Default Mode Network,Motor Network,Dorsal and Ventral Basal Ganglia Networks in the Rat Brain: Comparison to Human Networks Using Resting State-fMRI

Rodent models are developed to enhance understanding of the underlying biology of different brain disorders. However, before interpreting findings from animal models in a translational aspect to understand human disease, a fundamental step is to first have knowledge of similarities and differences of the biological systems studied. In this study, we analyzed and verified four known networks termed: default mode network, motor network, dorsal basal ganglia network, and ventral basal ganglia network using resting state functional MRI (rsfMRI) in humans and rats. Our work supports the notion that humans and rats have common robust resting state brain networks and that rsfMRI can be used as a translational tool when validating animal models of brain disorders. In the future, rsfMRI may be used, in addition to short-term interventions, to characterize longitudinal effects on functional brain networks after long-term intervention in humans and rats.     

Rat liver nuclear skeleton and ribonucleoprotein complexes containing HnRNA

Rat liver nuclei deprived of chromatin and nucleoplasm show a spongelike network which preserves its connection with nucleoli, the inner membrane of the nuclear envelope, and nuclear pore complexes. It contains all of the HnRNA, provided the endogenous proteolytic activity is inhibited by a proteolytic inhibitor such as phenylmethyl sulfonyl chloride (PMSC) or the fluoride form (PMSF). In the absence of these proteolytic inhibitors, HnRNA is dissociated from the spongelike network and sediments in a sucrose gradient as polydispersed ribonucleoprotein complexes. Furthermore, purified HnRNA as well as rRNA do not bind to the spongelike network when added to these nuclei. These observations demonstrate that the association of HnRNA to the nuclear skeleton is not an artifact. RNase treatment of the spongelike network digests the majority of the rapidly labeled RNA but does not alter the morphological aspect nor the architecture of this network. EDTA and heparin treatments affect neither the attachment of HnRNA nor the structural organization of this network. Electron microscope studies of the network reveal a characteristic flexuous configuration. Its relationship with diffused and condensed chromatin is discussed.     

河北坝上草原东沟植物群落生态梯度的数量分析

运用DCCA排序轴分类,将河北坝上草原东沟的植物群落划分为8类,效果较好．排序图表达了植物群落的环境梯度、结构梯度和人为干扰．第1轴反映了群落在海拔和坡度方面的空间梯度,第2轴反映了群落的坡向分异格局,两轴综合反映了群落沿水分梯度的空间分异．群落的层片构成和各层片物种组成也表现出相应的空间分布格局．白桦局限在阴坡高海拔陡峭处．阴坡灌木与草本层片优势种分别为金露梅与细叶苔草,阳坡则为蒿类和冰草．阳坡群落各层片优势种还存在海拔和坡度分布格局．另外,放牧、耕作和伐树等人为干扰对群落时空分布也有显著影响．一般来说,生境条件较好的群落,人为干扰较严重．     

Alpha-kinase 1, a new component in apical protein transport

A key aspect in the structure of epithelial cells is the maintenance of a polarized organization based on a highly specific sorting machinery for cargo destined for the apical or the basolateral membrane domain at the exit site of the trans-Golgi network. We could recently identify two distinct post-trans-Golgi network vesicle populations that travel along separate routes to the plasma membrane, a lipid raft-dependent and a lipid raft-independent pathway. A new component of raft-carrying apical vesicles is alpha-kinase 1 (ALPK1), which was identified in immunoisolated vesicles carrying raft-associated sucrase-isomaltase (SI). This kinase was absent from vesicles carrying raft-non-associated lactase-phlorizin hydrolase. The expression of ALPK1 increases by the time of epithelial cell differentiation, whereas the intracellular localization of ALPK1 on apical transport vesicles was confirmed by confocal analysis. A phosphorylation assay on isolated SI-carrying vesicles revealed the phosphorylation of a protein band of about 105 kDa, which could be identified as the motor protein myosin I. Finally, a specific reduction of ALPK1-expression by RNA interference results in a significant decrease in the apical delivery of SI. Taken together, our data suggest that the phosphorylation of myosin I by ALPK1 is an essential process in the apical trafficking of raft-associated SI.     

