MINT, the molecular interaction database: 2012 update

The Molecular INTeraction Database (MINT, http://mint.bio.uniroma2.it/mint/) is a public repository for protein-protein interactions (PPI) reported in peer-reviewed journals. The database grows steadily over the years and at September 2011 contains approximately 235,000 binary interactions captured from over 4750 publications. The web interface allows the users to search, visualize and download interactions data. MINT is one of the members of the International Molecular Exchange consortium (IMEx) and adopts the Molecular Interaction Ontology of the Proteomics Standard Initiative (PSI-MI) standards for curation and data exchange. MINT data are freely accessible and downloadable at http://mint.bio.uniroma2.it/mint/download.do. We report here the growth of the database, the major changes in curation policy and a new algorithm to assign a confidence to each interaction

Identification, semantic annotation and comparison of combinations of functional elements in multiple biological conditions

Motivation: Approaches such as chromatin immunoprecipitation followed by sequencing (ChIP-seq) represent the standard for the identification of binding sites of DNA-associated proteins, including transcription factors and histone marks. Public repositories of omics data contain a huge number of experimental ChIP-seq data, but their reuse and integrative analysis across multiple conditions remain a daunting task. Results: We present the Combinatorial and Semantic Analysis of Functional Elements (CombSAFE), an efficient computational method able to integrate and take advantage of the valuable and numerous, but heterogeneous, ChIP-seq data publicly available in big data repositories. Leveraging natural language processing techniques, it integrates omics data samples with semantic annotations from selected biomedical ontologies; then, using hidden Markov models, it identifies combinations of static and dynamic functional elements throughout the genome for the corresponding samples. CombSAFE allows analyzing the whole genome, by clustering patterns of regions with similar functional elements and through enrichment analyses to discover ontological terms significantly associated with them. Moreover, it allows comparing functional states of a specific genomic region to analyze their different behavior throughout the various semantic annotations. Such findings can provide novel insights by identifying unexpected combinations of functional elements in different biological conditions

About the cellular tropism of the gammaherpesvirus bovine herpesvirus type 4.

We read with interest the recent report by Egyed et al. (4) about the distribution in tissue, in the natural host, of bovine herpesvirus type 4 (BHV-4), a member of the gammaherpesvirus group. Using PCR, those authors were able to trace BHV-4 (Movar strain) in several tissues of experimentally infected cattle (mostly spleen, lung, trachea, and nasal epithelium tissues) at different times, ranging from 3 to 48 days postinfection. The authors also report consistent detection of BHV-4 DNA in what they consider to be a pure population of lymphocytes obtained from peripheral blood of the BHV-4- infected cattle, and then they describe how BHV-4 extensively replicated in these peripheral “lymphocytes” throughout the whole period of their study. According to Egyed et al. (4), their results would then prove that the target cell of this virus is the lymphocyte and not (or not only) macrophagic cells as we previously reported (8). Furthermore, Egyed et al. contend that their results on specific lymphocyte tropism of BHV-4 justify the classification of this bovine herpesvirus as a gammaherpesvirus closely related to Epstein-Barr virus (4). An analysis of the procedures used by these authors (4) and those referenced by them (1) lead us to conclude that, in spite of their plausible rationalization, their experimental results do not provide support for the notion that lymphocytes are the target cell for replication of BHV-4

Passive Transfer of Virus-Specific Antibodies Confers Protection against Reproductive Failure Induced by a Virulent Strain of Porcine Reproductive and Respiratory Syndrome Virus and Establishes Sterilizing Immunity

