Bacteria frequently need to adapt to altered environmental conditions. Adaptation requires changes in gene expression, often mediated by global regulators of transcription. The nucleoid-associated protein H-NS is a key global regulator in Gram-negative bacteria and is believed to be a crucial player in bacterial chromatin organization via its DNA-bridging activity. H-NS activity in vivo is modulated by physico-chemical factors (osmolarity, pH, temperature) and interaction partners. Mechanistically, it is unclear how functional modulation of H-NS by such factors is achieved. Here, we show that a diverse spectrum of H-NS modulators alter the DNA-bridging activity of H-NS. Changes in monovalent and divalent ion concentrations drive an abrupt switch between a bridging and non-bridging DNA-binding mode. Similarly, synergistic and antagonistic co-regulators modulate the DNA-bridging efficiency. Structural studies suggest a conserved mechanism: H-NS switches between a ‘closed’ and an ‘open’, bridging competent, conformation driven by environmental cues and interaction partners.

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In this paper, we address the risk estimation problem where one aims at estimating the probability of violation of safety constraints for a robot in the presence of bounded uncertainties with arbitrary probability distributions. In this problem, an unsafe set is described by level sets of polynomials that is, in general, a non-convex set. Uncertainty arises due to the probabilistic parameters of the unsafe set and probabilistic states of the robot. To solve this problem, we use a moment-based representation of probability distributions. We describe upper and lower bounds of the risk in terms of a linear weighted sum of the moments. Weights are coefficients of a univariate Chebyshev polynomial obtained by solving a sum-of-squares optimization problem in the offline step. Hence, given a finite number of moments of probability distributions, risk can be estimated in real-time. We demonstrate the performance of the provided approach by solving probabilistic collision checking problems where we aim to find the probability of collision of a robot with a non-convex obstacle in the presence of probabilistic uncertainties in the location of the robot and size, location, and geometry of the obstacle.In this paper, we leverage SOS based techniques to provide upper and lower bounds of the probability of violation of safety constraints described by level sets of n-variate polynomials. The proposed method can deal with bounded uncertainties with arbitrary probability distributions and also uncertain nonconvex safety constraints e.g., obstacles with uncertain location, size, and geometry. The provided method relies on a convex optimization that looks for a univariate polynomial indicator function. Using the proposed approach, we describe upper and lower bounds of the risk as a linear weighted sum of the moments of uncertainties. The weights are coefficients of a univariate Chebyshev polynomial obtained by solving a univariate SOS optimization.

DNA double strand breaks (DSB) are the most severe damages in chromatin induced by ionizing radiation. In response to such environmentally determined stress situations, cells have developed repair mechanisms. Although many investigations have contributed to a detailed understanding of repair processes, e.g., homologous recombination repair or non-homologous end-joining, the question is not sufficiently answered, how a cell decides to apply a certain repair process at a certain damage site, since all different repair pathways could simultaneously occur in the same cell nucleus. One of the first processes after DSB induction is phosphorylation of the histone variant H2AX to γH2AX in the given surroundings of the damaged locus. Since the spatial organization of chromatin is not random, it may be conclusive that the spatial organization of γH2AX foci is also not random, and rather, contributes to accessibility of special repair proteins to the damaged site, and thus, to the following repair pathway at this given site. The aim of this article is to demonstrate a new approach to analyze repair foci by their topology in order to obtain a cell independent method of categorization. During the last decade, novel super-resolution fluorescence light microscopic techniques have enabled new insights into genome structure and spatial organization on the nano-scale in the order of 10 nm. One of these techniques is single molecule localization microscopy (SMLM) with which the spatial coordinates of single fluorescence molecules can precisely be determined and density and distance distributions can be calculated. This method is an appropriate tool to quantify complex changes of chromatin and to describe repair foci on the single molecule level. Based on the pointillist information obtained by SMLM from specifically labeled heterochromatin and γH2AX foci reflecting the chromatin morphology and repair foci topology, we have developed a new analytical methodology of foci or foci cluster characterization, respectively, by means of persistence homology. This method allows, for the first time, a cell independent comparison of two point distributions (here the point distributions of two γH2AX clusters) with each other of a selected ensample and to give a mathematical measure of their similarity. In order to demonstrate the feasibility of this approach, cells were irradiated by low LET (linear energy transfer) radiation with different doses and the heterochromatin and γH2AX foci were fluorescently labeled by antibodies for SMLM. By means of our new analysis method, we were able to show that the topology of clusters of γH2AX foci can be categorized depending on the distance to heterochromatin. This method opens up new possibilities to categorize spatial organization of point patterns by parameterization of topological similarity.

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In the epidermal cells of onion (Allium cepa L.) bulb scales the endoplasmic reticulum (ER) can be subdivided into three domains: a peripheral tubular network, cisternae, and long tubular strands. The latter are the form in which the ER is moved in onion cells. During cold treatment the arrangement of the three domains changes drastically. The cisternae and long tubular strands disintegrate into short ER tubules which show rapid agitational motion. Long-distance movement is inhibited. The peripheral tubular ER network is presumably retained during cold treatment. Rewarming of previously chilled bulb scales initiates the reorganization of the ER into the three domains. The ER is partly relocated during recovery from cold treatment. Redistribution and reorganization of the ER is not affected by the microtubule-destabilizing herbicides oryzalin and trifluralin (5 μM). Cytochalasin D (2μM), however, inhibits not only the relocation of ER material, as is evident by the absence of long tubular ER strands, but also the movement of other cell organelles. The latter cluster on top of the cisternae in a manner which is characteristic of treatment with the actin-filament inhibitor. The array of actin filaments is similar in unstressed, cold-treated cells, and cells which recover from low temperatures in the presence of oryzalin or tap water alone. In the presence of cytochalasin D the actin filaments are severely fragmented. The results indicate that low temperatures most likely influence either the interaction of the force-generating system, probably myosin, with actin filaments, or the force-generating mechanism of the actomyosin-driven intracellular movement, but do not affect actin-filament integrity.

Recent humanoid control investigations have emphasized the importance of controlling whole-body angular momentum throughout a movement task. For typical movement tasks, such as normal walking, such controllers minimize fluctuations in angular momentum about the center of mass (CM). This minimization is consistent with observed behavior of humans for such tasks. However, there are cases where such minimization is not desirable. In this study, we investigate movement tasks where bipedal balance control requires a relaxation of the goal of minimizing whole-body angular moment. We construct a humanoid model having a human-like mass distribution, and a Moment-Exploiting Control algorithm that modulates whole-body angular momentum to enhance CM control. The model only requires reference trajectories for CM position and torso orientation. Joint reference trajectories are not required. While balancing on one leg, we show that the controller is capable of correcting errors in CM state by sacrificing angular postural goals for the swing leg, trunk and head. This prioritization capability provides robustness to significant disturbances, without the need to plan new reference trajectories. We compare the dynamic behavior of our humanoid model to that of human test participants. While standing on one leg, the model, like the human, is shown to reposition its CM just above the stance foot from an initial body state where CM velocity is zero, and the ground CM projection falls outside the foot envelope.