Structure of a translocation signal domain mediating conjugative transfer by Type IV secretion systems

Relaxases are proteins responsible for the transfer of plasmid and chromosomal DNA from one bacterium to another during conjugation. They covalently react with a specific phosphodiester bond within DNA origin of transfer sequences, forming a nucleo-protein complex which is subsequently recruited for transport by a plasmid-encoded type IV secretion system. In previous work we identified the targeting translocation signals presented by the conjugative relaxase TraI of plasmid R1. Here we report the structure of TraI translocation signal TSA. In contrast to known translocation signals we show that TSA is an independent folding unit and thus forms a bona fide structural domain. This domain can be further divided into three sub-domains with striking structural homology with helicase sub-domains of the SF1B family. We also show that TSA is part of a larger vestigial helicase domain which has lost its helicase activity but not its single-stranded DNA binding capability. Finally, we further delineate the binding site responsible for translocation activity of TSA by targeting single residues for mutations. Overall, this study provides the first evidence that translocation signals can be part of larger structural scaffolds, overlapping with translocation-independent activities

Path planning with far-away obstacles detection under uncertainty

[Resumen] Hoy en día se están investigando robots de exploración terrestre y espacial más rápidos en respuesta a la creciente demanda de capacidades de exploración e investigación más rápidas, eficaces y rentables. Para estas plataformas móviles rápidas la identificación y evasión de obstáculos lejanos son críticas, ya que su alta velocidad implica la necesidad de tener en cuenta el mayor número posible de obstáculos cercanos y lejanos para el cálculo de la trayectoria global, evitando cualquier posible accidente debido a su velocidad y al tiempo de cálculo de los algoritmos de replanificación. Debido a su distancia, los obstáculos lejanos no se incluyen en los mapas locales, que están limitados por el alcance de las cámaras de profundidad. Por estas razones, este artículo propone el uso de técnicas de Inteligencia Artificial para detectarlos a partir de imágenes y estimar sus tamaños y posiciones con un cierto grado de incertidumbre. Los obstáculos detectados se incluirán posteriormente en los mapas globales, corrigiendo la trayectoria global en caso de colisionar con ellos.[Abstract] Nowadays faster terrestrial and space exploration robots are being investigated, in response to the growing demand for faster, more efficient, and cost-effective exploration and research apabilities. For these rapid mobile platforms, the identification and avoidance of far obstacles are critical, since their high speed implies the need to take into account as many near and far obstacles as possible for the global path computation, avoiding any possible accident due to their speed and the computation time of the replanning algorithms. Due to their distance, the far obstacles are not included within the local maps, which are limited by the range of the depth cameras. For these reasons, this paper proposes the use of Artificial Intelligence techniques to detect them from images and estimate their sizes and positions with a certain degree of uncertainty. The detected obstacles will be later included in the global maps, correcting the global path in case it collides with them

Network Cournot Competition

Cournot competition is a fundamental economic model that represents firms competing in a single market of a homogeneous good. Each firm tries to maximize its utility---a function of the production cost as well as market price of the product---by deciding on the amount of production. In today's dynamic and diverse economy, many firms often compete in more than one market simultaneously, i.e., each market might be shared among a subset of these firms. In this situation, a bipartite graph models the access restriction where firms are on one side, markets are on the other side, and edges demonstrate whether a firm has access to a market or not. We call this game \emph{Network Cournot Competition} (NCC). In this paper, we propose algorithms for finding pure Nash equilibria of NCC games in different situations. First, we carefully design a potential function for NCC, when the price functions for markets are linear functions of the production in that market. However, for nonlinear price functions, this approach is not feasible. We model the problem as a nonlinear complementarity problem in this case, and design a polynomial-time algorithm that finds an equilibrium of the game for strongly convex cost functions and strongly monotone revenue functions. We also explore the class of price functions that ensures strong monotonicity of the revenue function, and show it consists of a broad class of functions. Moreover, we discuss the uniqueness of equilibria in both of these cases which means our algorithms find the unique equilibria of the games. Last but not least, when the cost of production in one market is independent from the cost of production in other markets for all firms, the problem can be separated into several independent classical \emph{Cournot Oligopoly} problems. We give the first combinatorial algorithm for this widely studied problem

