Energetics of the native energy landscape of a two-domain calcium sensor protein: distinct folding features of the two domains

The protein folding energy landscape allows a thorough understanding of the protein folding problem which in turn helps in understanding various aspects of biological functions. Characterizing the cooperative unfolding units and the intermediates along the folding funnel of a protein is a challenging task. In this paper, we investigated the native energy landscape of EhCaBP, a calcium sensor, belonging to the same EF-hand superfamily as calmodulin. EhCaBP is a two-domain EF-hand protein consisting of two EF-hands in each domain and binding to four Ca2+ cations. Native-state hydrogen exchange (HX) was used to assess the folding features of the landscape and also to throw light on the structure-folding function paradigm of calcium sensor proteins. HX measurements under the EX2 regime provided the thermodynamic information about the protein folding events under native conditions. HX studies revealed that the unfolding of EhCaBP is not a two-state process. Instead, it proceeds through cooperative units. The C-terminal domain exhibits less denaturant dependence than the N-terminal domain, suggesting that the former is dominated by local fluctuations. It is interesting to note that the N- and C-terminal domains of EhCaBP have distinct folding features. In fact, these observed differences can regulate the domain-dependent target recognition of two-domain Ca2+ sensor proteins.     

The energetics of T4 lysozyme reveal a hierarchy of conformations.

We have used native state exchange to examine the energy landscape of the well-characterized protein T4 lysozyme. Although the protein exhibits two-state behavior by traditional probes, the energy landscape determined here is much more complex. The average stability of the C-terminal subdomain is significantly higher than that for the N-terminus suggesting at least two regions of unfolding. At a more detailed level, there appears to be a broad continuum of stabilities throughout each region. The overall subdomain hierarchy of energies does not mirror data on the folding pathway for this protein, challenging the relationship between energy landscapes and folding trajectories.     

Natural disturbances are spatially diverse but temporally synchronized across temperate forest landscapes in Europe

Natural disturbance regimes are changing substantially in forests around the globe. However, large‐scale disturbance change is modulated by a considerable spatiotemporal variation within biomes. This variation remains incompletely understood particularly in the temperate forests of Europe, for which consistent large‐scale disturbance information is lacking. Here, our aim was to quantify the spatiotemporal patterns of forest disturbances across temperate forest landscapes in Europe using remote sensing data and determine their underlying drivers. Specifically, we tested two hypotheses: (1) Topography determines the spatial patterns of disturbance, and (2) climatic extremes synchronize natural disturbances across the biome. We used novel Landsat‐based maps of forest disturbances 1986–2016 in combination with landscape analysis to compare spatial disturbance patterns across five unmanaged forest landscapes with varying topographic complexity. Furthermore, we analyzed annual estimates of disturbances for synchronies and tested the influence of climatic extremes on temporal disturbance patterns. Spatial variation in disturbance patterns was substantial across temperate forest landscapes. With increasing topographic complexity, natural disturbance patches were smaller, more complex in shape, more dispersed, and affected a smaller portion of the landscape. Temporal disturbance patterns, however, were strongly synchronized across all landscapes, with three distinct waves of high disturbance activity between 1986 and 2016. All three waves followed years of pronounced drought and high peak wind speeds. Natural disturbances in temperate forest landscapes of Europe are thus spatially diverse but temporally synchronized. We conclude that the ecological effect of natural disturbances (i.e., whether they are homogenizing a landscape or increasing its heterogeneity) is strongly determined by the topographic template. Furthermore, as the strong biome‐wide synchronization of disturbances was closely linked to climatic extremes, large‐scale disturbance episodes are likely in Europe's temperate forests under climate changes.     

Evolution in alternating environments with tunable interlandscape correlations

Natural populations are often exposed to temporally varying environments. Evolutionary dynamics in varying environments have been extensively studied, although understanding the effects of varying selection pressures remains challenging. Here, we investigate how cycling between a pair of statistically related fitness landscapes affects the evolved fitness of an asexually reproducing population. We construct pairs of fitness landscapes that share global fitness features but are correlated with one another in a tunable way, resulting in landscape pairs with specific correlations. We find that switching between these landscape pairs, depending on the ruggedness of the landscape and the interlandscape correlation, can either increase or decrease steady‐state fitness relative to evolution in single environments. In addition, we show that switching between rugged landscapes often selects for increased fitness in both landscapes, even in situations where the landscapes themselves are anticorrelated. We demonstrate that positively correlated landscapes often possess a shared maximum in both landscapes that allows the population to step through sub‐optimal local fitness maxima that often trap single landscape evolution trajectories. Finally, we demonstrate that switching between anticorrelated paired landscapes leads to ergodic‐like dynamics where each genotype is populated with nonzero probability, dramatically lowering the steady‐state fitness in comparison to single landscape evolution.     

