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Dynamic Networks (dynamic + network)
Selected AbstractsVisualization of protein interactions in living plant cells using bimolecular fluorescence complementationTHE PLANT JOURNAL, Issue 3 2004Michael Walter Summary Dynamic networks of protein,protein interactions regulate numerous cellular processes and determine the ability to respond appropriately to environmental stimuli. However, the investigation of protein complex formation in living plant cells by methods such as fluorescence resonance energy transfer has remained experimentally difficult, time consuming and requires sophisticated technical equipment. Here, we report the implementation of a bimolecular fluorescence complementation (BiFC) technique for visualization of protein,protein interactions in plant cells. This approach relies on the formation of a fluorescent complex by two non-fluorescent fragments of the yellow fluorescent protein brought together by association of interacting proteins fused to these fragments (Hu et al., 2002). To enable BiFC analyses in plant cells, we generated different complementary sets of expression vectors, which enable protein interaction studies in transiently or stably transformed cells. These vectors were used to investigate and visualize homodimerization of the basic leucine zipper (bZIP) transcription factor bZIP63 and the zinc finger protein lesion simulating disease 1 (LSD1) from Arabidopsis as well as the dimer formation of the tobacco 14-3-3 protein T14-3c. The interaction analyses of these model proteins established the feasibility of BiFC analyses for efficient visualization of structurally distinct proteins in different cellular compartments. Our investigations revealed a remarkable signal fluorescence intensity of interacting protein complexes as well as a high reproducibility and technical simplicity of the method in different plant systems. Consequently, the BiFC approach should significantly facilitate the visualization of the subcellular sites of protein interactions under conditions that closely reflect the normal physiological environment. [source] Deletion of mdmB impairs mitochondrial distribution and morphology in Aspergillus nidulansCYTOSKELETON, Issue 2 2003Katrin V. Koch Abstract Mitochondria form a dynamic network of interconnected tubes in the cells of Saccharomyces cerevisiae or filamentous fungi such as Aspergillus nidulans,Neurospora crassa, or Podospora anserina. The dynamics depends on the separation of mitochondrial fragments, their movement throughout the cell, and their subsequent fusion with the other parts of the organelle. Interestingly, the microtubule network is required for the distribution in N. crassa and S. pombe, while S. cerevisiae and A. nidulans appear to use the actin cytoskeleton. We studied a homologue of S. cerevisiae Mdm10 in A. nidulans, and named it MdmB. The open reading frame is disrupted by two introns, one of which is conserved in mdm10 of P. anserina. The MdmB protein consists of 428 amino acids with a predicted molecular mass of 46.5 kDa. MdmB shares 26% identical amino acids to Mdm10 from S. cerevisiae, 35% to N. crassa, and 32% to the P. anserina homologue. A MdmB-GFP fusion protein co-localized evenly distributed along mitochondria. Extraction of the protein was only possible after treatment with a non-ionic and an ionic detergent (1% Triton X-100; 0.5% SDS) suggesting that MdmB was tightly bound to the mitochondrial membrane fraction. Deletion of the gene in A. nidulans affected mitochondrial morphology and distribution at 20°C but not at 37°C. mdmB deletion cells contained two populations of mitochondria at lower temperature, the normal tubular network plus some giant, non-motile mitochondria. Cell Motil. Cytoskeleton 55:114,124, 2003. © 2003 Wiley-Liss, Inc. [source] Factors affecting writing achievement: mapping teacher beliefsENGLISH IN EDUCATION, Issue 1 2004Claire Wyatt-Smith Abstract The intersection of teacher beliefs with writing achievement in schooling is a key concern of this paper. The paper reports part of a two-year Australian study that set out to examine in detail how it is that teachers judge Year 5 students' literacy achievement using writing as the case instance. In what follows, we examine the data in the form of concept maps that the teachers them selves made available showing their beliefs about, and insights into the factors that affect student writing achievement. Drawing on these maps, we highlight the range of teacher-identified factors, including those relating to in-class behaviour, motivation, attitudes to school learning, social and cultural backgrounds, oracy and even life circumstances. Additionally, we address how the identified factors function, operating either as standalone elements or within a dynamic network of inter-relationships. [source] AODV-RIP: improved security in mobile ad hoc networks through route investigation procedureCONCURRENCY AND COMPUTATION: PRACTICE & EXPERIENCE, Issue 7 2010Byung-Seok Kang Abstract Most routing protocols in mobile ad