Polypeptide folding with off-lattice Monte Carlo dynamics: the method

The MC dynamics of an off-lattice all-atom protein backbone model with rigid amide planes are studied. The only degrees of freedom are the dihedral angle pairs of the C-atoms. Conformational changes are generated by Monte Carlo (MC) moves. The MC moves considered are single rotations (simple moves, SM's) giving rise to global conformational changes or, alternatively, cooperative rotations in a window of amide planes (window moves, WM's) generating local conformational changes in the window. Outside the window the protein conformation is kept invariant by constraints. These constraints produce a bias in the distribution of dihedral angles. The WM's are corrected for this bias by suitable Jacobians. The energy function used is derived from the CHARMM force field. In a first application to polyalanine it is demonstrated that WM's sample the conformational space more efficiently than SM's.Abbreviations CPU Central Processing Unit - MC Monte Carlo - MCD Monte Carlo Dynamics - MD Molecular Dynamics - RMS Root-Mean-Square - RMSD Root-Mean-Square-Deviation - SM Simple Move - WM Window Move     

Acetylation of α-tubulin in male meiotic spindles ofPyrrhocoris apterus,an insect with holokinetic chromosomes

Summary Kinetochore structure was examined in metaphase spermatogonia and primary spermatocytes of the red firebug,Pyrrhocoris apterus (Pyrrhocoridae, Hemiptera). Chromosome spreads were analysed using light microscopy and serial sections through spindles were studied using electron microscopy. Mitotic chromosomes were rod-shaped bodies and did not possess primary constrictions. Trilaminar kinetochores occurred throughout about 72% of the chromosomal length. Numerous microtubules (MTs) were connected with the outer plates of the kinetochores and interactions between MTs and the remainder of the chromosomal surface were rare. The bivalents formed dumbbell-shaped bodies in metaphase I spermatocytes. At that stage, MTs were found in contact with the entire poleward surface of the chromosomes. Distinct kinetochore material was, however, not detectable and some MTs penetrated deeply into the chromatin. Mitotic and meiotic chromosomes ofP. apterus are holokinetic and consequently the number of kinetochore MTs is expected to be relatively high. In the second part of the study, the question whether holokinetic chromosomes affect spindle MT dynamics is addressed. To this end, primary spermatocytes ofP. apterus were labelled with a widely used antibody, 6-11B-1, directed against acetylated -tubulin. The acetylation of -tubulin is believed to indicate the presence of long-lived MTs. MT bundles were labelled in metaphase and anaphase I spindles, while prophase and prometaphase I spermatocytes did not contain acetylated MTs. MTs in early and mid telophase spindles were not acetylated. Only late telophase I spindles possessed small amounts of acetylated -tubulin. The acetylated MT bundles of metaphase and anaphase I spindles probably represent kinetochore MTs stabilized by their association with the holokinetic chromosomes at one end and the spindle poles at the opposite end.Abbreviations BSA bovine serum albumin - DAPI 4,6-diamidino-2-phenylindole · 2HCl - EGTA ethylene glycol-bis (-aminoethyl ether)-N,N-tetraacetic acid - FITC fluorescein-isothiocyanate - PBS phosphate-buffered saline - PIPES piperazine-N,N bis(2-ethane sulfonic acid) - MT microtubule     

Evolutionary dynamics of predator-prey systems: an ecological perspective

 Evolution takes place in an ecological setting that typically involves interactions with other organisms. To describe such evolution, a structure is needed which incorporates the simultaneous evolution of interacting species. Here a formal framework for this purpose is suggested, extending from the microscopic interactions between individuals – the immediate cause of natural selection, through the mesoscopic population dynamics responsible for driving the replacement of one mutant phenotype by another, to the macroscopic process of phenotypic evolution arising from many such substitutions. The process of coevolution that results from this is illustrated in the context of predator–prey systems. With no more than qualitative information about the evolutionary dynamics, some basic properties of predator–prey coevolution become evident. More detailed understanding requires specification of an evolutionary dynamic; two models for this purpose are outlined, one from our own research on a stochastic process of mutation and selection and the other from quantitative genetics. Much of the interest in coevolution has been to characterize the properties of fixed points at which there is no further phenotypic evolution. Stability analysis of the fixed points of evolutionary dynamical systems is reviewed and leads to conclusions about the asymptotic states of evolution rather different from those of game-theoretic methods. These differences become especially important when evolution involves more than one species. Received 10 November 1993; received in revised form 25 July 1994     

