Spiking buildings to avoid house martin (Delichon urban) nesting: is it a good choice?

Duarte, J., Farfán, M.A.,Vargas, J.M

Landfill habitat restoration can reduce the incidence of vertebrate pest species

Duarte, J., Zurita, F., Farfán, M.A., Vargas, J.M

Divergent evolution and purifying selection of the flaA gene sequences in Aeromonas

<p>Abstract</p> <p>Background</p> <p>The bacterial flagellum is the most important organelle of motility in bacteria and plays a key role in many bacterial lifestyles, including virulence. The flagellum also provides a paradigm of how hierarchical gene regulation, intricate protein-protein interactions and controlled protein secretion can result in the assembly of a complex multi-protein structure tightly orchestrated in time and space. As if to stress its importance, plants and animals produce receptors specifically dedicated to the recognition of flagella. Aside from motility, the flagellum also moonlights as an adhesion and has been adapted by humans as a tool for peptide display. Flagellar sequence variation constitutes a marker with widespread potential uses for studies of population genetics and phylogeny of bacterial species.</p> <p>Results</p> <p>We sequenced the complete flagellin gene <it>(flaA</it>) in 18 different species and subspecies of <it>Aeromonas</it>. Sequences ranged in size from 870 (<it>A. allosaccharophila</it>) to 921 nucleotides (<it>A. popoffii</it>). The multiple alignment displayed 924 sites, 66 of which presented alignment gaps. The phylogenetic tree revealed the existence of two groups of species exhibiting different FlaA flagellins (FlaA1 and FlaA2). Maximum likelihood models of codon substitution were used to analyze <it>flaA </it>sequences. Likelihood ratio tests suggested a low variation in selective pressure among lineages, with an ω ratio of less than 1 indicating the presence of purifying selection in almost all cases. Only one site under potential diversifying selection was identified (isoleucine in position 179). However, 17 amino acid positions were inferred as sites that are likely to be under positive selection using the branch-site model. Ancestral reconstruction revealed that these 17 amino acids were among the amino acid changes detected in the ancestral sequence.</p> <p>Conclusion</p> <p>The models applied to our set of sequences allowed us to determine the possible evolutionary pathway followed by the <it>flaA </it>gene in <it>Aeromonas</it>, suggesting that this gene have probably been evolving independently in the two groups of <it>Aeromonas </it>species since the divergence of a distant common ancestor after one or several episodes of positive selection.</p> <p>Reviewers</p> <p>This article was reviewed by Alexey Kondrashov, John Logsdon and Olivier Tenaillon (nominated by Laurence D Hurst).</p

Modelado numérico para estudiar interfases fluido-sólidas ante excitaciones dinámicas

ResumenEste trabajo trata sobre la propagación de ondas en interfases fluido-sólidas debidas a excitaciones dinámicas, que son conocidas como ondas de Scholte. Se ha estudiado una amplia gama de materiales sólidos elásticos empleados en la ingeniería. La interfase une un medio acústico (fluido) y otro sólido. Se ha demostrado que por medio de un análisis de ondas difractadas en un fluido es posible deducir las características mecánicas del medio sólido, específicamente sus velocidades de propagación. Para este propósito, el campo difractado de onda de presión y desplazamientos, debido a una onda inicial de presión en el fluido, se expresa mediante las representaciones integrales de frontera, las cuales satisfacen la ecuación de movimiento. La presión inicial en el fluido es representada mediante una función de Hankel de segunda especie y orden cero. La solución a este problema de propagación de ondas se obtiene por medio del método indirecto de elementos frontera, que es equivalente al bien conocido teorema de representación de Somigliana. La validación de los resultados se realiza por medio del método del número de onda discreto. En primer lugar, se muestran espectros de presiones que ilustran el comportamiento del fluido para cada material sólido considerado, y después se aplica la transformada rápida de Fourier para mostrar los resultados en el dominio del tiempo, donde se ejemplifica la aparición de las ondas de Scholte y la cantidad de energía que transportan.AbstractThis work shows the wave propagation in fluid-solid interfaces due to dynamic excitations, such interface waves are known as Scholte's waves. We studied a wide range of elastic solid materials used in engineering. The interface connects an acoustic medium (fluid) and another solid. It has been shown that by means of an analysis of diffracted waves in a fluid, it is possible to deduce the mechanical characteristics of the solid medium, specifically, its propagation velocities. For this purpose, the diffracted field of pressures and displacements, due to an initial pressure in the fluid, are expressed using boundary integral representations, which satisfy the equation of motion. The initial pressure in the fluid is represented by a Hankel's function of second kind and zero order. The solution to this problem of wave propagation is obtained by means of the Indirect Boundary Element Method, which is equivalent to the well-known Somigliana's representation theorem. The validation of the results was performed by means of the Discrete Wave Number Method. Firstly, spectra of pressures to illustrate the behavior of the fluid for each solid material considered are included, then, the Fast Fourier Transform algorithm to display the results in the time domain is applied, where the emergence of Scholte's waves and the amount of energy that they carry are highlighted