Metapopulation Persistence in Random Fragmented Landscapes

Habitat destruction and land use change are making the world in which natural populations live increasingly fragmented, often leading to local extinctions. Although local populations might undergo extinction, a metapopulation may still be viable as long as patches of suitable habitat are connected by dispersal, so that empty patches can be recolonized. Thus far, metapopulations models have either taken a mean-field approach, or have modeled empirically-based, realistic landscapes. Here we show that an intermediate level of complexity between these two extremes is to consider random landscapes, in which the patches of suitable habitat are randomly arranged in an area (or volume). Using methods borrowed from the mathematics of Random Geometric Graphs and Euclidean Random Matrices, we derive a simple, analytic criterion for the persistence of the metapopulation in random fragmented landscapes. Our results show how the density of patches, the variability in their value, the shape of the dispersal kernel, and the dimensionality of the landscape all contribute to determining the fate of the metapopulation. Using this framework, we derive sufficient conditions for the population to be spatially localized, such that spatially confined clusters of patches act as a source of dispersal for the whole landscape. Finally, we show that a regular arrangement of the patches is always detrimental for persistence, compared to the random arrangement of the patches. Given the strong parallel between metapopulation models and contact processes, our results are also applicable to models of disease spread on spatial networks.     

The side chain of aspartic acid 69 dictates the folding mechanism of Bacillus subtilis HPr

Many small, single-domain proteins show equilibrium and kinetic folding mechanisms that appear to be adequately described as two state. The two-state model makes several predictions that can be tested experimentally. First, the conformational stability determined at or extrapolated to a set of reference conditions should be independent of the measurement method (thermal or solvent denaturation or hydrogen exchange). Second, model-independent measures of the cardinal thermodynamic parameters (T(m), DeltaH) as determined from direct calorimetric means should be identical to those determined from the two-state analysis of thermal unfolding data. Third, the ratio of the kinetic folding and unfolding rate constants should be equal to K(eq) determined from an equilibrium measurement under the same conditions. Here, we show that the wild-type HPr protein from Bacillus subtilis does not meet all of these criteria under our standard conditions. However, if we replace the side chain of Asp69, or add moderate concentrations of salt, we find excellent two-state behavior in both equilibrium and kinetic folding. Thus, for this protein and possibly others, very subtle changes in the primary structure or in the solution conditions can dramatically alter the relative stabilities of the native intermediate, and unfolded ensembles can cause an observable change in the nature of the folding mechanism.     

A checklist for ecological management of landscapes for conservation

The management of landscapes for biological conservation and ecologically sustainable natural resource use are crucial global issues. Research for over two decades has resulted in a large literature, yet there is little consensus on the applicability or even the existence of general principles or broad considerations that could guide landscape conservation. We assess six major themes in the ecology and conservation of landscapes. We identify 13 important issues that need to be considered in developing approaches to landscape conservation. They include recognizing the importance of landscape mosaics (including the integration of terrestrial and aquatic areas), recognizing interactions between vegetation cover and vegetation configuration, using an appropriate landscape conceptual model, maintaining the capacity to recover from disturbance and managing landscapes in an adaptive framework. These considerations are influenced by landscape context, species assemblages and management goals and do not translate directly into on-the-ground management guidelines but they should be recognized by researchers and resource managers when developing guidelines for specific cases. Two crucial overarching issues are: (i) a clearly articulated vision for landscape conservation and (ii) quantifiable objectives that offer unambiguous signposts for measuring progress.     

Interactive effects of landscape and weather on dispersal

Over the last decades, many species have been forced to track their shifting climate envelopes, and at the same time man‐induced landscape fragmentation has led to the global decrease of natural habitat availability and connectivity. The interaction between these two co‐occurring global environmental changes might have very strong effects on biodiversity that are still understudied. Species‐specific responses to these environmental changes critically depend on individual dispersal, either to track suitable climatic conditions or to cope with landscape fragmentation. Here we study how dispersal in an ectotherm is affected by interactions between landscape fragmentation and weather conditions. We show that both the emigration rates out of suitable habitats and the topology of the trajectory of dispersing individuals were affected by temperature and landscape fragmentation. The emigration rate was temperature‐dependent in fragmented landscapes, with butterflies emigrating more at high temperatures. The emigration rate was temperature insensitive in more continuous landscapes. Move length was farther at low temperatures and less at high temperatures in fragmented landscapes. Move length was less at low temperatures and farther at high temperatures in more continuous landscapes. To our knowledge only two recent studies have documented patterns of interactions between climate and fragmentation, despite the fact that they are the two main drivers of biodiversity loss worldwide. Here, we go a step further by providing mechanistic explanations to such patterns.     

