Rate Of Reconfiguration Research Articles

Shield wall: Kelps are the last stand against corals in tropicalized reefs

Abstract Communities inhabiting biogeographic transition zones are shifting in composition as a result of progressive warming and heatwaves. In the marine environment, corals are expanding onto higher latitude reefs historically dominated by temperate kelp forests, initiating a shift towards warm affinity coral‐dominated states. Although these coral expansions are a global phenomenon, the mechanisms that are underpinning the expansion process remain poorly understood, which limits the projections of the rate and extent of ecosystem reconfiguration. Here, we investigated the interaction between the kelp Ecklonia radiata and the high latitude scleractinian coral Plesiastrea versipora in several of Western Australia's temperate reefs, where coral colony abundance has increased by 50% in recent years. Combining field surveys with field and laboratory experiments, we test the importance of physical (abrasion and light reduction) and chemical (allelopathic) effects of kelp canopies on coral tissue cover, photosynthetic parameters and calcification rates. In the field, kelp cover had a negative effect on coral density that was overwhelming in comparison to other dominant macroalgal taxa. Abrasion by kelp whiplash was the predominant mechanism by which kelp exerted a negative effect on P. versipora fitness, scraping up to 80% of live coenosarc from experimental colonies. In contrast, canopies had no effects on P. versipora photochemical efficiency and laboratory incubations showed that there were no allelochemical effects from kelp on P. versipora. We conclude that E. radiata inhibits P. versipora establishment and development through abrasion, and the survey data confirmed that recent climate‐driven kelp loss released corals from this effect, facilitating their expansion on high‐latitude reefs in Western Australia. This shows how competitive interactions actively shield against species expansion in biogeographic transition zones and suggests a continued decline of kelp canopies will increase the permeability of temperate reefs to warm affinity species such as scleractinian corals. Read the free Plain Language Summary for this article on the Journal blog.

Dynamic Functional Connectivity as a complex random walk: Definitions and the dFCwalk toolbox

Functional Connectivity, describing the interaction between brain regions beyond their anatomical interconnection, is highly dynamic even when no task is performed (“resting state”) and it remains a methodological challenge to properly describe its changes in time without strong assumptions. We have developed a framework to describe the dynamics of Functional Connectivity (dFC) estimated from brain activity time-series as a as a smooth reconfiguration process, combining “liquid” and “coordinated” aspects. Our framework considers dFC as a complex random walk in the space of possible functional networks. Unlike other previous approaches, our method does not require the explicit extraction of discrete connectivity states but tracks changes in a continuous time fashion.•We introduced several dFC random walk metrics. First, dFC speed analyses extract the distribution of the time-resolved rate of reconfiguration of FC along time. These distributions have a clear peak (typical dFC speed, that can already serve as a biomarker) and fat tails (denoting deviations from Gaussianity that can be detected by suitable scaling analyses of FC network streams).•Second, meta-connectivity (MC) analyses identify groups of functional links whose fluctuations co-vary in time and that define veritable dFC modules organized along specific dFC meta-hub controllers (differing from conventional FC modules and hubs). The decomposition of whole-brain dFC by MC allows performing dFC speed analyses separately for each of the detected dFC modules.•We present here blocks and pipelines for dFC random walk analyses that are made easily available through a dedicated MATLABⓇ toolbox (dFCwalk), openly downloadable. Although we applied such analyses mostly to fMRI resting state data, in principle our methods can be extended to any type of neural activity (from Local Field Potentials to EEG, MEG, fNIRS, etc.) or even non-neural time-series.

An Adaptive Reclosing Switch Based on Shunt Resistance

In order to solve problems that the low coincidence success rate of the automatic reclosure of distribution network and short-circuit current has a large impact on the system when it coincides with the permanent fault, a shunt resistance type of adaptive reclosing switch is proposed. In order to improve the success rate of reconfiguration of the distribution network. By selecting the appropriate shunt resistance, the switch can not only suppress the magnetizing inrush current, limit the short-circuit current, reduce the system impact, but also use the current characteristics flowing through the shunt resistance to determine whether there is a permanent fault in the downstream, and realize the adaptive reclosing. The shunt resistance type adaptive reclosing switch can be separately applied to the power distribution switch to replace the original reclosing mode, and as a switch with protection function, the safety of the fault handling process is improved.

