Annexation of the interchromosomal space during viral infection

The nucleus is known to be compartmentalized into units of function, but the processes leading to the spatial organization of chromosomes and nuclear compartments are not yet well defined. Here we report direct quantitative analysis of the global structural perturbations of interphase chromosome and interchromosome domain distribution caused by infection with herpes simplex virus-1 (HSV-1). Our results show that the peripheral displacement of host chromosomes that correlates with expansion of the viral replication compartment (VRC) is coupled to a twofold increase in nuclear volume. Live cell dynamic measurements suggest that viral compartment formation is driven by the functional activity of viral components and underscore the significance of spatial regulation of nuclear activities.     

Dynamic organization of the cell nucleus

The dynamic organization of the cell nucleus into subcompartments with distinct biological activities represents an important regulatory layer for cell function. Recent studies provide new insights into the principles, by which nuclear organelles form. This process frequently occurs in a self-organizing manner leading to the assembly of stable but plastic structures from multiple relatively weak interaction forces. These can rearrange into different functional states in response to specific modifications of the constituting components or changes in the nuclear environment.     

西方生态学近况

本文对美英等西方英语国家的近期生态学研究的研究趋向、流行概念,研究方式、前沿领域及新方法、新技术进行了综述分析,近期、西方英语国家的生态学理论研究中最受重视的问题是：在一定时空尺度上生物物种组成和各物种种群丰盛度的动态规律和特征,以及决定这种规律和特征的内在机制。这些机制包括：个体发育、生理、行为和遗传过程对生物与非生物环境的反应及这些过程对自身所在的种群、种落和栖息地的影响;种内种间相似或相异个     

基于时间聚类分析和独立成分分析的癫痫fMRI盲分析方法

提出了一种基于时间聚类分析和独立成分分析的癫痫fMRI数据盲分析方法,并将两种方法有效联合,提取发作间期的癫痫fMRI激活时空信息.该方法首先由时间聚类分析得到与激活相关的时间峰度特征曲线,以此特征作为时间参考信息;再由空间独立成分分析分解fMRI信号得到空间独立成分;最后将每个独立成分所对应的时间曲线与参考曲线做相关分析提取相应脑激活图.提出的方法无需任何关于癫痫fMRI的先验假设信息,有效解决了独立成分的排序问题,实现了对数据的盲分析.仿真试验结果阐明了这一方法的有效性及可靠性,对癫痫数据的试验结果显示空间定位准确性优于统计参数图方法.     

Parallel processing by a homogeneous group of coupled model neurons can enhance, reduce and generate signal correlations

 Correlated activities have been proposed as correlates of flexible association and assembly coding. We addressed the basic question of how signal correlations on parallel pathways are enhanced, reduced and generated by homogeneous groups of coupled neurons, and how this depends on the input activities and their interactions with internal coupling processes. For this we simulated a fully connected group of identical impulse-coded neurons with dynamic input and threshold processes and additive or multiplicative lateral coupling. Input signals were Gaussian white noise (GWN), completely independent or partially correlated on a subgroup of the parallel inputs. We show that in states of high average spike rates input-output correlations were weak while the network could generate correlated activities of stochastic, oscillatory and rhythmic bursting types depending exclusively on lateral coupling strength. In states of low average spike rates input-output correlations were high and the network could effectively enhance or reduce differences in spatial correlation applied to its parallel inputs. The correlation differences were more pronounced with multiplicative lateral coupling than with the additive interactions commonly used. As the different modes of correlation processing emerged already by global changes in the average spike rate and lateral coupling strength, we assume that in real cortical circuits changes in correlational processing may also be induced by unspecific modulations of activation and lateral coupling. Received: 11 December 1995 / Accepted in revised form: 29 November 1996     

Absolute stability and transitions in ecosystems with a multiplicity of stable states and dispersal

The principle that for a large class of spatially extended dynamic systems with several locally stable states there exists at most one absolutely stable state is applied to population dynamical models with diffusive spatial dispersal. The basic concepts and methods to characterize absolute stability and its limits are presented. Some interesting results concerning the significance of dispersal ability in competing and mutualistic systems are found. The concepts appear of practical importance since only absolutely stable states are resilient against all localized fluctuations and disturbances.     