Analgesic and Anti-inflammatory Activities of the Stem Bark of Yellow Flamboyant (Peltophorum pterocarpum)

Peltophorum pterocarpum (family; Fabaceae) is an evergreen perennial crop grown in tropical gardens. Different parts of this tree are being used for the management of many diseases. This study investigated the acute toxicity, analgesic and anti-inflammatory potentials of n-hexane extract of P. pterocarpum stem bark. Acute oral toxicity of n-hexane extract of P. pterocarpum stem bark was investigated using standard method. Analgesic activity was investigated by using acetic acid-induced writhing model, using indomethacin as a reference drug. Antiinflammatory activity of n-hexane extract of P. pterocarpum stem bark was investigated by using formalin-induced paw licking model, using aspirin as standard drug. In the acute toxicity study, mortality was observed at 500 and 2500 mg/kg body weight. In the acetic acid induced writhing test, the n-hexane extract of P. pterocarpum (100 and 200 mg/kg body weight) showed a significant reduction in the number of writhing with 55.5 % and 60 % of inhibition respectively. In formalin-induced rat paw oedema test for acute inflammation, the n-hexane extract of P. pterocarpum in 50, 100 and 200 mg/kg body weight showed 26.00 %, 27.89 % and 32.27 % inhibition of oedema respectively after 4hours, which is comparable to that of standard drug-aspirin (33.59 %). These results validated that the extract of P. pterocarpum possesses significant analgesic and anti-inflammatory properties.Keywords: Peltophorum pterocarpum, acute toxicity, analgesic activity, anti-inflammatory activit

Towards an understanding of the effect of adding a foam core on the blast performance of glass fibre reinforced epoxy laminate panels

This paper presents insights into the blast response of sandwich panels with lightweight foam cores and asymmetric (different thicknesses) glass fibre epoxy face sheets. Viscously damped elastic vibrations were observed in the laminates (no core), while the transient response of the sandwich panels was more complex, especially after the peak displacement was observed. The post-peak residual oscillations in the sandwich panels were larger and did not decay as significantly with time when compared to the equivalent mass laminate panel test. Delamination was the predominant mode of failure on the thinner facesheet side of the sandwich panel, whereas cracking and matrix failure were more prominent on the thicker side (which was exposed to the blast). The type of constituent materials used and testing conditions, including the clamping method, influenced the resulting failure modes observed. A probable sequence of damage in the sandwich panels was proposed, based on the transient displacement measurements, a post-test failure analysis, and consideration of the stress wave propagation through the multilayered, multimaterial structure. This work demonstrates the need for detailed understanding of the transient behaviour of multilayered structures with significant elastic energy capacity and a wide range of possible damage mechanisms. The work should prove valuable to structural engineers and designers considering the deployment of foam-core sandwich panels or fibre reinforced polymer laminates in applications when air-blast loading may pose a credible threat

Thermal conductivity of the Toda lattice with conservative noise

We study the thermal conductivity of the one dimensional Toda lattice perturbed by a stochastic dynamics preserving energy and momentum. The strength of the stochastic noise is controlled by a parameter $\gamma$. We show that heat transport is anomalous, and that the thermal conductivity diverges with the length $n$ of the chain according to $\kappa(n) \sim n^\alpha$, with $0 < \alpha \leq 1/2$. In particular, the ballistic heat conduction of the unperturbed Toda chain is destroyed. Besides, the exponent $\alpha$ of the divergence depends on $\gamma$

The Influence of Solar Flares on the Lower Solar Atmosphere: Evidence from the Na D Absorption Line Measured by GOLF/SOHO

