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Herrero J.,CSIC - Aula Dei Experimental Station
Land Degradation and Development | Year: 2017

Gypseous lands occur mainly in arid regions of the world, where irrigation is required for profitable agriculture. The study of gypseous soils has been neglected for years in the main stream of the soil science. Agriculture and, more recently, the environmental concerns are challenging research in the countries that have extensive gypsum outcrops. Those challenges have been obvious since at least the 1960s, when economic development in some of these countries led to the construction of new irrigation schemes and associated infrastructures. This paper presents examples of documents about agriculture on gypseous soils in Spain that might be applicable to similar situations elsewhere in the world. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Vicente-Serrano S.M.,CSIC - Pyrenean Institute of Ecology | Begueria S.,CSIC - Aula Dei Experimental Station | Lopez-Moreno J.I.,CSIC - Pyrenean Institute of Ecology
Journal of Climate | Year: 2010

The authors propose a new climatic drought index: the standardized precipitation evapotranspiration index (SPEI). The SPEI is based on precipitation and temperature data, and it has the advantage of combining multiscalar character with the capacity to include the effects of temperature variability on drought assessment. The procedure to calculate the index is detailed and involves a climatic water balance, the accumulation of deficit/surplus at different time scales, and adjustment to a log-logistic probability distribution. Mathematically, the SPEI is similar to the standardized precipitation index (SPI), but it includes the role of temperature. Because the SPEI is based on a water balance, it can be compared to the self-calibrated Palmer drought severity index (sc-PDSI). Time series of the three indices were compared for a set of observatories with different climate characteristics, located in different parts of the world. Under global warming conditions, only the sc-PDSI and SPEI identified an increase in drought severity associated with higher water demand as a result of evapotranspiration. Relative to the sc-PDSI, the SPEI has the advantage of being multiscalar, which is crucial for drought analysis and monitoring. © 2010 American Meteorological Society.

Contreras-Moreira B.,CSIC - Aula Dei Experimental Station | Vinuesa P.,National Autonomous University of Mexico
Applied and Environmental Microbiology | Year: 2013

GET_HOMOLOGUES is an open-source software package that builds on popular orthology-calling approaches making highly customizable and detailed pangenome analyses of microorganisms accessible to nonbioinformaticians. It can cluster homologous gene families using the bidirectional best-hit, COGtriangles, or OrthoMCL clustering algorithms. Clustering stringency can be adjusted by scanning the domain composition of proteins using the HMMER3 package, by imposing desired pairwise alignment coverage cutoffs, or by selecting only syntenic genes. The resulting homologous gene families can be made even more robust by computing consensus clusters from those generated by any combination of the clustering algorithms and filtering criteria. Auxiliary scripts make the construction, interrogation, and graphical display of core genome and pangenome sets easy to perform. Exponential and binomial mixture models can be fitted to the data to estimate theoretical core genome and pangenome sizes, and high-quality graphics can be generated. Furthermore, pangenome trees can be easily computed and basic comparative genomics performed to identify lineage-specific genes or gene family expansions. The software is designed to take advantage of modern multiprocessor personal computers as well as computer clusters to parallelize time-consuming tasks. To demonstrate some of these capabilities, we survey a set of 50 Streptococcus genomes annotated in the Orthologous Matrix (OMA) browser as a benchmark case. The package can be downloaded at http://www.eead.csic.es/compbio/soft/gethoms.php and http://maya.ccg.unam.mx/soft/gethoms.php. © 2013, American Society for Microbiology.

Lee Y.,University of Lausanne | Rubio M.C.,University of Lausanne | Rubio M.C.,CSIC - Aula Dei Experimental Station | Alassimone J.,University of Lausanne | Geldner N.,University of Lausanne
Cell | Year: 2013

The precise localization of extracellular matrix and cell wall components is of critical importance for multicellular organisms. Lignin is a major cell wall modification that often forms intricate subcellular patterns that are central to cellular function. Yet the mechanisms of lignin polymerization and the subcellular precision of its formation remain enigmatic. Here, we show that the Casparian strip, a lignin-based, paracellular diffusion barrier in plants, forms as a precise, median ring by the concerted action of a specific, localized NADPH oxidase, brought into proximity of localized peroxidases through the action of Casparian strip domain proteins (CASPs). Our findings in Arabidopsis provide a simple mechanistic model of how plant cells regulate lignin formation with subcellular precision. We speculate that scaffolding of NADPH oxidases to the downstream targets of the reactive oxygen species (ROS) that they produce might be a widespread mechanism to ensure specificity and subcellular precision of ROS action within the extracellular matrix. © 2013 Elsevier Inc.

