ER Network Research Articles

Random clique evolving network model and their communicability

We introduce a notion of random clique evolving network, this network start from a complete subgraph of a -clique, where a is the size of the clique. In every time step T , m nodes are chosen from this network randomly, and forming a new complete subgraph of a -clique. In this way, this network grows in time steps. The numerical investigation shows that the cumulative degree distribution of this network takes an exponential function, which is the property of the homogeneous networks, and the clustering coefficient of this network is larger than that of the ER network. However, the characteristic path length of this network is the similar to that of the ER network, so this network shows the behaviors of small-world networks. Subsequent study shows that this network exhibits hierarchical modular structure for the clustering spectrum vs. k takes power-law. These results are in good agreement with the empirical results on many real-world complex networks, such as urban bus translation network or urban subway network, our model can explain the evolutionary procedure of these spatial networks. Whats more, we present a numerical investigation on the communicability of our model by the Estrada index EE ( G ), the Estrada index EE ( G ) of this network increases with decreasing the rata m / a at the same size N and the same average degree k >. The communicability of the urban public translation networks is very important, our results have a certain guiding significance for the construction of urban bus translation network and urban subway network.

Percolation of a general network of networks

Percolation theory is an approach to study the vulnerability of a system. We develop an analytical framework and analyze the percolation properties of a network composed of interdependent networks (NetONet). Typically, percolation of a single network shows that the damage in the network due to a failure is a continuous function of the size of the failure, i.e., the fraction of failed nodes. In sharp contrast, in NetONet, due to the cascading failures, the percolation transition may be discontinuous and even a single node failure may lead to an abrupt collapse of the system. We demonstrate our general framework for a NetONet composed of n classic Erdős-Rényi (ER) networks, where each network depends on the same number m of other networks, i.e., for a random regular network (RR) formed of interdependent ER networks. The dependency between nodes of different networks is taken as one-to-one correspondence, i.e., a node in one network can depend only on one node in the other network (no-feedback condition). In contrast to a treelike NetONet in which the size of the largest connected cluster (mutual component) depends on n, the loops in the RR NetONet cause the largest connected cluster to depend only on m and the topology of each network but not on n. We also analyzed the extremely vulnerable feedback condition of coupling, where the coupling between nodes of different networks is not one-to-one correspondence. In the case of NetONet formed of ER networks, percolation only exhibits two phases, a second order phase transition and collapse, and no first order percolation transition regime is found in the case of the no-feedback condition. In the case of NetONet composed of RR networks, there exists a first order phase transition when the coupling strength q (fraction of interdependency links) is large and a second order phase transition when q is small. Our insight on the resilience of coupled networks might help in designing robust interdependent systems.

Percolation of interdependent networks with intersimilarity

Real data show that interdependent networks usually involve intersimilarity. Intersimilarity means that a pair of interdependent nodes have neighbors in both networks that are also interdependent [Parshani et al. Europhys. Lett. 92, 68002 (2010)]. For example, the coupled worldwide port network and the global airport network are intersimilar since many pairs of linked nodes (neighboring cities), by direct flights and direct shipping lines, exist in both networks. Nodes in both networks in the same city are regarded as interdependent. If two neighboring nodes in one network depend on neighboring nodes in the other network, we call these links common links. The fraction of common links in the system is a measure of intersimilarity. Previous simulation results of Parshani et al. suggest that intersimilarity has considerable effects on reducing the cascading failures; however, a theoretical understanding of this effect on the cascading process is currently missing. Here we map the cascading process with intersimilarity to a percolation of networks composed of components of common links and noncommon links. This transforms the percolation of intersimilar system to a regular percolation on a series of subnetworks, which can be solved analytically. We apply our analysis to the case where the network of common links is an Erdős-Rényi (ER) network with the average degree K, and the two networks of noncommon links are also ER networks. We show for a fully coupled pair of ER networks, that for any K≥0, although the cascade is reduced with increasing K, the phase transition is still discontinuous. Our analysis can be generalized to any kind of interdependent random network systems.