城市河流的景观生态学研究:概念框架

城市河流作为城市景观中一种重要的生态廊道,其功能的正常实现与否关系到整个城市的可持续发展。通过分析当前城市河流的研究概况,发现应用景观生态学原理对城市河流展开多尺度、多学科的综合研究是实现“自然-人类-水体”可持续发展的必然趋势。从景观生态学的角度出发,结合城市河流的特点,提出了更为综合的、景观水平上的城市河流研究的概念框架。特别针对景观生态学研究的核心问题,对城市河流的研究尺度、格局分析、干扰程度等重要方面进行了详细论述,以期在景观水平上构建城市河流的可持续发展预案。     

Heterogeneous folding of the trpzip hairpin: full atom simulation and experiment

The beta-hairpin trpzip2 can be tuned continuously from a two-state folder to folding on a rough energy landscape without a dominant refolding barrier. At high denaturant concentration, this extremely stable peptide exhibits a single apparent "two-state" transition temperature when monitored by different spectroscopic techniques. However, under optimal folding conditions the hairpin undergoes an unusual folding process with three clusters of melting transitions ranging from 15 degrees C to 160 degrees C, as monitored by 12 different experimental and computational observables. We explain this behavior in terms of a rough free energy landscape of the unfolded peptide caused by multiple tryptophan interactions and alternative backbone conformations. The landscape is mapped out by potentials of mean force derived from replica-exchange molecular dynamics simulations. Implications for deducing cooperativity from denaturant titrations, for the origin of folding cooperativity, and for the folding of thermophilic proteins are pointed out. trpzip is an excellent small tunable model system for the glass-like folding transitions predicted by landscape theory.     

Exploring the relationship between funneled energy landscapes and two-state protein folding

It should take an astronomical time span for unfolded protein chains to find their native state based on an unguided conformational random search. The experimental observation that folding is fast can be rationalized by assuming that protein energy landscapes are sloped towards the native state minimum, such that rapid folding can proceed from virtually any point in conformational space. Folding transitions often exhibit two-state behavior, involving extensively disordered and highly structured conformers as the only two observable kinetic species. This study employs a simple Brownian dynamics model of "protein particles" moving in a spherically symmetrical potential. As expected, the presence of an overall slope towards the native state minimum is an effective means to speed up folding. However, the two-state nature of the transition is eradicated if a significant energetic bias extends too far into the non-native conformational space. The breakdown of two-state cooperativity under these conditions is caused by a continuous conformational drift of the unfolded proteins. Ideal two-state behavior can only be maintained on surfaces exhibiting large regions that are energetically flat, a result that is supported by other recent data in the literature (Kaya and Chan, Proteins: Struct Funct Genet 2003;52:510-523). Rapid two-state folding requires energy landscapes exhibiting the following features: (i) A large region in conformational space that is energetically flat, thus allowing for a significant degree of random sampling, such that unfolded proteins can retain a random coil structure; (ii) a trapping area that is strongly sloped towards the native state minimum.     

Protein folding in the landscape perspective: Chevron plots and non-arrhenius kinetics

We use two simple models and the energy landscape perspective to study protein folding kinetics. A major challenge has been to use the landscape perspective to interpret experimental data, which requires ensemble averaging over the microscopic trajectories usually observed in such models. Here, because of the simplicity of the model, this can be achieved. The kinetics of protein folding falls into two classes: multiple-exponential and two-state (single-exponential) kinetics. Experiments show that two-state relaxation times have “chevron plot” dependences on denaturant and non-Arrhenius dependences on temperature. We find that HP and HP+ models can account for these behaviors. The HP model often gives bumpy landscapes with many kinetic traps and multiple-exponental behavior, whereas the HP+ model gives more smooth funnels and two-state behavior. Multiple-exponential kinetics often involves fast collapse into kinetic traps and slower barrier climbing out of the traps. Two-state kinetics often involves entropic barriers where conformational searching limits the folding speed. Transition states and activation barriers need not define a single conformation; they can involve a broad ensemble of the conformations searched on the way to the native state. We find that unfolding is not always a direct reversal of the folding process. Proteins 30:2–33, 1998. © 1998 Wiley-Liss, Inc.     

