Analysis of correlations between protein complex and protein-protein interaction and mRNA expression

Protein-protein interaction is a physical interaction of two proteins in living cells. In budding yeast Saccharomyces cerevisiae, large-seale protein-protein interaction data have been obtained through high-throughput yeast two-hybrid systems (Y2H) and protein complex purification techniques based on mass-spectrometry. Here, we collect 11855 interactions between total 2617 proteins. Through seriate genome-wide mRNA expression data, similarity between two genes could be measured. Protein complex data can also be obtained publicly and can be translated to pair relationship that any two proteins can only exist in the same complex or not. Analysis of protein complex data, protein-protein interaction data and mRNA expression data can elucidate correlations between them. The results show that proteins that have interactions or similar expression patterns have a higher possibility to be in the same protein complex than randomized selected proteins, and proteins which have interactions and similar expression patterns are even more possible to exist in the same protein complex. The work indirates that comprehensive integration and analysis of public large-seale bioinformatical data, such as protein complex data, protein-protein interaction data and mRNA expression data, may help to uncover their relationships and common biological information underlying these data. The strategies described here may help to integrate and analyze other functional genomic and proteomic data, such as gene expression profiling, protein-localization mapping and large-scale phenotypic data, both in yeast and in other organisms.     

Local interactions predict large-scale pattern in empirically derived cellular automata.

An important unanswered question in ecology is whether processes such as species interactions that occur at a local scale can generate large-scale patterns seen in nature. Because of the complexity of natural ecosystems, developing an adequate theoretical framework to scale up local processes has been challenging. Models of complex systems can produce a wide array of outcomes; therefore, model parameter values must be constrained by empirical information to usefully narrow the range of predicted behaviour. Under some conditions, spatially explicit models of locally interacting objects (for example, cells, sand grains, car drivers, or organisms), variously termed cellular automata or interacting particle models, can self-organize to develop complex spatial and temporal patterning at larger scales in the absence of any externally imposed pattern. When these models are based on transition probabilities of moving between ecological states at a local level, relatively complex versions of these models can be linked readily to empirical information on ecosystem dynamics. Here, I show that an empirically derived cellular automaton model of a rocky intertidal mussel bed based on local interactions correctly predicts large-scale spatial patterns observed in nature.     

Variance in ecological consumer-resource interactions

Food-web models use the effect size of trophic interactions to predict consumer-resource dynamics. These models anticipate that strong effects of consumers increase spatial and temporal variability in abundance of species, whereas weak effects dampen fluctuations. Empirical evidence indicates that opposite patterns may occur in natural assemblages. Here I show that spatial variance in the distribution of resource populations is sensitive to changes in the variance of the trophic interaction, in addition to the mean effect of consumers, relative to other causes of spatial variability. Simulations indicate that both strong and weak direct effects of consumers can promote spatial variability in abundance of resources, but only trophic interactions with a large mean effect size can reduce variation. Predictions of the model agree with the results of repeated field experiments and are consistent with data from published consumer-resource interactions, proving to be robust across widely varying environmental conditions and species' life histories. Thus, food-web models that embody variance in trophic interactions may have increased capacity to explain the wide range of effects of consumers documented in empirical studies.     

Non-fluorous polymers with very high solubility in supercritical CO2 down to low pressures

Liquid and supercritical carbon dioxide have attracted much interest as environmentally benign solvents, but their practical use has been limited by the need for high CO2 pressures to dissolve even small amounts of polar, amphiphilic, organometallic, or high-molecular-mass compounds. So-called 'CO2-philes' efficiently transport insoluble or poorly soluble materials into CO2 solvent, resulting in the development of a broad range of CO2-based processes, including homogeneous and heterogeneous polymerization, extraction of proteins and metals, and homogeneous catalysis. But as the most effective CO2-philes are expensive fluorocarbons, such as poly(perfluoroether), the commercialization of otherwise promising CO2-based processes has met with only limited success. Here we show that copolymers can act as efficient, non-fluorous CO2-philes if their constituent monomers are chosen to optimize the balance between the enthalpy and entropy of solute-copolymer and copolymer-copolymer interactions. Guided by heuristic rules regarding these interactions, we have used inexpensive propylene and CO2 to synthesize a series of poly(ether-carbonate) copolymers that readily dissolve in CO2 at low pressures. Even though non-fluorous polymers are generally assumed to be CO2-phobic, we expect that our design principles can be used to create a wide range of non-fluorous CO2-philes from low-cost raw materials, thus rendering a variety of CO2-based processes economically favourable, particularly in cases where recycling of CO2-philes is difficult.     

