Correlation studies of open and closed states fluctuations in an ion channel: Analysis of ion current through a large conductance locust potassium channel

Ion current fluctuations occurring within open and closed states of large conductance locust potassium channel (BK channel) were investigated for the existence of correlation. Both time series, extracted from the ion current signal, were studied by the autocorrelation function (AFA) and the detrended fluctuation analysis (DFA) methods. The persistent character of the short- and middle-range correlations of time series is shown by the slow decay of the autocorrelation function. The DFA exponent $\alpha$ is significantly larger than 0.5. The existence of strongly-persistent long-range correlations was detected only for closed-states fluctuations, with $\alpha=0.98\pm0.02$. The long-range correlation of the BK channel action is therefore determined by the character of closed states. The main outcome of this study is that the memory effect is present not only between successive conducting states of the channel but also independently within the open and closed states themselves. As the ion current fluctuations give information about the dynamics of the channel protein, our results point to the correlated character of the protein movement regardless whether the channel is in its open or closed state.Comment: 12 pages, 5 figures; to be published in Phys. Rev.

Dirac Mixture Density Approximation Based on Minimization of the Weighted Cramér-von Mises Distance

This paper proposes a systematic procedure for approximating arbitrary probability density functions by means of Dirac mixtures. For that purpose, a distance measure is required, which is in general not well defined for Dirac mixture densities. Hence, a distance measure comparing the corresponding cumulative distribution functions is employed. Here, we focus on the weighted Cramer-von Mises distance, a weighted integral quadratic distance measure, which is simple and intuitive. Since a closed-form solution of the given optimization problem is not possible in general, an efficient solution procedure based on a homotopy continuation approach is proposed. Compared to a standard particle approximation, the proposed procedure ensures an optimal approximation with respect to a given distance measure. Although useful in their own respect, the results also provide the basis for a recursive nonlinear filtering mechanism as an alternative to the popular particle filter

Strategies for tropical forest protection and sustainable supply chains: challenges and opportunities for alignment with the UN sustainable development goals

Governance for sustainable development increasingly involves diverse stakeholder groups, with the promise of enhanced legitimacy and effectiveness in decision-making and implementation. The UN sustainable development goals (SDGs) emphasise the important role of multiple (non-state) actors, including businesses and non-governmental organisations, including in efforts to ensure the sustainability of supply chains, and to reduce tropical deforestation and forest degradation. This paper critically analyses sustainability strategies to examine how the UN SDG agendas related to ‘sustainable supply chains’ and ‘tropical forest protection’ are framed and enacted by two contrasting non-state actors: (1) Instituto Centro de Vida (ICV), an NGO in Brazil working to address deforestation, including by supporting farmers to produce commodities, and (2) Unilever, a global consumer goods manufacturer and major buyer of such commodities. By identifying areas of variability in the discursive techniques used by ICV and Unilever, we unearth particular power dynamics that can shape the processes and outcomes of sustainability strategies. This paper finds that the two organisations use diverse strategies at different levels of governance, both participate actively in multi-stakeholder forums to advance their organisations’ goals, but have divergent framings of ‘sustainability’. Despite being considered ‘non-state’ actors, the strategies of the two organisations examined both reflect, and influence, the structural effects of the state in the implementation of non-state organisations’ strategies, and progress towards the SDGs. Although there is alignment of certain strategies related to tropical forest protection, in some cases, there is a risk that more sustainable, alternative approaches to governing forests and supply chains may be excluded

Optimal Parametric Density Estimation by Minimizing an Analytic Distance Measure

In this paper, we present a novel approach to parametric density estimation from given samples. The samples are treated as a parametric density function by means of a Dirac mixture, which allows for applying analytic optimization techniques. The method is based on minimizing a distance measure between the integral of the approximation function and the empirical cumulative distribution function (EDF) of the given samples, where the EDF is represented by the integral of the Dirac mixture. Since this minimization problem cannot be solved directly in general, a progression technique is applied. Increased performance of the approach in comparison to iterative maximum likelihood approaches is shown in simulations

