The Experts below are selected from a list of 321 Experts worldwide ranked by ideXlab platform
Yue Wang - One of the best experts on this subject based on the ideXlab platform.
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cdc28 cln3 phosphorylation of sla1 regulates actin Patch Dynamics in different modes of fungal growth
Molecular Biology of the Cell, 2012Co-Authors: Guisheng Zeng, Yan-ming Wang, Yue WangAbstract:A dynamic balance between targeted transport and endocytosis is critical for polarized cell growth. However, how actin-mediated endocytosis is regulated in different growth modes remains unclear. Here we report differential regulation of cortical actin Patch Dynamics between the yeast and hyphal growth in Candida albicans. The mechanism involves phosphoregulation of the endocytic protein Sla1 by the cyclin-dependent kinase (CDK) Cdc28-Cln3 and the actin-regulating kinase Prk1. Mutational studies of the CDK phosphory- lation sites of Sla1 revealed that Cdc28-Cln3 phosphorylation of Sla1 enhances its further phosphorylation by Prk1, weakening Sla1 association with Pan1, an activator of the actin- nucleating Arp2/3 complex. Sla1 is rapidly dephosphorylated upon hyphal induction and re- mains so throughout hyphal growth. Consistently, cells expressing a phosphomimetic version of Sla1 exhibited markedly reduced actin Patch Dynamics, impaired endocytosis, and defec- tive hyphal development, whereas a nonphosphorylatable Sla1 had the opposite effect. Tak- en together, our findings establish a molecular link between CDK and a key component of the endocytic machinery, revealing a novel mechanism by which endocytosis contributes to cell morphogenesis.
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Cdc28–Cln3 phosphorylation of Sla1 regulates actin Patch Dynamics in different modes of fungal growth
Molecular biology of the cell, 2012Co-Authors: Guisheng Zeng, Yan-ming Wang, Yue WangAbstract:A dynamic balance between targeted transport and endocytosis is critical for polarized cell growth. However, how actin-mediated endocytosis is regulated in different growth modes remains unclear. Here we report differential regulation of cortical actin Patch Dynamics between the yeast and hyphal growth in Candida albicans. The mechanism involves phosphoregulation of the endocytic protein Sla1 by the cyclin-dependent kinase (CDK) Cdc28-Cln3 and the actin-regulating kinase Prk1. Mutational studies of the CDK phosphorylation sites of Sla1 revealed that Cdc28-Cln3 phosphorylation of Sla1 enhances its further phosphorylation by Prk1, weakening Sla1 association with Pan1, an activator of the actin-nucleating Arp2/3 complex. Sla1 is rapidly dephosphorylated upon hyphal induction and remains so throughout hyphal growth. Consistently, cells expressing a phosphomimetic version of Sla1 exhibited markedly reduced actin Patch Dynamics, impaired endocytosis, and defective hyphal development, whereas a nonphosphorylatable Sla1 had the opposite effect. Taken together, our findings establish a molecular link between CDK and a key component of the endocytic machinery, revealing a novel mechanism by which endocytosis contributes to cell morphogenesis.
James T. Cronin - One of the best experts on this subject based on the ideXlab platform.
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Patch Dynamics of a native grass in relation to the spread of invasive smooth brome (Bromus inermis)
Biological Invasions, 2008Co-Authors: Forrest P. Dillemuth, Erick A. Rietschier, James T. CroninAbstract:The effects of invasive species on the Patch Dynamics (establishment, growth, and local extinction) of native species are not well studied, owing to the need for relatively fine-scale data on the distribution of species. Within the prairie pothole region of the United States and Canada, the grass, Bromus inermis (smooth brome) has become established by invading disturbed prairies, and through repeated introductions for soil retention and animal graze. In this study, the impact of smooth brome on the Patch Dynamics of a dominant native grass species, Spartina pectinata (prairie cordgrass), was assessed using fine-scale (sub-meter) mapping of the distribution of cordgrass and brome in three prairie fragments from 2000 to 2006. Using GIS spatial analyses, we determined that cordgrass Patch growth was two times greater in areas not invaded by smooth brome versus areas that were heavily infested with smooth brome. Among sites and time periods, there was a consistent significant negative relationship between the amount of smooth brome surrounding a Patch of cordgrass and the growth of that cordgrass Patch. The probability of establishment of a new Patch of cordgrass averaged 1.3 times higher in areas of low brome coverage ( 75%). Conversely, existing cordgrass Patches were 7.8 times more likely to go extinct in areas of high than low brome coverage. This is one of only a few field studies to provide evidence of the negative impact of smooth brome on native flora and hopefully will serve as justification for the development of a formal management plan to limit the distribution of this species in tallgrass prairie ecosystems.