Charge‐Transfer States at Organic–Organic Interfaces: Impact of Static and Dynamic Disorders

Molecular dynamics simulations are combined with density functional theory calculations to evaluate the impact of static and dynamic disorders on the energy distribution of charge‐transfer (CT) states at donor–acceptor heterojunctions, such as those found in the active layers of organic solar cells. It is shown that each of these two disorder components can be partitioned into contributions related to the energetic disorder of the transport states and to the disorder associated with the hole–electron electrostatic interaction energies. The methodology is applied to evaluate the energy distributions of the CT states in representative bulk heterojunctions based on poly‐3‐hexyl‐thiophene and phenyl‐C₆₁‐butyric‐acid methyl ester. The results indicate that the torsional fluctuations of the polymer backbones are the main source of both static and dynamic disorders for the CT states as well as for the transport levels. The impact of static and dynamic disorders on radiative and nonradiative geminate recombination processes is also discussed.     

Biophysical nanotools for single-molecule dynamics

The focus of the cell biology field is now shifting from characterizing cellular activities to organelle and molecular behaviors. This process accompanies the development of new biophysical visualization techniques that offer high spatial and temporal resolutions with ultra-sensitivity and low cell toxicity. They allow the biology research community to observe dynamic behaviors from scales of single molecules, organelles, cells to organoids, and even live animal tissues. In this review, we summarize these biophysical techniques into two major classes: the mechanical nanotools like dynamic force spectroscopy (DFS) and the optical nanotools like single-molecule and super-resolution microscopy. We also discuss their applications in elucidating molecular dynamics and functionally mapping of interactions between inter-cellular networks and intra-cellular components, which is key to understanding cellular processes such as adhesion, trafficking, inheritance, and division.     

三江平原沼泽湿地景观空间格局变化

景观空间格局是指大小和形状不一的景观斑块在空间上的排列,它是景观异质性的重要表现,同时又是各种生态过程在不同尺度上作用的结果。这一研究可为环境资源的合理管理提供有价值的资料,已成为景观生态学研究的核心之一。通过选取斑块连接指数、分布质心和扩展等模型,来表征三江平原沼泽湿地景观近20a来空间格局变化情况。结果表明：（1）三江平原沼泽湿地的破碎化较为严重,斑块数量增加了46％,斑块密度净增加2倍。与1980年相比,1996年最大斑块面积缩小了63.57％,最大斑块周长缩短了52.47％。（2）三江平原沼泽湿地斑块间隙在不同时期都较大,且随着沼泽湿地面积的减小和斑块数量的增加,其斑块间隙越来越大,进一步说明沼泽湿地的破碎化较为厉害。（3）1980-1996年间三江平原沼泽湿地的分布质心向西南方向偏移了7.05km,1996-2000年向西北方向偏移了6.01km。（4）1980、1996、2000年三江平原沼泽湿地的扩展度分别接近于14.222、11.101和11.262。其值都远大于1,说明斑块形状与圆形相差较大,形状不规则。近20a来,人类活动对沼泽湿地空间格局变化的影响程度较大,1980-1996年尤为明显,而在1996-2000年,由于采取了保护措施,其影响程度开始变弱。     

Complex dynamics of microbial competition in the gradostat

We examine the conditions necessary for the emergence of complex dynamic behavior in systems of microbial competition. In particular, we study the effect of spatial heterogeneity and substrate-inhibition on the dynamics of such a system. This is accomplished through the study of a mathematical model of two microbial populations competing for a single nutrient in a configuration of two interconnected chemostats. Microbial growth is assumed to follow substrate-inhibited kinetics for both species. Such a system with sterile feed has been shown in a previous work to exhibit stable periodic states. In the present work we study the system for the case of non-sterile feed, i.e., when the two species are present in the feed of the chemostats. The analysis is done by numerical bifurcation theory methods. We demonstrate that, in addition to periodic states, the system possesses stable quasi-periodic states resulting from Neimark-Sacker bifurcations of limit cycles. Also, periodic states may undergo successive period doublings leading to periodic states of increasing period and indicating that chaotic states might be possible. Multistability is also observed, consisting in the coexistence of several stable steady states and possibly stable periodic or quasi-periodic states for given operating conditions. It appears that substrate-inhibition, spatial heterogeneity and presence of microorganisms in the inflow are all necessary conditions for complex dynamics to arise in a microbial system of pure and simple competition.     