Immune mechanisms mediating protective immunity against porcine reproductive and respiratory syndrome virus (PRRSV) are not well understood. The PRRSV-specific humoral immune response has been dismissed as being ineffective and perhaps deleterious for the host. The function of PRRSV antibodies in protective immunity against infection with a highly abortifacient strain of this virus was examined by passive transfer experiments in pregnant swine. All of a group of pregnant gilts (n = 6) that received PRRSV immunoglobulin (Ig) from PRRSV-convalescent, hyperimmune animals were fully protected from reproductive failure as judged by 95% viability of offspring at weaning (15 days of age). On the other hand, the totality of animals in a matched control group (n = 6) receiving anti-pseudorabies virus (PRV) Ig exhibited marked reproductive failure with 4% survival at weaning. Besides protecting the pregnant females from clinical reproductive disease, the passive transfer of PRRSV Ig prevented the challenge virus from infecting the dams and precluded its vertical transmission, as evidenced by the complete absence of infectious PRRSV from the tissues of the dams and lack of infection in their offspring. In summary, these results indicate that PRRSV-Igs are capable of conferring protective immunity against PRRSV and furthermore that these Igs can provide sterilizing immunity in vivo

"Seismic analyis of complex masonry buildings"

The 6th of April 2009, a catastrophic earthquake of magnitude ML=5.8 (Mw=6.3), stroke down the city of L'Aquila. The seismic event caused serious injure to several masonry buildings, putting at imminent risk a valuable historical and architectural heritage. Partial collapses or severe damages affected several constructions in the city centre, which consist primarily of masonry-type buildings. The present paper approaches the multi-faceted task of evaluating the seismic performance of a complex masonry building located in the centre of the city, hosting an important bank institution. The building possesses many peculiarities characterizing its dynamical behaviour, such as a C-shaped non-regular plan, a vertically-varying geometry, and a complex resistant scheme, coming out from an important partial demolition and rebuilding intervention, dating to the early 70\u2019s. The current structure is realized by a reinforced concrete frame, superimposed to the original masonry wall scheme, at the second floor level. The paper includes a comprehensive discussion on the current limit capacity of the building, based on the observations from repeated visual inspections of the earthquake occurred damage, the experimental data from a wide campaign of in-situ tests on the material properties, the results of numerical simulations from different finite element models of the damaged and undamaged structur

"Il ruolo della conoscenza e dell'analisi dei materiali e delle strutture nei progetti di intervento sui palazzi storici dell'Universit\ue0 dell'Aquila"

Il 6 Aprile 2009 un terremoto di magnitudo ML=5.8 (MW=6.3) ha colpito la citt\ue0 dell\u2019Aquila. L\u2019evento sismico ha causato seri e diffusi danni al tessuto edilizio cittadino, soprattutto a quello storico in muratura, compromettendo la quasi totalit\ue0 di un pregevole patrimonio monumentale ed architettonico. Crolli parziali o comunque danni gravi hanno interessato la maggior parte delle costruzioni nel centro citt\ue0. Il lavoro sintetizza uno sforzo sinergico volto allo sviluppo di ricerca e di conoscenza nell\u2019ambito dell\u2019analisi dei materiali e delle strutture dei beni monumentali. Sono pertanto dapprima evidenziati i risultati di diverse esperienze nel settore delle indagini distruttive e non distruttive per la caratterizzazione dei materiali e delle strutture tipici della citt\ue0 dell\u2019Aquila. Quindi \ue8 presentata in forma organica ed integrata l\u2019attivit\ue0 di ricerca svolta nell\u2019ambito della modellazione strutturale di edifici monumentali in muratura con inserti di telai in cemento armato. In particolare, sono confrontati diversi approcci per la modellazione strutturale di edifici storici in muratura, paragonandone le prestazioni anche alla luce dell\u2019esperienza accumulata durante le numerose ispezioni visive post-sisma finalizzate al rilievo del danno e alla prima valutazione del comportamento sismico. Come casi studio si presentano gli edifici storici di Palazzo Carli, di Palazzo Camponeschi e della sede della Direzione Generale della CarispAq, al fine di illustrare con esempi diversi le conclusioni desunte dall\u2019elaborazione della grande messe di dati proveniente dalle attivit\ue0 condott