Using IR-n for information retrieval of Genomics Track

Nowadays there is a big amount of biomedical literature which uses complex nouns and acronyms of biological entities thus complicating the task of retrieval specific information. The Genomics Track works for this goal and this paper describes the approach we used to take part of this track of TREC 2007. As this is the first time we participate in this track, we configurated a new system consisting of the following diferenciated parts: preprocessing, passage generation, document retrieval and passage (with the answer) extraction. We want to call special attention to the textual retrieval system used, which was developed by the University of Alicante. Adapting the resources for the propouse, our system has obtained precision results over the mean and median average of the 66 official runs for the Document, Aspect and Passage2 MAP; and in the case of Passage MAP we get nearly the median and mean value. We want to emphasize we have obtained these results without incorporating specific information about the domain of the track. For the future, we would like to further develop our system in this direction.

From community approaches to single-cell genomics: the discovery of ubiquitous hyperhalophilic Bacteroidetes generalists

The microbiota of multi-pond solar salterns around the world has been analyzed using a variety of culture-dependent and molecular techniques. However, studies addressing the dynamic nature of these systems are very scarce. Here we have characterized the temporal variation during 1 year of the microbiota of five ponds with increasing salinity (from 18% to >40%), by means of CARD-FISH and DGGE. Microbial community structure was statistically correlated with several environmental parameters, including ionic composition and meteorological factors, indicating that the microbial community was dynamic as specific phylotypes appeared only at certain times of the year. In addition to total salinity, microbial composition was strongly influenced by temperature and specific ionic composition. Remarkably, DGGE analyses unveiled the presence of most phylotypes previously detected in hypersaline systems using metagenomics and other molecular techniques, such as the very abundant Haloquadratum and Salinibacter representatives or the recently described low GC Actinobacteria and Nanohaloarchaeota. In addition, an uncultured group of Bacteroidetes was present along the whole range of salinity. Database searches indicated a previously unrecognized widespread distribution of this phylotype. Single-cell genome analysis of five members of this group suggested a set of metabolic characteristics that could provide competitive advantages in hypersaline environments, such as polymer degradation capabilities, the presence of retinal-binding light-activated proton pumps and arsenate reduction potential. In addition, the fairly high metagenomic fragment recruitment obtained for these single cells in both the intermediate and hypersaline ponds further confirm the DGGE data and point to the generalist lifestyle of this new Bacteroidetes group.