03098nas a2200325 4500008004100000245012300041210006900164260001600233520197300249100001902222700001902241700002402260700002102284700001702305700003102322700002002353700003002373700002502403700002402428700001902452700001902471700002102490700002602511700002402537700002902561700001802590700002002608700001902628856012502647 2010 eng d00aFine-scale evolution: genomic, phenotypic and ecological differentiation in two coexisting Salinibacter ruber strains.0 aFinescale evolution genomic phenotypic and ecological differenti c2010 Feb 183 a

Genomic and metagenomic data indicate a high degree of genomic variation within microbial populations, although the ecological and evolutive meaning of this microdiversity remains unknown. Microevolution analyses, including genomic and experimental approaches, are so far very scarce for non-pathogenic bacteria. In this study, we compare the genomes, metabolomes and selected ecological traits of the strains M8 and M31 of the hyperhalophilic bacterium Salinibacter ruber that contain ribosomal RNA (rRNA) gene and intergenic regions that are identical in sequence and were simultaneously isolated from a Mediterranean solar saltern. Comparative analyses indicate that S. ruber genomes present a mosaic structure with conserved and hypervariable regions (HVRs). The HVRs or genomic islands, are enriched in transposases, genes related to surface properties, strain-specific genes and highly divergent orthologous. However, the many indels outside the HVRs indicate that genome plasticity extends beyond them. Overall, 10% of the genes encoded in the M8 genome are absent from M31 and could stem from recent acquisitions. S. ruber genomes also harbor 34 genes located outside HVRs that are transcribed during standard growth and probably derive from lateral gene transfers with Archaea preceding the M8/M31 divergence. Metabolomic analyses, phage susceptibility and competition experiments indicate that these genomic differences cannot be considered neutral from an ecological perspective. The results point to the avoidance of competition by micro-niche adaptation and response to viral predation as putative major forces that drive microevolution within these Salinibacter strains. In addition, this work highlights the extent of bacterial functional diversity and environmental adaptation, beyond the resolution of the 16S rRNA and internal transcribed spacers regions.The ISME Journal advance online publication, 18 February 2010; doi:10.1038/ismej.2010.6.

1 aPeña, Arantxa1 aTeeling, Hanno1 aHuerta-Cepas, Jaime1 aSantos, Fernando1 aYarza, Pablo1 aBrito-Echeverría, Jocelyn1 aLucio, Marianna1 aSchmitt-Kopplin, Philippe1 aMeseguer, Inmaculada1 aSchenowitz, Chantal1 aDossat, Carole1 aBarbe, Valerie1 aDopazo, Joaquín1 aRosselló-Mora, Ramon1 aSchüler, Margarete1 aGlöckner, Frank, Oliver1 aAmann, Rudolf1 aGabaldón, Toni1 aAntón, Josefa uhttps://clinbioinfosspa.es/content/fine-scale-evolution-genomic-phenotypic-and-ecological-differentiation-two-coexisting02515nas a2200337 4500008004100000022001400041245007300055210006900128260001600197300000800213490000600221520148900227653001501716653002301731653002401754653003001778653002301808653002101831653002401852653001301876653002001889653002801909100002501937700002101962700002001983700002402003700001902027700002002046700002002066856009102086 2007 eng d a1471-210500aFrom genes to functional classes in the study of biological systems.0 aFrom genes to functional classes in the study of biological syst c2007 Apr 03 a1140 v83 a

BACKGROUND: With the popularization of high-throughput techniques, the need for procedures that help in the biological interpretation of results has increased enormously. Recently, new procedures inspired in systems biology criteria have started to be developed.

RESULTS: Here we present FatiScan, a web-based program which implements a threshold-independent test for the functional interpretation of large-scale experiments that does not depend on the pre-selection of genes based on the multiple application of independent tests to each gene. The test implemented aims to directly test the behaviour of blocks of functionally related genes, instead of focusing on single genes. In addition, the test does not depend on the type of the data used for obtaining significance values, and consequently different types of biologically informative terms (gene ontology, pathways, functional motifs, transcription factor binding sites or regulatory sites from CisRed) can be applied to different classes of genome-scale studies. We exemplify its application in microarray gene expression, evolution and interactomics.

CONCLUSION: Methods for gene set enrichment which, in addition, are independent from the original data and experimental design constitute a promising alternative for the functional profiling of genome-scale experiments. A web server that performs the test described and other similar ones can be found at: http://www.babelomics.org.

10aAlgorithms10aChromosome Mapping10aComputer Simulation10aGene Expression Profiling10aModels, Biological10aMultigene Family10aSignal Transduction10aSoftware10aSystems biology10aUser-Computer Interface1 aAl-Shahrour, Fátima1 aArbiza, Leonardo1 aDopazo, Hernán1 aHuerta-Cepas, Jaime1 aMinguez, Pablo1 aMontaner, David1 aDopazo, Joaquin uhttps://clinbioinfosspa.es/content/genes-functional-classes-study-biological-systems-0