GLOSSary: the GLobal Ocean 16S subunit web accessible resource.

BACKGROUND: Environmental metagenomics is a challenging approach that is exponentially spreading in the scientific community to investigate taxonomic diversity and possible functions of the biological components. The massive amount of sequence data produced, often endowed with rich environmental metadata, needs suitable computational tools to fully explore the embedded information. Bioinformatics plays a key role in providing methodologies to manage, process and mine molecular data, integrated with environmental metagenomics collections. One such relevant example is represented by the Tara Ocean Project. RESULTS: We considered the Tara 16S miTAGs released by the consortium, representing raw sequences from a shotgun metagenomics approach with similarities to 16S rRNA genes. We generated assembled 16S rDNA sequences, which were classified according to their lengths, the possible presence of chimeric reads, the putative taxonomic affiliation. The dataset was included in GLOSSary (the GLobal Ocean 16S Subunit web accessible resource), a bioinformatics platform to organize environmental metagenomics data. The aims of this work were: i) to present alternative computational approaches to manage challenging metagenomics data; ii) to set up user friendly web-based platforms to allow the integration of environmental metagenomics sequences and of the associated metadata; iii) to implement an appropriate bioinformatics platform supporting the analysis of 16S rDNA sequences exploiting reference datasets, such as the SILVA database. We organized the data in a next-generation NoSQL "schema-less" database, allowing flexible organization of large amounts of data and supporting native geospatial queries. A web interface was developed to permit an interactive exploration and a visual geographical localization of the data, either raw miTAG reads or 16S contigs, from our processing pipeline. Information on unassembled sequences is also available. The taxonomic affiliations of contigs and miTAGs, and the spatial distribution of the sampling sites and their associated sequence libraries, as they are contained in the Tara metadata, can be explored by a query interface, which allows both textual and visual investigations. In addition, all the sequence data were made available for a dedicated BLAST-based web application alongside the SILVA collection. CONCLUSIONS: GLOSSary provides an expandable bioinformatics environment, able to support the scientific community in current and forthcoming environmental metagenomics analyses.

[Quantitative evaluation methods of the chemoantibiotic associations (author's transl)]. / Metodi di valutazione quantitativa delle associazioni chemioantibiotiche.

In the introductory part a new classification of joint drug actions is submitted, according which three fundamental types are distincted, named respectively interference, cooperation and true interaction. In its turn, interaction is subdivided in three classes (uni-effectual, bis-ineffectual, bis-effectual) in the last of which is placed the most relevant of the interactions, that is synergism, subclassified, at its turn, as additive, super and infra-additive. The second part is devoted to the classification of the bacteriological techniques hitherto proposed in order to evaluate in vitro and in vivo the antibacterial interaction of chemoantibiotics. The third part is devoted to the classification and critical analysis of biometrical techniques hitherto applied to above quoted bacteriological techniques in order to obtain a quantitative evaluation of interaction. Criticism versus isobolic model is pointed out. In the final part a new procedure, named isoeffectual, is proposed. According to such a procedure a close grid of single and joint concentrations of a couple of chemoantibiotics, broad enough in order to cover the whole of the effects to be explored, is tested in vitro adopting the one-center agar diffusion test or a liquid medium. The experimental data so obtained are related in a planar diagram to the log of the sum obtained by adding to the concentrations of the first the concentrations of the second agent, converted into equi-effectual concentrations of the first. By this way a series of curvilinear regressions is obtained, which may be all explained by a mathematical formula according which the data may be submitted to statistical analysis and elaborated in order to draw the parameters able to define quantitatively the interaction. The model so applied is discussed as a general model for joint drug action.

Pharmacological properties of the anti-inflammatory agent pyridyl-biphenylyl-acetamide (diphenpyramide).

Pyridyl-biphenylyl-acetamide (diphenpyramide, Z-876) is a new bisphenylalcanoic derivative with marked anti-inflammatory, analgesic, antipyretic and uricosuric properties. It is more active than phenylbutazone in the adjuvant polyarthritis in the rat when given prophylactically or therapeutically. It is thrice as active as phenylbutazone and ten times as active as acetylsalicylic acid (ASA) on the carrageenin-induced edema of the hind-paw. Diphenpyramide is characterized by low acute toxicity and by weak ulcerogenic activity. On the carrageenin-induced edema the therapeutic index of diphenpyramide is 30 times higher than that of indometacin and the ratio between the ED50 and the UD50 (ulcerogenic dose in 50% of the treated rats) is 39 times higher than that of ASA.