Satisfiability of constraint specifications on XML documents

Jose Meseguer is one of the earliest contributors in the area of Algebraic Specification. In this paper, which we are happy to dedicate to him on the occasion of his 65th birthday, we use ideas and methods coming from that area with the aim of presenting an approach for the specification of the structure of classes of XML documents and for reasoning about them. More precisely, we specify the structure of documents using sets of constraints that are based on XPath and we present inference rules that are shown to define a sound and complete refutation procedure for checking satisfiability of a given specification using tableaux.Peer ReviewedPostprint (author's final draft

Embryo and larval biology of the deepsea octocoral Dentomuricea aff. meteor under different temperature regimes

Deep-sea octocorals are common habitat-formers in deep-sea ecosystems, however, our knowledge on their early life history stages is extremely limited. The present study focuses on the early life history of the species Dentomuricea aff. meteor, a common deep-sea octocoral in the Azores. The objective was to describe the embryo and larval biology of the target species under two temperature regimes, corresponding to the minimum and maximum temperatures in its natural environment during the spawning season. At temperature of 13 ±0.5 °C, embryos of the species reached the planula stage after 96h and displayed a median survival of 11 days. Planulae displayed swimming only after stimulation, swimming speed was 0.24 ±0.16 mm s−1 and increased slightly but significantly with time. Under a higher temperature (15 °C ±0.5 °C) embryos reached the planula stage 24 h earlier (after 72 h), displayed a median survival of 16 days and had significantly higher swimming speed (0.3 ±0.27 mm s−1). Although the differences in survival were not statistically significant, our results highlight how small changes in temperature can affect embryo and larval characteristics with potential cascading effects in larval dispersal and success. In both temperatures, settlement rates were low and metamorphosis occurred even without settlement. Such information is rarely available for deep-sea corals, although essential to achieve a better understanding of dispersal, connectivity and biogeographical patterns of benthic species.Versión del edito

L-Rhamnose induction of Aspergillus nidulans α-L-rhamnosidase genes is glucose repressed via a CreA-independent mechanism acting at the level of inducer uptake

<p>Abstract</p> <p>Background</p> <p>Little is known about the structure and regulation of fungal α-L-rhamnosidase genes despite increasing interest in the biotechnological potential of the enzymes that they encode. Whilst the paradigmatic filamentous fungus <it>Aspergillus nidulans </it>growing on L-rhamnose produces an α-L-rhamnosidase suitable for oenological applications, at least eight genes encoding putative α-L-rhamnosidases have been found in its genome. In the current work we have identified the gene (<it>rhaE</it>) encoding the former activity, and characterization of its expression has revealed a novel regulatory mechanism. A shared pattern of expression has also been observed for a second α-L-rhamnosidase gene, (AN10277/<it>rhaA</it>).</p> <p>Results</p> <p>Amino acid sequence data for the oenological α-L-rhamnosidase were determined using MALDI-TOF mass spectrometry and correspond to the amino acid sequence deduced from AN7151 (<it>rhaE</it>). The cDNA of <it>rhaE </it>was expressed in <it>Saccharomyces cerevisiae </it>and yielded <it>p</it>NP-rhamnohydrolase activity. Phylogenetic analysis has revealed this eukaryotic α-L-rhamnosidase to be the first such enzyme found to be more closely related to bacterial rhamnosidases than other α-L-rhamnosidases of fungal origin. Northern analyses of diverse <it>A. nidulans </it>strains cultivated under different growth conditions indicate that <it>rhaA </it>and <it>rhaE </it>are induced by L-rhamnose and repressed by D-glucose as well as other carbon sources, some of which are considered to be non-repressive growth substrates. Interestingly, the transcriptional repression is independent of the wide domain carbon catabolite repressor CreA. Gene induction and glucose repression of these <it>rha </it>genes correlate with the uptake, or lack of it, of the inducing carbon source L-rhamnose, suggesting a prominent role for inducer exclusion in repression.</p> <p>Conclusions</p> <p>The <it>A. nidulans rhaE </it>gene encodes an α-L-rhamnosidase phylogenetically distant to those described in filamentous fungi, and its expression is regulated by a novel CreA-independent mechanism. The identification of <it>rhaE </it>and the characterization of its regulation will facilitate the design of strategies to overproduce the encoded enzyme - or homologs from other fungi - for industrial applications. Moreover, <it>A. nidulans </it>α-L-rhamnosidase encoding genes could serve as prototypes for fungal genes coding for plant cell wall degrading enzymes regulated by a novel mechanism of CCR.</p

CSIC High Specialization Course on Cultural Heritage Intervention Models: Research, Protection, Conservation and Valorization: A training Experience from a complex research programme.