hoc networks (MANETs) place an emphasis on finding paths in dynamic networks without considering security. As a result, there are a number of attacks that can be used to manipulate the routing in MANET. A malicious node that sends a modified control message to an intermediate node can disturb the network using a control message. To solve this problem, we introduce AODV protocol with route investigation procedure (AODV-RIP). It uses two additional control messages to defeat security attacks that can occur in AODV routing protocol. When an intermediate node that is on the path between the source node and the destination node receives a control message, it sends a Rroute Investigation Request (IREQ) message to the destination node in order to check the reliability of the control message. According to the existence of Route Investigation Reply (IREP), the intermediate node decides whether it transmits the control message to the source node or not. Consequently, the intermediate node that receives the control message confirms that it is using two additive control messages: IREQ and IREP. Through this investigation procedure, the source node can obtain a reliable path for transmitting data packets to an intentional destination node. The simulation results show an improvement in the packet delivery ratio and end-to-end delay at the expense of a moderate increase of the control message overhead compared with the current routing protocols. Copyright © 2009 John Wiley & Sons, Ltd. [source] BIOTIC INTERACTIONS AND MACROEVOLUTION: EXTENSIONS AND MISMATCHES ACROSS SCALES AND LEVELSEVOLUTION, Issue 4 2008David Jablonski Clade dynamics in the fossil record broadly fit expectations from the operation of competition, predation, and mutualism, but data from both modern and ancient systems suggest mismatches across scales and levels. Indirect effects, as when antagonistic or mutualistic interactions restrict geographic range and thereby elevate extinction risk, are probably widespread and may flow in both directions, as when species- or organismic-level factors increase extinction risk or speciation probabilities. Apparent contradictions across scales and levels have been neglected, including (1) the individualistic geographic shifts of species on centennial and millennial timescales versus evidence for fine-tuned coevolutionary relationships; (2) the extensive and dynamic networks of interactions faced by most species versus the evolution of costly enemy-specific defenses and finely attuned mutualisms; and (3) the macroevolutionary lags often seen between the origin and the diversification of a clade or an evolutionary novelty versus the rapid microevolution of advantageous phenotypes and the invasibility of most communities. Resolution of these and other cross-level tensions presumably hinges on how organismic interactions impinge on genetic population structures, geographic ranges, and the persistence of incipient species, but generalizations are not yet possible. Paleontological and neontological data are both incomplete and so the most powerful response to these problems will require novel integrative approaches. Promising research areas include more realistic approaches to modeling and empirical analysis of large-scale diversity dynamics of ostensibly competing clades; spatial and phylogenetic dissections of clades involved in escalatory dynamics (where prey respond evolutionarily to a broad and shifting array of enemies); analyses of the short- versus long-term consequences of mutualistic symbioses; and fuller use of abundant natural experiments on the evolutionary impacts of ecosystem engineers. [source] Knowledge, Market Structure, and Economic Coordination: Dynamics of Industrial DistrictsGROWTH AND CHANGE, Issue 3 2002Ron A. Boschma The industrial rise of the Third Italy has been characterized by the growth of dynamic networks of flexible small and medium,sized enterprises (SMEs) that are spatially concentrated in specialized industrial districts. This network type of coordination has been associated with horizontal, trust,based relations rather than vertical relations of power and dependency between local organizations. This would lower transaction costs (essential for local systems with an extreme division of labor), facilitate the transmission and exchange of (tacit) knowledge (and thus, learning and innovation), encourage cooperation mechanisms (such as the establishment of research centers), and stimulate political,institutional performance (e.g. through regulation of potential social conflicts). From an evolutionary perspective, the focus is on the dynamics of industrial districts drawing from current experiences in Italy. In this respect, this paper concentrates on two main features of industrial districts that have largely contributed to their economic success in the past, that is, their network organization and the collective learning process. The evolution of industrial districts is described in terms of organizational adjustments to structural change. The way in which the size distribution of firms