Protein co-evolution, co-adaptation and interactions

Co-evolution has an important function in the evolution of species and it is clearly manifested in certain scenarios such as host–parasite and predator–prey interactions, symbiosis and mutualism. The extrapolation of the concepts and methodologies developed for the study of species co-evolution at the molecular level has prompted the development of a variety of computational methods able to predict protein interactions through the characteristics of co-evolution. Particularly successful have been those methods that predict interactions at the genomic level based on the detection of pairs of protein families with similar evolutionary histories (similarity of phylogenetic trees: mirrortree). Future advances in this field will require a better understanding of the molecular basis of the co-evolution of protein families. Thus, it will be important to decipher the molecular mechanisms underlying the similarity observed in phylogenetic trees of interacting proteins, distinguishing direct specific molecular interactions from other general functional constraints. In particular, it will be important to separate the effects of physical interactions within protein complexes (‘co-adaptation') from other forces that, in a less specific way, can also create general patterns of co-evolution

Testing outer boundary treatments for the Einstein equations

Various methods of treating outer boundaries in numerical relativity are compared using a simple test problem: a Schwarzschild black hole with an outgoing gravitational wave perturbation. Numerical solutions computed using different boundary treatments are compared to a `reference' numerical solution obtained by placing the outer boundary at a very large radius. For each boundary treatment, the full solutions including constraint violations and extracted gravitational waves are compared to those of the reference solution, thereby assessing the reflections caused by the artificial boundary. These tests use a first-order generalized harmonic formulation of the Einstein equations. Constraint-preserving boundary conditions for this system are reviewed, and an improved boundary condition on the gauge degrees of freedom is presented. Alternate boundary conditions evaluated here include freezing the incoming characteristic fields, Sommerfeld boundary conditions, and the constraint-preserving boundary conditions of Kreiss and Winicour. Rather different approaches to boundary treatments, such as sponge layers and spatial compactification, are also tested. Overall the best treatment found here combines boundary conditions that preserve the constraints, freeze the Newman-Penrose scalar Psi_0, and control gauge reflections.Comment: Modified to agree with version accepted for publication in Class. Quantum Gra

The action of obestatin in skeletal muscle repair: stem cell expansion, muscle growth, and microenvironment remodeling

The development of therapeutic strategies for skeletal muscle diseases, such as physical injuries and myopathies, depends on the knowledge of regulatory signals that control the myogenic process. The obestatin/GPR39 system operates as an autocrine signal in the regulation of skeletal myogenesis. Using a mouse model of skeletal muscle regeneration after injury and several cellular strategies, we explored the potential use of obestatin as a therapeutic agent for the treatment of trauma-induced muscle injuries. Our results evidenced that the overexpression of the preproghrelin, and thus obestatin, and GPR39 in skeletal muscle increased regeneration after muscle injury. More importantly, the intramuscular injection of obestatin significantly enhanced muscle regeneration by simulating satellite stem cell expansion as well as myofiber hypertrophy through a kinase hierarchy. Added to the myogenic action, the obestatin administration resulted in an increased expression of VEGF/VEGFR2 and the consequent microvascularization, with no effect on collagen deposition in skeletal muscle. Furthermore, the potential inhibition of myostatin during obestatin treatment might contribute to its myogenic action improving muscle growth and regeneration. Taken together, our data demonstrate successful improvement of muscle regeneration, indicating obestatin is a potential therapeutic agent for skeletal muscle injury and would benefit other myopathies related to muscle regeneration

Gravitational perturbations of Schwarzschild spacetime at null infinity and the hyperboloidal initial value problem

We study gravitational perturbations of Schwarzschild spacetime by solving a hyperboloidal initial value problem for the Bardeen-Press equation. Compactification along hyperboloidal surfaces in a scri-fixing gauge allows us to have access to the gravitational waveform at null infinity in a general setup. We argue that this hyperboloidal approach leads to a more accurate and efficient calculation of the radiation signal than the common approach where a timelike outer boundary is introduced. The method can be generalized to study perturbations of Kerr spacetime using the Teukolsky equation.Comment: 14 pages, 9 figure

Ultraefficient Thermophotovoltaic Power Conversion By Band-Edge Spectral Filtering