Comunicación presentada en la 18th Annual Meeting of the European Association of Archaeologists, celebrada en Helsinki del 29 de agosto al 1 de septiembre de 2012.In late 2007 the then called Ministry of Education and Science funded the Research Program on Technologies for the Conservation and Valorization of Cultural Heritage (TCP) within the CONSOLIDER -INGENIO 2010 call. In it 16 research groups take part, from the CSIC and 4 Spanish universities, articulating traditionally distant disciplines directly involved with Cultural Heritage. The base for working is the culture of cooperation and collaboration between groups in an interdisciplinary way. TCP was the only funded proposal of the call that focused on the study of Cultural Heritage. One of the main objectives of the project included training, so after valorizing different options, it was finally decided to opt for a CSIC High Specialization Course model. The aim was to create a postgraduate training strategy for preparing, in a truly specialized way, professionals with technical or scientific profile, who can become the best professionals working on cultural heritage. This course was an alternative possibility, different from formal university education. It also benefited from greater freedom in designing the course, choosing the participating teachers, and establishing the relationship between practical and theoretical aspects. This goal lies at the very foundations of the Consolider call and more specifically, also within TCP: strengthen and highlight the link between the interdisciplinary research, the professional practice and the social visibility of research through training, dissemination and knowledge transfer.Peer Reviewe

Physiological performance of the cold-water coral Dendrophyllia cornigera reveals its preference for temperate environments

Cold-water corals (CWCs) are key ecosystem engineers in deep-sea benthic communities around the world. Their distribution patterns are related to several abiotic and biotic factors, of which seawater temperature is arguably one of the most important due to its role in coral physiological processes. The CWC Dendrophyllia cornigera has the particular ability to thrive in several locations in which temperatures range from 11 to 17 °C, but to be apparently absent from most CWC reefs at temperatures constantly below 11 °C. This study thus aimed to assess the thermal tolerance of this CWC species, collected in the Mediterranean Sea at 12 °C, and grown at the three relevant temperatures of 8, 12, and 16 °C. This species displayed thermal tolerance to the large range of seawater temperatures investigated, but growth, calcification, respiration, and total organic carbon (TOC) fluxes severely decreased at 8 °C compared to the in situ temperature of 12 °C. Conversely, no significant differences in calcification, respiration, and TOC fluxes were observed between corals maintained at 12 and 16 °C, suggesting that the fitness of this CWC is higher in temperate rather than cold environments. The capacity to maintain physiological functions between 12 and 16 °C allows D. cornigera to be the most abundant CWC species in deep-sea ecosystems where temperatures are too warm for other CWC species (e.g., Canary Islands). This study also shows that not all CWC species occurring in the Mediterranean Sea (at deep-water temperatures of 12-14 °C) are currently living at their upper thermal tolerance limit. © 2014 Springer-Verlag Berlin Heidelber

Controlling Reuse in Pattern-Based Model-to-Model Transformations

Model-to-model transformation is a central activity in Model-Driven Engineering that consists of transforming models from a source to a target language. Pattern-based model-to-model transformation is our approach for specifying transformations in a declarative, relational and formal style. The approach relies on patterns describing allowed or forbidden relations between two models. These patterns are compiled into operational mechanisms to perform forward and backward transformations. Inspired by QVT-Relations, in this paper we incorporate into our framework the so-called check-before-enforce semantics, which checks the existence of suitable elements before creating them (i.e. it promotes reuse). Moreover, we enable the use of keys in order to describe when two elements are considered equal. The presented techniques are illustrated with a bidirectional transformation between Web Services Description Language and Enterprise Java Beans models.Work partially supported by the Spanish Ministry of Science and Innovation, with projects METEORIC (TIN2008-02081) and FORMALISM (TIN2007-66523), and the R&D program of the Community of Madrid (S2009/TIC-1650, project “e-Madrid”). Moreover, part of this work was done during a post-doctoral stay of the first author at the University of York, and sabbatical leaves of the second and third authors to the University of York and TU Berlin respectively, all with financial support from the Spanish Ministry of Science and Innovation (grant refs. JC2009-00015, PR2009-0019 and PR2008-0185).Publicad