ALBERT

Description: The CRISPR/Cas technology is enabling targeted genome editing in multiple organisms with unprecedented accuracy and specificity by using RNA-guided nucleases. A critical point when planning a CRISPR/Cas experiment is the design of the guide RNA (gRNA), which directs the nuclease and associated machinery to the desired genomic location. This gRNA has to fulfil the requirements of the nuclease and lack homology with other genome sites that could lead to off-target effects. Here we introduce the Breaking-Cas system for the design of gRNAs for CRISPR/Cas experiments, including those based in the Cas9 nuclease as well as others recently introduced. The server has unique features not available in other tools, including the possibility of using all eukaryotic genomes available in ENSEMBL (currently around 700), placing variable PAM sequences at 5' or 3' and setting the guide RNA length and the scores per nucleotides. It can be freely accessed at: http://bioinfogp.cnb.csic.es/tools/breakingcas , and the code is available upon request.

Description: Metabolites Biological Role (MBROLE) is a server that performs functional enrichment analysis of a list of chemical compounds derived from a metabolomics experiment, which allows this list to be interpreted in biological terms. Since its release in 2011, MBROLE has been used by different groups worldwide to analyse metabolomics experiments from a variety of organisms. Here we present the latest version of the system, MBROLE2, accessible at http://csbg.cnb.csic.es/mbrole2 . MBROLE2 has been supplemented with 10 databases not available in the previous version, which allow analysis over a larger, richer set of vocabularies including metabolite–protein and drug–protein interactions. This new version performs automatic conversion of compound identifiers from different databases, thus simplifying usage. In addition, the user interface has been redesigned to generate an interactive, more intuitive representation of the results.

Description: Motivation : Many diseases are related by shared associated molecules and pathways, exhibiting comorbidities and common phenotypes, an indication of the continuous nature of the human pathological landscape. Although it is continuous, this landscape is always partitioned into discrete diseases when studied at the molecular level. Clinical signs are also important phenotypic descriptors that can reveal the molecular mechanisms that underlie pathological states, but have seldom been the subject of systemic research. Here, we quantify the modular nature of the clinical signs associated with genetic diseases in the human interactome. Results : We found that clinical signs are reflected as modules at the molecular network level, to at least to the same extent as diseases. They can thus serve as a valid complementary partition of the human pathological landscape, with implications for etiology research, diagnosis and treatment. Contact: monica.chagoyen@cnb.csic.es Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Motivation: The evolution of proteins cannot be fully understood without taking into account the coevolutionary linkages entangling them. From a practical point of view, coevolution between protein families has been used as a way of detecting protein interactions and functional relationships from genomic information. The most common approach to inferring protein coevolution involves the quantification of phylogenetic tree similarity using a family of methodologies termed mirrortree. In spite of their success, a fundamental problem of these approaches is the lack of an adequate statistical framework to assess the significance of a given coevolutionary score (tree similarity). As a consequence, a number of ad hoc filters and arbitrary thresholds are required in an attempt to obtain a final set of confident coevolutionary signals. Results: In this work, we developed a method for associating confidence estimators ( P values) to the tree-similarity scores, using a null model specifically designed for the tree comparison problem. We show how this approach largely improves the quality and coverage (number of pairs that can be evaluated) of the detected coevolution in all the stages of the mirrortree workflow, independently of the starting genomic information. This not only leads to a better understanding of protein coevolution and its biological implications, but also to obtain a highly reliable and comprehensive network of predicted interactions, as well as information on the substructure of macromolecular complexes using only genomic information. Availability and implementation: The software and datasets used in this work are freely available at: http://csbg.cnb.csic.es/pMT/ . Contact: pazos@cnb.csic.es Supplementary Information: Supplementary data are available at Bioinformatics online.

Description: Determining the residues that are important for the molecular activity of a protein is a topic of broad interest in biomedicine and biotechnology. This knowledge can help understanding the protein’s molecular mechanism as well as to fine-tune its natural function eventually with biotechnological or therapeutic implications. Some of the protein residues are essential for the function common to all members of a family of proteins, while others explain the particular specificities of certain subfamilies (like binding on different substrates or cofactors and distinct binding affinities). Owing to the difficulty in experimentally determining them, a number of computational methods were developed to detect these functional residues, generally known as ‘specificity-determining positions’ (or SDPs), from a collection of homologous protein sequences. These methods are mature enough for being routinely used by molecular biologists in directing experiments aimed at getting insight into the functional specificity of a family of proteins and eventually modifying it. In this review, we summarize some of the recent discoveries achieved through SDP computational identification in a number of relevant protein families, as well as the main approaches and software tools available to perform this type of analysis.