Spatial and temporal components of the mating systems of kudu bulls and red deer stags

Observations were made on greater kudu (Tragelaphus strepsiceros) in the Kruger National Park in South Africa. Data on movement patterns, courtship, dominance interactions and proportion of time spent in various activities by males during the breeding season are presented. Comparative data on the apportionment of time by red deer (Cervus elaphus) setages were obtained on the Isle of Rhum, Scotland. While spatial components of male reproductive behaviour were similar in the two species, time-investments differed markedly. Kudu bulls showed little change in time spent feeding and moving during the breeding season, did not herd females and tolerated the presence of younger males. In contrast, red deer stags almost ceased feeding and greatly increased their time spent moving and in sexual or dominance-related activities. Thus the spatial and temporal components of male mating strategies can vary independently and require separate evolutionary explanaions. Comparative data for other ungulates are sparse, but suggest that time-investments are influenced by the duration of the breeding season and the breeding sex ratio. However, kudu bulls incur high mortality costs despite their low time-investments in reproductive activities.     

Metabolic control at the cytosol–mitochondria interface in different growth phases of CHO cells

Metabolism at the cytosol–mitochondria interface and its regulation is of major importance particularly for efficient production of biopharmaceuticals in Chinese hamster ovary (CHO) cells but also in many diseases. We used a novel systems-oriented approach combining dynamic metabolic flux analysis and determination of compartmental enzyme activities to obtain systems level information with functional, spatial and temporal resolution. Integrating these multiple levels of information, we were able to investigate the interaction of glycolysis and TCA cycle and its metabolic control. We characterized metabolic phases in CHO batch cultivation and assessed metabolic efficiency extending the concept of metabolic ratios. Comparing in situ enzyme activities including their compartmental localization with in vivo metabolic fluxes, we were able to identify limiting steps in glycolysis and TCA cycle. Our data point to a significant contribution of substrate channeling to glycolytic regulation. We show how glycolytic channeling heavily affects the availability of pyruvate for the mitochondria. Finally, we show that the activities of transaminases and anaplerotic enzymes are tailored to permit a balanced supply of pyruvate and oxaloacetate to the TCA cycle in the respective metabolic states. We demonstrate that knowledge about metabolic control can be gained by correlating in vivo metabolic flux dynamics with time and space resolved in situ enzyme activities.     

Protection Enhances Community and Habitat Stability: Evidence from a Mediterranean Marine Protected Area

Rare evidences support that Marine Protected Areas (MPAs) enhance the stability of marine habitats and assemblages. Based on nine years of observation (2001–2009) inside and outside a well managed MPA, we assessed the potential of conservation and management actions to modify patterns of spatial and/or temporal variability of Posidonia oceanica meadows, the lower midlittoral and the shallow infralittoral rock assemblages. Significant differences in both temporal variations and spatial patterns were observed between protected and unprotected locations. A lower temporal variability in the protected vs. unprotected assemblages was found in the shallow infralittoral, demonstrating that, at least at local scale, protection can enhance community stability. Macrobenthos with long-lived and relatively slow-growing invertebrates and structurally complex algal forms were homogeneously distributed in space and went through little fluctuations in time. In contrast, a mosaic of disturbed patches featured unprotected locations, with small-scale shifts from macroalgal stands to barrens, and harsh temporal variations between the two states. Opposite patterns of spatial and temporal variability were found for the midlittoral assemblages. Despite an overall clear pattern of seagrass regression through time, protected meadows showed a significantly higher shoot density than unprotected ones, suggesting a higher resistance to local human activities. Our results support the assumption that the exclusion/management of human activities within MPAs enhance the stability of the structural components of protected marine systems, reverting or arresting threat-induced trajectories of change.     

海河流域景观空间梯度格局及其与环境因子的关系

基于GIS技术,以海河流域为对象,首先,分别采用Fragstats3.3的标准法和移动视窗法先后分析了流域整体景观格局及其空间分异特征;然后,针对流域本身自然地理梯度特点,分别沿流域纵向(河流流向)梯度和横向(垂直与河流流向)梯度设置了两条样带,应用移动视窗法计算了景观层次下的斑块面积(AREA_MN)、蔓延度指数(CONTAG)、边界密度(ED)、形状指数(LSI)、斑块密度(PD)、多样性指数(SHDI),获得了景观沿两个样带方向的梯度格局;最后,以高程、降水、气温、人口和GDP为环境因子,以上述6个指数值为目标物种,利用去趋势典范对应分析(DCCA)方法研究了景观梯度格局与环境因子的关系。结果表明:2000年海河流域内景观基质为农田,面积占55.9%,流域内景观结构以块状结构为主,并零散分布有圈层和带状(廊道)结构;景观梯度格局在两条样带上均表现为类似的特征,即随景观类型变化呈现不同幅度的波动,两条样带上均存在较为明显的过渡带;DCCA分析表明:景观梯度格局与环境因子关系密切,区域高程、降水量、温度对流域尺度的景观格局起决定性作用,人口数量、GDP则在局部地区对景观格局有着重要影响。     

