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  • 1
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    Variability of Depth to Tosca in Udolls and Soil Classification, Buenos Aires Province, Argentina (2002)
    Wiley
    Details
    Publication Date: 2002-05-01
    Print ISSN: 0361-5995
    Electronic ISSN: 1435-0661
    Topics: Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by Wiley
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  • 2
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    Breaking-Cas--interactive design of guide RNAs for CRISPR-Cas experiments for ENSEMBL genomes (2016)
    Oxford University Press
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    Publication Date: 2016-07-06
    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.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    MBROLE 2.0--functional enrichment of chemical compounds (2016)
    Oxford University Press
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    Publication Date: 2016-07-06
    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.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 4
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    Characterization of clinical signs in the human interactome (2016)
    Oxford University Press
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    Publication Date: 2016-06-16
    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.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 5
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    Detection of significant protein coevolution (2015)
    Oxford University Press
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    Publication Date: 2015-06-27
    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.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 6
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    JDet: interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures (2012)
    Oxford University Press
    Details
    Publication Date: 2012-02-17
    Description: : We have implemented in a single package all the features required for extracting, visualizing and manipulating fully conserved positions as well as those with a family-dependent conservation pattern in multiple sequence alignments. The program allows, among other things, to run different methods for extracting these positions, combine the results and visualize them in protein 3D structures and sequence spaces. Availability and implementation: JDet is a multiplatform application written in Java. It is freely available, including the source code, at http://csbg.cnb.csic.es/JDet . The package includes two of our recently developed programs for detecting functional positions in protein alignments ( Xdet and S3Det ), and support for other methods can be added as plug-ins. A help file and a guided tutorial for JDet are also available. Contact: pazos@cnb.csic.es
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 7
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    Advances in the Electro-Fenton Process for Remediation of Recalcitrant Organic Compounds (2012)
    Wiley
    Details
    Publication Date: 2012-04-15
    Description: The electro-Fenton (EF) process is a promising method combining electrochemical reactions and Fenton's reagent. In this hybrid process, the electrical current induces the in situ generation of H 2 O 2 via reduction of oxygen, and the catalytic reaction is propagated by Fe 2+ regeneration, which can take place by reduction of Fe 3+ with H 2 O 2 , hydroperoxyl radical, organic radical intermediates, or directly at the cathode. Recent advances in the EF process are discussed and several key variables analyzed, including electrode material, initial pH, and Fenton's reagents, in order to extend the applicability of this technology. A brief survey of the electro-Fenton (EF) process for the removal of different pollutants is presented. Special attention is focused on improving the technology by optimization of the fundamental variables governing the process, including pH, electrode material, and identity of Fenton's reagents in order to extend the applicability of this process.
    Print ISSN: 0930-7516
    Electronic ISSN: 1521-4125
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Published by Wiley
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  • 8
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    Advances in the Electro-Fenton Process for Remediation of Recalcitrant Organic Compounds (2012)
    Wiley
    Details
    Publication Date: 2012-03-07
    Description: The electro-Fenton (EF) process is a promising method combining electrochemical reactions and Fenton's reagent. In this hybrid process, the electrical current induces the in situ generation of H 2 O 2 via reduction of oxygen, and the catalytic reaction is propagated by Fe 2+ regeneration, which can take place by reduction of Fe 3+ with H 2 O 2 , hydroperoxyl radical, organic radical intermediates, or directly at the cathode. Recent advances in the EF process are discussed and several key variables analyzed, including electrode material, initial pH, and Fenton's reagents, in order to extend the applicability of this technology. A brief survey of the electro-Fenton (EF) process for the removal of different pollutants is presented. Special attention is focused on improving the technology by optimization of the fundamental variables governing the process, including pH, electrode material, and identity of Fenton's reagents in order to extend the applicability of this process.
    Print ISSN: 0930-7516
    Electronic ISSN: 1521-4125
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Published by Wiley
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  • 9
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    Crustal thickness variations in northern Morocco (2012)
    Wiley
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    Publication Date: 2012-02-23
    Description: During the TopoIberia experiment, a total of 26 seismic broadband stations were recording in northern Morocco, providing for the first time extended regional coverage for investigating structure and seismotectonics of the southern branch of the Betic-Rif arc, its foreland, and the Atlas domain. Here, we analyze P-to-S converted waves in teleseismic receiver functions to infer gross crustal properties as thickness and Vp/Vs ratio. Strong lateral variations of the crustal thickness are observed throughout the region. Crustal thicknesses vary between 22 and 44 km and display a simple geographic pattern that divides the study area into three domains: entire northwestern Morocco underlain by a thickened crust with crustal thicknesses between 35 and 44 km; northeastern Morocco affected by significant crustal thinning, with crustal thicknesses ranging from 22 to 30 km, with the shallowest Moho along the Mediterranean coast; and an extended domain of 27–34 km thick crust, farther south which includes the Atlas domain and its foreland regions. Vp/Vs ratios show normal values of ∼1.75 for most stations except for the Atlas domain, where several stations give low Vp/Vs ratios of around 1.71. The very sharp transition from thick crust in northwestern Morocco to thin crust in northeastern Morocco is attributed to regional geodynamics, possibly the realm of present-day subcrustal dynamics in the final stage of western Mediterranean subduction. Crustal thicknesses just slightly above 30 km in the southern domain are intriguing, showing that high topography in this region is not isostatically compensated at crustal level.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 10
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    Hybrid Technologies for the Remediation of Diesel Fuel Polluted Soil (2011)
    Wiley
    Details
    Publication Date: 2011-11-04
    Description: Diesel fuel may be released into soil due to anthropogenic activities, such as accidental spills or leaks in underground storage tanks or pipelines. Since diesel fuel is mainly composed of hydrophobic organic compounds, it has low water solubility. Therefore, treating contaminated areas with conventional techniques is difficult. In this study, electrokinetic treatment of soil contaminated with diesel fuel was carried out. Two different hybrid approaches to pollutant removal were tested. A surfactant was used as a processing fluid during electrokinetic treatment to increase desorption and the solubility of diesel fuel. Additionally, a hybrid technology combining a Fenton reaction and electrokinetic remediation (EK-Fenton) was tested in an attempt to generate favorable in situ degradation of pollutants. The efficiency of each treatment was determined based on diesel fuel removal. After 30 days of treatment, the highest removal of diesel fuel was found to be achieved with the EK-Fenton process. Several approaches to the electrokinetic treatment of soil polluted with diesel fuel were evaluated. The use of surfactants as processing fluid was tested with the aim of increasing desorption and the solubility of diesel fuel, leading to improved removal by electroosmosis. Additionally, the EK-Fenton process was investigated as a method of promoting in situ degradation of diesel fuel.
    Print ISSN: 0930-7516
    Electronic ISSN: 1521-4125
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Published by Wiley
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