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

Acciones para categorizar profesores de Educación Física como árbitros y jueces en deportes motivo de estudio (Original)

In Cuba the strategies applied to improve the quality of education involve new requirements to achieve the categorization Physical Education professors as referees and judges in the study-motive sports as a parameter of efficient performance in the teaching- learning process of each institution. As a methodological foundation of this research the materialist-dialectic method is used as well as methods of theoretical and empiric level that allowed the fulfillment of the proposed objectives. As consequence, in this article results of the diagnosis are offered as a foundation of the problémica situation as well as the actions to categorize Physical Education professors as referees and judges in the study-motive sports. The effects of its partial application show transformation and effectivity of the proposal of the actions conceived as a scientific result.En Cuba, las estrategias aplicadas para mejorar la calidad de la educación, plantean nuevas demandas para lograr la categorización de los profesores de Educación Física como árbitros y jueces de los deportes motivo estudio como un parámetro de desempeño eficiente dentro del proceso docente educativo de cada institución. Se emplea como base metodológica de la investigación el método dialéctico-materialista, así como métodos del nivel teórico&nbsp; y del nivel empírico que permitieron el cumplimiento de los objetivos propuestos. En consecuencias en el presente artículo se ofrecen los resultados del diagnóstico que fundamentan la situación problémica así como las acciones para categorizar a los profesores de Educación Física como&nbsp; árbitros y jueces en deportes motivo de estudio. Los efectos de su aplicación parcial revelan las transformaciones y efectividad de la propuesta de las acciones concebidas como resultado científico

Draft genome sequence of Pseudomonas stutzeri strain B1SMN1, a nitrogen-fixing and naphthalene-degrading strain isolated from wastewater

Peer Reviewe

Meningioma vs. migraña.Reporte de caso

Introducción: Los meningiomas son tumores benignos que se originan en células aracnoideas y como consecuencia pueden crecer en cualquier lugar donde exista duramadre. Suelen aparecer generalmente entre los 35 y 55 años de edad y son más frecuentes en mujeres.Objetivo: Presentar un caso clínico cuyo diagnóstico pudo realizarse antes teniendo en cuenta la forma de presentación.Caso clínico: Mujer de 38 años de edad con antecedentes de estar diagnosticada de migraña de más de 1 año de evolución y que ingresa en el Servicio de Medicina Interna del Hospital General Docente Enrique Cabrera, de La Habana, con síntomas en los últimos 3 meses de intensificación de la cefalea y modificación de sus características, con hipertensión intracraneal y focalización motora. El examen clínico y la realización de TAC definen el diagnóstico y se corrobora con tratamiento quirúrgico. Posterior al tratamiento evoluciona satisfactoriamente.Conclusiones. Un correcto interrogatorio y examen del paciente, y el uso adecuado y preciso de las imágenes en los diagnósticos reduce la posibilidad de errores en la práctica clínica.Palabras clave: cefalea, hipertensión intracraneal, meningioma, tumores intracraneales, tomografía axial computarizada (TAC)</p

Living a Pandemic

SARS-CoV-2 first appeared in Wuhan (China) in December 2019 and from that moment it spread throughout the rest of the world causing a pandemic such as had not been seen recently. A rapid virus diagnosis and appropriate infection prevention measures have been seen to be the fundamental tools to contain the virus. This article describes how this pandemic was experienced from a laboratory of Virology.El SARS-CoV-2 apareció por primera vez en diciembre de 2019 en Wuhan (China) y desde ese momento se expandió por el resto del mundo causando una pandemia como no se había visto recientemente. El rápido diagnóstico del virus y las medidas de prevención de la infección se ha visto que son las herramientas fundamentales para contener el virus. En este artículo se relata cómo se vivió esta pandemia desde un laboratorio de virología

Scarce evidence of the causal role of germline mutations in UNC5C in hereditary colorectal cancer and polyposis

Germline mutations in UNC5C have been suggested to increase colorectal cancer (CRC) risk, thus causing hereditary CRC. However, the evidence gathered thus far is insufficient to include the study of the UNC5C gene in the routine genetic testing of familial CRC. Here we aim at providing a more conclusive answer about the contribution of germline UNC5C mutations to genetically unexplained hereditary CRC and/or polyposis cases. To achieve this goal we sequenced the coding region and exon-intron boundaries of UNC5C in 544 familial CRC or polyposis patients (529 families), using a technique that combines pooled DNA amplification and massively parallel sequencing. A total of eight novel or rare variants, all missense, were identified in eight families. Co-segregation data in the families and association results in case-control series are not consistent with a causal effect for 7 of the 8 identified variants, including c.1882_1883delinsAA (p.A628K), previously described as a disease-causing mutation. One variant, c.2210G > A (p.S737N), remained unclassified. In conclusion, our results suggest that the contribution of germline mutations in UNC5C to hereditary colorectal cancer and to polyposis cases is negligible

Association between long term exposure to particulate matter and incident hypertension in Spain

Exposure to air particulate matter has been linked with hypertension and blood pressure levels. The metabolic risks of air pollution could vary according to the specific characteristics of each area, and has not been sufficiently evaluated in Spain. We analyzed 1103 individuals, participants in a Spanish nationwide population based cohort study ([email protected]), who were free of hypertension at baseline (2008-2010) and completed a follow-up exam of the cohort (2016-2017). Cohort participants were assigned air pollution concentrations for particulate matter < 10 mu m (PM10) and < 2.5 mu m (PM2.5) during follow-up (2008-2016) obtained through modeling combined with measurements taken at air quality stations (CHIMERE chemistry-transport model). Mean and SD concentrations of PM10 and PM2.5 were 20.17 +/- 3.91 mu g/m(3) and 10.83 +/- 2.08 mu g/m(3) respectively. During follow-up 282 cases of incident hypertension were recorded. In the fully adjusted model, compared with the lowest quartile of PM10, the multivariate weighted ORs (95% CIs) for developing hypertension with increasing PM10 exposures were 0.82 (0.59-1.14), 1.28 (0.93-1.78) and 1.45 (1.05-2.01) in quartile 2, 3 and 4 respectively (p for a trend of 0.003). The corresponding weighted ORs according to PM2.5 exposures were 0.80 (0.57-1.13), 1.11 (0.80-1.53) and 1.48 (1.09-2.00) (p for trend 0.004). For each 5-mu g/m(3) increment in PM10 and PM2.5 concentrations, the odds for incident hypertension increased 1.22 (1.06-1.41) p = 0.007 and 1.39 (1.07-1.81) p = 0.02 respectively. In conclusion, our study contributes to assessing the impact of particulate pollution on the incidence of hypertension in Spain, reinforcing the need for improving air quality as much as possible in order to decrease the risk of cardiometabolic disease in the population

Degradació aeròbica d’hidrocarburs aromàtics per Pseudomonas i Roseobacters

Abstract not availabl

Aprendizaje-servicio y Trabajo Social

Es una propuesta metodológica aplicada a los estudios de Trabajo Social. Su objetivo es incorporar el método aprendizaje-servicio a la docencia presencial para incrementar el interés y la satisfacción de la comunidad científica y la sociedad civil