Full-field dual-color 100-nm super-resolution imaging reveals organization and dynamics of mitochondrial and ER networks

Most structured illumination microscopes use a physical or synthetic grating that is projected into the sample plane to generate a periodic illumination pattern. Albeit simple and cost-effective, this arrangement hampers fast or multi-color acquisition, which is a critical requirement for time-lapse imaging of cellular and sub-cellular dynamics. In this study, we designed and implemented an interferometric approach allowing large-field, fast, dual-color imaging at an isotropic 100-nm resolution based on a sub-diffraction fringe pattern generated by the interference of two colliding evanescent waves. Our all-mirror-based system generates illumination pat-terns of arbitrary orientation and period, limited only by the illumination aperture (NA = 1.45), the response time of a fast, piezo-driven tip-tilt mirror (10 ms) and the available fluorescence signal. At low µW laser powers suitable for long-period observation of life cells and with a camera exposure time of 20 ms, our system permits the acquisition of super-resolved 50 µm by 50 µm images at 3.3 Hz. The possibility it offers for rapidly adjusting the pattern between images is particularly advantageous for experiments that require multi-scale and multi-color information. We demonstrate the performance of our instrument by imaging mitochondrial dynamics in cultured cortical astrocytes. As an illustration of dual-color excitation dual-color detection, we also resolve interaction sites between near-membrane mitochondria and the endoplasmic reticulum. Our TIRF-SIM microscope provides a versatile, compact and cost-effective arrangement for super-resolution imaging, allowing the investigation of co-localization and dynamic interactions between organelles--important questions in both cell biology and neurophysiology.

Concentration and Stability of Community-Detecting Functions on Random Networks

We propose a general form of community detecting functions for finding the communities or the optimal partition of a random network, and examine the concentration and stability of the function values using the bounded difference martingale method. We derive LDP inequalities for both the general case and several specific community detecting functions: modularity, graph bipartitioning and q-Potts community structure. We also discuss the concentration and stability of community detecting functions on different types of random networks: the sparse and non-sparse networks and some examples such as ER and CL networks.

Nucleocapsid of Tomato spotted wilt tospovirus forms mobile particles that traffic on an actin/endoplasmic reticulum network driven by myosin XI‐K

A number of viral proteins from plant viruses, other than movement proteins, have been shown to traffic intracellularly along actin filaments and to be involved in viral infection. However, there has been no report that a viral capsid protein may traffic within a cell by utilizing the actin/endoplasmic reticulum (ER) network. We used Tomato spotted wilt tospovirus (TSWV) as a model virus to study the cell biological properties of a nucleocapsid (N) protein. We found that TSWV N protein was capable of forming highly motile cytoplasmic inclusions that moved along the ER and actin network. The disruption of actin filaments by latrunculin B, an actin-depolymerizing agent, almost stopped the intracellular movement of N inclusions, whereas treatment with a microtubule-depolymerizing reagent, oryzalin, did not. The over-expression of a myosin XI-K tail, functioning in a dominant-negative manner, completely halted the movement of N inclusions. Latrunculin B treatment strongly inhibited the formation of TSWV local lesions in Nicotiana tabacum cv Samsun NN and delayed systemic infection in N.benthamiana. Collectively, our findings provide the first evidence that the capsid protein of a plant virus has the novel property of intracellular trafficking. The findings add capsid protein as a new class of viral protein that traffics on the actin/ER system.

Synchronization of mobile chaotic agents on connected networks

This work studies the synchronization of a number of mobile agents on a substrate network. Each agent carries a chaotic map and randomly walks on a connected network. The collection of agents consists of another time-varying network derived from the substrate network. It is found that the synchronization conditions of this agent network depend on the average degree of the substrate network’s connectivity, the coupling strength between interacting agents, and the agent density in the network. Synchronization of the agent network on scale-free and ER networks is considered here, and it is found that the scale-free topology is more applicable to synchronize mobile chaotic agents. To get analytical insights, the star graph is taken and considered as a substrate network.