Thermophotovoltaic power conversion utilizes thermal radiation from a local heat source to generate electricity in a photovoltaic cell. It was shown in recent years that the addition of a highly reflective rear mirror to a solar cell maximizes the extraction of luminescence. This, in turn, boosts the voltage, enabling the creation of record-breaking solar efficiency. Now we report that the rear mirror can be used to create thermophotovoltaic systems with unprecedented high thermophotovoltaic efficiency. This mirror reflects low-energy infrared photons back into the heat source, recovering their energy. Therefore, the rear mirror serves a dual function; boosting the voltage and reusing infrared thermal photons. This allows the possibility of a practical \u3e50% efficient thermophotovoltaic system. Based on this reflective rear mirror concept, we report a thermophotovoltaic efficiency of 29.1 ± 0.4% at an emitter temperature of 1,207 °C

Three axis vector magnet set-up for cryogenic scanning probe microscopy

We describe a three axis vector magnet system for cryogenic scanning probe microscopy measurements. We discuss the magnet support system and the power supply, consisting of a compact three way 100 A current source. We obtain tilted magnetic fields in all directions with maximum value of 5T along z-axis and of 1.2T for XY-plane magnetic fields. We describe a scanning tunneling microscopy-spectroscopy (STM-STS) set-up, operating in a dilution refrigerator, which includes a new high voltage ultralow noise piezodrive electronics and discuss the noise level due to vibrations. STM images and STS maps show atomic resolution and the tilted vortex lattice at 150 mK in the superconductor β-Bi2Pd. We observe a strongly elongated hexagonal lattice, which corresponds to the projection of the tilted hexagonal vortex lattice on the surface. We also discuss Magnetic Force Microscopy images in a variable temperature insertThis work was supported by Convocatoria Doctorados en el Exterior 568-2012 COLCIENCIAS, the Spanish MINECO (FIS2011-23488, MAT2011-27470-C02-02, CSD2009-00013), by the Comunidad de Madrid through program Nanofrontmag-CM (S2013/MIT-2850) and by Marie-Curie actions under the project FP7-PEOPLE-2013- CIG-618321. The research leading to these results has received funding from the European Union Seventh Framework Programme under Grant Agreement No. 604391 Graphene Flagship. We also acknowledge Banco Santander, COST MP1201. J.A. and C.M. acknowledge the FPI (BES- 2012-058600) and Juan de la Cierva (JCI-2011-08815) programs, respectivel

Distribution, occurrence and biotoxin composition of the main

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Assessment of Arthrobacter viscosus as reactive medium for forming permeable reactive biobarrier applied to PAHs remediation

Polycyclic aromatic hydrocarbons (PAHs) are significant environmental contaminants as they are present naturally as well as anthropogenically in soil, air and water. In spite of their low solubility, PAHs are spread to the environment, and they are present in surface water, industrial effluent or groundwater. Amongst all remediation technologies for treating groundwater contaminated with PAHs, the use of a permeable reactive biobarrier (PRBB) appears to be the most cost-effective, energy efficient, and environmentally sound approach. In this technology, the microorganisms are used as reactive medium to degrade or stabilize the contaminants. The main limits of this approach are that the microorganisms or consortium used for forming the PRBB should show adequate characteristics. They must be retained in the barrier-forming biofilm, and they should also have degradative ability for the target pollutants. The aim of the present work is to evaluate the viability of Arthrobacter viscosus as bioreactive medium for forming PRBB. Initially, the ability of A. viscosus to remove PAHs, benzo[a]anthracene 100 μM and phenanthrene 100 μM was evaluated operating in a batch bench-scale bioreactor. In both cases, total benzo[a]anthracene and phenanthrene removals were obtained after 7 and 3 days, respectively. Furthermore, the viability of the microorganisms was evaluated in the presence of chromium in a continuous mode. As a final point, the adhesion of A. viscosus to sepiolite forming a bioreactive material to build PRBB was demonstrated. In view of the attained results, it can be concluded that A. viscosus could be a suitable microorganism to form a bioreactive medium for PAHs remediation.This work has been supported by the Spanish Ministry of Economy and Competitiveness and FEDER Funds (Project CTM 2011-25389). Marta Pazos received financial support under the Ramon y Cajal programme and Marta Cobas under the final project master grant "Campus do Mar Knowledge in depth"

Field testing for toxic algae with a microarray: initial results from the MIDTAL project

One of the key tasks in the project MIDTAL (MIcroarrays for the Detection of Toxic ALgae) is to demonstrate the applicability of microarrays to monitor harmful algae across a broad range of ecological niches and toxic species responsible for harmful algal events. Water samples are collected from a series of sites used in national phytoplankton and biotoxin monitoring programmes across Europe. The samples are filtered; the rRNA is extracted, labelled with a fluorescent dye and applied to a microarray chip. The signal intensity from >120 probes previously spotted on the chip is measured and analysed. Preliminary results comparing microarray signal intensities with actual field counts are presented