Abstract. This paper presents a minimalist program for RDF, by showing how one can do without several predicates and keywords of the RDF Schema vocabulary, obtaining a simpler language which preserves the original semantics. This approach is beneficial in at least two directions: (a) To have a simple abstract fragment of RDFS easy to formalize and to reason about, which captures the essence of RDFS; (b) To obtain algorithmic properties of deduction and optimizations that are relevant for particular fragments. Among our results are: the identification of a simple fragment of RDFS; the proof that it encompasses the main features of RDFS; a formal semantics and a deductive system for it; sound and complete deductive systems for their sub-fragments; and an O(n log n) complexity bound for ground entailment in this fragment.

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Halophilic organisms inhabit hypersaline environments where the extreme ionic conditions and osmotic pressure have driven the evolution of molecular adaptation mechanisms. Understanding such mechanisms is limited by the common difficulties encountered in cultivating such organisms. Within the Euryarchaeota, for example, only the Halobacteria and the order Methanosarcinales include readily cultivable halophilic species. Furthermore, only the former have been extensively studied in terms of their component proteins. Here, in order to redress this imbalance, we investigate the halophilic adaptation of glycolytic enzymes from the ADP-dependent phosphofructokinase/glucokinase family (ADP-PFK/GK) derived from organisms of the order Methanosarcinales. Structural analysis of proteins from non-halophilic and halophilic Methanosarcinales shows an almost identical composition and distribution of amino acids on both the surface and within the core. However, these differ from those observed in Halobacteria or Eukarya. Proteins from Methanosarcinales display a remarkable increase in surface lysine content and have no reduction to the hydrophobic core, contrary to the features ubiquitously observed in Halobacteria and which are thought to be the main features responsible for their halophilic properties. Biochemical characterization of recombinant ADP-PFK/GK from M. evestigatum (halophilic) and M. mazei (non-halophilic) shows the activity of both these extant enzymes to be only moderately inhibited by salt. Nonetheless, its activity over time is notoriously stabilized by salt. Furthermore, glycine betaine has a protective effect against KCl inhibition and enhances the thermal stability of both enzymes. The resurrection of the last common ancestor of ADP-PFK/GK from Methanosarcinales shows that the ancestral enzyme displays an extremely high salt tolerance and thermal stability. Structure determination of the ancestral protein reveals unique traits such as an increase in the Lys and Glu content at the protein surface and yet no reduction to the volume of the hydrophobic core. Our results suggest that the halophilic character is an ancient trait in the evolution of this protein family and that proteins from Methanosarcinales have adapted to highly saline environments by a non-canonical strategy, different from that currently proposed for Halobacteria. These results open up new avenues for the search and development of novel salt tolerant biocatalysts.

The use of parasite body size (i.e. body mass) is a promising proxy to improve the study of patterns in parasite infracommunities, which are usually analysed using only numerical descriptors. This study deals with the importance and effect of the presence of a large endoparasite species, the cestode Anonchocephalus chilensis in a marine fish species, Genypterus maculatus, on the structure of the parasite infracommunities. Numerical and volumetric measures of aggregated properties of parasite infracommunities were compared and their correlation examined. The highly dominant presence of A. chilensis by volume causes a dramatic change in the patterns observed, including a smaller total volume of the remaining species when this volumetrically dominant species is present. However, C-scores and V-ratios, both indices based on null models of species occurrence, do not support the idea of communities structured by interspecific competition. Analyses reveal that numerical and volumetric community descriptors are complementary ways to search for patterns and to reveal processes within these systems.

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