The Diverse Functions of Small Heat Shock Proteins in the Proteostasis Network

The protein quality control (PQC) system maintains protein homeostasis by counteracting the accumulation of misfolded protein conformers. Substrate degradation and refolding activities executed by ATP-dependent proteases and chaperones constitute major strategies of the proteostasis network. Small heat shock proteins represent ATP-independent chaperones that bind to misfolded proteins, preventing their uncontrolled aggregation. sHsps share the conserved α-crystallin domain (ACD) and gain functional specificity through variable and largely disordered N- and C-terminal extensions (NTE, CTE). They form large, polydisperse oligomers through multiple, weak interactions between NTE/CTEs and ACD dimers. Sequence variations of sHsps and the large variability of sHsp oligomers enable sHsps to fulfill diverse tasks in the PQC network. sHsp oligomers represent inactive yet dynamic resting states that are rapidly deoligomerized and activated upon stress conditions, releasing substrate binding sites in NTEs and ACDs Bound substrates are usually isolated in large sHsp/substrate complexes. This sequestration activity of sHsps represents a third strategy of the proteostasis network. Substrate sequestration reduces the burden for other PQC components during immediate and persistent stress conditions. Sequestered substrates can be released and directed towards refolding pathways by ATP-dependent Hsp70/Hsp100 chaperones or sorted for degradation by autophagic pathways. sHsps can also maintain the dynamic state of phase-separated stress granules (SGs), which store mRNA and translation factors, by reducing the accumulation of misfolded proteins inside SGs and preventing unfolding of SG components. This ensures SG disassembly and regain of translational capacity during recovery periods.     

Translation of EEG spatial filters from resting to motor imagery using independent component analysis

Electroencephalogram (EEG)-based brain-computer interfaces (BCIs) often use spatial filters to improve signal-to-noise ratio of task-related EEG activities. To obtain robust spatial filters, large amounts of labeled data, which are often expensive and labor-intensive to obtain, need to be collected in a training procedure before online BCI control. Several studies have recently developed zero-training methods using a session-to-session scenario in order to alleviate this problem. To our knowledge, a state-to-state translation, which applies spatial filters derived from one state to another, has never been reported. This study proposes a state-to-state, zero-training method to construct spatial filters for extracting EEG changes induced by motor imagery. Independent component analysis (ICA) was separately applied to the multi-channel EEG in the resting and the motor imagery states to obtain motor-related spatial filters. The resultant spatial filters were then applied to single-trial EEG to differentiate left- and right-hand imagery movements. On a motor imagery dataset collected from nine subjects, comparable classification accuracies were obtained by using ICA-based spatial filters derived from the two states (motor imagery: 87.0%, resting: 85.9%), which were both significantly higher than the accuracy achieved by using monopolar scalp EEG data (80.4%). The proposed method considerably increases the practicality of BCI systems in real-world environments because it is less sensitive to electrode misalignment across different sessions or days and does not require annotated pilot data to derive spatial filters.     

Temporal-to-spatial dynamic mapping,flexible recognition,and temporal correlations in an olfactory cortex model

 This paper proposes temporal-to-spatial dynamic mapping inspired by neural dynamics of the olfactory cortex. In our model the temporal structure of olfactory-bulb patterns is mapped to the spatial dynamics of the ensemble of cortical neurons. This mapping is based on the following biological mechanism: while anterior part of piriform cortex can be excited by the afferent input alone, the posterior areas require both afferent and association signals, which are temporally correlated in a specific way. One of the functional types of the neurons in our model corresponds to the cortical spatial dynamics and encodes odor components, and another represents temporal activity of association-fiber signals, which, we suggest, may be relevant to the encoding of odor concentrations. The temporal-to-spatial mapping and distributed representation of the model enable simultaneous rough cluster classification and fine recognition of patterns within a cluster as parts of the same dynamic process. The model is able to extract and segment the components of complex odor patterns which are spatiotemporal sequences of neural activity. Received: 16 October 2001 / Accepted in revised form: 7 February 2002