Multiprotein DNA looping

DNA looping plays a fundamental role in a wide variety of biological processes, providing the backbone for long range interactions on DNA. Here we develop the first model for DNA looping by an arbitrarily large number of proteins and solve it analytically in the case of identical binding. We uncover a switch-like transition between looped and unlooped phases and identify the key parameters that control this transition. Our results establish the basis for the quantitative understanding of fundamental cellular processes like DNA recombination, gene silencing, and telomere maintenance.Comment: 11 pages, 4 figure

Conservation Laws in Smooth Particle Hydrodynamics: the DEVA Code

We describe DEVA, a multistep AP3M-like-SPH code particularly designed to study galaxy formation and evolution in connection with the global cosmological model. This code uses a formulation of SPH equations which ensures both energy and entropy conservation by including the so-called \bn h terms. Particular attention has also been paid to angular momentum conservation and to the accuracy of our code. We find that, in order to avoid unphysical solutions, our code requires that cooling processes must be implemented in a non-multistep way. We detail various cosmological simulations which have been performed to test our code and also to study the influence of the \bn h terms. Our results indicate that such correction terms have a non-negligible effect on some cosmological simulations, especially on high density regions associated either to shock fronts or central cores of collapsed objects. Moreover, they suggest that codes paying a particular attention to the implementation of conservation laws of physics at the scales of interest, can attain good accuracy levels in conservation laws with limited computational resources.Comment: 36 pages, 10 figures. Accepted for publication in The Astrophysical Journa

Variations in soil chemical and physical properties explain basin-wide Amazon forest soil carbon concentrations

We investigate the edaphic, mineralogical and climatic controls of soil organic carbon (SOC) concentration utilising data from 147 primary forest soils (0–30 cm depth) sampled in eight different countries across the Amazon Basin. Sampled across 14 different World Reference Base soil groups, our data suggest that stabilisation mechanism varies with pedogenetic level. Specifically, although SOC concentrations in Ferralsols and Acrisols were best explained by simple variations in clay content – this presumably being due to their relatively uniform kaolinitic mineralogy – this was not the case for less weathered soils such as Alisols, Cambisols and Plinthosols for which interactions between Al species, soil pH and litter quality are argued to be much more important. Although for more strongly weathered soils the majority of SOC is located within the aggregate fraction, for the less weathered soils most of the SOC is located within the silt and clay fractions. It thus seems that for highly weathered soils SOC storage is mostly influenced by surface area variations arising from clay content, with physical protection inside aggregates rendering an additional level of protection against decomposition. On the other hand, most of the SOC in less weathered soils is associated with the precipitation of aluminium–carbon complexes within the fine soil fraction, with this mechanism enhanced by the presence of high levels of aromatic, carboxyl-rich organic matter compounds. Also examined as part of this study were a relatively small number of arenic soils (viz. Arenosols and Podzols) for which there was a small but significant influence of clay and silt content variations on SOM storage, with fractionation studies showing that particulate organic matter may account for up to 0.60 of arenic soil SOC. In contrast to what were in all cases strong influences of soil and/or litter quality properties, after accounting for these effects neither wood productivity, above-ground biomass nor precipitation/temperature variations were found to exert any significant influence on SOC stocks. These results have important implications for our understanding of how Amazon forest soils are likely to respond to ongoing and future climate changes

A Multilayer Approach to Fabricate Bioactive Glass Coatings on Ti Alloys

Glasses in the system Si-Ca-Na-Mg-P-K-O with thermal expansion coefficients close to that of Ti6Al4V were used to coat the titanium alloy by a simple enameling technique. Firings were done in air at temperatures between 800 and 840 C and times up to 1 minute. Graded compositions were obtained by firing multilayered glass coatings. Hydroxyapatite (HA) particles were mixed with the glass powder and the mixture was placed on the outer surface of the coatings to render them more bioactive. Coatings with excellent adhesion to the substrate and able to form apatite when immersed in a simulated body fluid (SBF) can be fabricated by this methodology