基于启发式群聚算法的机器人全局任务调度策略

提出了一种基于启发式群聚算法的机器人全局任务调度策略，在任务划分阶段采用一种启发式群聚算法对随机划分的各子任务按能否使总的运行时间缩短进行各子任务间的聚合，以使各子任务粒度和相互之间的通讯量达到一种优化状态，并在此基础上对群聚之后的各子群任务采用集中式动态调度策略，在程序运行过程中实现各处理器的负载平衡，提高各处理器的利用率，缩短总的运行时间．在一个由5个DSP（digital signal processor）处理器组成的同构型松耦合MIMD（multi instruction multidata）并行处理平台上，对平面四自由度连杆机器人在关节锁定下的运动控制任务采用上述先随机划分，再聚合，最后集中式调度的方法进行了并行实时仿真实验，取得了满意的并行性能指标．     

Species diversity enhances ecosystem functioning through interspecific facilitation.

Facilitation between species is thought to be a key mechanism by which biodiversity affects the rates of resource use that govern the efficiency and productivity of ecosystems; however, there is no direct empirical evidence to support this hypothesis. Here we show that increasing the species diversity of a functional group of aquatic organisms induces facilitative interactions, leading to non-additive changes in resource consumption. We increased the richness and evenness of suspension-feeding caddisfly larvae (Insecta, Trichoptera) in stream mesocosms and found that the increased topographical complexity of the benthic habitat alters patterns of near-bed flow such that the feeding success of individuals is enhanced. Species diversity reduces 'current shading' (that is, the deceleration of flow from upstream to downstream neighbours), allowing diverse assemblages to capture a greater fraction of suspended resources than is caught by any species monoculture. The fundamental nature of this form of hydrodynamic facilitation suggests that it is broadly applicable to freshwater and marine habitats; in addition, it has several analogues in terrestrial ecosystems where fluxes of energy and matter can be influenced by biophysical complexity. Thus, changes in species diversity may alter the probability of positive species interactions, resulting in disproportionately large changes in the functioning of ecosystems.     

Resilient circadian oscillator revealed in individual cyanobacteria

Circadian oscillators, which provide internal daily periodicity, are found in a variety of living organisms, including mammals, insects, plants, fungi and cyanobacteria. Remarkably, these biochemical oscillators are resilient to external and internal modifications, such as temperature and cell division cycles. They have to be 'fluctuation (noise) resistant' because relative fluctuations in the number of messenger RNA and protein molecules forming the intracellular oscillators are likely to be large. In multicellular organisms, the strong temporal stability of circadian clocks, despite molecular fluctuations, can easily be explained by intercellular interactions. Here we study circadian rhythms and their stability in unicellular cyanobacteria Synechoccocus elongatus. Low-light-level microscopy has allowed us to measure gene expression under circadian control in single bacteria, showing that the circadian clock is indeed a property of individual cells. Our measurements show that the oscillators have a strong temporal stability with a correlation time of several months. In contrast to many circadian clocks in multicellular organisms, this stability seems to be ensured by the intracellular biochemical network, because the interactions between oscillators seem to be negligible.     

