MPI-LIT: a literature-curated dataset of microbial binary protein--protein interactions.

UNLABELLED: Prokaryotic protein-protein interactions are underrepresented in currently available databases. Here, we describe a 'gold standard' dataset (MPI-LIT) focusing on microbial binary protein-protein interactions and associated experimental evidence that we have manually curated from 813 abstracts and full texts that were selected from an initial set of 36 852 abstracts. The MPI-LIT dataset comprises 1237 experimental descriptions that describe a non-redundant set of 746 interactions of which 659 (88%) are not reported in public databases. To estimate the curation quality, we compared our dataset with a union of microbial interaction data from IntAct, DIP, BIND and MINT. Among common abstracts, we achieve a sensitivity of up to 66% for interactions and 75% for experimental methods. Compared with these other datasets, MPI-LIT has the lowest fraction of interaction experiments per abstract (0.9) and the highest coverage of strains (92) and scientific articles (813). We compared methods that evaluate functional interactions among proteins (such as genomic context or co-expression) which are implemented in the STRING database. Most of these methods discriminate well between functionally relevant protein interactions (MPI-LIT) and high-throughput data. AVAILABILITY: http://www.jcvi.org/mpidb/interaction.php?dbsource=MPI-LIT. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Environmental quality assessment of Port Blair in Andaman islands.

The Andman and Nicobar archipelago comprises of about 556 small and big islands covering an area of 8493 sq. kms in the Bay of Bengal. The very remoteness of these islands from the mainland has preserved their pristine environment and spectacular natural beauty. The Andman and Nicobar Administration is going for major developmental projects to cope with the increasing needs of the people, which ultimately results in significant changes in environmental quality. This paper describes the existing environmental quality around Port Blair city, which will give baseline scenario to assess the environmental impacts due to developments in the future.In order to monitor the air quality of the region, sampling stations were selected based on the locations of various industries and domestic activities. Suspended Particulate Matter (SPM), Sulphur dioxide (SO2) and Nitrogen Oxides (NOx) were monitored for a period of one month during winter season. In addition, micrometeorological data, viz. wind speed and direction were also recorded and analysed to obtain the representative meteorological scenario of the air basin. The monitored values of ambient air quality was found to be within the NAAQ standards of India.Similarly, noise levels were also measured at various locations viz., residential areas, commercial centres, villages, stone quarry sites and construction sites. Noise levels were found to exceed the standards at stone quarry, construction sites and other locations.Water quality studies were carried out with respect to surface and ground water. The various physico- chemical and bacteriological parameters were analysed. It was observed that the physico-chemical parameters of surface and ground water lie within the standards stipulated for Indian subcontinent except for heavy metals which exceed the limits in ground water samples. Bacteriological analysis of sea water and ground water indicate that they are contaminated with faecal matters. Further, the ground water can be used for drinking purposes only after adequate treatment.