Discovering functions and revealing mechanisms at molecular level from biological networks

With the increasingly accumulated data from high-throughput technologies, study on biomolecular networks has become one of key focuses in systems biology and bioinformatics. In particular, various types of molecular networks (e.g., protein-protein interaction (PPI) network; gene regulatory network (GRN); metabolic network (MN); gene coexpression network (GCEN)) have been extensively investigated, and those studies demonstrate great potentials to discover basic functions and to reveal essential mechanisms for various biological phenomena, by understanding biological systems not at individual component level but at a system-wide level. Recent studies on networks have created very prolific researches on many aspects of living organisms. In this paper, we aim to review the recent developments on topics related to molecular networks in a comprehensive manner, with the special emphasis on the computational aspect. The contents of the survey cover global topological properties and local structural characteristics, network motifs, network comparison and query, detection of functional modules and network motifs, function prediction from network analysis, inferring molecular networks from biological data as well as representative databases and software tools.     

A particular structure associated to the nucleoid of cyanobacteria

Regressive staining as well as beta-radiations or trypsin treatment on Synechocystis PCC6803 and Spirulina platensis (Gom,-Geilteri.) whole cells or permeaplasts, respectively, have demonstrated the presence of a particular structure associated to the nucleoid of cyanobacteria. This structure with a tridimensional network aspect has been called scaffold-like. We presume that it represents the cellular-molecular support for the supercoiling of the nucleoid of cyanobacteria.     

基于GIS的广州市中心城区城市森林可达性分析

城市森林是城市中主要的生态功能景观,已经成为城市生态环境建设的主体。基于居民方便获取城市森林服务的要求,根据大型城市森林斑块、道路网和街区单元数据,利用ArcGIS9.2的Network Analyst工具,分析了广州市中心城区在2km步行距离内街区单元到达城市森林斑块的可达性以及城市森林斑块的承载力,并结合航片解译的树冠覆盖数据对具有不同可达性的街区单元进行了分析。分析结果表明：广州中心城区的外环高速以内的区域范围,分别有73%、46%和18%的的街区单元在步行2km、1km和0.5km距离内能够到达大型城市森林绿地斑块。从街区单元的行政归属看,以越秀区的街区可达性最好,而海珠区和原芳村区的街区可达性较差。研究范围内,0.5km内不能到达大型城市森林斑块且树冠覆盖超过30%的街区类型中,以公共管理单位类型为主,单位绿化对于树冠覆盖的贡献率大;而绝大多数以住宅类型为主的街区单元的树冠覆盖率低于10%,其中64%的街区树冠覆盖率低于5%。以街区单元为基本对象进行可达性度量,分析城市森林斑块现状分布和服务状况,并结合其树冠覆盖特征,可以明确需要重点关注区域的空间分布,可为广州市在较小尺度上的城市森林空间布局优化提供参考。     

基于形态空间格局分析和最小累积阻力模型的广州市生态网络构建

构建生态网络对改善快速城市化背景下城市生态环境问题具有重要作用.本研究以广州市为研究区,采用形态学空间分析方法(MSPA)和景观指数法,提取景观连通性较好的核心区作为生态源地,并基于最小累积阻力模型(MCR)构建广州市生态廊道网络,通过重力模型和连通性指数定量分析生态网络结构,最后提出生态网络的优化对策.结果表明: 广州市共有10块核心区可作为生态源地,重要廊道有18条,一般廊道有27条,主要分布在研究区东北部;优化后的生态网络增加了5个生态源地和13条规划廊道,其结构指数有所改善;林地是生态廊道的主要组成景观,重要廊道的适宜宽度为60～100 m,规划廊道的适宜宽度为30～60 m.研究结果可为城市生态廊道规划提供科学参考.     

基于地形因素的高寒草甸土壤温湿度和物种多样性与初级生产力关系研究

山地是高寒草甸的主要分布区,地形变化引起了土壤温湿度和物种的差异性分布,进而影响到草地生态系统生产功能。为明晰高寒草甸山地环境因子(土壤温湿度)和物种多样性(丰富度、多度、均匀度、优势度)与初级生产力的关系,本研究以青藏高原东北缘马牙雪山支脉的高寒草甸山体为研究对象,选择阶地、阴坡、山脊和阳坡与3个海拔梯度段,调查了189个样方的植物群落组成和土壤温湿度。采用线性回归法分析土壤温湿度和物种多样性与初级生产力之间的关系。结果表明:(1)以山地高寒草甸整体为研究单元,初级生产力只随物种多度的增加而显著增加(R~2=0.07 P=0.01)。(2)坡向影响初级生产力的因素不同,阴坡初级生产力与物种丰富度正线性相关;山脊初级生产力与土壤湿度正线性相关,也随物种丰富度增加而显著增加;阳坡初级生产力与物种多度正线性相关;阶地初级生产力随均匀度增加而显著增加,随优势度增加而显著降低。(3)只有低海拔区(2860-2910 m)初级生产力随物种多度和丰富度的增加而显著增加。综上所述,山地高寒草甸土壤温湿度和物种多样性与初级生产力关系受坡向比海拔的影响更大,且物种多样性对初级生产力的影响大于土壤温湿度。建议山地高寒草甸生态系统生产和生态管理过程中要重点考虑坡向对植物多样性和初级生产力的影响。     

