Les coses que no tene preu, amb Antoni Alcover, Xavier Pastor, Joan David Tàbara, Frances Triay i Andreu Ramis

Abstract not availabl

PseudoMLSA: a database for multigenic sequence analysis of Pseudomonas species

<p>Abstract</p> <p>Background</p> <p>The genus <it>Pseudomonas </it>comprises more than 100 species of environmental, clinical, agricultural, and biotechnological interest. Although, the recommended method for discriminating bacterial species is DNA-DNA hybridisation, alternative techniques based on multigenic sequence analysis are becoming a common practice in bacterial species discrimination studies. Since there is not a general criterion for determining which genes are more useful for species resolution; the number of strains and genes analysed is increasing continuously. As a result, sequences of different genes are dispersed throughout several databases. This sequence information needs to be collected in a common database, in order to be useful for future identification-based projects.</p> <p>Description</p> <p>The PseudoMLSA Database is a comprehensive database of multiple gene sequences from strains of <it>Pseudomonas </it>species. The core of the database is composed of selected gene sequences from all <it>Pseudomonas </it>type strains validly assigned to the genus through 2008. The database is aimed to be useful for MultiLocus Sequence Analysis (MLSA) procedures, for the identification and characterisation of any <it>Pseudomonas </it>bacterial isolate. The sequences are available for download via a direct connection to the National Center for Biotechnology Information (NCBI). Additionally, the database includes an online BLAST interface for flexible nucleotide queries and similarity searches with the user's datasets, and provides a user-friendly output for easily parsing, navigating, and analysing BLAST results.</p> <p>Conclusions</p> <p>The PseudoMLSA database amasses strains and sequence information of validly described <it>Pseudomonas </it>species, and allows free querying of the database via a user-friendly, web-based interface available at <url>http://www.uib.es/microbiologiaBD/Welcome.html</url>. The web-based platform enables easy retrieval at strain or gene sequence information level; including references to published peer-reviewed articles, and direct external links to more specialized strain information databases (StrainInfo) and GeneBank (NCBI). The PseudoMLSA is intended to provide helpful strain-sequence information for a better and more comprehensive discriminative multigenic sequence based analysis of this special group of bacteria, contributing to enhance our understanding of the evolution of <it>Pseudomonas </it>species.</p

Phylogenomics and systematics in Pseudomonas

© 2015 Gomila, Peña, Mulet, Lalucat and García-Valdés. The genus Pseudomonas currently contains 144 species, making it the genus of Gram-negative bacteria that contains the largest number of species. Currently, multilocus sequence analysis (MLSA) is the preferred method for establishing the phylogeny between species and genera. Four partial gene sequences of housekeeping genes (16S rRNA, gyrB, rpoB, and rpoD) were obtained from 112 complete or draft genomes of strains related to the genus Pseudomonas that were available in databases. These genes were analyzed together with the corresponding sequences of 133 Pseudomonas type strains of validly published species to assess their correct phylogenetic assignations. We confirmed that 30% of the sequenced genomes of non-type strains were not correctly assigned at the species level in the accepted taxonomy of the genus and that 20% of the strains were not identified at the species level. Most of these strains had been isolated and classified several years ago, and their taxonomic status has not been updated by modern techniques. MLSA was also compared with indices based on the analysis of whole-genome sequences that have been proposed for species delineation, such as tetranucleotide usage patterns (TETRA), average nucleotide identity (ANIm, based on MUMmer and ANIb, based on BLAST) and genome-to-genome distance (GGDC). TETRA was useful for discriminating Pseudomonas from other genera, whereas ANIb and GGDC clearly separated strains of different species. ANIb showed the strongest correlation with MLSA. The correct species classification is a prerequisite for most diversity and evolutionary studies. This work highlights the necessity for complete genomic sequences of type strains to build a phylogenomic taxonomy and that all new genome sequences submitted to databases should be correctly assigned to species to avoid taxonomic inconsistencies.Financial support was obtained from the Spanish MINECO through projects CGL2011-24318 and Consolider CSD2009-00006, as well as funds for competitive research groups from the Government of the Balearic Islands (the last two funds with FEDER cofunding). MG and AP were supported by a postdoctoral contract from the University of the Balearic IslandsPeer Reviewe

Degradació aeròbica d’hidrocarburs aromàtics per Pseudomonas i Roseobacters

Abstract not availabl

Sharing, Living Together and Understanding. A Journey Through our Experiences

S’exposen les metodologies i objectius d’un recull d’experiències educatives que ajuden als infants a comprendre el món mitjançant l’ús d’eines i recursos culturals matemàtics. Aquestes experiències s’han realitzat amb nins d’Educació Infantil de diferents escoles públiques de les Illes Balears. Així mateix, dues experiències, Xishun i Codi de barres, s’han realitzat amb alumnat de primer cicle d’Educació PrimàriaSe exponen las metodologías y objetivos de una recopilación de experiencias educativas que ayudan a los niños a comprender el mundo mediante el uso de herramientas y recursos culturales matemáticos. Estas experiencias se han realizado con niños de Educación Infantil de diferentes escuelas públicas de las Illes Balears. Asimismo, dos experiencias: Xishun y Código de barras, se han realizado con alumnado de primer ciclo de Educación Primaria.This paper presents the methodologies and objectives of a collection of educational experiences that help children understand the world and ourselves through the use of mathematical and cultural tools and resources. These experiences were implemented with 3, 4 and 5-year-old preschool children in different Balearic schools and two of them, “Xishun” and “Codi de Barres”, were implemented with first-cycle primary school students