Harvard y otros centros de prestigio, más cerca de las universidades españolas gracias al programa IM

El programa IMP es una iniciativa española que se encuadra dentro de una mayor, IMFAHE (International Mentoring Foundation for the Advancement of Higher Education).IMP ha creado una red de talento español en el extranjero, presente en 4 continentes del mundo, que pretende conectar el talento en el extranjero con estu- diantes de universidades españolas para guiarles en su desarrollo profesional. Todo esto sin ánimo de lucro, consiguiendo ?nanciación a través de la colaboración con las universidades y distintas entidades

Distribution modelling of wild rabbit hunting yields in its original area (S Iberian Peninsula)

In this work we used the information of the Annual Hunting Reports (AHRs) to obtain a high-resolution model of the potential favourableness for wild rabbit harvesting in Andalusia (southern Spain), using environmental and land-use variables as predictors. We analysed 32,134 AHRs from the period 1993/2001 reported by 6049 game estates to estimate the average hunting yields of wild rabbit in each Andalusian municipality (n5771). We modelled the favourableness for obtaining good hunting yields using stepwise logistic regression on a set of climatic, orographical, land use, and vegetation variables. The favourability equation was used to create a downscaled image representing the favourableness of obtaining good hunting yields for the wild rabbit in 161 km squares in Andalusia, using the Idrisi Image Calculator. The variables that affected hunting yields of wild rabbit were altitude, dry wood crops (mainly olive groves, almond groves, and vineyards), temperature, pasture, slope, and annual number of frost days. The 161 km squares with high favourableness values are scattered throughout the territory, which seems to be caused mainly by the effect of vegetation. Finally, we obtained quality categories for the territory by combining the probability values given by logistic regression with those of the environmental favourability function

Allelic diversity and population structure in Vibrio cholerae O139 Bengal based on nucleotide sequence analysis

Comparative analysis of gene fragments of six housekeeping loci, distributed around the two chromosomes of Vibrio cholerae, has been carried out for a collection of 29 V. cholerae O139 Bengal strains isolated from India during the first epidemic period (1992 to 1993). A toxigenic O1 ElTor strain from the seventh pandemic and an environmental non-O1/non-O139 strain were also included in this study. All loci studied were polymorphic, with a small number of polymorphic sites in the sequenced fragments. The genetic diversity determined for our O139 population is concordant with a previous multilocus enzyme electrophoresis study in which we analyzed the same V. cholerae O139 strains. In both studies we have found a higher genetic diversity than reported previously in other molecular studies. The results of the present work showed that O139 strains clustered in several lineages of the dendrogram generated from the matrix of allelic mismatches between the different genotypes, a finding which does not support the hypothesis previously reported that the O139 serogroup is a unique clone. The statistical analysis performed in the V. cholerae O139 isolates suggested a clonal population structure. Moreover, the application of the Sawyer's test and split decomposition to detect intragenic recombination in the sequenced gene fragments did not indicate the existence of recombination in our O139 population

Divergent evolution and purifying selection of the flaA gene sequences in Aeromonas

