primers4clades: a web server that uses phylogenetic trees to design lineage-specific PCR primers for metagenomic and diversity studies

Primers4clades is an easy-to-use web server that implements a fully automatic PCR primer design pipeline for cross-species amplification of novel sequences from metagenomic DNA, or from uncharacterized organisms, belonging to user-specified phylogenetic clades or taxa. The server takes a set of non-aligned protein coding genes, with or without introns, aligns them and computes a neighbor-joining tree, which is displayed on screen for easy selection of species or sequence clusters to design lineage-specific PCR primers. Primers4clades implements an extended CODEHOP primer design strategy based on both DNA and protein multiple sequence alignments. It evaluates several thermodynamic properties of the oligonucleotide pairs, and computes the phylogenetic information content of the predicted amplicon sets from Shimodaira–Hasegawa-like branch support values of maximum likelihood phylogenies. A non-redundant set of primer formulations is returned, ranked according to their thermodynamic properties. An amplicon distribution map provides a convenient overview of the coverage of the target locus. Altogether these features greatly help the user in making an informed choice between alternative primer pair formulations. Primers4clades is available at two mirror sites: http://maya.ccg.unam.mx/primers4clades/and http://floresta.eead.csic.es/primers4clades/. Three demo data sets and a comprehensive documentation/tutorial page are provided for easy testing of the server's capabilities and interface

El grau de satisfacció dels usuaris i la seva relació amb la qualitat del servei, al programa de senderisme de la Diputació de Granada. Anàlisi i estudi dels diferents programes de senderisme a la província de Granada

Els gestors esportius han de garantir l’eficiència i l’eficàcia dels recursos públics assignats als serveis esportius, basant-se en estudis sistemàtics, que impedeixin de deixar coses a l’atzar. De la mateixa manera, les polítiques socials, que permeten aquests serveis, han de garantir la satisfacció de necessitats socials reals i ajustades a cada realitat en particular. Realitat que es viu diferent entre la població d’una Entitat Local, i encara més entre poblacions de diferents Entitats Locals. Per això, el tipus d’informació que cal aplegar és qualitatiu, atès que s’han de conèixer els sentiments, opinions, motius, necessitats, expectatives, desigs per practicar un tipus d’activitat física i/o esport. Caldrà conèixer les eines, els mitjans necessaris per aconseguir aquesta informació. Això permetrà d’assignar recursos i esforços a millorar les característiques a les quals hom atribueix més importància i eliminar els esforços en les valorades com a no importants i que no estan donant satisfacció als senderistes. L’estudi se centra en l’anàlisi de l’oferta pública de 12 Entitats Locals Granadines que ofereixen el servei esportiu de senderisme en la temporada 2002-2003. Es va estudiar, entre d’altres coses, la valoració de qualitat de cada un, i també la satisfacció que reportava als senderistes. Els tres qüestionaris utilitzats van ser els següents: Qüestionari 1. Per estudiar la banda de tolerància de les dimensions de qualitat de cada programa de senderisme per als seus usuaris. Creat i validat en el procés d’investigació. Els instruments que es van utilitzar van ser l’entrevista telefònica i el qüestionari autogestionat per realitzar l’observació sociològica. Per delimitar-ne la llista de dimen­sions de qualitat, es va utilitzar el mètode de l’incident crític. Aquest mètode es basa a identificar sota aquesta terminologia les descripcions, tant positives com negatives, que el client fa sobre el servei. Qüestionari 2. Per conèixer el perfil del senderista granadí. Aquest qüestionari es va desenvolupar a través de preguntes sociodemogràfiques i psicogràfiques. A més a més, es van formular preguntes per conèixer el judici de satisfacció i qualitat global, i preguntes per conèixer la fidelitat del senderista al programa de senderisme que realitzava. Qüestionari 3. Anomenat MODE, per estudiar les motiva­cions esportives que porten el senderista a realitzar l’esport

High-resolution simulations of a turbulent boundary layer impacting two obstacles in tandem

High-fidelity large-eddy simulations of the flow around two rectangular obstacles are carried out at a Reynolds number of 10 000 based on the freestream velocity and the obstacle height. The incoming flow is a developed turbulent boundary layer. Mean-velocity components, turbulence fluctuations, and the terms of the turbulent-kinetic-energy budget are analyzed for three flow regimes: skimming flow, wake interference, and isolated roughness. Three regions are identified where the flow undergoes the most significant changes: the first obstacle's wake, the region in front of the second obstacle, and the region around the second obstacle. In the skimming-flow case, turbulence activity in the cavity between the obstacles is limited and mainly occurs in a small region in front of the second obstacle. In the wake-interference case, there is a strong interaction between the freestream flow that penetrates the cavity and the wake of the first obstacle. This interaction results in more intense turbulent fluctuations between the obstacles. In the isolated-roughness case, the wake of the first obstacle is in good agreement with that of an isolated obstacle. Separation bubbles with strong turbulent fluctuations appear around the second obstacle

