HuR biological function involves RRM3-mediated dimerization and RNA binding by all three RRMs

HuR/ELAVL1 is an RNA-binding protein involved in differentiation and stress response that acts primarily by stabilizing messenger RNA (mRNA) targets. HuR comprises three RNA recognition motifs (RRMs) where the structure and RNA binding of RRM3 and of full-length HuR remain poorly understood. Here, we report crystal structures of RRM3 free and bound to cognate RNAs. Our structural, NMR and biochemical data show that RRM3 mediates canonical RNA interactions and reveal molecular details of a dimerization interface localized on the α-helical face of RRM3. NMR and SAXS analyses indicate that the three RRMs in full-length HuR are flexibly connected in the absence of RNA, while they adopt a more compact arrangement when bound to RNA. Based on these data and crystal structures of tandem RRM1,2-RNA and our RRM3-RNA complexes, we present a structural model of RNA recognition involving all three RRM domains of full-length HuR. Mutational analysis demonstrates that RRM3 dimerization and RNA binding is required for functional activity of full-length HuR in vitro and to regulate target mRNAs levels in human cells, thus providing a fine-tuning for HuR activity in vivo.España, MINECO BFU2015-71017España, Junta de Andalucía CVI-BIO198; P11-CVI7216 to I.D.M

Wetting phenomenon in the liquid-vapor phase coexistence of a partially miscible Lennard-Jones binary mixture

We have carried out extensive equilibrium molecular dynamics (MD) simulations to study the structure and the interfacial properties in the liquid-vapor (LV) phase coexistence of partially miscible binary Lennard-Jones (LJ) mixtures. By analyzing the structural properties as a function of the miscibility parameter, $\alpha$, we found that at relatively low temperatures the system separates forming a liquid A-liquid B interface in coexistence with the vapor phase. At higher temperatures and, $0<\alpha\leq 0.5$, we found a temperature range, $T^{*}_{w}(\alpha) \leq T^{*} < T^{*}_{cons}(\alpha)$, where the liquid phases are wet by the vapor phase. Here, $T^{*}_{w}(\alpha)$ represents the wetting transition temperature (WTT) and $T^{*}_{cons}(\alpha)$ is the consolute temperature of the mixture. However, for $0.5< \alpha < 1$, no wetting phenomenon occurs. For the particular value, $\alpha=0.25$, we analyzed quantitatively the $T^{*}$ versus $\rho^{*}$, and $P^{*}$ versus $T^{*}$ phase diagrams and found, $T^{*}_{c}\simeq 1.25$, and $T^{*}_{cons}\simeq1.25$. We also studied quantitatively, as a function of temperature, the surface tension and the adsorption of molecules at the liquid-liquid interface. It was found that the adsorption shows a jump from a finite negative value up to minus infinity, when the vapor wets the liquid phases, suggesting that the wetting transition (WT) is of first order. The calculated phase diagram together with the wetting phenomenon strongly suggest the existence of a tricritical point. These results agree well with some experiments carried out in fluid binary mixtures.Comment: Enlarged version that include results of more extensive simulations. A total of 24 LaTeX pages that include 12 encapsulated poscript figures. To appear in PRE, Vol. 70, issue Sept. 1st (2004

Synchronization in Random Geometric Graphs

In this paper we study the synchronization properties of random geometric graphs. We show that the onset of synchronization takes place roughly at the same value of the order parameter that a random graph with the same size and average connectivity. However, the dependence of the order parameter with the coupling strength indicates that the fully synchronized state is more easily attained in random graphs. We next focus on the complete synchronized state and show that this state is less stable for random geometric graphs than for other kinds of complex networks. Finally, a rewiring mechanism is proposed as a way to improve the stability of the fully synchronized state as well as to lower the value of the coupling strength at which it is achieved. Our work has important implications for the synchronization of wireless networks, and should provide valuable insights for the development and deployment of more efficient and robust distributed synchronization protocols for these systems.Comment: 5 pages, 4 figure

High-trhoughput screening of cytochrome C novel partners chlamydomonas ReindhartII

Comunicaciones a congreso

Diffusion dynamics on multiplex networks

We study the time scales associated to diffusion processes that take place on multiplex networks, i.e. on a set of networks linked through interconnected layers. To this end, we propose the construction of a supra-Laplacian matrix, which consists of a dimensional lifting of the Laplacian matrix of each layer of the multiplex network. We use perturbative analysis to reveal analytically the structure of eigenvectors and eigenvalues of the complete network in terms of the spectral properties of the individual layers. The spectrum of the supra-Laplacian allows us to understand the physics of diffusion-like processes on top of multiplex networks.Comment: 6 Pages including supplemental material. To appear in Physical Review Letter

The hydration structure of Cu2+: More tetrahedral than octahedral?