BACKGROUND: The bacterial flagellum is the most important organelle of motility in bacteria and plays a key role in many bacterial lifestyles, including virulence. The flagellum also provides a paradigm of how hierarchical gene regulation, intricate protein-protein interactions and controlled protein secretion can result in the assembly of a complex multi-protein structure tightly orchestrated in time and space. As if to stress its importance, plants and animals produce receptors specifically dedicated to the recognition of flagella. Aside from motility, the flagellum also moonlights as an adhesion and has been adapted by humans as a tool for peptide display. Flagellar sequence variation constitutes a marker with widespread potential uses for studies of population genetics and phylogeny of bacterial species. RESULTS: We sequenced the complete flagellin gene (flaA) in 18 different species and subspecies of Aeromonas. Sequences ranged in size from 870 (A. allosaccharophila) to 921 nucleotides (A. popoffii). The multiple alignment displayed 924 sites, 66 of which presented alignment gaps. The phylogenetic tree revealed the existence of two groups of species exhibiting different FlaA flagellins (FlaA1 and FlaA2). Maximum likelihood models of codon substitution were used to analyze flaA sequences. Likelihood ratio tests suggested a low variation in selective pressure among lineages, with an omega ratio of less than 1 indicating the presence of purifying selection in almost all cases. Only one site under potential diversifying selection was identified (isoleucine in position 179). However, 17 amino acid positions were inferred as sites that are likely to be under positive selection using the branch-site model. Ancestral reconstruction revealed that these 17 amino acids were among the amino acid changes detected in the ancestral sequence. CONCLUSION: The models applied to our set of sequences allowed us to determine the possible evolutionary pathway followed by the flaA gene in Aeromonas, suggesting that this gene have probably been evolving independently in the two groups of Aeromonas species since the divergence of a distant common ancestor after one or several episodes of positive selection. REVIEWERS: This article was reviewed by Alexey Kondrashov, John Logsdon and Olivier Tenaillon (nominated by Laurence D Hurst)

Biochemical identification and numerical taxonomy of Aeromonas spp. isolated from environmental and clinical samples in Spain

Aims: To study the phenotypic characteristics of Aeromonas spp. from environmental and clinical samples in Spain and to cluster these strains by numerical taxonomy. Methods and Results: A collection of 202 Aeromonas strains isolated from bivalve molluscs, water and clinical samples was tested for 64 phenotypic properties; 91% of these isolates were identified at species level. Aeromonas caviae was predominant in bivalve molluscs and Aerom. bestiarum in freshwater samples. Cluster analyses revealed eight different phena: three containing more than one DNA-DNA hybridization group but including strains that belong to the same phenospecies complex (Aerom. hydrophila, Aerom. sobria and Aerom. caviae), Aerom. encheleia, Aerom. trota and three containing unidentified Aeromonas strains isolated from bivalve molluscs. Conclusions: Aeromonas spp. are widely distributed in environmental and clinical sources. A selection of 16 of the phenotypical tests chosen allowed the identification of most isolates (91%), although some strains remain unidentified, mainly isolates from bivalve molluscs, suggesting the presence of new Aeromonas species. Numerical taxonomy was not in total concordance with the identification of the studied strains. Significance and Impact of the Study: Numerical taxonomy of Aeromonas strains isolated from different sources revealed the presence of potentially pathogenic Aeromonas spp., especially in bivalve molluscs, and phena with unidentified strains that suggest new Aeromonas species

The reference strain Aeromonas hydrophicla CIP 57.50 should be reclassified as Aeromonas salmonicida CIP 57.50

The use of reference strains is a critical element for the quality control of different assays, from the development of molecular methods to the evaluation of antimicrobial activities. Most of the strains used in these assays are not type strains and some of them are cited erroneously because of subsequent reclassifications and descriptions of novel species. In this study, we propose that the reference strain Aeromonas hydrophila CIP 57.50 be reclassified as Aeromonas salmonicida CIP 57.50 based on phenotypic characterization and sequence analyses of the cpn60, dnaJ, gyrB and rpoD genes