Monomer Dynamics of Alzheimer Peptides and Kinetic Control of Early Aggregation in Alzheimer's Disease.

The rate of reconfiguration-or intramolecular diffusion-of monomeric Alzheimer (Aβ) peptides is measured and, under conditions that aggregation is more likely, peptide diffusion slows down significantly, which allows bimolecular associations to be initiated. By using the method of Trp-Cys contact quenching, the rate of reconfiguration is observed to be about five times faster for Aβ40 , which aggregates slowly, than that for Aβ42 , which aggregates quickly. Furthermore, the rate of reconfiguration for Aβ42 speeds up at higher pH, which slows aggregation, and in the presence of the aggregation inhibitor curcumin. The measured reconfiguration rates are able to predict the early aggregation behavior of the Aβ peptide and provide a kinetic basis for why Aβ42 is more prone to aggregation than Aβ40 , despite a difference of only two amino acids.

Intramolecular diffusion controls aggregation of the PAPf39 peptide

The 39-residue fragment of human prostatic acidic phosphatase (PAP) is found in high concentrations in semen and easily form fibrils. Previous work has shown that fibrillization is accelerated with a deletion of the first 8, mostly charged residues and it was hypothesized that fibrillization depended on the dynamics of these peptides. To test this hypothesis we have measured the intramolecular diffusion of the full length and 8-residue deletion peptides at two different pHs and found a correlation with fibrillization lag time. These results can be explained by a simple kinetic model of the early stages of aggregation in which oligomerization is controlled by the rate of peptide reconfiguration.

Effects of Mutations on the Reconfiguration Rate of α-Synuclein.

It is still poorly understood why α-synuclein, the intrinsically disordered protein involved in Parkinson's and other neurodegenerative diseases, is so prone to aggregation. Recent work has shown a correlation between the aggregation rate and the rate of diffusional reconfiguration by varying temperature and pH. Here we examine the effects of several point mutations in the sequence on the conformational ensemble and reconfiguration rate. We find that at lower temperatures the PD causing aggregation enhancing mutations slow down and aggregation reducing mutations drastically speed up intramolecular diffusion, as compared to the wild type sequence. However, at higher temperatures, one of three familial mutations that enhance aggregation slows intramolecular diffusion while non-natural mutations that inhibit aggregation speed up intramolecular diffusion. These results support the hypothesis that the first step of aggregation is kinetically controlled by reconfiguration in which the protein chain cannot reconfigure rapidly enough to escape oligomerization. Finally we provide physical and chemical insights into why small point mutations cause these dramatic changes in the conformational ensemble and dynamics.

An improved Cauchy number approach for predicting the drag and reconfiguration of flexible vegetation

An improved model to describe the drag and reconfiguration of flexible riparian vegetation is proposed. The key improvement over previous models is the use of a refined ‘vegetative’ Cauchy number to explicitly determine the magnitude and rate of the vegetation's reconfiguration. After being derived from dimensional consideration, the model is applied to two experimental data sets. The first contains high-resolution drag force and physical property measurements for twenty-one foliated and defoliated full-scale trees, including specimens of Alnus glutinosa, Populus nigra and Salix alba. The second data set is independent and of a different scale, consisting of drag force and physical property measurements for natural and artificial branches of willow and poplar, under partially and fully submerged flow conditions. Good agreement between the measured and predicted drag forces is observed for both data sets, especially when compared to a more typical ‘rigid’ approximation, where the effects of reconfiguration are neglected.