Agent-based model approach to optimal foraging in heterogeneous landscapes: effects of patch clumpiness

Optimal foraging theory concerns animal behavior in landscapes where food is concentrated in patches. The efficiency of foraging is an effect of both the animal behavior and the geometry of the landscape; furthermore, the landscape is itself affected by the foraging of animals. We investigated the effect of landscape heterogeneity on the efficiency of an optimal forager. The particular aspect of heterogeneity we considered was "clumpiness"– the degree to which food resource patches are clustered together. The starting point for our study was the framework of the Mean Value Theorem (MVT) by Charnov. Since MVT is not spatially explicit, and thus not apt to investigate effects of clumpiness, we built an agent-based (or individual-based) model for animal movement in discrete landscapes extending the MVT. We also constructed a model for generating landscapes where the clumpiness of patches can be easily controlled, or "tuned", by an input parameter. We evaluated the agent based model by comparing the results with what the MTV would give, i.e. if the spatial effects were removed. The MVT matched the simulations best on landscapes with random patch configuration and high food recovery rates. As for our main question about the effects of clumpiness, we found that, when landscapes were highly productive (rapid food replenishment), foraging efficiency was greatest in clumped landscapes. In less productive landscapes, however, foraging efficiency was lowest in landscapes with a clumped patch distribution.     

苏南快速城市化地区景观生态优化调控研究

城市化是经济快速发展的必然结果和要求.以苏锡常为代表的快速城市化苏南板块正在导致原有的城乡景观发生快速的变化（优化与恶化并存）.基于城市景观生态调控方法,通过城市景观生态规划（整体共生的理念）、城市景观生态工程（循环再生的理念）和城市景观生态管理（竞争自生的理念）,提出快速城市化过程中城市景观生态优化调控的构想.以苏南地区的常州市武进区为例,从其地理环境背景及景观演化出发,提出可持续发展的景观生态优化的基本原则和目标.将城镇整合成以中心城区斑块为核心的向外辐射的4个城镇景观生态发展斑块,即5大斑块平衡组团的景观格局,协调各行政区域的城市化、工业化发展;典型景观生态片区建设以淹城保护区斑块为核心,以滆湖-太湖斑块和绿色空间基底景观生态建设为主体,依托＂二纵三横＂的生态廊道网络,形成整个武进富有韵律的生态网架,从区域整体上改善、优化城乡景观生态,有效避免景观破碎与退化和生态环境恶化.     

Scaling properties of multivariate landscape structure

Analyses of landscape context is essential for understanding how ecological patterns and processes relate to space. This requires that we quantify variation patterns of different landscape parameters, which may change relative to one another at different spatial scales. Here, we analyzed how statistical relationships of land-use composition parameters changed as a function of extent in 20 real agricultural landscapes. Furthermore, we tested the generality of these scaling relations in numerical simulations using 300 artificial landscapes. We analyzed proportions of artificial habitat types at different extent and compared these patterns with three dominant habitat types in real landscapes (forest, arable land and grassland) at four spatial scales (quadrates of 1–4 km). Both real and simulated landscapes showed that variance of landscape parameters (data differentiation) decreased and their correlations (data consistency) increased as scale increased, thereby suggesting general scaling laws. The potential statistical impact of these scaling relationships is revealed in simultaneous analyses of variation of (local) site parameters of 20 arable fields and their surrounding landscape context. At small and medium extent (quadrates of 1–3 km), variability of local site parameters (e.g. fertilization, pH-value) was high relative to those of landscape parameters. In contrast, at large extent (quadrates of 4 km) variability of landscape parameters was greater than that of site parameters indicating a fundamental shift in the relationship between these sets of parameters at different scales. Hence, it is clear that there is a high risk of artefactual correlations in hierarchical multi-scale landscape analyses when ecological data are related to the landscape context. Accordingly, there is a necessity for multi-scale analyses in landscape ecology to accurately evaluate the relative importance of landscape context at different spatial scales.     