Description: Although ecologists and managers have been increasingly preoccupied with the crowding consequences of overabundant herbivores, the potential role of territorial behavior as a self-regulatory agent has seldom been considered. The crowding mechanism underlies most regulation models in ungulate demography and relies on the assumption of an equal share of available supplies among individuals. In contrast, in territorial systems dominant individuals monopolize resources, predicting deviations from the expected demographic outcomes under the crowding approach. We used empirical data on a protected guanaco ( Lama guanicoe ) population to test competing hypotheses about crowding and territorial defense as the mechanism driving density regulation in a resource-defense polygyny ungulate. We assessed density dependence on recruitment at different spatial scales and density effects on preferred forage availability. The guanaco density inside the reserve increased rapidly and then stabilized during the last third of the study period. The absence of density effects on recruitment questions the existence of crowding mechanisms. Guanaco numbers stabilized below the environmental carrying capacity predicted by an equal share of available forage, supporting territorial defense as the mechanism shaping population density in the area. Variability in forage cover was independent from changes in population density, rejecting crowding effects on food supplies. These results are consistent with the hypothesis of a self-regulatory mechanism derived from resource defense that may prevent overgrazing. Our findings suggest that other factors in addition to food availability may determine the demographic carrying capacity under resource defense systems, stressing the importance of accounting for behavioral traits when addressing management issues.

Description: The Gibraltar arc and surrounding areas are a complex tectonic region and its tectonic evolution since Miocene is still under debate. Knowledge of its lithospheric structure will help to understand the mechanisms that produced extension and westward motion of the Alboran domain, simultaneously with NW–SE compression driven by Africa–Europe plates convergence. We perform a P -wave receiver function analysis in which we analyse new data recorded at 83 permanent and temporary seismic broad-band stations located in the South of the Iberian peninsula. These data are stacked and combined with data from a previous study in northern Morocco to build maps of thickness and average v P / v S ratio for the crust, and cross-sections to image the lithospheric discontinuities beneath the Gibraltar arc, the Betic and Rif Ranges and their Iberian and Moroccan forelands. Crustal thickness values show strong lateral variations in the southern Iberia peninsula, ranging from ~19 to ~46 km. The Variscan foreland is characterized by a relatively flat Moho at ~31 km depth, and an average v P / v S ratio of ~1.72, similar to other Variscan terranes, which may indicate that part of the lower crustal orogenic root was lost. The thickest crust is found at the contact between the Alboran domain and the External Zones of the Betic Range, while crustal thinning is observed southeastern Iberia (down to 19 km) and in the Guadalquivir basin where the thinning at the Iberian paleomargin could be still preserved. In the cross-sections, we see a strong change between the eastern Betics, where the Iberian crust underthrusts and couples to the Alboran crust, and the western Betics, where the underthrusting Iberian crust becomes partially delaminated and enters into the mantle. The structures largely mirror those on the Moroccan side where a similar detachment was observed in northern Morocco. We attribute a relatively shallow strong negative-polarity discontinuity to the lithosphere-asthenosphere boundary. This means relatively thin lithosphere ranging from ~50 km thickness in southeastern Iberia and northeastern Morocco to ~90–100 km beneath the western Betics and the Rif, with abrupt changes of ~30 km under the central Betics and northern Morocco. Our observations support a geodynamic scenario where in western Betics oceanic subduction has developed into ongoing continental subduction/delamination while in eastern Betics this process is inactive.

Description: Daily work in molecular biology presently depends on a large number of computational tools. An in-depth, large-scale study of that ‘ecosystem’ of Web tools, its characteristics, interconnectivity, patterns of usage/citation, temporal evolution and rate of decay is crucial for understanding the forces that shape it and for informing initiatives aimed at its funding, long-term maintenance and improvement. In particular, the long-term maintenance of these tools is compromised because of their specific development model. Hundreds of published studies become irreproducible de facto, as the software tools used to conduct them become unavailable. In this study, we present a large-scale survey of 〉5400 publications describing Web servers within the two main bibliographic resources for disseminating new software developments in molecular biology. For all these servers, we studied their citation patterns, the subjects they address, their citation networks and the temporal evolution of these factors. We also analysed how these factors affect the availability of these servers (whether they are alive). Our results show that this ecosystem of tools is highly interconnected and adapts to the ‘trendy’ subjects in every moment. The servers present characteristic temporal patterns of citation/usage, and there is a worrying rate of server ‘death’, which is influenced by factors such as the server popularity and the institutions that hosts it. These results can inform initiatives aimed at the long-term maintenance of these resources.