Sebastian A.,CSIC - Aula Dei Experimental Station | Contreras-Moreira B.,CSIC - Aula Dei Experimental Station
Bioinformatics | Year: 2014

Motivation: Traditional and high-throughput techniques for determining transcription factor (TF) binding specificities are generating large volumes of data of uneven quality, which are scattered across individual databases.Results: FootprintDB integrates some of the most comprehensive freely available libraries of curated DNA binding sites and systematically annotates the binding interfaces of the corresponding TFs. The first release contains 2422 unique TF sequences, 10 112 DNA binding sites and 3662 DNA motifs. A survey of the included data sources, organisms and TF families was performed together with proprietary database TRANSFAC, finding that footprintDB has a similar coverage of multicellular organisms, while also containing bacterial regulatory data. A search engine has been designed that drives the prediction of DNA motifs for input TFs, or conversely of TF sequences that might recognize input regulatory sequences, by comparison with database entries. Such predictions can also be extended to a single proteome chosen by the user, and results are ranked in terms of interface similarity. Benchmark experiments with bacterial, plant and human data were performed to measure the predictive power of footprintDB searches, which were able to correctly recover 10, 55 and 90% of the tested sequences, respectively. Correctly predicted TFs had a higher interface similarity than the average, confirming its diagnostic value. © 2013 The Author.

Losada J.M.,CSIC - Aula Dei Experimental Station
Annals of botany | Year: 2012

Stigmatic receptivity plays a clear role in pollination dynamics; however, little is known about the factors that confer to a stigma the competence to be receptive for the germination of pollen grains. In this work, a developmental approach is used to evaluate the acquisition of stigmatic receptivity and its relationship with a possible change in arabinogalactan-proteins (AGPs). Flowers of the domestic apple, Malus × domestica, were assessed for their capacity to support pollen germination at different developmental stages. Stigmas from these same stages were characterized morphologically and different AGP epitopes detected by immunocytochemistry. Acquisition of stigmatic receptivity and the secretion of classical AGPs from stigmatic cells occurred concurrently and following the same spatial distribution. While in unpollinated stigmas AGPs appeared unaltered, in cross-pollinated stigmas AGPs epitopes vanished as pollen tubes passed by. The concurrent secretion of AGPs with the acquisition of stigmatic receptivity, together with the differential response in unpollinated and cross-pollinated pistils point out a role of AGPs in supporting pollen tube germination and strongly suggest that secretion of AGPs is associated with the acquisition of stigma receptivity.

Yruela I.,CSIC - Aula Dei Experimental Station
Metallomics | Year: 2013

Transition metals are involved in essential biological processes in plants since they are cofactors of metalloproteins and also act as regulator elements. Particularly, plant chloroplasts are organelles with high transition metal ion demand because metalloproteins are involved in the photosynthetic electron transport chain. The transition metal requirement of photosynthetic organisms greatly exceeds that of non-photosynthetic organisms, and either metal deficiency or metal excess strongly impacts photosynthetic functions. In chloroplasts, the transition metal ion requirement needs a homeostasis network that strictly regulates metal uptake, chelation, trafficking and storage since under some conditions metals cause toxicity. This review gives an overview of the current understanding of main features concerning the role of copper (Cu), iron (Fe), manganese (Mn) and zinc (Zn) in plant photosynthesis as well as the mechanisms involved in their homeostasis within chloroplasts. The metalloproteins functioning in photosynthetic proteins of plants as well as those proteins participating in the metal transport and metal binding assembly are reviewed. Furthermore, the role of nickel (Ni) in artificial photosynthesis will be discussed. © 2013 The Royal Society of Chemistry.