High-resolution large-eddy simulations of simplified urban flows

High-fidelity large-eddy simulations of the flow around two rectangular obstacles are carried out at a Reynolds number of 10,000 based on the free-stream velocity and the obstacle height. The incoming flow is a developed turbulent boundary layer. Mean-velocity components, turbulence fluctuations, and the terms of the turbulent-kinetic-energy budget are analyzed for three flow regimes: skimming flow, wake interference, and isolated roughness. Three regions are identified where the flow undergoes the most significant changes: the first obstacle's wake, the region in front of the second obstacle, and that around the second obstacle. In the skimming-flow case, turbulence activity in the cavity between the obstacles is limited and mainly occurs in a small region in front of the second obstacle. In the wake-interference case, there is a strong interaction between the free-stream flow that penetrates the cavity and the wake of the first obstacle. This interaction results in more intense turbulent fluctuations between the obstacles. In the isolated-roughness case, the wake of the first obstacle is in good agreement with that of an isolated obstacle. Separation bubbles with strong turbulent fluctuations appear around the second obstacle

Social representations of climate change in a group of college students from the University of Santiago de Compostela: common culture vs. scientific culture

College students are a sector of the population that is called to play a fundamental role in the future societies. This responsibility with and for society cannot obviate humanity's main challenge nowadays, the anthropogenic climate change. To this end, it is necessary to understand the climatic problem in all its dimensions, in order to propose and accept strategies and measures of adaptation and mitigation. In this paper we present a research on college students of the Universidade de Santiago de Compostela (N = 644). A closedend questionnaire was used to explore college students´ climate literacy level. Outcomes were compared according to academic discipline and year course. There were statistically significant differences in the distributions of responses (ANOVA) between areas of knowledge and of university degree fields. Nevertheless, in the case of comparing 1st year students with 4th year students there is not statistical significance. Outcomes suggest that most of the information with which college students build their representation of climate change comes from their stage in secondary education and experiences out of the educational system

Caracterización de la investigación educativa sobre el cambio climático y los estudiantes de educación secundaria

Trabajo realizado en el marco del proyecto Resclima, dentro del grupo de investigación en Pedagoxía Social e Educación Ambiental, SEPA-interea (GI-1447)La finalidad de este estudio es aportar evidencias bibliométricas que permitan caracterizar la investigación educativa sobre la representación del cambio climático en alumnado de educación secundaria (12-18 años). A través de una revisión sistematizada se seleccionaron 84 artículos (1993-2017) sobre los que se realizó un análisis bibliométrico. Se recurrió a las bases de datos Scopus y Web of Science para artículos publicados en inglés, y a Redalyc, Scielo y Dialnet para los de castellano, portugués y gallego. Se ofrecen resultados sobre tendencias de publicación por año, país y revista, así como sobre el perfil de los principales autores, las referencias bibliográficas utilizadas y las palabras clave como indicadoras de sus orientaciones metodológicas y temáticasThe purpose of this study is to contribute bibliometric evidence that permits characterizing educational research on the representation of climate change among secondary school students (ages 12 to 18). Through a systematized review, 84 articles were selected (1993-2017) for the bibliometric analysis. The Scopus and Web of Science databases were used for articles published in English, and Redalyc, Scielo, and Dialnet for articles published in Spanish, Portuguese, and the Galician language. Publication trends are given by year, by nation, and by journal, as well as author profiles, bibliographic references, and keywords as indicators of methodological and thematic orientationsEDU 2015-63572-P. Ministerio de Economía y Competitividad (Cofinanciamiento con fondos FEDER - Programa Operativo 2014-2020)S

Genomic lineages of Rhizobium etli revealed by the extent of nucleotide polymorphisms and low recombination

<p>Abstract</p> <p>Background</p> <p>Most of the DNA variations found in bacterial species are in the form of single nucleotide polymorphisms (SNPs), but there is some debate regarding how much of this variation comes from mutation versus recombination. The nitrogen-fixing symbiotic bacteria <it>Rhizobium etli </it>is highly variable in both genomic structure and gene content. However, no previous report has provided a detailed genomic analysis of this variation at nucleotide level or the role of recombination in generating diversity in this bacterium. Here, we compared draft genomic sequences versus complete genomic sequences to obtain reliable measures of genetic diversity and then estimated the role of recombination in the generation of genomic diversity among <it>Rhizobium etli</it>.</p> <p>Results</p> <p>We identified high levels of DNA polymorphism in <it>R. etli</it>, and found that there was an average divergence of 4% to 6% among the tested strain pairs. DNA recombination events were estimated to affect 3% to 10% of the genomic sample analyzed. In most instances, the nucleotide diversity (π) was greater in DNA segments with recombinant events than in non-recombinant segments. However, this degree of recombination was not sufficiently large to disrupt the congruence of the phylogenetic trees, and further evaluation of recombination in strains quartets indicated that the recombination levels in this species are proportionally low.</p> <p>Conclusion</p> <p>Our data suggest that <it>R. etli </it>is a species composed of separated lineages with low homologous recombination among the strains. Horizontal gene transfer, particularly via the symbiotic plasmid characteristic of this species, seems to play an important role in diversity but the lineages maintain their evolutionary cohesiveness.</p