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an invasive plant promotes unstable host parasitoid Patch Dynamics
Ecology, 2004Co-Authors: James T. Cronin, Kyle J. HaynesAbstract:In theory, the rate of interPatch dispersal significantly influences the population Dynamics of predators and their prey, yet there are relatively few field experiments that provide a strong link between these two processes. In tallgrass prairies of North America, the planthopper, Prokelisia crocea, and its specialist parasitoid, Anagrus columbi, exist among discrete host-plant Patches (prairie cordgrass, Spartina pectinata). In many areas, the matrix, or habitat between Patches, has become dominated by the invasive exotic grass, smooth brome (Bromus inermis). We performed a landscape-level field study in which replicate cordgrass networks (identical in number, size, quality, and distribution of cordgrass Patches) were embedded in a matrix composed of either mudflat (a native matrix habitat) or smooth brome. Mark–recapture experiments with the planthopper and parasitoid revealed that the rate of movement among cordgrass Patches for both species was 3–11 times higher in smooth brome than in mudflat. Within three generations, planthopper and parasitoid densities per Patch were on average ∼50% lower and spatially 50–87% more variable for Patches embedded in a brome as compared to a mudflat matrix. A brome-dominated landscape also promoted extinction rates per Patch that were 4–5 times higher than the rates per Patch in native mudflat habitat. The effect was more acute for the parasitoid. We suggest that the differences in population Dynamics between networks of Patches in brome and those in mudflat were driven by underlying differences in interPatch dispersal (i.e., Patch connectivity). To our knowledge, this is the first experimental study to reveal that matrix composition, in particular, the presence of an invasive plant species, affects the spatial and temporal Dynamics of an herbivore and its natural enemy.
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AN INVASIVE PLANT PROMOTES UNSTABLE HOST–PARASITOID Patch Dynamics
Ecology, 2004Co-Authors: James T. Cronin, Kyle J. HaynesAbstract:In theory, the rate of interPatch dispersal significantly influences the population Dynamics of predators and their prey, yet there are relatively few field experiments that provide a strong link between these two processes. In tallgrass prairies of North America, the planthopper, Prokelisia crocea, and its specialist parasitoid, Anagrus columbi, exist among discrete host-plant Patches (prairie cordgrass, Spartina pectinata). In many areas, the matrix, or habitat between Patches, has become dominated by the invasive exotic grass, smooth brome (Bromus inermis). We performed a landscape-level field study in which replicate cordgrass networks (identical in number, size, quality, and distribution of cordgrass Patches) were embedded in a matrix composed of either mudflat (a native matrix habitat) or smooth brome. Mark–recapture experiments with the planthopper and parasitoid revealed that the rate of movement among cordgrass Patches for both species was 3–11 times higher in smooth brome than in mudflat. Within three generations, planthopper and parasitoid densities per Patch were on average ∼50% lower and spatially 50–87% more variable for Patches embedded in a brome as compared to a mudflat matrix. A brome-dominated landscape also promoted extinction rates per Patch that were 4–5 times higher than the rates per Patch in native mudflat habitat. The effect was more acute for the parasitoid. We suggest that the differences in population Dynamics between networks of Patches in brome and those in mudflat were driven by underlying differences in interPatch dispersal (i.e., Patch connectivity). To our knowledge, this is the first experimental study to reveal that matrix composition, in particular, the presence of an invasive plant species, affects the spatial and temporal Dynamics of an herbivore and its natural enemy.
Brian W Mcardell - One of the best experts on this subject based on the ideXlab platform.
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Patch Dynamics and stability in steep, rough streams
Journal of Geophysical Research: Earth Surface, 2012Co-Authors: Elowyn M Yager, J. W. Kirchner, W. E. Dietrich, Brian W McardellAbstract:The beds of steep streams are typically composed of relatively immobile\nboulders and more mobile Patches of gravel and cobbles. Little is\nknown about how variability in flow and sediment flux affect the\narea, thickness, composition, and grain mobility of sediment Patches.\nTo better understand Patch Dynamics, we measured flow, sediment transport,\nand bed properties in two steep channels. Patches close to the thalweg\nvaried in area, thickness, and grain size, whereas those outside\nthe thalweg did not. Local variations in transport of several orders\nof magnitude occurred, even on a Patch with a spatially homogeneous\ngrain size distribution. During moderate flow events, partial to\nselective transport dominated on the entire channel bed and all individual\nPatches. Tracer particles moved freely between different Patch classes\n(e.g., fine and coarse Patches exchanged particles), and relatively\nfine sediment on all Patch classes began motion at the same shear\nstress. Therefore, the selective transport observed for the entire\nbed was not a result of the preferential transport of only fine Patches,\nbut the high relative mobility of finer sediment on all Patches.\nOur results suggest that local flow and sediment supply, and not\nspatial grain size variations, were the primary drivers of local\nbed load transport variability. The use of reach-averaged flow properties\nto understand local Patch Dynamics may not be applicable.