Reconfiguration of the Alzheimer's Peptide Kinetically Controls Aggregation in Alzheimer's Disease

Protein aggregation is a complex, multistep process, but the first step is likely the formation of a dimer through non-specific interactions of two disordered monomers. In this work we measure the rate of reconfiguration, or intramolecular diffusion, of monomeric Abeta peptides and find a correlation between this rate and the aggregation rate. Using the method of Trp-Cys contact quenching we find that the rate of reconfiguration is ∼5 times faster for Abeta40, which aggregates slowly, than for Abeta42, which aggregates quickly. Furthermore, the rate of reconfiguration for Abeta42 speeds up at higher pH, which slows aggregation, and in the presence of the aggregation inhibitor curcumin. These results are commensurate with a model of the first step of aggregation, described here, that is a kinetic competition between reconfiguration and bimolecular diffusion.

Molecular Basis for Preventing α-Synuclein Aggregation by a Molecular Tweezer

Recent work on α-synuclein has shown that aggregation is controlled kinetically by the rate of reconfiguration of the unstructured chain, such that the faster the reconfiguration, the slower the aggregation. In this work we investigate this relationship by examining α-synuclein in the presence of a small molecular tweezer, CLR01, which binds selectively to Lys side chains. We find strong binding to multiple Lys within the chain as measured by fluorescence and mass-spectrometry and a linear increase in the reconfiguration rate with concentration of the inhibitor. Top-down mass-spectrometric analysis shows that the main binding of CLR01 to α-synuclein occurs at the N-terminal Lys-10/Lys-12. Photo-induced cross-linking of unmodified proteins (PICUP) analysis shows that under the conditions used for the fluorescence analysis, α-synuclein is predominantly monomeric. The results can be successfully modeled using a kinetic scheme in which two aggregation-prone monomers can form an encounter complex that leads to further oligomerization but can also dissociate back to monomers if the reconfiguration rate is sufficiently high. Taken together, the data provide important insights into the preferred binding site of CLR01 on α-synuclein and the mechanism by which the molecular tweezer prevents self-assembly into neurotoxic aggregates by α-synuclein and presumably other amyloidogenic proteins.

Aggregation of α-synuclein is kinetically controlled by intramolecular diffusion

We hypothesize that the first step of aggregation of disordered proteins, such as α-synuclein, is controlled by the rate of backbone reconfiguration. When reconfiguration is fast, bimolecular association is not stable, but as reconfiguration slows, association is more stable and subsequent aggregation is faster. To investigate this hypothesis, we have measured the rate of intramolecular diffusion in α-synuclein, a protein involved in Parkinson's disease, under solvent conditions that accelerate or decelerate aggregation. Using the method of tryptophan-cysteine (Trp-Cys) quenching, the rate of intramolecular contact is measured in four different loops along the chain length. This intrinsically disordered protein is highly diffusive at low temperature at neutral pH, when aggregation is slow, and compacts and diffuses more slowly at high temperature or low pH, when aggregation is rapid. Diffusion also slows with the disease mutation A30P. This work provides unique insights into the earliest steps of α-synuclein aggregation pathway and should provide the basis for the development of drugs that can prevent aggregation at the initial stage.

Influence of microstructure on the resistivity of Al-Cu-Si thin-film interconnects

The rate of resistivity decay in Al-2Cu-1Si thin-film conductors was studied as a function of temperature and grain size distribution. The decay kinetics were assumed to be governed by the rate of precipitate reconfiguration to grain boundaries. This assumption was confirmed by transmission electron microscopy (TEM) observations of the microstructure during resistance decay, and by studies of lines of two different widths. The results can be explained qualitatively from the microstructure of the lines. In particular, increasing the mean grain size slows the rate of resistivity decay, and establishing a bimodal distribution with a significant population of relatively large grains has the same effect. A simple model was developed to treat these effects quantitatively. The model assumes a cylindrical grain geometry and a uniform initial distribution of Cu and ignores the effect of intragranular precipitation. The model yields reasonable values for the activation energy for Cu diffusion in thin films, and predicts the correct dependence of the decay rate on grain size and grain distribution; however, it appears to overestimate the value of the preexponential factor D0.