The Aspergillus nidulans Peripheral ER: Disorganization by ER Stress and Persistence during Mitosis

The genetically amenable fungus Aspergillus nidulans is well suited for cell biology studies involving the secretory pathway and its relationship with hyphal tip growth by apical extension. We exploited live-cell epifluorescence microscopy of the ER labeled with the translocon component Sec63, endogenously tagged with GFP, to study the organization of ‘secretory’ ER domains. The Sec63 A. nidulans ER network includes brightly fluorescent peripheral strands and more faintly labeled nuclear envelopes. In hyphae, the most abundant peripheral ER structures correspond to plasma membrane-associated strands that are polarized, but do not invade the hyphal tip dome, at least in part because the subapical collar of endocytic actin patches constrict the cortical strands in this region. Thus the subapical endocytic ring might provide an attachment for ER strands, thereby ensuring that the growing tip remains ‘loaded’ with secretory ER. Acute disruption of secretory ER function by reductive stress-mediated induction of the unfolded protein response results in the reversible aggregation of ER strands, cessation of exocytosis and swelling of the hyphal tips. The secretory ER is insensitive to brefeldin A treatment and does not undergo changes during mitosis, in agreement with the reports that apical extension continues at normal rates during this period.

Membrane assembly during the infection cycle of the giant Mimivirus.

Although extensively studied, the structure, cellular origin and assembly mechanism of internal membranes during viral infection remain unclear. By combining diverse imaging techniques, including the novel Scanning-Transmission Electron Microscopy tomography, we elucidate the structural stages of membrane biogenesis during the assembly of the giant DNA virus Mimivirus. We show that this elaborate multistage process occurs at a well-defined zone localized at the periphery of large viral factories that are generated in the host cytoplasm. Membrane biogenesis is initiated by fusion of multiple vesicles, ∼70 nm in diameter, that apparently derive from the host ER network and enable continuous supply of lipid components to the membrane-assembly zone. The resulting multivesicular bodies subsequently rupture to form large open single-layered membrane sheets from which viral membranes are generated. Membrane generation is accompanied by the assembly of icosahedral viral capsids in a process involving the hypothetical major capsid protein L425 that acts as a scaffolding protein. The assembly model proposed here reveals how multiple Mimivirus progeny can be continuously and efficiently generated and underscores the similarity between the infection cycles of Mimivirus and Vaccinia virus. Moreover, the membrane biogenesis process indicated by our findings provides new insights into the pathways that might mediate assembly of internal viral membranes in general.

Untangling the web: Mechanisms underlying ER network formation

The ER is a continuous membrane system consisting of the nuclear envelope, flat sheets often studded with ribosomes, and a polygonal network of highly-curved tubules extending throughout the cell. Although protein and lipid biosynthesis, protein modification, vesicular transport, Ca2+dynamics, and protein quality control have been investigated in great detail, mechanisms that generate the distinctive architecture of the ER have been uncovered only recently. Several protein families including the reticulons and REEPs/DP1/Yop1p harbor hydrophobic hairpin domains that shape high-curvature ER tubules and mediate intramembrane protein interactions. Members of the atlastin/RHD3/Sey1p family of dynamin-related GTPases interact with the ER-shaping proteins and mediate the formation of three-way junctions responsible for the polygonal structure of the tubular ER network, with Lunapark proteins acting antagonistically. Additional classes of tubular ER proteins including some REEPs and the M1 spastin ATPase interact with the microtubule cytoskeleton. Flat ER sheets possess a different complement of proteins such as p180, CLIMP-63 and kinectin implicated in shaping, cisternal stacking and cytoskeletal interactions. The ER is also in constant motion, and numerous signaling pathways as well as interactions among cytoskeletal elements, the plasma membrane, and organelles cooperate to position and shape the ER dynamically. Finally, many proteins involved in shaping the ER network are mutated in the most common forms of hereditary spastic paraplegia, indicating a particular importance for proper ER morphology and distribution in large, highly-polarized cells such as neurons. This article is part of a Special Issue entitled: Functional and structural diversity of endoplasmic reticulum.

