteristics and bird densities, it was possible to indicate which characteristics were important for these birds and which conservation measures would be necessary to apply for this forest.     

Free Energy Perturbations in Ribonuclease T1 Substrate Binding. A Study of the Influence of Simulation Length,Internal Degrees of Freedom and Structure in Free Energy Perturbations

Abstract

We have studied the reliability of free energy perturbation calculations with respect to simulation protocol and simulation length in a real biological system, the binding of two different ligands to wildtype Ribonuclease T ₁ (RNT1) and to a mutant of RNT1 with Glu-46 replaced by Gln (RNT1-Gln46). The binding of the natural substrate 3′ GMP has been compared with the binding of a fluorescent probe, 2-aminopurine 3′ mono phosphate (2AP3′MP). These simulations predict that the mutant binds 2AP3′MP better than 3′GMP. Four complete free energy perturbations were performed that form a closed loop of four free energy differences, which should sum up to zero. This could be used as a tool for searching for systematic errors that are not detected by standard forward ? backward perturbations. The perturbation between 2AP3′MP and 3′GMP is quite straightforward and similar to what has been done by other groups. The perturbation between Glu46 and Gln46 is much more complex, involving as many as twelve atoms and a change of charge. This perturbation needs much longer simulation time, 500-600 ps, than used in free energy perturbations before. The increased simulation time is needed both to reach an equilibrium and to include several phases of fluctuations of the observed parameters in the production run. The extremely long simulation time is not such a severe problem as much of the work might be done on several different machines in parallel and cheap workstations are excellent for these calculations. Problems may also occur with values of the coupling parameter Λ close to 0 or 1, due to the high mobility of atoms as well as insertion/deletion in a previously unoccupied space involved in the perturbation.     

Evolutionary game dynamics with impulsive effects

The jumps in population size due to the occurrence of an unfavorable physical environment (e.g. the effects of periodic climate disaster on the population size), or due to the intrinsic physiological and reproductive mechanisms of the population (e.g. the seasonal reproduction of most animal populations), can be called impulsive perturbations. A two-phenotype evolutionary game dynamics with impulsive effects is investigated. The main goal is to show how the evolutionary game dynamics is affected by the impulsive perturbations. The results show that the impulsive perturbations not only result in periodic behavior, but also it is possible that an ESS strategy based on the traditional concept of evolutionary stability can be replaced successfully by a non-ESS strategy.     

Robustness: predicting the effects of life history perturbations on stage-structured population dynamics

Matrix-based models lie at the core of many applications across the physical, engineering and life sciences. In ecology, matrix models arise naturally via population projection matrices (PPM). The eigendata of PPMs provide detailed quantitative and qualitative information on the dynamic behaviour of model populations, especially their asymptotic rates of growth or decline. A fundamental task in modern ecology is to assess the effect that perturbations to life-cycle transition rates of individuals have on such eigendata. The prevailing assessment tools in ecological applications of PPMs are direct matrix simulations of eigendata and linearised extrapolations to the typically non-linear relationship between perturbation magnitude and the resulting matrix eigenvalues. In recent years, mathematical systems theory has developed an analytical framework, called 'Robustness Analysis and Robust Control', encompassing also algorithms and numerical tools. This framework provides a systematic and precise approach to studying perturbations and uncertainty in systems represented by matrices. Here we lay down the foundations and concepts for a 'robustness' inspired approach to predictive analyses in population ecology. We treat a number of application-specific perturbation problems and show how they can be formulated and analysed using these robustness methodologies.     

具收获与脉冲的时滞捕食模型研究

研究了与生物资源管理相关的食饵具脉冲扰动与成年捕食者具连续收获的阶段结构时滞捕食-食饵模型.利用离散动力系统的频闪映射和脉冲时滞微分方程理论,得到了捕食者灭绝周期解的全局吸引和系统持久的充分条件,也证明了系统的所有解的一致完全有界.结论为现实的可再生生物资源管理提供了可靠的策略依据.     