Positive feedbacks promote power-law clustering of Kalahari vegetation

The concept of local-scale interactions driving large-scale pattern formation has been supported by numerical simulations, which have demonstrated that simple rules of interaction are capable of reproducing patterns observed in nature. These models of self-organization suggest that characteristic patterns should exist across a broad range of environmental conditions provided that local interactions do indeed dominate the development of community structure. Readily available observations that could be used to support these theoretical expectations, however, have lacked sufficient spatial extent or the necessary diversity of environmental conditions to confirm the model predictions. We use high-resolution satellite imagery to document the prevalence of self-organized vegetation patterns across a regional rainfall gradient in southern Africa, where percent tree cover ranges from 65% to 4%. Through the application of a cellular automata model, we find that the observed power-law distributions of tree canopy cluster sizes can arise from the interacting effects of global-scale resource constraints (that is, water availability) and local-scale facilitation. Positive local feedbacks result in power-law distributions without entailing threshold behaviour commonly associated with criticality. Our observations provide a framework for integrating a diverse suite of previous studies that have addressed either mean wet season rainfall or landscape-scale soil moisture variability as controls on the structural dynamics of arid and semi-arid ecosystems.     

Symmetry perception in an insect

Symmetrical visual patterns have a salient status in human perception, as evinced by their prevalent occurrence in art, and also in animal perception, where they may be an indicator of phenotypic and genotypic quality. Symmetry perception has been demonstrated in humans, birds, dolphins and apes. Here we show that bees trained to discriminate bilaterally symmetrical from non-symmetrical patterns learn the task and transfer it appropriately to novel stimuli, thus demonstrating a capacity to detect and generalize symmetry or asymmetry. We conclude that bees, and possibly flower-visiting insects in general, can acquire a generalized preference towards symmetrical or, alternatively, asymmetrical patterns depending on experience, and that symmetry detection is preformed or can be learned as perceptual category by insects, because it can be extracted as an independent visual pattern feature. Bees show a predisposition for learning and generalized symmetry because, if trained to it, they choose it more frequently, come closer to and hover longer in front of the novel symmetrical stimuli than the bees trained for asymmetry do for the novel asymmetrical stimuli. Thus, even organisms with comparatively small nervous systems can generalize about symmetry, and favour symmetrical over asymmetrical patterns.     

Captivity masks inbreeding effects on male mating success in butterflies

Small isolated populations are frequently genetically less diverse than core populations, resulting in higher homozygosity that can hamper their long-term survival. The decrease in fitness of organisms owing to matings between relatives is well known from captive and laboratory animals. Such inbreeding can have strongly deleterious effects on life-history traits and survival, and can be critical to the success of population conservation. Because pedigrees are hard to follow in the wild, most field studies have used marker loci to establish that fitness declines with increasing homozygosity. Very few have experimentally explored the effects of inbreeding in the wild, or compared observations in the laboratory with field conditions. Here, using a technique involving the transfer of marker dusts during copulation, we show that a small decrease in mating success of captive inbred male butterflies in cages is greatly accentuated in conditions with unconstrained flight. Our results have important implications for conservation and for studies of sexual selection because they show that the behaviours underlying patterns of mating can be profoundly influenced by a history of inbreeding or by any restraining experimental conditions.     

高值空间聚类的精确检测

提出了一个数据调整的方法来弥补通常空间聚类检测的不足，从而能够对高值聚类进行精确检测。利用Matlab软件将该方法在模拟的空间类型中应用于Moran’I检测。结果表明，当有高值聚类趋势时，经该方法调整数据后利用Moran’I可以显著地检测出高值聚类的存在。     

Bacterial chromatin organization by H-NS protein unravelled using dual DNA manipulation