Using historical ecology to understand patterns of biodiversity in fragmented agricultural landscapes

Aim To enhance current attempts to understand biodiversity patterns by using an historical ecology approach to highlight the over‐riding influence of land‐use history in creating past, current and future patterns of biodiversity in fragmented agricultural landscapes. Methods We develop an integrative conceptual framework for understanding spatial and temporal variations in landscape patterns in fragmented agricultural landscapes by presenting five postulates (hypotheses) which highlight the important role of historical, anthropogenic disturbance regimes. We then illustrate each of these postulates with examples drawn from fragmented woodlands in agricultural areas of south‐eastern Australia, and discuss these findings in an international context. Location examples are drawn from agricultural areas in south‐eastern Australia. Results We conclude that there is limited potential to refine our understanding of patterns of biodiversity in human‐modified landscapes based on traditional concepts of island biogeography, or simple assumptions of ongoing destruction and degradation. Instead, we propose that in agricultural landscapes that were largely cleared over a century ago: (1) present‐day remnant vegetation patterns are not accidental, but are logically arrayed due to historic land‐use decisions, (2) historic anthropogenic disturbances have a major influence on current ecosystem conditions and diversity patterns, and (3) the condition of remnant ecosystems is not necessarily deteriorating rapidly. Main conclusions An historical ecology approach can enhance our understanding of why different species and ecosystem states occur where they do, and can explain internal variations in ecological conditions within remnant ecosystems, too often casually attributed to the ‘mess of history’. This framework emphasizes temporal changes (both past and future) in biotic patterns and processes in fragmented agricultural landscapes. Integration of spatially and temporally explicit historical land‐use information into ecological studies can prove extremely useful to test hypotheses of the effects of changes in landscape processes, and to enhance future research, restoration and conservation management activities.     

The effect of phenotypic plasticity on evolution in multipeaked fitness landscapes

When facing the challenge of developing an individual that best fits its environment, nature demonstrates an interesting combination of two fundamentally different adaptive mechanisms: genetic evolution and phenotypic plasticity. Following numerous computational models, it has become the accepted wisdom that lifetime acclimation (e.g. via learning) smooths the fitness landscape and consequently accelerates evolution. However, analytical studies, focusing on the effect of phenotypic plasticity on evolution in simple unimodal landscapes, have often found that learning hinders the evolutionary process rather than accelerating it. Here, we provide a general framework for studying the effect of plasticity on evolution in multipeaked landscapes and introduce a rigorous mathematical analysis of these dynamics. We show that the convergence rate of the evolutionary process in a given arbitrary one-dimensional fitness landscape is dominated by the largest descent (drawdown) in the landscape and provide numerical evidence to support an analogous dominance also in multidimensional landscapes. We consider several schemes of phenotypic plasticity and examine their effect on the landscape drawdown, identifying the conditions under which phenotypic plasticity is advantageous. The lack of such a drawdown in unimodal landscapes vs. its dominance in multipeaked landscapes accounts for the seemingly contradictory findings of previous studies.     

On the role of spatial stochastic models in understanding landscape indices in ecology

Spatial stochastic models play an important role in understanding and predicting the behaviour of complex systems. Such models may be implemented with explicit knowledge of only a limited number of parameters relating to spatial relationships among locations. Consequently, they are often used instead of deterministic‐mechanistic models, which may potentially require an unrealistically large number of parameters. Currently, in contrast to spatial stochastic models, the parameterization of the joint spatial distribution of objects in landscape models is more often implicit than explicit. Here, we investigate the similarities and differences between bona fide spatial stochastic models and landscape models by focusing mostly on the relationships between processes, their realizations (patterns), representation and measurement, and their use in exploratory as well as confirmatory data analysis. One of the most important outcomes of recognizing the importance of stochastic processes is the acknowledgement that the spatial pattern observed in a landscape is only one realization of that process. Hence, while ecologists have been using landscape pattern indices (LPIs) to characterize landscape heterogeneity and/or make inferences about processes shaping the landscape, no stochastic modelling framework has been developed for their proper statistical elucidation. Consequently, several (mis)uses of LPIs draw conclusions about landscapes which are suspect. We show that several reports about sensitivities of LPIs to measurements have common roots that can be made explicitly manageable by adopting stochastic models of spatial structure. The key parameters of these stochastic models are composition and configuration, which, in general, cannot be estimated independently from each other. We outline how to develop the stochastic framework to interpret observations and make some recommendations to practitioners about everyday usage. The conceptual linkages between patterns and processes are particularly important in light of recent efforts to bridge the static‐structural and the dynamic‐analytic traditions of ecology.