Sebastian A.,CSIC - Aula Dei Experimental Station | Contreras-Moreira B.,CSIC - Aula Dei Experimental Station
Nucleic Acids Research | Year: 2013

Sequence alignment of proteins and nucleic acids is a routine task in bioinformatics. Although the comparison of complete peptides, genes or genomes can be undertaken with a great variety of tools, the alignment of short DNA sequences and motifs entails pitfalls that have not been fully addressed yet. Here we confront the structural superposition of transcription factors with the sequence alignment of their recognized cis elements. Our goals are (i) to test TFcompare (http://floresta.eead.csic.es/tfcompare), a structural alignment method for protein-DNA complexes; (ii) to benchmark the pairwise alignment of regulatory elements; (iii) to define the confidence limits and the twilight zone of such alignments and (iv) to evaluate the relevance of these thresholds with elements obtained experimentally. We find that the structure of cis elements and protein-DNA interfaces is significantly more conserved than their sequence and measures how this correlates with alignment errors when only sequence information is considered. Our results confirm that DNA motifs in the form of matrices produce better alignments than individual sequences. Finally, we report that empirical and theoretically derived twilight thresholds are useful for estimating the natural plasticity of regulatory sequences, and hence for filtering out unreliable alignments. © 2012 The Author(s) 2012. Published by Oxford University Press.

Gaspar L.,CSIC - Aula Dei Experimental Station | Navas A.,CSIC - Aula Dei Experimental Station
Geoderma | Year: 2013

The fallout radionuclide 137Cs has been used widely as an environmental tracer in the study of soil redistribution processes. An understanding of the relationships between 137Cs and soil properties and physiographic factors is essential for a sound interpretation of the estimates of soil redistribution derived from 137Cs data. The purpose of this study was to investigate the relationships of 137Cs with main soil properties in cultivated and uncultivated soils located in the northern border of central part of the Ebro basin in order to infer the behavior of 137Cs in representative soils of Mediterranean mountain hillslopes. The depth distribution of 137Cs and the physicochemical properties of the soils were measured in 59 soil profiles along five soil toposequences that differed in orientation, slope gradient, land uses, soil types and lithologies, and were representative of Mediterranean mountain agroecosystems. The 137Cs mass activities and inventories varied widely (between b.d.l. and 38Bqkg-1, and between 0 and 2633Bqm-2, respectively). The highest values were found in surface layers of uncultivated Leptosols (mean: 21.9Bqkg-1, 1052.0Bqm-2) associated with steep slopes and high SOM content (mean: 8.3%), and the lowest values (b.d.l.) were found at deep layers of uncultivated and cultivated soils. In uncultivated soils most 137Cs was found in the upper 12cm with a clear exponential decay with depth. Cultivated soils had longer mixed 137Cs profiles extending to 47cm. 137Cs inventories were significantly higher in uncultivated soils (mean: 1616.1Bqm-2) than in cultivated soils (mean: 1174.1Bqm-2). The 137Cs contents were significantly positively correlated with SOM and stoniness, respectively, but weakly negatively correlated with clay content. Multivariate analyses were used to test the hypothesis that soil properties and physiographic factors influence the distribution of 137Cs. As much as 80% and over 60% of the variance of 137Cs was explained by SOM contents in stepwise model and adding land use and depth intervals in GLM models evidencing the strong control of land use. The results of this study improve our understanding of the effects of soil properties and physiographic factors on the behavior of 137Cs in the Spanish south-central Pyrenees. © 2013 Elsevier B.V.

Navas A.,CSIC - Aula Dei Experimental Station
Environmental Modelling and Software | Year: 2014

Flow accumulation algorithms (FAAs) predict the cumulative upstream drainage but each FAA generates a different map and this uncertainty still remains unsolved. This study makes advances in flow path research by testing 8 FAAs and analyzing the uncertainties of 15 simulations. The DR2-2013© SAGAv1.0 hydrological software is presented in a study carried out for two catchment lakes (NE Spain) over a 69-month test period. The best simulations were obtained with two single flow (Rho8 and Deterministic Infinity) and two multiple flow (Multiple Flow with threshold value and Triangular Multiple Flow) algorithms. Correlations between runoff depths and lake levels improved when the test period was split into wet and dry seasons. Correlations also improved with a one-month delay in response time and no delay in the large and small lakes. The DR2-2013© tool helped predict changes in lake volume and the highest model efficiencies were obtained with the multiple flow algorithms. © 2014 Elsevier Ltd.

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