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

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

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

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

Optimización del proceso kraft en maderas de Eucalyptus globulus

Se ha estudiado en maderas de E. globulus como afecta el factor H y la carga de álcali activo en cocción sobre la facilidad de la deslignificación, el contenido en carbohidratos y la eliminación de extractos de las pastas crudas obtenidas a un mismo nivel de lignina residual. Los resultados obtenidos mostraron que trabajar con bajas cargas de álcali activo y temperaturas en cocción más elevadas, aumenta el rendimiento de pasta en cocción y eliminan más sitosterol. Sin embargo, las blancuras más altas se obtienen trabajando con alta carga de álcali activo. Los xilanos son los compuestos más sensibles a la alta carga de álcali y se eliminan en gran extensión. Las pastas obtenidas con bajo álcali residual en cocción tienen mejor estallido y tracción pero peor drenabilidad, volumen, opacidad y porosidad.___________________________________This paper studies how H factor and active alkali loads in cooking affect E. globulus woods with regard to ease of delignification, carbohydrate content or removal of extractives. The results obtained demonstrated that working with low alkali loads and higher cooking temperatures increase pulp production and remove greater amounts of sitosterol. However, the greatest brightness is achieved by working with a high active alkali load. Xylans are the most sensitive compounds to high alkali loads and to a large extent are removed. Pulp produced with low residual alkali in the cooking stage has better burst index and tensile strength, but lower dewatering, bulk, opacity and air permeability

A Gene Encoding Arginyl-tRNA Synthetase Is Located in the Upstream Region of the lysA Gene in Brevibacterium lactofermentum: Regulation of argS-lysA Cluster Expression by Arginine

International audienceThe Brevibacterium lactofermentum argS gene, which encodes an arginyl-tRNA synthetase, was identified in the upstream region of the lysA gene. The cloned gene was sequenced; it encodes a 550-amino-acid protein with an Mr of 59,797. The deduced amino acid sequence showed 28% identical and 49% similar residues when compared with the sequence of the Escherichia coli arginyl-tRNA synthetase. The B. lactofermentum enzyme showed the highly conserved motifs of class I aminoacyl-tRNA synthetases. Expression of the argS gene in B. lactofermentum and E. coli resulted in an increase in aminoacyl-tRNA synthetase activity, correlated with the presence in sodium dodecyl sulfate-polyacrylamide gels of a clear protein band that corresponds to this enzyme. One single transcript of about 3,000 nucleotides and corresponding to the B. lactofermentum argS-lysA operon was identified. The transcription of these genes is repressed by lysine and induced by arginine, showing an interesting pattern of biosynthetic interlock between the pathways of both amino acids in corynebacteria

Transcriptome Metabolic Characterization of Tuber borchii SP1—A New Spanish Strain for In Vitro Studies of the Bianchetto Truffle

Truffles are ascomycete hypogeous fungi belonging to the Tuberaceae family of the Pezizales order that grow in ectomycorrhizal symbiosis with tree roots, and they are known for their peculiar aromas and flavors. The axenic culture of truffle mycelium is problematic because it is not possible in many cases, and the growth rate is meager when it is possible. This limitation has prompted searching and characterizing new strains that can be handled in laboratory conditions for basic and applied studies. In this work, a new strain of Tuber borchii (strain SP1) was isolated and cultured, and its transcriptome was analyzed under different in vitro culture conditions. The results showed that the highest growth of T. borchii SP1 was obtained using maltose-enriched cultures made with soft-agar and in static submerged cultures made at 22 °C. We analyzed the transcriptome of this strain cultured in different media to establish a framework for future comparative studies, paying particular attention to the central metabolic pathways, principal secondary metabolite gene clusters, and the genes involved in producing volatile aromatic compounds (VOCs). The results showed a transcription signal for around 80% of the annotated genes. In contrast, most of the transcription effort was concentrated on a limited number of genes (20% of genes account for 80% of the transcription), and the transcription profile of the central metabolism genes was similar in the different conditions analyzed. The gene expression profile suggests that T. borchii uses fermentative rather than respiratory metabolism in these cultures, even in aerobic conditions. Finally, there was a reduced expression of genes belonging to secondary metabolite clusters, whereas there was a significative transcription of those involved in producing volatile aromatic compounds

Comparative profiling identifies C13orf3 as a component of the Ska complex required for mammalian cell division

Proliferation of mammalian cells requires the coordinated function of many proteins to accurately divide a cell into two daughter cells. Several RNAi screens have identified previously uncharacterised genes that are implicated in mammalian cell division. The molecular function for these genes needs to be investigated to place them into pathways. Phenotypic profiling is a useful method to assign putative functions to uncharacterised genes. Here, we show that the analysis of protein localisation is useful to refine a phenotypic profile. We show the utility of this approach by defining a function of the previously uncharacterised gene C13orf3 during cell division. C13orf3 localises to centrosomes, the mitotic spindle, kinetochores, spindle midzone, and the cleavage furrow during cell division and is specifically phosphorylated during mitosis. Furthermore, C13orf3 is required for centrosome integrity and anaphase onset. Depletion by RNAi leads to mitotic arrest in metaphase with an activation of the spindle assembly checkpoint and loss of sister chromatid cohesion. Proteomic analyses identify C13orf3 (Ska3) as a new component of the Ska complex and show a direct interaction with a regulatory subunit of the protein phosphatase PP2A. All together, these data identify C13orf3 as an important factor for metaphase to anaphase progression and highlight the potential of combined RNAi screening and protein localisation analyses