Lindsey Gillson - One of the best experts on this subject based on the ideXlab platform.
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Patch Dynamics
Ecology, 2013Co-Authors: Lindsey GillsonAbstract:Patch Dynamics is the study of spatial patterns in landscapes and the ecological and environmental processes that generate these patterns, plus the internal Dynamics of how Patches change over time. “Patches” are spatial units differing from their neighbors. They are not necessarily internally homogeneous, but may be further decomposable to smaller spatial scales. For example, a forest ecosystem is composed of stands of trees, but each stand is composed of individual trees. By studying the Dynamics of Patches over space and time, ecologists have sought to address one of the fundamental matters in ecology—understanding the linkages between pattern, process, and scale. This theme underpins landscape ecology, disturbance ecology, and the spatial aspects of population ecology, which is the basis for metapopulation theory and metacommunity theory. All of these branches of ecology are concerned with flux/nonequilibrium: dynamic, heterogeneous systems, may appear stable at some spatial and temporal scales and stable at others. The persistence of Patch dynamic landscapes despite their dynamism led to the concept of the shifting mosaic steady state. Pursuing the question of how to bridge the gaps between processes at different spatial scales led to the amalgam of Patch Dynamics and hierarchy theory. Covering the dimensions of both space and time, Patch Dynamics has been of fundamental importance in biodiversity conservation, and it provides a spatial and temporal basis for natural resource management and managing and conserving complex systems. Patch Dynamics intersects with numerous other important concepts in ecology, including the island theory of biogeography, Metapopulation Theory, succession, and disturbance ecology.
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evidence of hierarchical Patch Dynamics in an east african savanna
Landscape Ecology, 2004Co-Authors: Lindsey GillsonAbstract:The Hierarchical Patch Dynamics Paradigm provides a conceptual framework for linking pattern, process and scale in ecosystems, but there have been few attempts to test this theory because most ecological studies focus on only one spatial scale, or are limited in their temporal scope. Here I use palaeoecological techniques (analysis of fossil pollen and stable carbon isotopes) to compare vegetation heterogeneity in an east African savanna at three spatial scales, over hundreds of years. The data show that patterns of vegetation change are different at the three spatial scales of observation, and suggest that different ecological processes dominate tree abundance at micro, local and landscape scales. Interactions between plants, disturbance (e.g., by fire and herbivores), climate and soil type may influence tree density at differing spatial and temporal scales. This hierarchical explanation of savanna vegetation Dynamics could inform future biodiversity conservation and management in savannas.
Ioannis G. Kevrekidis - One of the best experts on this subject based on the ideXlab platform.
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Accuracy of Patch Dynamics with Mesoscale Temporal Coupling for Efficient Massively Parallel Simulations
SIAM Journal on Scientific Computing, 2016Co-Authors: Judith Bunder, Anthony J. Roberts, Ioannis G. KevrekidisAbstract:Massive parallelization has lead to a dramatic increase in available computational power. However, data transfer speeds have failed to keep pace and are the major limiting factor in the development of exascale computing. New algorithms must be developed which minimize the transfer of data. Patch Dynamics is a computational macroscale modeling scheme which provides a coarse macroscale solution of a problem defined on a fine microscale by dividing the domain into many nonoverlapping, coupled Patches. Patch Dynamics is readily adaptable to massive parallelization as each processor can evaluate the Dynamics on one, or a few, Patches. However, Patch coupling conditions interpolate across the unevaluated parts of the domain between Patches, and are typically reevaluated at every microscale time step, thus requiring almost continuous data transfer. We propose a modified Patch Dynamics scheme which minimizes data transfer by only reevaluating the Patch coupling conditions at “mesoscale” time scales which are sign...