A UK scheme for reporting serious adverse events and reactions associated with ocular tissue transplantation

Reporting and investigation of serious adverse events and reactions associated with tissue and cell transplantation is a fundamental aspect of ensuring adequate levels of safety and quality and is a requirement of the European Union Directives on tissues and cells. In the UK, a system for the reporting and analysis of events and reactions associated with ocular tissue transplantation is well established. It is operated by a network of individuals and organisations, each with clearly defined roles and responsibilities, following written procedures for reporting and investigation. Analysis of reports indicates that the most important adverse reactions associated with this type of tissue transplantation are endophthalmitis (0.58%) and primary graft failure (0.3%). This system allows the analysis of all types of events and reactions by the professionals involved so that trends can be identified and services improved. Tools to evaluate the severity and imputability of individual events or reactions, such as those developed by the EUSTITE project, can be utilised to facilitate the selection of those cases meeting the criteria for reporting to the Competent Authority. This vigilance model has been shown to be effective and could be applied in other fields of tissue or cell transplantation.     

Actin cytoskeletal network in aging and cancer.

The cytoskeleton is being recognized as an important modulator of metabolic functions of the cell. The actin cytoskeletal network, in particular, is involved in events regulating cell proliferation and differentiation. The state of actin in a variety of cell types is regulated by signals arising from the cell surface through a wide spectrum of interactions. In this review, we explore the role of actin cytoskeletal network in a series of events which are known to influence cell proliferation and differentiation. These include interaction of actin network with extracellular matrix proteins, cell surface membranes, second messengers, cytoplasmic enzymes and the nucleus. Because of the involvement of the actin network in such diverse interactions, we propose that alterations in the actin cytoskeletal function may be an important aspect of generalized decrease in cellular functions associated with aging. Preliminary data indicate that alterations in the cytoskeletal network do occur in cells obtained from older individuals. Alterations in actin state are also reported during malignant transformation of cells in culture, and in naturally occurring tumors. Taken together, the existing data seem to suggest that changes in the actin cytoskeletal network may be a part of the aging process as well as malignant transformation. Therefore, the study of the actin cytoskeletal network and its regulation has the potential to yield important information regarding cellular senescence and neoplastic transformation.     

Kunyenga, "real sex," and survival: assessing the risk of HIV infection among urban street boys in Tanzania

This article examines possible avenues of HIV infection among urban street boys in Tanzania. In doing so, it questions the ways that AIDS researchers have defined and approached the phenomenon of "survival sex" in East and Central Africa. The article specifically examines the boys' sexual networks, sexual practices, and attitudes regarding their own sexual behavior, including their perceived risk of HIV/AIDS infection. Seventy-five street boys aged eight to 20 from the city of Mwanza were interviewed. Results suggest that almost all street boys are involved in a sexual network in which homosexual and heterosexual behavior occurs. Homosexual practices are rooted in a complex set of behaviors and ideologies known as kunyenga, which is a situated aspect of life on the streets and helps maintain the boys' strong dependence on one another. A key aspect of the boys' sexual careers involves a decrease in kunyenga activity as they approach the age of 18 and an increase in heterosexual encounters after the age of 11. There appears to be a critical period between these ages in which heterosexual and kunyenga activities overlap. It is suggested that boys between these ages represent a potential bridge for HIV/AIDS infection between the general population and the relatively enclosed sexual network of street boys.     