has changed is discussed (in particular the role of large companies), how the (power) relationships between local organizations have evolved, what are the current sources and mechanisms of learning, and to what extent institutional lock,in has set in. Finally, a number of trajectories districts may go through in the near future are presented. [source] Parallel Algorithms for Dynamic Shortest Path ProblemsINTERNATIONAL TRANSACTIONS IN OPERATIONAL RESEARCH, Issue 3 2002Ismail Chabini The development of intelligent transportation systems (ITS) and the resulting need for the solution of a variety of dynamic traffic network models and management problems require faster-than-real-time computation of shortest path problems in dynamic networks. Recently, a sequential algorithm was developed to compute shortest paths in discrete time dynamic networks from all nodes and all departure times to one destination node. The algorithm is known as algorithm DOT and has an optimal worst-case running-time complexity. This implies that no algorithm with a better worst-case computational complexity can be discovered. Consequently, in order to derive algorithms to solve all-to-one shortest path problems in dynamic networks, one would need to explore avenues other than the design of sequential solution algorithms only. The use of commercially-available high-performance computing platforms to develop parallel implementations of sequential algorithms is an example of such avenue. This paper reports on the design, implementation, and computational testing of parallel dynamic shortest path algorithms. We develop two shared-memory and two message-passing dynamic shortest path algorithm implementations, which are derived from algorithm DOT using the following parallelization strategies: decomposition by destination and decomposition by transportation network topology. The algorithms are coded using two types of parallel computing environments: a message-passing environment based on the parallel virtual machine (PVM) library and a multi-threading environment based on the SUN Microsystems Multi-Threads (MT) library. We also develop a time-based parallel version of algorithm DOT for the case of minimum time paths in FIFO networks, and a theoretical parallelization of algorithm DOT on an ,ideal' theoretical parallel machine. Performances of the implementations are analyzed and evaluated using large transportation networks, and two types of parallel computing platforms: a distributed network of Unix workstations and a SUN shared-memory machine containing eight processors. Satisfactory speed-ups in the running time of sequential algorithms are achieved, in particular for shared-memory machines. Numerical results indicate that shared-memory computers constitute the most appropriate type of parallel computing platforms for the computation of dynamic shortest paths for real-time ITS applications. [source] Adversarial models for priority-based networks,NETWORKS: AN INTERNATIONAL JOURNAL, Issue 1 2005C. Ŕlvarez Abstract In this article, we propose several variations of the adversarial queueing model and address stability issues of networks and protocols in those proposed models. The first such variation is the priority model, which is directed at static network topologies and takes into account the case in which packets can have different priorities. Those priorities are assigned by an adversary at injection time. A second variation, the variable priority model, is an extension of the priority model in which the adversary may dynamically change the priority of packets at each time step. Two more variations, namely the failure model and the reliable model, are proposed to cope with dynamic networks. In the failure and reliable models the adversary controls, under different constraints, the failures that the links of the topology might suffer. Concerning stability of networks in the proposed adversarial models, we show that the set of universally stable networks in the adversarial model remains the same in the priority, variable priority, failure, and reliable models. From the point of view of protocols (or queueing policies), we show that several protocols that are universally stable in the adversarial queueing model remain so in the priority, failure, and reliable models. However, we show that the longest-in-system (LIS) protocol, which is universally stable in the adversarial queueing model, is not universally stable in any of the other models we propose. Moreover, we show that no queueing policy is universally stable in the variable priority model. Finally, we analyze the problem of deciding stability of a given network under a fixed protocol. We provide a characterization of the networks that are stable under first-in-first-out (FIFO) and LIS in the failure model (and therefore in the reliable and priority models). This characterization allows us to show that the stability problem under FIFO and LIS in the failure model can be solved in polynomial time. © 2004 Wiley Periodicals, Inc. NETWORKS, Vol. 45(1), 23,35 2005 [source] | ||||||||||