A navigation search model based on subnet of maximum controllability

In this paper, we propose a concept of subnet of maximum controllability based on the model of network controllability, and set up the navigation search model based on the subnet of maximum controllability, called NMSMC. The strategy of adding links that is based on the subnet of maximum controllability is to solve, with the minimum cost, the terminating search, the problem that arises from no way for particles to search in the directed network. Based on the subnet of maximum controllability to deploy navigation nodes,the search time of the whole network can be made close to the average shortest path of the navigation network,which the number of navigation nodes is only 2% of the total nodes. The experimental results of the ER and SF networks show that the search efficiency is strongly correlated with the network controllability. The better the controllability, the less the adding links are, which can lead to the fact that the more the navigation nodes are distributed in the network, the more the search efficiency of the network can be enhanced.

Network controllability based on node overloaded failure

Liu and Barabasi applied the modern control theory to the network controllability of linear dynamical systems and proposed a method to calculate the minimal set of driver node which controls the states of all nodes in a linear time invariant complex network with any topology. The network controllability model solves the computable problems of the network controllability. Facing the problem of node overloaded failure in real networks, in the paper we investigate the model of network controllability based on node overloaded failure. Through the simulation of betweenness and Weibull failure model, the results demonstrate that the difficulty in maintaining the controllability of SF network is significantly greater than that of ER network. In the target failure mechanism, even if the failure signals input rarely to the networks, they can greatly increase the difficulty of network controllability. Besides, the node failure based high betweenness centrality is more efficient than failure based high degree on damaging network controllability, which indicates the nodes with high betweenness centrality play an important role in maintaining the network controllability. Furthermore, taking the reasonable measures for different load failure model can prevent the networks from inducing a step uncontrollable phenomenon.

Rumor spreading model considering forgetting and remembering mechanisms in inhomogeneous networks

The SIHR rumor spreading model with consideration of the forgetting and remembering mechanisms was studied in homogeneous networks. We further investigate the properties of the SIHR model in inhomogeneous networks. The SIHR model is refined and mean-field equations are derived to describe the dynamics of the rumor spreading model in inhomogeneous networks. Steady-state analysis is carried out, which shows no spreading threshold existing. Numerical simulations are conducted in a BA scale-free network. The simulation results show that the network topology exerts significant influences on the rumor spreading: In comparison with the ER network, the rumor spreads faster and the final size of the rumor is smaller in BA scale-free network; the forgetting and remembering mechanisms greatly impact the final size of the rumor. Finally, through the numerical simulation, we examine the effects that the spreading rate and the stifling rate have on the the influence of the rumor. In addition, the no threshold result is verified.

Robustness of a network formed byninterdependent networks with a one-to-one correspondence of dependent nodes