Both prokaryotic and eukaryotic organisms contain DNA bridging proteins, which can have regulatory or architectural functions. The molecular and mechanical details of such proteins are hard to obtain, in particular if they involve non-specific interactions. The bacterial nucleoid consists of hundreds of DNA loops, shaped in part by non-specific DNA bridging proteins such as histone-like nucleoid structuring protein (H-NS), leucine-responsive regulatory protein (Lrp) and SMC (structural maintenance of chromosomes) proteins. We have developed an optical tweezers instrument that can independently handle two DNA molecules, which allows the systematic investigation of protein-mediated DNA-DNA interactions. Here we use this technique to investigate the abundant non-specific nucleoid-associated protein H-NS, and show that H-NS is dynamically organized between two DNA molecules in register with their helical pitch. Our optical tweezers also allow us to carry out dynamic force spectroscopy on non-specific DNA binding proteins and thereby to determine an energy landscape for the H-NS-DNA interaction. Our results explain how the bacterial nucleoid can be effectively compacted and organized, but be dynamic in nature and accessible to DNA-tracking motor enzymes. Finally, our experimental approach is widely applicable to other DNA bridging proteins, as well as to complex DNA interactions involving multiple DNA molecules.     

Trophic cascades across ecosystems

Predation can be intense, creating strong direct and indirect effects throughout food webs. In addition, ecologists increasingly recognize that fluxes of organisms across ecosystem boundaries can have major consequences for community dynamics. Species with complex life histories often shift habitats during their life cycles and provide potent conduits coupling ecosystems. Thus, local interactions that affect predator abundance in one ecosystem (for example a larval habitat) may have reverberating effects in another (for example an adult habitat). Here we show that fish indirectly facilitate terrestrial plant reproduction through cascading trophic interactions across ecosystem boundaries. Fish reduce larval dragonfly abundances in ponds, leading to fewer adult dragonflies nearby. Adult dragonflies consume insect pollinators and alter their foraging behaviour. As a result, plants near ponds with fish receive more pollinator visits and are less pollen limited than plants near fish-free ponds. Our results confirm that strong species interactions can reverberate across ecosystems, and emphasize the importance of landscape-level processes in driving local species interactions.     

一种基于一致性分片FCM的图像分割算法

针对传统FCM(fuzzy c-means)算法抗噪性差的问题,提出了一种基于一致性分片的模糊c均值聚类算法.为避免额外的空间邻域约束项带来的控制变量设置问题,该算法直接将FCM应用于图像片空间.为减弱空间邻域对图像边缘的模糊,采用基于置信区间的局部多项式交叉近似技术(local polynomial approximation and intersection of confidenec intervals,LPA-ICI)构造自适应形状一致性分片.在脑磁共振图像上的实验表明,与传统的FCM算法相比,该算法具有更高的分割精度和运行效率.     

Species interactions can explain Taylor's power law for ecological time series

One of the few generalities in ecology, Taylor's power law, describes the species-specific relationship between the temporal or spatial variance of populations and their mean abundances. For populations experiencing constant per capita environmental variability, the regression of log variance versus log mean abundance gives a line with a slope of 2. Despite this expectation, most species have slopes of less than 2 (refs 2, 3-4), indicating that more abundant populations of a species are relatively less variable than expected on the basis of simple statistical grounds. What causes abundant populations to be less variable has received considerable attention, but an explanation for the generality of this pattern is still lacking. Here we suggest a novel explanation for the scaling of temporal variability in population abundances. Using stochastic simulation and analytical models, we demonstrate how negative interactions among species in a community can produce slopes of Taylor's power law of less than 2, like those observed in real data sets. This result provides an example in which the population dynamics of single species can be understood only in the context of interactions within an ecological community.     

基于模糊聚类理论的入侵检测数据分析

入侵检测系统是网络和信息安全构架的重要组成部分,主要用于区分系统的正常活动和可疑及入侵模式,但是它所面临的挑战是如何有效的检测网络入侵行为以降低误报率和漏报率.基于已有入侵检测方法的不足提出利用模糊C-均值聚类方法对入侵检测数据进行分析,从而发现异常的网络行为模式.通过对CUP99数据集的检测试验表明该方法不但可行而且准确性及效率较高.     

