Ground temperatures, landforms and processes in an Atlantic mountain. Cantabrian Mountains (Northern Spain)

This research was supported by the Formación de Profesorado Universitario FPU13/05837 (Ministerio de Educación Cultura y Deporte) program, by the OAPN 053/2010 (Organismo Autónomo Parques Nacionales, MAGRAMA) project, by the I + D + I CGL2015-68144-R (Ministerio de Economia y Competitividad) project, by the Leverhulme Trust International Network Grant IN-2012-140 and the Royal Geographical Society Dudley Stamp Memorial Award.Peer reviewedPostprin

Molecular tools for breeding basidiomycetes

The industrial production of edible basidiomycetes is increasing every year as a response to the increasing public demand of them because of their nutritional properties. About a dozen of fungal species can be currently produced for food with sound industrial and economic bases. Notwithstanding, this production is threatened by biotic and abiotic factors that make it necessary to improve the fungal strains currently used in industry. Breeding of edible basidiomycetes, however, has been mainly empirical and slow since the genetic tools useful in the selection of the new genetic material to be introduced in the commercial strains have not been developed for these fungi as it was for other organisms. In this review we will discuss the main genetic factors that should be considered to develop breeding approaches and tools for higher basidiomycetes. These factors are (i) the genetic system controlling fungal mating; (ii) the genomic structure and organisation of these fungi; and (iii) the identification of genes involved in the control of quantitative traits. We will discuss the weight of these factors using the oyster mushroom Pleurotus ostreatus as a model organism for most of the edible fungi cultivated industrially

Docking glycosaminoglycans to proteins: analysis of solvent inclusion

Glycosaminoglycans (GAGs) are anionic polysaccharides, which participate in key processes in the extracellular matrix by interactions with protein targets. Due to their charged nature, accurate consideration of electrostatic and water-mediated interactions is indispensable for understanding GAGs binding properties. However, solvent is often overlooked in molecular recognition studies. Here we analyze the abundance of solvent in GAG-protein interfaces and investigate the challenges of adding explicit solvent in GAG-protein docking experiments. We observe PDB GAG-protein interfaces being significantly more hydrated than protein–protein interfaces. Furthermore, by applying molecular dynamics approaches we estimate that about half of GAG-protein interactions are water-mediated. With a dataset of eleven GAG-protein complexes we analyze how solvent inclusion affects Autodock 3, eHiTs, MOE and FlexX docking. We develop an approach to de novo place explicit solvent into the binding site prior to docking, which uses the GRID program to predict positions of waters and to locate possible areas of solvent displacement upon ligand binding. To investigate how solvent placement affects docking performance, we compare these results with those obtained by taking into account information about the solvent position in the crystal structure. In general, we observe that inclusion of solvent improves the results obtained with these methods. Our data show that Autodock 3 performs best, though it experiences difficulties to quantitatively reproduce experimental data on specificity of heparin/heparan sulfate disaccharides binding to IL-8. Our work highlights the current challenges of introducing solvent in protein-GAGs recognition studies, which is crucial for exploiting the full potential of these molecules for rational engineering

Geomatic methods applied to the change study of the la Paúl Rock Glacier, Spanish Pyrenees

Producción CientíficaRock glaciers are one of the most important features of the mountain permafrost in the Pyrenees. La Paúl is an active rock glacier located in the north face of the Posets massif in the La Paúl glacier cirque (Spanish Pyrenees). This study presents the preliminary results of the La Paúl rock glacier monitoring works carried out through two geomatic technologies since 2013: Global Navigation Satellite System (GNSS) receivers and Terrestrial Laser Scanning (TLS) devices. Displacements measured on the rock glacier surface have demonstrated both the activity of the rock glacier and the utility of this equipment for the rock glaciers dynamic analysis. The glacier has exhibited the fastest displacements on its west side (over 35 cm yr-1), affected by the Little Ice Age, and frontal area (over 25 cm yr-1). As an indicator of permafrost in marginal environments and its peculiar morphology, La Paúl rock glacier encourages a more prolonged study and to the application of more geomatic techniques for its detailed analysis.Ministerio de Economía, Industria y Competitividad - Fondo Europeo de Desarrollo Regional (project CGL2015-68144-R)Junta de Extremadura - Fondo Europeo de Desarrollo Regional (project GR10071

SCOWLP: a web-based database for detailed characterization and visualization of protein interfaces