Many real-world networks interact with and depend upon other networks. We develop an analytical framework for studying a network formed by n fully interdependent randomly connected networks, each composed of the same number of nodes N. The dependency links connecting nodes from different networks establish a unique one-to-one correspondence between the nodes of one network and the nodes of the other network. We study the dynamics of the cascades of failures in such a network of networks (NON) caused by a random initial attack on one of the networks, after which a fraction p of its nodes survives. We find for the fully interdependent loopless NON that the final state of the NON does not depend on the dynamics of the cascades but is determined by a uniquely defined mutual giant component of the NON, which generalizes both the giant component of regular percolation of a single network (n=1) and the recently studied case of the mutual giant component of two interdependent networks (n=2). We also find that the mutual giant component does not depend on the topology of the NON and express it in terms of generating functions of the degree distributions of the network. Our results show that, for any n≥2 there exists a critical p=p(c)>0 below which the mutual giant component abruptly collapses from a finite nonzero value for p≥p(c) to zero for p<p(c), as in a first-order phase transition. This behavior holds even for scale-free networks where p(c)=0 for n=1. We show that, if at least one of the networks in the NON has isolated or singly connected nodes, the NON completely disintegrates for sufficiently large n even if p=1. In contrast, in the absence of such nodes, the NON survives for any n for sufficiently large p. We illustrate this behavior by comparing two exactly solvable examples of NONs composed of Erdős-Rényi (ER) and random regular (RR) networks. We find that the robustness of n coupled RR networks of degree k is dramatically higher compared to the n-coupled ER networks of the same average degree k[over ¯]=k. While for ER NONs there exists a critical minimum average degree k[over ¯]=k[over ¯](min)∼lnn below which the system collapses, for RR NONs k(min)=2 for any n (i.e., for any k>2, a RR NON is stable for any n with p(c)<1). This results arises from the critical role played by singly connected nodes which exist in an ER NON and enhance the cascading failures, but do not exist in a RR NON.

ATI1, a newly identified atg8-interacting protein, binds two different Atg8 homologs

Autophagy is a mechanism used for the transport of macromolecules to the vacuole for degradation. It can be either non-selective or selective, resulting from the specific binding of target proteins to Atg8, an essential autophagy-related protein. Nine Atg8 homologs exist in the model plant Arabidopsis thaliana, suggesting possible different roles for different homologs. In a previous report published in the Plant Cell, our group identified two plant-specific proteins, termed ATI1 and ATI2, which bind Atg8f, as a representative of the nine Atg8 homologs. The proteins were shown to associate with novel starvation-induced bodies that move on the ER network and reach the lytic vacuole. Altered expression level of the proteins was also shown to affect the ability of seeds to germinate in the presence of the germination inhibiting hormone ABA. In the present addendum article, we demonstrate that, in addition to Atg8f, ATI1 binds Atg8h, an Atg8 homolog from a different sub-family, indicating that ATI1 is not a specific target of Atg8f.

CRSBP-1/LYVE-1 ligands stimulate contraction of the CRSBP-1-associated ER network in lymphatic endothelial cells

CRSBP-l/LYVE-1 ligands (PDGF-BB, VEGF-A165 and hyaluronic acid) have been shown to induce opening of lymphatic intercellular junctions in vitro and in vivo by stimulating contraction of lymphatic endothelial cells (LECs). The mechanism by which CRSBP-1 ligands stimulate contraction of LECs is not understood. Here we demonstrate that CRSBP-1 is localized to the plasma membrane as well as intracellular fibrillar structures in LECs, including primary human dermal LECs and SVEC4-10 cells. CRSBP-1-associated fibrillar structures are identical to the ER network as evidenced by the co-localization of CRSBP-1 and BiP in these cells. CRSBP-1 ligands stimulate contraction of the ER network in a CRSBP-1-dependent and paclitaxel (a microtubule-stabilizing agent)-sensitive manner. These results suggest that ligand-stimulated ER contraction is associated with ligand-stimulated contraction in LECs.

通信网络设计: 传输容量、设计代价和可扩展性

Despite the growing number of works centering around the traffic dynamics on complex networks, these researches still have some common shortcomings, e.g., too simple traffic flow model and lack of considerations for the designing cost and scalability issues. This paper builds on a more realistic traffic flow model, and offers a holistic view on the network designing problem. In addition to the extensively studied transmission capacity, this paper takes designing cost and scalability as two other designing objectives, and presents a quantitative study of how different designing choices independently and collectively influence these objectives by the introduction of a cartesian coordinate system. It is shown that different kinds of network topologies display different shapes of achievable solution spaces and exhibit different abilities to achieve cost-effective and scalable designing. In particular, we find the philosophy underlying empirical network designing and engineering today fails to meet the cost-effective and scalable designing requirements, and propose a cost-effective and scalable designing scheme for BA-like networks, i.e., the efficient routing combined with effective betweenness based link bandwidth allocation. In addition, when designing a thoroughly new network from the beginning, we find that ER network is a good candidate to achieve cost-effective and scalable designing in most settings.