Membrane protein sequestering by ionic protein-lipid interactions

Neuronal exocytosis is catalysed by the SNAP receptor protein syntaxin-1A, which is clustered in the plasma membrane at sites where synaptic vesicles undergo exocytosis. However, how syntaxin-1A is sequestered is unknown. Here we show that syntaxin clustering is mediated by electrostatic interactions with the strongly anionic lipid phosphatidylinositol-4,5-bisphosphate (PIP2). Using super-resolution stimulated-emission depletion microscopy on the plasma membranes of PC12 cells, we found that PIP2 is the dominant inner-leaflet lipid in microdomains about 73 nanometres in size. This high accumulation of PIP2 was required for syntaxin-1A sequestering, as destruction of PIP2 by the phosphatase synaptojanin-1 reduced syntaxin-1A clustering. Furthermore, co-reconstitution of PIP2 and the carboxy-terminal part of syntaxin-1A in artificial giant unilamellar vesicles resulted in segregation of PIP2 and syntaxin-1A into distinct domains even when cholesterol was absent. Our results demonstrate that electrostatic protein-lipid interactions can result in the formation of microdomains independently of cholesterol or lipid phases.     

Host-parasitoid associations in patchy environments

Studies of insect host-parasitoid interactions have contributed much to the consensus that spatial patchiness is important in the regulation of natural populations. A variety of theoretical models predict that host and parasitoid populations, although unstable in the absence of environmental heterogeneity, may persist at roughly steady overall densities in a patchy environment owing to variation in levels of parasitism from patch to patch. Observed patterns of parasitism, however, have a variety of forms (with variation in attack rates among patches depending directly or indirectly on host density, or showing variation uncorrelated with host density). There is some confusion about the dynamical consequences of these different forms. Here we first show how the dynamical effects of all these forms of environmental heterogeneity can be assessed by a common criterion. This 'CV2 greater than 1 rule' states that the overall population densities will remain roughly steady from generation to generation if the coefficient of variation squared (CV2) of the density of searching parasitoids in the vicinity of each host exceeds approximately unity. By partitioning CV2 into components, we show that both direct and inverse patterns of dependence on host density, and density-independent patterns, all contribute to population regulation in the same way. Second, we show how a maximum-likelihood method can be applied to the kind of field data that are usually available (that is, percentage parasitism versus local host density) to estimate the components of CV2. This analysis indicates that heterogeneity is large enough to stabilize dynamics in 9 of 34 published studies, and that density-independent heterogeneity is the main factor in most cases.     

Policing stabilizes construction of social niches in primates

All organisms interact with their environment, and in doing so shape it, modifying resource availability. Termed niche construction, this process has been studied primarily at the ecological level with an emphasis on the consequences of construction across generations. We focus on the behavioural process of construction within a single generation, identifying the role a robustness mechanism--conflict management--has in promoting interactions that build social resource networks or social niches. Using 'knockout' experiments on a large, captive group of pigtailed macaques (Macaca nemestrina), we show that a policing function, performed infrequently by a small subset of individuals, significantly contributes to maintaining stable resource networks in the face of chronic perturbations that arise through conflict. When policing is absent, social niches destabilize, with group members building smaller, less diverse, and less integrated grooming, play, proximity and contact-sitting networks. Instability is quantified in terms of reduced mean degree, increased clustering, reduced reach, and increased assortativity. Policing not only controls conflict, we find it significantly influences the structure of networks that constitute essential social resources in gregarious primate societies. The structure of such networks plays a critical role in infant survivorship, emergence and spread of cooperative behaviour, social learning and cultural traditions.     

基于免疫聚类的Web日志挖掘

Web日志挖掘旨在使用数据挖掘技术从Web服务器日志文件中挖掘出有用的规律和模式,以此改进网站结构以及实现Web个性化服务。本文提出基于免疫聚类的Web日志挖掘算法,利用人工免疫系统的基本原理来进行用户聚类分析,从而发现相似客户群体、挖掘潜在客户。免疫聚类通过模拟免疫系统体液免疫应答的基本过程,提取出数据的基本特征,以此概括数据的分布特征,从而实现Web日志数据的无监督自组织聚类。通过在真实数据集上的实验证明了该算法的可行性和有效性。