Impact of density of Aphis craccivora (Aphididae) on growth and yield of susceptible and resistant cowpea cultivars

Impact of initial density of cowpea aphid Aphis craccivora Koch (Aphididae) at infestation on the growth and yield of aphid-susceptible cowpea cultivar ICV-1 and aphid-resistant cultivar ICV-12, was investigated. Plants at the seedling, flowering and podding stages of development were infested with five aphid densities consisting of 0, 2, 5, 10 and. 20 aphids per plant and maintained for 22 days. Extended leaf heights of plants and aphid counts were recorded at 7, 12, 17 and 22 days after infestation. Two crop growth parameters (biomass duration and leaf area duration), and two plant yield parameters (number of pods per plant and number of seeds per pod) were recorded. Due to the occurrence of parthenogenesis and changes in population dynamics during infestations, aphid densities were converted into cumulative cowpea aphid-days, to facilitate data analyses and interpretation. ANOVA indicated that there was significant (P=s 0.05) difference in aphid-day accumulations between the two cultivars when infested at the seedling stage. Accumulations on cv. ICV-1 were greater than on cv. ICV-12. However, no such differences between the cultivars were detected when plants were infested at flowering and podding stages. Therefore, the seedling stage was used for comparisons of the impact of cowpea aphid-days on the growth and yield parameters of the two cultivars. At the 95% confidence intervals, ICV-12 plants were consistently taller than ICV-1 plants. Infested ICV-1 seedlings showed stunting and other growth deformities which were not observed on ICV-12 plants. Regression analyses revealed substantial reductions in the growth and yield parameters of ICV-1 relative to ICV-12. Overall, cowpea aphid-days provided a convenient and reliable method for studying the aphid population dynamics and the subsequent impact on plant growth and yield performance.     

The status and ecology of a Juniperus excelsa subsp. polycarpos woodland in the northern mountains of Oman

Juniperus excelsa subsp. polycarpos (K. Koch) Takhtajan is found in mountain areas from Turkey through to India and as an isolated population on Jebel Akhadar in the northern mountains of Oman. Juniperus is one of the dominant plant species in these mountains and a major landscape feature of several proposed National Nature and Scenic Reserves and of Hayl Juwari, a wooded valley at 2250 m altitude proposed as a Botanical Site of Special Interest. Above 2400 m altitude the Juniperus woodlands generally appear to be regenerating and in good condition, both on exposed slopes and in wadis and sheltered gullies, whereas below 2400 m most stands are in poor condition and exhibit few signs of regeneration. If the apparently poor condition of the lower altitude woodlands is due to any long term change in climatic conditions, both tree status and regeneration would be poorer in relatively more xeric habitats. To test this prediction we have carried out a detailed survey of the status and ecology of a 32 ha area of Hayl Juwari, and analysed differences in tree status and regeneration between wadis (relatively more nesic sites) and non-wadi areas (relatively more xeric). Approximately one third of the trees are dead, and an analysis of the height, condition, regeneration, female cone production, preferred germination sites and spatial distribution of trees indicates the importance of topography, hydrology and microclimate for growth. However, although there are relatively greater numbers of dead and poor-condition trees in the more xeric non-wadi habitat, there is no unequivocal evidence that the present distribution of small, sexually immature trees in both habitats could not form a pattern of larger, sexually mature trees similar to that seen today. We speculate, however, that the climate at this altitude may be marginal for the survival of a J. excelsa subsp. polycarpos woodland and that even small increases in climatic stress could imperil the woodland's present status.     

Plant growth and reproduction along CO2 gradients: non-linear responses and implications for community change

The effects of rising atmospheric CO₂ concentrations on natural plant communities will depend upon the cumulative responses of plant growth and reproduction to gradual, incremental changes in climatic conditions. We analysed published studies of plant responses to elevated CO₂ to address whether reproductive and total biomass exhibit similar enhancement to elevated vs. ambient CO₂ concentrations, and to assess the patterns of plant response along gradients of CO₂ concentrations. In six annual plant species, mean enhancement at double ambient vs. ambient CO₂ was 1.13 for total biomass and 1.30 for reproductive biomass. The two measures were significantly correlated, but there was considerable scatter in the relationship, indicating that reproductive responses cannot be consistently predicted from enhancement of total biomass. Along experimental CO₂ gradients utilizing three concentrations, there was a great diversity of response patterns, including positive, negative, non-monotonic and non-significant (flat) responses. The distribution of response patterns differed for plants grown in stands compared to those grown individually. Positive responses were less frequent in competitive environments, and non-monotonic responses were more frequent. These results emphasize that interpolation of plant response based on enhancement ratios measured at elevated vs. ambient CO₂ concentrations is not sufficient to predict community responses to incremental changes in atmospheric conditions. The consequences of differential response patterns were assessed in a simulation of community dynamics for four species of annual plants. The model illustrates that the final community composition at a future point in time depends critically on both the magnitude and the rate of increase of atmospheric CO₂.     