Sequence learning,prediction, and replay in networks of spiking neurons

Sequence learning, prediction and replay have been proposed to constitute the universal computations performed by the neocortex. The Hierarchical Temporal Memory (HTM) algorithm realizes these forms of computation. It learns sequences in an unsupervised and continuous manner using local learning rules, permits a context specific prediction of future sequence elements, and generates mismatch signals in case the predictions are not met. While the HTM algorithm accounts for a number of biological features such as topographic receptive fields, nonlinear dendritic processing, and sparse connectivity, it is based on abstract discrete-time neuron and synapse dynamics, as well as on plasticity mechanisms that can only partly be related to known biological mechanisms. Here, we devise a continuous-time implementation of the temporal-memory (TM) component of the HTM algorithm, which is based on a recurrent network of spiking neurons with biophysically interpretable variables and parameters. The model learns high-order sequences by means of a structural Hebbian synaptic plasticity mechanism supplemented with a rate-based homeostatic control. In combination with nonlinear dendritic input integration and local inhibitory feedback, this type of plasticity leads to the dynamic self-organization of narrow sequence-specific subnetworks. These subnetworks provide the substrate for a faithful propagation of sparse, synchronous activity, and, thereby, for a robust, context specific prediction of future sequence elements as well as for the autonomous replay of previously learned sequences. By strengthening the link to biology, our implementation facilitates the evaluation of the TM hypothesis based on experimentally accessible quantities. The continuous-time implementation of the TM algorithm permits, in particular, an investigation of the role of sequence timing for sequence learning, prediction and replay. We demonstrate this aspect by studying the effect of the sequence speed on the sequence learning performance and on the speed of autonomous sequence replay.     

Modifications of microfilaments and microtubules induced by two hepatic tumor promoters,phenobarbital and biliverdin in non-transformed and transformed hepatic cell lines

Microfilaments and microtubules are components of the cytoskeleton which could be implicated in neoplastic transformation. We studied the effect of two hepatic tumor promoters, phenobarbital (PB) and biliverdin (BV), on microfilaments and microtubules of non-transformed (Cl₃) and transformed (FV) hepatic epithelial cells. Cl₃ non-transformed cells cultured in the presence of 1 × 10^–6M BV for 48 h showed a loss of F-actin, fragmentation of actin and the appearance of star-like structures in the cytoplasm, as well as loosening of the peripheral bundle of actin, and some ruffling of cell membranes. In Cl₃ cells exposed to 0.2 × 10^–3M PB a similar disappearance of F-actin staining and a very prominent ruffling of cell membrane were observed. BV and PB also produced in these cells modifications of microtubules characterized by a disappearance of centrosome staining in numerous cells, a condensed ring of tubulin around the nucleus and a depolymerized aspect of the microtubular network. All these modifications of microfilaments and microtubules closely resembled those observed in FV transformed cells in the absence of any treatment (Solvent DMSO only). We did not observe an effect of BV and PB on FV cells.The present data demonstrate that the cytoskeleton of non-transformed epithelial liver cells is sensitive to the action of liver tumor promoters suggesting that it might play a role as to yet be defined in the promotion mechanism.Abbreviations PB phenobarbital - BV biliverdin - TPA 12-0-tetradecanoyl-phorbol 13 acetate - GGT gamma-glutamyl-transpeptidase - DMSO dimethylsulfoxyde     

Interdependent Multi-Layer Networks: Modeling and Survivability Analysis with Applications to Space-Based Networks

This article develops a novel approach and algorithmic tools for the modeling and survivability analysis of networks with heterogeneous nodes, and examines their application to space-based networks. Space-based networks (SBNs) allow the sharing of spacecraft on-orbit resources, such as data storage, processing, and downlink. Each spacecraft in the network can have different subsystem composition and functionality, thus resulting in node heterogeneity. Most traditional survivability analyses of networks assume node homogeneity and as a result, are not suited for the analysis of SBNs. This work proposes that heterogeneous networks can be modeled as interdependent multi-layer networks, which enables their survivability analysis. The multi-layer aspect captures the breakdown of the network according to common functionalities across the different nodes, and it allows the emergence of homogeneous sub-networks, while the interdependency aspect constrains the network to capture the physical characteristics of each node. Definitions of primitives of failure propagation are devised. Formal characterization of interdependent multi-layer networks, as well as algorithmic tools for the analysis of failure propagation across the network are developed and illustrated with space applications. The SBN applications considered consist of several networked spacecraft that can tap into each other''s Command and Data Handling subsystem, in case of failure of its own, including the Telemetry, Tracking and Command, the Control Processor, and the Data Handling sub-subsystems. Various design insights are derived and discussed, and the capability to perform trade-space analysis with the proposed approach for various network characteristics is indicated. The select results here shown quantify the incremental survivability gains (with respect to a particular class of threats) of the SBN over the traditional monolith spacecraft. Failure of the connectivity between nodes is also examined, and the results highlight the importance of the reliability of the wireless links between spacecraft (nodes) to enable any survivability improvements for space-based networks.     