A comprehensive multi-technique approach has been used to address the controversial question of the preferred geometric form of the Cu2+ aqua-ion hydration shell. A combination of H/D isotopic substitution neutron scattering and X-ray scattering has been used to refine atomistic models of 0.5 m and 2.0 m solutions of Cu(ClO4)2, that have also been constrained to simultaneously reproduce detailed local structure information about the cation environment obtained by X-ray Absorption spectroscopy. The adoption of the Empirical Potential Structure Refinement (EPSR) technique as a single unified analytical framework minimises the chances for biasing the result in favour of a specific pre-conceived outcome. The results are consistent with an average coordination for each Cu2+ ion of 4.5 ± 0.6 water molecules that matches the more recent picture of five-fold coordination in a 2.0 m solution, but interestingly this combined study highlights that the preferred local geometry of the ion sites is found to have a mixed character of tetrahedral, trigonal bipyramidal and octahedral components. A further point to note is that this new model adds support to a largely ignored result in the literature relating to the linear electric field effect induced g-shifts observed in the electron paramagnetic resonance spectra of glassy Cu2+ complexes (Peisach and Mims, Chem. Phys. Lett., 1976, 37, 307–310) that first highlighted the importance of tetrahedral distortions in the cation's hydration shell structure

El contacto entre las zonas de Ossa Morena y Sudportuguesa. Características y significado de la banda metamórfica de Aracena, en su sector central entre Aroche y Aracena (Huelva)

El contacto entre las zonas de Ossa Morena y Sudportuguesa está subrayado por la banda metamórfica de Aracena. Las características principales de esta región del macizo Ibérico pueden considerarse desde distintos puntos de vista: litológico, estructural, metamórfico, magmático, geoquímica, isotópico y experimental, y así se presentan en este artículo. La banda metamórfica de Aracena está dividida en dos dominios principales: el dominio oceánico está formado por metabasitas derivadas de un MORB (las metabasitas de Acebuches) y por un antiguo prisma de acrección. El dominio continental incluye gneises y migmatitas alumínicos, rocas de silicatos cálcicos, gneises leucocráticos, mármoles, anfibolitas, intrusiones sin/post-tectónicas de noritas ricas en Mg (con afinidad boninítica), así como rocas intrusivas post-tectónicas de composición ácida a básica. Las metabasitas de Acebuches sufrieron, en primer lugar, un metamorfismo de alta temperatura/baja presión que, en la actualidad, presenta un gradiente metamórfico invertido, y que estaba relacionado con un cabalgamiento vergente al SO. El pico térmico asociado a este evento metamórfico muestra un gradiente de edad, de forma que las edades más antiguas han sido obtenidas en el extremo oeste. La mitad inferior de la pila metabasítica de Acebuches fue afectada posteriormente por una deformación milonítica y un retrometamorfismo asociados a la zona de cizalla Sudibérica. Cuatro fases de deformación dúctil han sido definidas en el dominio continental: la fase CD-D1 estuvo relacionada con la generación de pliegues recumbentes de escala kilométrica. La fase CD-D2 se puede asociar a un colapso extensional, y es contemporánea con un metamorfismo de alta temperatura/baja presión que afectó al dominio continental y generó diversos complejos migmatíticos. La fase CD-D3 produjo pliegues simétricos verticales, mientras que la fase CD-D4 dio lugar a cabalgamientos vergentes al sur a los que se asociaron pliegues de propagación.Las principales características de la banda metamórfica de Aracena se interpretan como el resultado de la evolución de un punto triple de tipo fosa-fosa-dorsal. De acuerdo con el modelo propuesto, la interacción entre la dorsal y la zona de subducción dio como resultado la formación de una ventana astenosférica bajo el margen continental cabalgante, lo cual provocó el ascenso de la astenosfera y el consecuente rebote térmico. Esta unión triple migro a lo largo del margen continental hacia el este, lo que generó un cinturón metamórfico de alta temperatura/baja presión en el contacto entre las zonas de Ossa Morena y Sudportuguesa

Heat-pulse measurements of sap flow in olives for automating irrigation: tests, root flow and diagnostics of water stress