A protocol for classifying regional dynamics,exemplified by using woodland birds in southeastern Australia

Abstract Communities of forest and woodland birds are usually studied intensively at only one or a few locations. This provides a perspective that perhaps emphasizes local phenomena at the expense of placing local dynamics in the context of processes operating at the landscape or regional scale. The present paper seeks to redress partially this imbalance by studying the dynamics of individual bird species among several habitat types (all Eucalyptus-dominated forests or woodlands) over the annual cycle. This regional-scale (250km), continental study reveals that species exhibit idiosyncratic dynamics of various kinds: restricted or more ubiquitous occupation of habitats and three forms of seasonal dynamics at the regional scale (resident, migrant and itinerant). By using this classificatory scheme, it becomes evident that the bird communities found in different habitats consist of diverse collections of strategists and that the level of diversity differs among habitat types. The difficulties that many field workers have had in reconciling their observations with community theory most likely reflect the underlying dynamism of bird communities, especially in the temperate regions on continents where seasonal fluxes are pronounced.     

Leaf dynamics and insect herbivory in a Eucalyptus camaldulensis forest under moisture stress

Abstract The influence of soil moisture content on leaf dynamics and insect herbivory was examined between September 1991 and March 1992 in a river red gum (Eucalyptus camaldulensis) forest in southern central New South Wales. Long-term observations of leaves were made in trees standing either within intermittently flooded waterways or at an average of 37. 5m from the edge of the waterways. The mean soil moisture content was significantly (P≤0.05) greater in the waterways than in the non-flooded areas. Trees in the higher soil moisture regime produced significantly larger basal area increments and increased canopy leaf area. This increase in canopy leaf area was achieved, in part, through a significant increase in leaf longevity and mean leaf size. Although a greater number of leaves was initiated and abscissed per shoot from the non-flooded trees, more leaves were collected from litter traps beneath the denser canopies of the flooded trees. Consumption of foliage by insects on the trees subjected to flooding compared to the non-flooded trees was not significantly different. However, the relative impact of insect herbivory was significantly greater on the non-flooded trees. Leaf chewing was the most common form of damage by insects, particularly Chryso-melidae and Curculionidae. No species was present in outbreak during this study. Leaf survival decreased as the per cent area eaten per leaf increased. In addition, irrespective of the level of herbivory, leaf abscission tended to be higher in E. camaldulensis under moisture deficit. The influence of soil moisture content on the balance between river red gum growth and insect herbivory is discussed.     

陆地表层系统动力学机制研究Ⅰ．──陆地表层系统和动力学方程

对陆地表层动力学的研究对象、研究内容及其基本理论方法作了阐述,以多学科综合的观点定义了陆地表层系统,包括时空尺度范围的约定、状态变量的选择、物质循环以及外界因子等的讨论;依据物质和能量守恒原理建立了陆地表层系统的非线性控制方程组,表述了各圈层之间物质循环和能量循环过程、反馈关系及其动力学联系;讨论了控制方程组的整体运作功能以及人类活动对陆地表层系统的影响．     

大鹏湾反曲原甲藻种群动态机理模型辨识

建立了我国南海大鹏湾反曲原甲藻种群动态机理模型,在温度、盐度、溶解氧（ＤＯ）、可溶性无机磷（ＤＩＰ）、可溶性亚硝态氮、可溶性硝态氮和酸碱度（ＰＨ值）等７个因子的分析中,辨识出温度为反曲原甲藻的限制因子;种群数量变动中引入自回归平稳随机模拟,并建立３个站位６个层面的６个自回归与非线性回归联立模型,以动态递阶的方式对反曲原甲藻种群动态进行回代,研究模型对实测值的拟合结果,拟合率达８１．７％。