土壤微生物群落抵抗力和恢复力研究进展

人类活动的不断加剧使得土壤生态系统承受着环境干扰压力。土壤微生物受到环境干扰的响应程度（抵抗力）及恢复至原来状态的能力（恢复力）决定着土壤生态系统的可持续性。梳理和总结了土壤微生物群落对环境干扰的抵抗力和恢复力方面的研究进展。首先,在介绍土壤微生物群落抵抗力和恢复力概念的基础上,阐述了通过评估微生物群落的结构和功能的变化来系统表征抵抗力和恢复力;随后,分析了最近十年（2012-2021年）有关文献,发现土壤微生物群落的结构和（或）功能在环境干扰后的恢复力总体较弱,但耕作、有机物料添加和轮作等农田管理措施下的响应趋势表现出一定的规律性;继而,从个体水平的休眠和胁迫忍耐、种群水平的生存策略、群落水平的多样性和相互作用以及生态系统水平的历史遗留效应等方面分析了土壤微生物群落抵抗力和恢复力的维持机制;最后,从功能性状、多功能性和植物-土壤微生物整体性对未来研究做出了展望,以期为构建土壤健康评价体系及预测环境干扰对土壤功能的影响提供科学依据。     

Differential effect of ethanol on muscarinic cholinergic binding to rat and locust neural membranes

We have compared the effect of ethanol, a membrane perturbant, on the muscarinic binding sites in neural membranes from a vertebrate (rat) and an insect (locust). The binding of the muscarinic antagonist [³H]quinuclidinyl benzilate ([³H]QNB) to both rat and locust neural membranes was inhibited by ethanol at 10–500 mM concentrations; but this inhibition was greater in the locust. Ethanol (500 mM) increased the apparent dissociation constant (K d) of [³H]QNB binding to rat membranes from 0.13±0.01 nM in control to 0.20±0.02 nM; there was also an small but significant reduction in the number of binding sitesB _max. In locust, 500 mM ethanol reduced theB _max of [³H]QNB binding from 590±30 in control to 320±40 pmol/g protein; no significant alteration in theK _D was detected. The dissociation rate constant (k _off) of [³H]QNB increased from 0.020±0.003 in controls to 0.031±0.004 (min^–1) in the presence of 500mM ethanol, the association rate constant (k _on) did not change significantly. In locust, 500 mM ethanol did not affect eitherk _on ork _off. Competition experiments revealed that the binding affinities of both the agonist carbamylcholine and the antagonist atropine to the rat membranes were reduced in the presence of ethanol. In contrast, ethanol caused no alteration in the binding affinities of these ligands to the locust membranes. This differential effect of ethanol on rat and locust muscarinic binding suggests a difference in the hydrophobic domains and/or the membrane interactions of the muscarinic receptors in the two species.     

Sudden weather deterioration but not brood size affects baseline corticosterone levels in nestling Alpine swifts

While evidence is accumulating that stress-induced glucocorticoid responses help organisms to quickly adjust their physiology and behaviour to life-threatening environmental perturbations, the function and the ecological factors inducing variation in baseline glucocorticoid levels remain poorly understood. In this study we investigated the effects of brood size by experimentally manipulating the number of nestlings per brood and the effect of weather condition on baseline corticosterone levels of nestling Alpine swifts (Apus melba). We also examined the potential negative consequences of an elevation of baseline corticosterone on nestling immunity by correlating corticosterone levels with ectoparasite intensity and the antibody production towards a vaccine. Although nestlings reared in enlarged broods were in poorer condition than nestlings reared in reduced broods, they showed similar baseline corticosterone levels. In contrast, nestling baseline corticosterone levels were higher immediately after cold and rainy episodes with strong winds. Neither nestling infestation rate by ectoparastic flies nor nestling antibody production against a vaccine was correlated with baseline corticosterone levels. Thus, our results suggest that altricial Alpine swift nestlings can quickly modulate baseline corticosterone levels in response to unpredictable variations in meteorological perturbation but not to brood size which may be associated with the degree of sibling competition. Apparently, short-term elevations of baseline corticosterone have no negative effects on nestling immunocompetence.     

Delay model of circadian gene expression with two negative feedback loops

In this theoretical paper we propose a quantitative minimal model for circadian gene expression based on two negative feedback loops. We perform numerical simulations to analyse its dynamics and parameter sensitivities in free-running conditions, and verify the entrainability by a single periodic driver. We furthermore apply two simultaneously acting external drivers, leading to aperiodic oscillations in the case of a single-loop system. These can be turned into regular periodic oscillations by introduction of a second loop. Our studies confirm the increasing evidence that multiple feedback loops increase the robustness of regulatory systems, and stress the particular situation of systems that are close to transition from free-running oscillation to steady-state behaviour. We discuss possible molecular realisations of the featured feedback loops and suggest the application of complex patterns of external stimulation as a generally useful approach to assess the functionality of models of circadian systems.