Solar flares presumably have an impact on the deepest layers of the solar atmosphere and yet the observational evidence for such an impact is scarce. Using ten years of measurements of the Na D$_{1}$ and Na D$_2$ Fraunhofer lines, measured by GOLF onboard SOHO, we show that this photospheric line is indeed affected by flares. The effect of individual flares is hidden by solar oscillations, but a statistical analysis based on conditional averaging reveals a clear signature. Although GOLF can only probe one single wavelength at a time, we show that both wings of the Na line can nevertheless be compared. The varying line asymmetry can be interpreted as an upward plasma motion from the lower solar atmosphere during the peak of the flare, followed by a downward motion.Comment: 13 pages, 7 figure

TomograPy: A Fast, Instrument-Independent, Solar Tomography Software

Solar tomography has progressed rapidly in recent years thanks to the development of robust algorithms and the availability of more powerful computers. It can today provide crucial insights in solving issues related to the line-of-sight integration present in the data of solar imagers and coronagraphs. However, there remain challenges such as the increase of the available volume of data, the handling of the temporal evolution of the observed structures, and the heterogeneity of the data in multi-spacecraft studies. We present a generic software package that can perform fast tomographic inversions that scales linearly with the number of measurements, linearly with the length of the reconstruction cube (and not the number of voxels) and linearly with the number of cores and can use data from different sources and with a variety of physical models: TomograPy (http://nbarbey.github.com/TomograPy/), an open-source software freely available on the Python Package Index. For performance, TomograPy uses a parallelized-projection algorithm. It relies on the World Coordinate System standard to manage various data sources. A variety of inversion algorithms are provided to perform the tomographic-map estimation. A test suite is provided along with the code to ensure software quality. Since it makes use of the Siddon algorithm it is restricted to rectangular parallelepiped voxels but the spherical geometry of the corona can be handled through proper use of priors. We describe the main features of the code and show three practical examples of multi-spacecraft tomographic inversions using STEREO/EUVI and STEREO/COR1 data. Static and smoothly varying temporal evolution models are presented.Comment: 21 pages, 6 figures, 5 table

Salerno's model of DNA reanalysed: could solitons have biological significance?

We investigate the sequence-dependent behaviour of localised excitations in a toy, nonlinear model of DNA base-pair opening originally proposed by Salerno. Specifically we ask whether ``breather'' solitons could play a role in the facilitated location of promoters by RNA polymerase. In an effective potential formalism, we find excellent correlation between potential minima and {\em Escherichia coli} promoter recognition sites in the T7 bacteriophage genome. Evidence for a similar relationship between phage promoters and downstream coding regions is found and alternative reasons for links between AT richness and transcriptionally-significant sites are discussed. Consideration of the soliton energy of translocation provides a novel dynamical picture of sliding: steep potential gradients correspond to deterministic motion, while ``flat'' regions, corresponding to homogeneous AT or GC content, are governed by random, thermal motion. Finally we demonstrate an interesting equivalence between planar, breather solitons and the helical motion of a sliding protein ``particle'' about a bent DNA axis.Comment: Latex file 20 pages, 5 figures. Manuscript of paper to appear in J. Biol. Phys., accepted 02/09/0

Invariant higher-order variational problems II

Motivated by applications in computational anatomy, we consider a second-order problem in the calculus of variations on object manifolds that are acted upon by Lie groups of smooth invertible transformations. This problem leads to solution curves known as Riemannian cubics on object manifolds that are endowed with normal metrics. The prime examples of such object manifolds are the symmetric spaces. We characterize the class of cubics on object manifolds that can be lifted horizontally to cubics on the group of transformations. Conversely, we show that certain types of non-horizontal geodesics on the group of transformations project to cubics. Finally, we apply second-order Lagrange--Poincar\'e reduction to the problem of Riemannian cubics on the group of transformations. This leads to a reduced form of the equations that reveals the obstruction for the projection of a cubic on a transformation group to again be a cubic on its object manifold.Comment: 40 pages, 1 figure. First version -- comments welcome