Revealing the process of edge-based-attack cascading failures

In this paper, concerned with the highest-load attack (HL) and random attack (RA) on one edge or one node, we model the cascading dynamics in scale-free networks (SF), WS small-world networks (WS) and ER random networks (ER). How long the cascade propagation in networks will persist and what features the avalanche edges or nodes at each time step will show in cascading failures are questions investigated. We find that, under both HL and RA attack, the persistent time of cascade propagation in SF networks is always longer than in ER and WS networks (except p=0.1). Under HL attack, there exists a threshold αc of tolerance parameter α making the cascading propagation in SF and WS networks longest-running. Moreover, under HL attack, the avalanche edges and nodes in WS and ER networks always reach a peak over a period of time, while the SF network shows similar characteristics only in some field of α. However, under RA attack, in the case of big α, most of the avalanche edges and nodes in SF, WS and ER networks always occur at the beginning of the cascading failures. Furthermore, under node-targeted attack, SF shows to be more vulnerable than under edge-targeted attack and most of avalanche nodes occur at the beginning of failures. The results remind us to grasp the rhythm of controlling disasters according to the features of cascading failures in different networks.

The ER/Golgi Interface - Is There Anything in-between?

OPINION article Front. Plant Sci., 18 April 2012Sec. Plant Cell Biology Volume 3 - 2012 | https://doi.org/10.3389/fpls.2012.00073

ER Import Sites and Their Relationship to ER Exit Sites: A New Model for Bidirectional ER-Golgi Transport in Higher Plants

Per definition, ER exit sites are COPII vesiculation events at the surface of the ER and in higher plants are only visualizable in the electron microscope through cryofixation techniques. Fluorescent COPII labeling moves with Golgi stacks and locates to the interface between the ER and the Golgi. In contrast, the domain of the ER where retrograde COPI vesicles fuse, i.e., ER import sites (ERIS), has remained unclear. To identify ERIS we have employed ER-located SNAREs and tethering factors. We screened several SNAREs (SYP81, the SYP7 family, and USE1) to find a SNARE whose overexpression did not disrupt ER-Golgi traffic and which gave rise to discrete fluorescent punctae when expressed with an XFP tag. Only the Qc-SNARE SYP72 fulfilled these criteria. When coexpressed with SYP72-YFP, both the type I-membrane protein RFP-p24δ5 and the luminal marker CFP-HDEL whose ER localization are due to an efficient COPI-mediated recycling, form nodules along the tubular ER network. SYP72-YFP colocalizes with these nodules which are not seen when RFP-p24δ5 or CFP-HDEL is expressed alone or when SYP72-YFP is coexpressed with a mutant form of RFP-p24δ5 that cannot exit the ER. SYP72-YFP does not colocalize with Golgi markers, except when the Golgi stacks are immobilized through actin depolymerization. Endogenous SYP7 SNAREs, also colocalize with immobilized COPII/Golgi. In contrast, XFP-tagged versions of plant homologs to TIP20 of the Dsl1 COPI-tethering factor complex, and the COPII-tethering factor p115 colocalize perfectly with Golgi stacks irrespective of the motile status. These data suggest that COPI vesicle fusion with the ER is restricted to periods when Golgi stacks are stationary, but that when moving both COPII and COPI vesicles are tethered and collect in the ER-Golgi interface. Thus, the Golgi stack and an associated domain of the ER thereby constitute a mobile secretory and recycling unit: a unique feature in eukaryotic cells.