26 páginas, 10 figuras, 1 tabla, 32 referencias.-- [email protected] compensation heat-pulse method for measuring sap flow is tested here in olive trees (Olea europaea L.). We describe a rigorous three-way examination of the robustness of the technique for this species, and examine the potential of the technique for an automatic control of the irrigation system. Two tests were carried out using heat-pulse gear inserted into the stem of 12-year-old ‘Manzanilla’ olive trees. One test used forced-flow through a stem section, and the other involved measured water uptake by an excised tree. The measured sap flow in these two tests was in agreement with calculations from heat-pulse velocities when using a standard ‘wound correction’ to account for the presence of the probes and the disruption to the sap flow. Thus, this technique for monitoring transpiration can, we feel, be used with confidence in olives. The third experiment was carried out in the field, where we analysed sap flow data from two 29- year-old olive trees—one tree was under regular drip irrigation and the other was from dry-farming conditions. We use measurements of sap flow in the trunk to examine the hydraulic functioning of the tree, and to explore some diagnostics of water stress. Our heat-pulse measurements in the irrigated olive tree exhibited a profile of sap flow that was weighted towards the outer xylem of the tree trunk while the water-stressed trees in the field showed a profile of sap flow weighted towards the centre of the trunk. The loss of hydraulic functioning in the outermost section of the vascular system, as a result of water stress, we consider to be due both to stomatal control and to embolisms in the xylem vessels. The fourth experiment was also carried out in the field, in which sap flow measurements were made at three locations in the trunk as well as in two roots of another 29-year-old olive tree. The soil explored by each root, on opposite sides of the trunk, was differentially wetted by separate irrigation of each side. Our data showed that the surface roots were able to absorb water immediately after wetting, despite a reasonably prolonged period of moderate drought. Root activity quickly shifted to the regions where the soil had been wetted. A root in dry soil exhibited no flow at night, whereas sap flows of about 0.02 l h 1 were measured around midnight in the root drawing water from the wetter soil. Our observations suggest that the hydraulic behaviour of the trunk and surface roots might be used as a diagnostic of the onset, or severity, of water stress. Here there is not the imperative to replicate, for the prime goal is not transpiration estimation. Rather interpretation of the diurnal dynamics is used to infer the onset, or severity of water stress. The compensation heat-pulse seems a suitable technique for automatically controlling the irrigation system of olives, and probably other trees, based either on the estimation of the short-time dynamics of transpiration, or on changes in the hydraulic behaviour of the trees.The Comisión Interministerial de Ciencia y Tecnología of the Spanish Ministry of Education and Science financial support this project.Peer reviewe

Heat-pulse measurements of sap flow in olives for automating irrigation: tests, root flow and diagnostics of water stress

26 páginas, 10 figuras, 1 tabla, 32 referencias.-- [email protected] compensation heat-pulse method for measuring sap flow is tested here in olive trees (Olea europaea L.). We describe a rigorous three-way examination of the robustness of the technique for this species, and examine the potential of the technique for an automatic control of the irrigation system. Two tests were carried out using heat-pulse gear inserted into the stem of 12-year-old ‘Manzanilla’ olive trees. One test used forced-flow through a stem section, and the other involved measured water uptake by an excised tree. The measured sap flow in these two tests was in agreement with calculations from heat-pulse velocities when using a standard ‘wound correction’ to account for the presence of the probes and the disruption to the sap flow. Thus, this technique for monitoring transpiration can, we feel, be used with confidence in olives. The third experiment was carried out in the field, where we analysed sap flow data from two 29- year-old olive trees—one tree was under regular drip irrigation and the other was from dry-farming conditions. We use measurements of sap flow in the trunk to examine the hydraulic functioning of the tree, and to explore some diagnostics of water stress. Our heat-pulse measurements in the irrigated olive tree exhibited a profile of sap flow that was weighted towards the outer xylem of the tree trunk while the water-stressed trees in the field showed a profile of sap flow weighted towards the centre of the trunk. The loss of hydraulic functioning in the outermost section of the vascular system, as a result of water stress, we consider to be due both to stomatal control and to embolisms in the xylem vessels. The fourth experiment was also carried out in the field, in which sap flow measurements were made at three locations in the trunk as well as in two roots of another 29-year-old olive tree. The soil explored by each root, on opposite sides of the trunk, was differentially wetted by separate irrigation of each side. Our data showed that the surface roots were able to absorb water immediately after wetting, despite a reasonably prolonged period of moderate drought. Root activity quickly shifted to the regions where the soil had been wetted. A root in dry soil exhibited no flow at night, whereas sap flows of about 0.02 l h 1 were measured around midnight in the root drawing water from the wetter soil. Our observations suggest that the hydraulic behaviour of the trunk and surface roots might be used as a diagnostic of the onset, or severity, of water stress. Here there is not the imperative to replicate, for the prime goal is not transpiration estimation. Rather interpretation of the diurnal dynamics is used to infer the onset, or severity of water stress. The compensation heat-pulse seems a suitable technique for automatically controlling the irrigation system of olives, and probably other trees, based either on the estimation of the short-time dynamics of transpiration, or on changes in the hydraulic behaviour of the trees.The Comisión Interministerial de Ciencia y Tecnología of the Spanish Ministry of Education and Science financial support this project.Peer reviewe

Cytochrome c speeds up caspase cascade activation by blocking 14-3-3¿-dependent Apaf-1 inhibition article

Apoptosis is a highly regulated form of programmed cell death, essential to the development and homeostasis of multicellular organisms. Cytochrome c is a central figure in the activation of the apoptotic intrinsic pathway, thereby activating the caspase cascade through its interaction with Apaf-1. Our recent studies have revealed 14-3-3€ (a direct inhibitor of Apaf-1) as a cytosolic cytochrome c target. Here we explore the cytochrome c / 14-3-3€ interaction and show the ability of cytochrome c to block 14-3-3€-mediated Apaf-1 inhibition, thereby unveiling a novel function for cytochrome c as an indirect activator of caspase-9/3. We have used calorimetry, NMR spectroscopy, site mutagenesis and computational calculations to provide an insight into the structural features of the cytochrome c / 14-3-3€ complex. Overall, these findings suggest an additional cytochrome c-mediated mechanism to modulate apoptosome formation, shedding light onto the rigorous apoptotic regulation network