Efficient Inclusion Checking for Deterministic Tree Automata and DTDs

International audienceWe present a new algorithm for testing language inclusion L(A) ⊆ L(B)L(A) between tree automata in time O(|A| |B|) where B is deterministic. We extend this algorithm for testing inclusion between automata for unranked trees A and deterministic DTDs D in time O(|A| |Σ| |D|). No previous algorithms with these complexities exist. A journal extension is available at http://hal.inria.fr/inria-00366082

Schema-Guided Induction of Monadic Queries

International audienceThe induction of monadic node selecting queries from partially annotated XML-trees is a key task in Web information extraction. We show how to integrate schema guidance into an RPNI-based learning algorithm, in which monadic queries are represented by pruning node selecting tree transducers. We present experimental results on schema guidance by the DTD of HTML

Efficient Inclusion Checking for Deterministic Tree Automata and XML Schemas

Special issue of LATA'08.International audienceWe present algorithms for testing language inclusion L(A) ⊆ L(B) between tree automata in time O(|A| |B|) where B is deterministic (bottom-up or top-down). We extend our algorithms for testing inclusion of automata for unranked trees A in deterministic DTDs or deterministic EDTDs with restrained competition D in time O(|A| |Σ| |D|). Previous algorithms were less efficient or less general

Query Induction with Schema-Guided Pruning Strategies

International audienceInference algorithms for tree automata that define node selecting queries in unranked trees rely on tree pruning strategies. These impose additional assumptions on node selection that are needed to compensate for small numbers of annotated examples. Pruning-based heuristics in query learning algorithms for Web information extraction often boost the learning quality and speed up the learning process. We will distinguish the class of regular queries that are stable under a given schema-guided pruning strategy, and show that this class is learnable with polynomial time and data. Our learning algorithm is obtained by adding pruning heuristics to the traditional learning algorithm for tree automata from positive and negative examples. While justified by a formal learning model, our learning algorithm for stable queries also performs very well in practice of XML information extraction

Lipoteichoic Acid in Streptomyces hygroscopicus: Structural Model and Immunomodulatory Activities

Gram positive bacteria produce cell envelope macroamphiphile glycopolymers, i.e. lipoteichoic acids or lipoglycans, whose functions and biosynthesis are not yet fully understood. We report for the first time a detailed structure of lipoteichoic acid isolated from a Streptomyces species, i.e. Streptomyces hygroscopicus subsp. hygroscopicus NRRL 2387T. Chemical, MS and NMR analyses revealed a polyglycerolphosphate backbone substituted with α-glucosaminyl and α-N-acetyl-glucosaminyl residues but devoid of any amino-acid substituent. This structure is very close, if not identical, to that of the wall teichoic acid of this organism. These data not only contribute to the growing recognition that lipoteichoic acid is a cell envelope component of Gram positive Actinobacteria but also strongly support the recently proposed hypothesis of an overlap between the pathways of lipoteichoic acid and wall teichoic acid synthesis in these bacteria. S. hygroscopicus lipoteichoic acid induced signalling by human innate immune receptor TLR2, confirming its role as a microbe-associated molecular pattern. Its activity was partially dependant on TLR1, TLR6 and CD14. Moreover, it stimulated TNF-α and IL-6 production by a human macrophage cell line to an extent similar to that of Staphylococcus aureus lipoteichoic acid. These results provide new clues on lipoteichoic acid structure/function relationships, most particularly on the role of the polyglycerolphosphate backbone substituents

Modeling and analysis of adipocytes dynamic with a differentiation process

We propose in this article a model describing the dynamic of a system of adipocytes, structured by their sizes. This model takes into account the differentiation of a population of mesenchymal cells into preadipocytes and of preadipocytes into adipocytes; the differentiation rates depend on the mean adipocyte radius. The considered equations are therefore ordinary differential equations, coupled with an advection equation, the growth rate of which depends on food availability and on the total surface of adipocytes. Since this velocity is discontinuous, we need to introduce a convenient notion of solutions coming from Filippov theory. We are consequently able to determine the stationary solutions of the system, to prove the existence and uniqueness of solutions and to describe the asymptotic behavior of solutions in some simple cases. Finally, the parameters of the model are fitted thanks to some experimental data and numerical simulations are displayed; a spatial extension of the model is studied numerically