Towards Intuitive Human-Robot Cooperation

Human-robot cooperation calls for the treatment of human-machine communication channels, especially if humanoid robots are involved. In this paper, we consider implicit nonverbal channels given by recognizing the partner\u27s intention and proactive execution of tasks. We propose a method that keeps the human in the loop and allows for the systematic reduction of uncertainty inherent in implicit cooperation. We present a benchmark scenario as well as preliminary implementation results

Overview of the PALM model system 6.0

In this paper, we describe the PALM model system 6.0. PALM (formerly an abbreviation for Parallelized Largeeddy Simulation Model and now an independent name) is a Fortran-based code and has been applied for studying a variety of atmospheric and oceanic boundary layers for about 20 years. The model is optimized for use on massively parallel computer architectures. This is a follow-up paper to the PALM 4.0 model description in Maronga et al. (2015). During the last years, PALM has been significantly improved and now offers a variety of new components. In particular, much effort was made to enhance the model with components needed for applications in urban environments, like fully interactive land surface and radiation schemes, chemistry, and an indoor model. This paper serves as an overview paper of the PALM 6.0 model system and we describe its current model core. The individual components for urban applications, case studies, validation runs, and issues with suitable input data are presented and discussed in a series of companion papers in this special issue

Fungal chitinases: diversity, mechanistic properties and biotechnological potential

Chitin derivatives, chitosan and substituted chito-oligosaccharides have a wide spectrum of applications ranging from medicine to cosmetics and dietary supplements. With advancing knowledge about the substrate-binding properties of chitinases, enzyme-based production of these biotechnologically relevant sugars from biological resources is becoming increasingly interesting. Fungi have high numbers of glycoside hydrolase family 18 chitinases with different substrate-binding site architectures. As presented in this review, the large diversity of fungal chitinases is an interesting starting point for protein engineering. In this review, recent data about the architecture of the substrate-binding clefts of fungal chitinases, in connection with their hydrolytic and transglycolytic abilities, and the development of chitinase inhibitors are summarized. Furthermore, the biological functions of chitinases, chitin and chitosan utilization by fungi, and the effects of these aspects on biotechnological applications, including protein overexpression and autolysis during industrial processes, are discussed in this review

The proapoptotic influenza A virus protein PB1-F2 forms a nonselective ion channel

Background: PB1-F2 is a proapoptotic influenza A virus protein of approximately 90 amino acids in length that is located in the nucleus, cytosol and in the mitochondria membrane of infected cells. Previous studies indicated that the molecule destabilizes planar lipid bilayers and has a strong inherent tendency for multimerization. This may be correlate with its capacity to induce mitochondrial membrane depolarization. Methodology/Principal Findings: Here, we investigated whether PB1-F2 is able to form ion channels within planar lipid bilayers and microsomes. For that purpose, a set of biologically active synthetic versions of PB1-F2 (sPB1-F2) derived from the IAV isolates A/Puerto Rico/8/34(H1N1)( IAV(PR8)), from A/Brevig Mission/1/1918( H1N1) (IAV(SF2)) or the H5N1 consensus sequence (IAV(BF2)) were used. Electrical and fluorimetric measurements show that all three peptides generate in planar lipid bilayers or in liposomes, respectively, a barely selective conductance that is associated with stochastic channel type fluctuations between a closed state and at least two defined open states. Unitary channel fluctuations were also generated when a truncated protein comprising only the 37 c-terminal amino acids of sPB1-F2 was reconstituted in bilayers. Experiments were complemented by extensive molecular dynamics simulations of the truncated fragment in a lipid bilayer. The results indicate that the c-terminal region exhibits a slightly bent helical fold, which is stable and remains embedded in the bilayer for over 180 ns. Conclusion/Significance: The data support the idea that PB1-F2 is able to form protein channel pores with no appreciable selectivity in membranes and that the c-terminus is important for this function. This information could be important for drug development