Social traits,social networks and evolutionary biology

The social environment is both an important agent of selection for most organisms, and an emergent property of their interactions. As an aggregation of interactions among members of a population, the social environment is a product of many sets of relationships and so can be represented as a network or matrix. Social network analysis in animals has focused on why these networks possess the structure they do, and whether individuals’ network traits, representing some aspect of their social phenotype, relate to their fitness. Meanwhile, quantitative geneticists have demonstrated that traits expressed in a social context can depend on the phenotypes and genotypes of interacting partners, leading to influences of the social environment on the traits and fitness of individuals and the evolutionary trajectories of populations. Therefore, both fields are investigating similar topics, yet have arrived at these points relatively independently. We review how these approaches are diverged, and yet how they retain clear parallelism and so strong potential for complementarity. This demonstrates that, despite separate bodies of theory, advances in one might inform the other. Techniques in network analysis for quantifying social phenotypes, and for identifying community structure, should be useful for those studying the relationship between individual behaviour and group‐level phenotypes. Entering social association matrices into quantitative genetic models may also reduce bias in heritability estimates, and allow the estimation of the influence of social connectedness on trait expression. Current methods for measuring natural selection in a social context explicitly account for the fact that a trait is not necessarily the property of a single individual, something the network approaches have not yet considered when relating network metrics to individual fitness. Harnessing evolutionary models that consider traits affected by genes in other individuals (i.e. indirect genetic effects) provides the potential to understand how entire networks of social interactions in populations influence phenotypes and predict how these traits may evolve. By theoretical integration of social network analysis and quantitative genetics, we hope to identify areas of compatibility and incompatibility and to direct research efforts towards the most promising areas. Continuing this synthesis could provide important insights into the evolution of traits expressed in a social context and the evolutionary consequences of complex and nuanced social phenotypes.     

On the relation between residue flexibility and residue interactions in proteins

B-factor from X-ray crystal structure can well measure protein structural flexibility, which plays an important role in different biological processes, such as catalysis, binding and molecular recognition. Understanding the essence of flexibility can be helpful for the further study of the protein function. In this study, we attempted to correlate the flexibility of a residue to its interactions with other residues by representing the protein structure as a residue contact network. Here, several well established network topological parameters were employed to feature such interactions. A prediction model was constructed for B-factor of a residue by using support vector regression (SVR). Pearson correlation coefficient (CC) was used as the performance measure. CC values were 0.63 and 0.62 for single amino acid and for the whole sequence, respectively. Our results revealed well correlations between B-factors and network topological parameters. This suggests that the protein structural flexibility could be well characterized by the inter-amino acid interactions in a protein.     

模糊聚类分析在中国伞形科当归亚族分类中的应用

针对伞形科前胡族当归亚族上属间界线划分的分歧,采用模糊聚类分析方法,在形态方面以属为分类单位,定量阐明了属间亲缘关系。化学方面,以裂解－气相色谱信息为分类依据肉获得的２７个种的数据揭示了当归亚族中属间的分类关系,结果表明,当归属和在中国分布的山芹属与广义当归属类群相近,并显示了东北长鞘当归和骨缘当归是一个较特殊的类群。     

An affine micro-sphere-based constitutive model,accounting for junctional sliding,can capture F-actin network mechanics

Actin filaments are a major component of the cytoskeleton and play a crucial role in cell mechanotransduction. F-actin networks can be reconstituted in vitro and their mechanical behaviour has been studied experimentally. Constitutive models that assume an idealised network structure, in combination with a non-affine network deformation, have been successful in capturing the elastic response of the network. In this study, an affine network deformation is assumed, in which we propose an alternative 3D finite strain constitutive model. The model makes use of a micro-sphere to calculate the strain energy density of the network, which is represented as a continuous distribution of filament orientations in space. By incorporating a simplified sliding mechanism at the filament-to-filament junctions, premature filament locking, inherent to affine network deformation, could be avoided. The model could successfully fit experimental shear data for a specific cross-linked F-actin network, demonstrating the potential of the novel model.