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On the acceleration of spatially distributed agent-based computations
Applied Numerical Mathematics, 2015Co-Authors: Ping Liu, Giovanni Samaey, C. William Gear, Ioannis G. KevrekidisAbstract:In recent years, individual-based/agent-based modeling has been applied to study a wide range of applications, ranging from engineering problems to phenomena in sociology, economics and biology. Simulating such agent-based models over extended spatiotemporal domains can be prohibitively expensive due to stochasticity and the presence of multiple scales. Nevertheless, many agent-based problems exhibit smooth behavior in space and time on a macroscopic scale, suggesting that a useful coarse-grained continuum model could be obtained. For such problems, the equation-free framework 16-18 can significantly reduce the computational cost. Patch Dynamics is an essential component of this framework. This scheme is designed to perform numerical simulations of an unavailable macroscopic equation on macroscopic time and length scales; it uses appropriately initialized simulations of the fine-scale agent-based model in a number of small "Patches", which cover only a fraction of the spatiotemporal domain. In this work, we construct a finite-volume-inspired conservative Patch Dynamics scheme and apply it to a financial market agent-based model based on the work of Omurtag and Sirovich 22. We first apply our Patch Dynamics scheme to a continuum approximation of the agent-based model, to study its performance and analyze its accuracy. We then apply the scheme to the agent-based model itself. Our computational experiments indicate that here, typically, the Patch Dynamics-based simulation needs to be performed in only 20% of the full agent simulation space, and in only 10% of the temporal domain.
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On the acceleration of spatially distributed agent-based computations: a Patch Dynamics scheme
arXiv: Numerical Analysis, 2014Co-Authors: Ping Liu, Giovanni Samaey, C. William Gear, Ioannis G. KevrekidisAbstract:In recent years, individual-based/agent-based modeling has been applied to study a wide range of applications, ranging from engineering problems to phenomena in sociology, economics and biology. Simulating such agent-based models over extended spatiotemporal domains can be prohibitively expensive due to stochasticity and the presence of multiple scales. Nevertheless, many agent-based problems exhibit smooth behavior in space and time on a macroscopic scale, suggesting that a useful coarse-grained continuum model could be obtained. For such problems, the equation-free framework [16-18] can significantly reduce the computational cost. Patch Dynamics is an essential component of this framework. This scheme is designed to perform numerical simulations of an unavailable macroscopic equation on macroscopic time and length scales; it uses appropriately initialized simulations of the fine-scale agent-based model in a number of small "Patches", which cover only a fraction of the spatiotemporal domain. In this work, we construct a finite-volume-inspired conservative Patch Dynamics scheme and apply it to a financial market agent-based model based on the work of Omurtag and Sirovich [22]. We first apply our Patch Dynamics scheme to a continuum approximation of the agent-based model, to study its performance and analyze its accuracy. We then apply the scheme to the agent-based model itself. Our computational experiments indicate that here, typically, the Patch Dynamics-based simulation requires only 20% of the full agent-based simulation in space, and need occur over only 10% of the temporal domain.
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Patch Dynamics with buffers for homogenization problems
Journal of Computational Physics, 2006Co-Authors: Giovanni Samaey, Ioannis G. Kevrekidis, Dirk RooseAbstract:An important class of problems exhibits smooth behaviour on macroscopic space and time scales, while only a microscopic evolution law is known. For such time-dependent multi-scale problems, an ''equation-free'' framework has been proposed, of which Patch Dynamics is an essential component. Patch Dynamics is designed to perform numerical simulations of an unavailable macroscopic equation on macroscopic time and length scales; it uses appropriately initialized simulations of the available microscopic model in a number of small boxes (Patches), which cover only a fraction of the space-time domain. We show that it is possible to use arbitrary boundary conditions for these Patches, provided that suitably large buffer regions ''shield'' the boundary artefacts from the interior of the Patches. We analyze the accuracy of this scheme for a diffusion homogenization problem with periodic heterogeneity and illustrate the approach with a set of numerical examples, which include a non-linear reaction-diffusion equation and the Kuramoto-Sivashinsky equation.
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Patch Dynamics with buffers for homogenization problems
arXiv: Computational Physics, 2004Co-Authors: Giovanni Samaey, Ioannis G. Kevrekidis, Dirk RooseAbstract:An important class of problems exhibits smooth behaviour on macroscopic space and time scales, while only a microscopic evolution law is known. For such time-dependent multi-scale problems, an "equation-free" framework has been proposed, of which Patch Dynamics is an essential component. Patch Dynamics is designed to perform numerical simulations of an unavailable macroscopic equation on macroscopic time and length scales; it uses appropriately initialized simulations of the available microscopic model in a number of small boxes (Patches), which cover only a fraction of the space-time domain. To reduce the effect of the artificially introduced box boundaries, we use buffer regions to "shield" the boundary artefacts from the interior of the domain for short time intervals. We analyze the accuracy of this scheme for a diffusion homogenization problem with periodic heterogeneity, and propose a simple heuristic to determine a sufficient buffer size. The algorithm performance is illustrated through a set of numerical examples, which include a non-linear reaction-diffusion equation and the Kuramoto--Sivashinsky equation.