Mycobacterium marinum MMAR_2380, a predicted transmembrane acyltransferase, is essential for the presence of the mannose cap on lipoarabinomannan

Lipoarabinomannan (LAM) is a major glycolipid in the mycobacterial cell envelope. LAM consists of a mannosylphosphatidylinositol (MPI) anchor, a mannan core and a branched arabinan domain. The termini of the arabinan branches can become substituted with one to three α(1→2)-linked mannosyl residues, the mannose cap, producing ManLAM. ManLAM has been associated with a range of different immunomodulatory properties of Mycobacterium tuberculosis during infection of the host. In some of these effects, the presence of the mannose cap on ManLAM appears to be crucial for its activity. So far, in the biosynthesis of the mannose cap on ManLAM, two enzymes have been reported to be involved: a mannosyltransferase that adds the first mannosyl residue of the mannose caps to the arabinan domain of LAM, and another mannosyltransferase that elongates the mannose cap up to three mannosyl residues. Here, we report that a third gene is involved, MMAR_2380, which is the Mycobacterium marinum orthologue of Rv1565c. MMAR_2380 encodes a predicted transmembrane acyltransferase. In M. marinum ΔMMAR_2380, the LAM arabinan domain is still intact, but the mutant LAM lacks the mannose cap. Additional effects of mutation of MMAR_2380 on LAM were observed: a higher degree of branching of both the arabinan domain and the mannan core, and a decreased incorporation of [1,2-14C]acetate into the acyl chains in mutant LAM as compared with the wild-type form. This latter effect was also observed for related lipoglycans, i.e. lipomannan (LM) and phosphatidylinositol mannosides (PIMs). Furthermore, the mutant strain showed increased aggregation in liquid cultures as compared with the wild-type strain. All phenotypic traits of M. marinum ΔMMAR_2380, the deficiency in the mannose cap on LAM and changes at the cell surface, could be reversed by complementing the mutant strain with MMAR_2380. Strikingly, membrane preparations of the mutant strain still showed enzymic activity for the arabinan mannose-capping mannosyltransferase similar to that of the wild-type strain. Although the exact function of MMAR_2380 remains unknown, we show that the protein is essential for the presence of a mannose cap on LAM

Lipoglycans Contribute to Innate Immune Detection of Mycobacteria

Innate immune recognition is based on the detection, by pattern recognition receptors (PRRs), of molecular structures that are unique to microorganisms. Lipoglycans are macromolecules specific to the cell envelope of mycobacteria and related genera. They have been described to be ligands, as purified molecules, of several PRRs, including the C-type lectins Mannose Receptor and DC-SIGN, as well as TLR2. However, whether they are really sensed by these receptors in the context of a bacterium infection remains unclear. To address this question, we used the model organism Mycobacterium smegmatis to generate mutants altered for the production of lipoglycans. Since their biosynthesis cannot be fully abrogated, we manipulated the biosynthesis pathway of GDP-Mannose to obtain some strains with either augmented (∼1.7 fold) or reduced (∼2 fold) production of lipoglycans. Interestingly, infection experiments demonstrated a direct correlation between the amount of lipoglycans in the bacterial cell envelope on one hand and the magnitude of innate immune signaling in TLR2 reporter cells, monocyte/macrophage THP-1 cell line and human dendritic cells, as revealed by NF-κB activation and IL-8 production, on the other hand. These data establish that lipoglycans are bona fide Microbe-Associated Molecular Patterns contributing to innate immune detection of mycobacteria, via TLR2 among other PRRs

Implication de la connexine 43 et de ses partenaires dans les processus physiologiques (proliférations, différenciation et apoptose) et physiopathologiques (cancer) testiculaires

LE KREMLIN-B.- PARIS 11-BU Méd (940432101) / SudocSudocFranceF