BACKGROUND: Currently there is a strong need for methods that help to obtain an accurate description of protein interfaces in order to be able to understand the principles that govern molecular recognition and protein function. Many of the recent efforts to computationally identify and characterize protein networks extract protein interaction information at atomic resolution from the PDB. However, they pay none or little attention to small protein ligands and solvent. They are key components and mediators of protein interactions and fundamental for a complete description of protein interfaces. Interactome profiling requires the development of computational tools to extract and analyze protein-protein, protein-ligand and detailed solvent interaction information from the PDB in an automatic and comparative fashion. Adding this information to the existing one on protein-protein interactions will allow us to better understand protein interaction networks and protein function. DESCRIPTION: SCOWLP (Structural Characterization Of Water, Ligands and Proteins) is a user-friendly and publicly accessible web-based relational database for detailed characterization and visualization of the PDB protein interfaces. The SCOWLP database includes proteins, peptidic-ligands and interface water molecules as descriptors of protein interfaces. It contains currently 74,907 protein interfaces and 2,093,976 residue-residue interactions formed by 60,664 structural units (protein domains and peptidic-ligands) and their interacting solvent. The SCOWLP web-server allows detailed structural analysis and comparisons of protein interfaces at atomic level by text query of PDB codes and/or by navigating a SCOP-based tree. It includes a visualization tool to interactively display the interfaces and label interacting residues and interface solvent by atomic physicochemical properties. SCOWLP is automatically updated with every SCOP release. CONCLUSION: SCOWLP enriches substantially the description of protein interfaces by adding detailed interface information of peptidic-ligands and solvent to the existing protein-protein interaction databases. SCOWLP may be of interest to many structural bioinformaticians. It provides a platform for automatic global mapping of protein interfaces at atomic level, representing a useful tool for classification of protein interfaces, protein binding comparative studies, reconstruction of protein complexes and understanding protein networks. The web-server with the database and its additional summary tables used for our analysis are available at

Analysis of the impact of solvent on contacts prediction in proteins

<p>Abstract</p> <p>Background</p> <p>The correlated mutations concept is based on the assumption that interacting protein residues coevolve, so that a mutation in one of the interacting counterparts is compensated by a mutation in the other. Approaches based on this concept have been widely used for protein contacts prediction since the 90s. Previously, we have shown that water-mediated interactions play an important role in protein interfaces. We have observed that current "dry" correlated mutations approaches might not properly predict certain interactions in protein interfaces due to the fact that they are water-mediated.</p> <p>Results</p> <p>The goal of this study has been to analyze the impact of including solvent into the concept of correlated mutations. For this purpose we use linear combinations of the predictions obtained by the application of two different similarity matrices: a standard "dry" similarity matrix (DRY) and a "wet" similarity matrix (WET) derived from all water-mediated protein interfacial interactions in the PDB. We analyze two datasets containing 50 domains and 10 domain pairs from PFAM and compare the results obtained by using a combination of both matrices. We find that for both intra- and interdomain contacts predictions the introduction of a combination of a "wet" and a "dry" similarity matrix improves the predictions in comparison to the "dry" one alone.</p> <p>Conclusion</p> <p>Our analysis, despite the complexity of its possible general applicability, opens up that the consideration of water may have an impact on the improvement of the contact predictions obtained by correlated mutations approaches.</p

Discovery of Nigri/nox and Panto/pox site-specific recombinase systems facilitates advanced genome engineering

Precise genome engineering is instrumental for biomedical research and holds great promise for future therapeutic applications. Site-specific recombinases (SSRs) are valuable tools for genome engineering due to their exceptional ability to mediate precise excision, integration and inversion of genomic DNA in living systems. The ever-increasing complexity of genome manipulations and the desire to understand the DNA-binding specificity of these enzymes are driving efforts to identify novel SSR systems with unique properties. Here, we describe two novel tyrosine site-specific recombination systems designated Nigri/nox and Panto/pox. Nigri originates from Vibrio nigripulchritudo (plasmid VIBNI_pA) and recombines its target site nox with high efficiency and high target-site selectivity, without recombining target sites of the well established SSRs Cre, Dre, Vika and VCre. Panto, derived from Pantoea sp. alpha B, is less specific and in addition to its native target site, pox also recombines the target site for Dre recombinase, called rox. This relaxed specificity allowed the identification of residues that are involved in target site selectivity, thereby advancing our understanding of how SSRs recognize their respective DNA targets

Introducción de una etapa ácida en la secuencia TCF

El oxígeno y el peróxido no son capaces de eliminar los ácidos hexenurónicos (HexA) en gran extensión, por lo que las pastas TCF de mercado blanqueadas con la secuencia Q-POP, tienen alta reversión. La introducción de una etapa ácida A-Q-POP en la secuencia actual, mediante la adición de ácido fórmico y ácido sulfúrico para conseguir un pH final 3,0-3,5, elimina los HexA significativamente. En este trabajo la etapa ácida se llevó a cabo a temperaturas elevadas 110-115ºC. Los mejores resultados se obtuvieron a 115ºC y una hora de tiempo de retención. En estas condiciones se consigue un índice kappa final de 2,0, un nivel de HexA de 6,0 mEq/kg y una reversión de blancura de solo el 9,4 % tras envejecimiento en cámara climática a 80ºC y 65%HR durante 48 h. Las pastas obtenidas tienen menor índice de tracción pero mejor desgote, permeabilidad al aire y opacidad.____________________________________To a large extent, oxygen and peroxide stages are unable to remove hexenuronic acids (HexA), so that bleached TCF market pulps, using a Q-POP sequence, have high reversion. The introduction of an acid stage by adding formic acid and sulphuric acid at a pH of 3,0 – 3,5 improves selectivity and removes a significant amount of HexA. Optimum conditions were seen to be 115ºC and a retention time of 1 hour. Such conditions were able to produce a final Kappa number of 2,0, a HexA level of 6,0 mEq/kg, and a reversion in controlled-climate chamber of only 9,4%. The pulp thus produced had lower tensile strength, but also greater dewatering, air permeability and opacity