The Spanish SpaceWeather Service SeNMEs. A Case Study on the Sun-Earth Chain

Comunicación presentada en el Coimbra Solar Physics Meeting, 5-9 October 2015, Coimbra, PortugalThe Spanish Space Weather Service SeNMEs, www.senmes.es, is a portal created by the SRG-SW of the Universidad de Alcalá, Spain, to meet societal needs of near real-time space weather services. This webpage-portal is divided in different sections to fulfill users needs about space weather effects: radio blackouts, solar energetic particle events, geomagnetic storms and presence of geomagnetically induced currents. In less than one year of activity, this service has released a daily report concerning the solar current status and interplanetary medium, informing about the chances of a solar perturbation to hit the Earth’s environment. There are also two different forecasting tools for geomagnetic storms, and a daily ionospheric map. These tools allow us to nowcast a variety of solar eruptive events and forecast geomagnetic storms and their recovery, including a new local geomagnetic index, LDiñ, along with some specific new scaling. In this paper we also include a case study analysed by SeNMEs. Using different high resolution and cadence data from space-borne solar telescopes SDO, SOHO and GOES, along with ionospheric and geomagnetic data, we describe the Sun-Earth feature chain for the event.MINECO project AYA2013-47735PPeer reviewe

wild birds in Serbia during 2012: first isolation and characterisation of WNV strains from Serbia

Monitoring West Nile virus (WNV) infection i

The influence of C3 and C4 vegetation on soil organic matter dynamics in contrasting semi-natural tropical ecosystems

This is a freely-available open access publication. Please cite the published version which is available via the DOI link in this record.Variations in the carbon isotopic composition of soil organic matter (SOM) in bulk and fractionated samples were used to assess the influence of C3 and C4 vegetation on SOM dynamics in semi-natural tropical ecosystems sampled along a precipitation gradient in West Africa. Differential patterns in SOM dynamics in C3/C4 mixed ecosystems occurred at various spatial scales. Relative changes in C/ N ratios between two contrasting SOM fractions were used to evaluate potential site-scale differences in SOM dynamics between C3- and C4-dominated locations. These differences were strongly controlled by soil texture across the precipitation gradient, with a function driven by bulk δ 13C and sand content explaining 0.63 of the observed variability. The variation of δ 13C with soil depth indicated a greater accumulation of C3-derived carbon with increasing precipitation, with this trend also being strongly dependant on soil characteristics. The influence of vegetation thickening on SOM dynamics was also assessed in two adjacent, but structurally contrasting, transitional ecosystems occurring on comparable soils to minimise the confounding effects posed by climatic and edaphic factors. Radiocarbon analyses of sand-size aggregates yielded relatively short mean residence times (τ ) even in deep soil layers, while the most stable SOM fraction associated with silt and clay exhibited shorter τ in the savanna woodland than in the neighbouring forest stand. These results, together with the vertical variation observed in δ 13C values, strongly suggest that both ecosystems are undergoing a rapid transition towards denser closed canopy formations. However, vegetation thickening varied in intensity at each site and exerted contrasting effects on SOM dynamics. This study shows that the interdependence between biotic and abiotic factors ultimately determine whether SOM dynamics of Published by Copernicus Publications on behalf of the European Geosciences Union. 5042 G. Saiz et al.: Influence of C3/C4 on SOM in tropical biomes C3- and C4-derived vegetation are at variance in ecosystems where both vegetation types coexist. The results highlight the far-reaching implications that vegetation thickening may have for the stability of deep SOM.UK National Environment Research CouncilAustralian Institute of Nuclear Science and Engineering (AINSE Ltd

Observation of inhibited electron-ion coupling in strongly heated graphite

Creating non-equilibrium states of matter with highly unequal electron and lattice temperatures (Tele≠Tion) allows unsurpassed insight into the dynamic coupling between electrons and ions through time-resolved energy relaxation measurements. Recent studies on low-temperature laser-heated graphite suggest a complex energy exchange when compared to other materials. To avoid problems related to surface preparation, crystal quality and poor understanding of the energy deposition and transport mechanisms, we apply a different energy deposition mechanism, via laser-accelerated protons, to isochorically and non-radiatively heat macroscopic graphite samples up to temperatures close to the melting threshold. Using time-resolved x ray diffraction, we show clear evidence of a very small electron-ion energy transfer, yielding approximately three times longer relaxation times than previously reported. This is indicative of the existence of an energy transfer bottleneck in non-equilibrium warm dense matter