The Copernicus Marine Environment Monitoring Service Ocean State Report

The Copernicus Marine Environment Monitoring Service (CMEMS) Ocean State Report (OSR) provides an annual report of the state of the global ocean and European regional seas for policy and decision-makers with the additional aim of increasing general public awareness about the status of, and changes in, the marine environment. The CMEMS OSR draws on expert analysis and provides a 3-D view (through reanalysis systems), a view from above (through remote-sensing data) and a direct view of the interior (through in situ measurements) of the global ocean and the European regional seas. The report is based on the unique CMEMS monitoring capabilities of the blue (hydrography, currents), white (sea ice) and green (e.g. Chlorophyll) marine environment. This first issue of the CMEMS OSR provides guidance on Essential Variables, large-scale changes and specific events related to the physical ocean state over the period 1993–2015. Principal findings of this first CMEMS OSR show a significant increase in global and regional sea levels, thermosteric expansion, ocean heat content, sea surface temperature and Antarctic sea ice extent and conversely a decrease in Arctic sea ice extent during the 1993–2015 period. During the year 2015 exceptionally strong large-scale changes were monitored such as, for example, a strong El Niño Southern Oscillation, a high frequency of extreme storms and sea level events in specific regions in addition to areas of high sea level and harmful algae blooms. At the same time, some areas in the Arctic Ocean experienced exceptionally low sea ice extent and temperatures below average were observed in the North Atlantic Ocean

Análisis de secuencias multilocus en estudios de taxonomía, filogenia y evolución de Pseudomonas

[spa] El género Pseudomonas comprende muchas especies de interés ambiental, clínico, agrícola o biotecnológico. A pesar de estar bien definido desde los puntos de vista fenotípico y genotípico se están describiendo continuamente nuevas especies dentro del género. La enorme diversidad genética de algunas de las especies del género está claramente demostrada, como sucede en P. stutzeri y hay que ver cómo se manifiesta en otras especies del género. El método actualmente aceptado para discriminar entre especies bacterianas es la hibridación DNA-DNA, pero este método tiene sus limitaciones (tiempo requerido, necesidad de experiencia en desarrollo, no define distancias entre especies, no es acumulativo). En este proyecto proponemos el desarrollo de un nuevo método, fiable y acumulativo para la definición de especies en el género Pseudomonas, basado en la técnica de tipado multilocus de secuencias (MLST). La enorme diversidad genética de las especies de este género ha hacen un banco de pruebas ideal en el que se pueden validar nuevos métodos. La técnica de MLST permitirá además elucidar la diversidad genética del género, su filogenia y su taxonomía. Para ello habrá que aplicar nuevas herramientas bioinformáticas. Además, el conjunto de datos debe ser accesible a través de Internet y, para que sea útil a la comunidad científica, debe ir acompañado de una buena colección de microorganismos que aseguren el material biológico necesario para estudios comparativos

Genomics in Bacterial Taxonomy: Impact on the Genus Pseudomonas

This article belongs to the Section Microbial Genetics and Genomics.The introduction of genomics is profoundly changing current bacterial taxonomy. Phylogenomics provides accurate methods for delineating species and allows us to infer the phylogeny of higher taxonomic ranks as well as those at the subspecies level. We present as a model the currently accepted taxonomy of the genus Pseudomonas and how it can be modified when new taxonomic methodologies are applied. A phylogeny of the species in the genus deduced from analyses of gene sequences or by whole genome comparison with different algorithms allows three main conclusions: (i) several named species are synonymous and have to be reorganized in a single genomic species; (ii) many strains assigned to known species have to be proposed as new genomic species within the genus; and (iii) the main phylogenetic groups defined by 4-, 100- and 120-gene multilocus sequence analyses are concordant with the groupings in the whole genome analyses. Moreover, the boundaries of the genus Pseudomonas are also discussed based on phylogenomic analyses in relation to other genera in the family Pseudomonadaceae. The new technologies will result in a substantial increase in the number of species and probably split the current genus into several genera or subgenera, although these classifications have to be supported by a polyphasic taxonomic approach.This research was funded by the Spanish Ministry of Economy and Competitiveness, grant number CGK2015-70925, co-funded by the European Regional Development Fund/European Social Fund ‘Investing in your future’ (FEDER)