El sector frutihortícola

En el presente trabajo se analizan los distintos organismos de control sanitario y de calidad de los alimentos en nuestro pais y su relación con al industria frutihortícola.Academia Nacional de Agronomía y Veterinari

El sector frutihortícola

En el presente trabajo se analizan los distintos organismos de control sanitario y de calidad de los alimentos en nuestro pais y su relación con al industria frutihortícola.Academia Nacional de Agronomía y Veterinari

A Reduced Number of mtSNPs Saturates Mitochondrial DNA Haplotype Diversity of Worldwide Population Groups

BACKGROUND: The high levels of variation characterising the mitochondrial DNA (mtDNA) molecule are due ultimately to its high average mutation rate; moreover, mtDNA variation is deeply structured in different populations and ethnic groups. There is growing interest in selecting a reduced number of mtDNA single nucleotide polymorphisms (mtSNPs) that account for the maximum level of discrimination power in a given population. Applications of the selected mtSNP panel range from anthropologic and medical studies to forensic genetic casework. METHODOLOGY/PRINCIPAL FINDINGS: This study proposes a new simulation-based method that explores the ability of different mtSNP panels to yield the maximum levels of discrimination power. The method explores subsets of mtSNPs of different sizes randomly chosen from a preselected panel of mtSNPs based on frequency. More than 2,000 complete genomes representing three main continental human population groups (Africa, Europe, and Asia) and two admixed populations ("African-Americans" and "Hispanics") were collected from GenBank and the literature, and were used as training sets. Haplotype diversity was measured for each combination of mtSNP and compared with existing mtSNP panels available in the literature. The data indicates that only a reduced number of mtSNPs ranging from six to 22 are needed to account for 95% of the maximum haplotype diversity of a given population sample. However, only a small proportion of the best mtSNPs are shared between populations, indicating that there is not a perfect set of "universal" mtSNPs suitable for all population contexts. The discrimination power provided by these mtSNPs is much higher than the power of the mtSNP panels proposed in the literature to date. Some mtSNP combinations also yield high diversity values in admixed populations. CONCLUSIONS/SIGNIFICANCE: The proposed computational approach for exploring combinations of mtSNPs that optimise the discrimination power of a given set of mtSNPs is more efficient than previous empirical approaches. In contrast to precedent findings, the results seem to indicate that only few mtSNPs are needed to reach high levels of discrimination power in a population, independently of its ancestral background

La bioinformática al servicio de la genómica

Este trabajo de tesis aborda distintos ámbitos de aplicación de técnicas bioinformáticas a la resolución de problemas surgidos del manejo, análisis, almacenamiento y consulta de grandes volúmenes de datos genómicos. Los principales retos a los que esta tesis ha tratado de dar respuesta han sido los siguientes: - Procesar la información más básica de las tecnologías de genotipado de alto rendimiento, a fin de permitir obtener de manera rápida y sencilla una serie de parámetros y estadísticas básicas características de un experimento independientemente de la tecnología elegida. - Facilitar la publicación y consulta de resultados de genotipado a baja y media escala, tanto de SNPs como de STRs, así como su interacción con los repositorios de variabilidad accesibles públicamente. - Estudiar la viabilidad de gestionar localmente un repositorio propio de variabilidad humana basado en los recursos disponibles, tanto de información externa como de infraestructura interna. - Transferir el conocimiento obtenido. Aportar herramientas existentes o soluciones ad hoc a los problemas que pueda presentar la investigación genética en el campo de la biología computacional

El español de ?sol y playa?. Reflexiones sobre la docencia de culturemas en E/LE

Esta experiencia práctica pretende explorar la función de asesores culturales quenormalmente desempeñan los auxiliares de conversación en los centros de enseñanzasecundaria de Reino Unido dentro de la docencia en Sixth Form (el equivalente a losdos cursos de Bachillerato LOGSE en España), en especial en su labor de enseñaraspectos culturales que van más allá del ámbito tradicional conocido por los alumnos (elespañol de ?sol y playa? o español básico de supervivencia para venir a España devacaciones)

ENGINES: exploring single nucleotide variation in entire human genomes

<p>Abstract</p> <p>Background</p> <p>Next generation ultra-sequencing technologies are starting to produce extensive quantities of data from entire human genome or exome sequences, and therefore new software is needed to present and analyse this vast amount of information. The 1000 Genomes project has recently released raw data for 629 complete genomes representing several human populations through their Phase I interim analysis and, although there are certain public tools available that allow exploration of these genomes, to date there is no tool that permits comprehensive population analysis of the variation catalogued by such data.</p> <p>Description</p> <p>We have developed a genetic variant site explorer able to retrieve data for Single Nucleotide Variation (SNVs), population by population, from entire genomes without compromising future scalability and agility. ENGINES (ENtire Genome INterface for Exploring SNVs) uses data from the 1000 Genomes Phase I to demonstrate its capacity to handle large amounts of genetic variation (>7.3 billion genotypes and 28 million SNVs), as well as deriving summary statistics of interest for medical and population genetics applications. The whole dataset is pre-processed and summarized into a data mart accessible through a web interface. The query system allows the combination and comparison of each available population sample, while searching by rs-number list, chromosome region, or genes of interest. Frequency and F_STfilters are available to further refine queries, while results can be visually compared with other large-scale Single Nucleotide Polymorphism (SNP) repositories such as HapMap or Perlegen.</p> <p>Conclusions</p> <p>ENGINES is capable of accessing large-scale variation data repositories in a fast and comprehensive manner. It allows quick browsing of whole genome variation, while providing statistical information for each variant site such as allele frequency, heterozygosity or F_STvalues for genetic differentiation. Access to the data mart generating scripts and to the web interface is granted from <url>http://spsmart.cesga.es/engines.php</url></p

Performance evaluation of deleteriousness prediction methods for intronic SNVs in next generation sequences

Introduction: Alterations in splicing sites (ss) are estimated to explain approximately 10% of human disease causal variants. Mutations outside the ss but affecting ?regulatory elements? can be up to 25%. Accurate deleteriousness prediction for intronic variants is crucial for diagnostic purposes. Many deleteriousness prediction methods have been developed, but their relative values are still unclear in practical applications. We comprehensively evaluated the predictive performance of two complementary deleteriousness-scoring methods using information from real patients. Material and Methods: We selected the dbscSNV (both ADA and RF scores) and SPIDEX algorithms, that study variants in splicing consensus regions or in regulatory regions respectively. The tools, either alone or in combination, were tested on 29294 gene intronic SNVs that have previously been characterised by ClinVar as either ?pathogenic? (430) or ?benign? (28864). The sensitivity, specificity and positive and negative predictive values were calculated. Moreover, we applied the algorithms to WES data from undiagnosed patients, and we analysed the mRNA sequence from genes that fitted the patient?s phenotype. Results: The highest sensitivity corresponds to dbscSNV with 96.55% while the best specificity is for SPIDEX with 95.78%. When considering the 3 scores (SPIDEX, dbscSNV ADA and RF Score), the sensitivity and specificity values were 60.7% and 94.6%. The Positive and Negative Predictive Value were 14.45% and 99.39%. The results for 20 undiagnosed cases are presented. Conclusions: Besides the low positive predictive value, the combination of both algorithms leads less than 1% of false negatives, so their routine use can be recommended for diagnostic purposes

A Generalized Model to Estimate the Statistical Power in Mitochondrial Disease Studies Involving 2×k Tables

Mitochondrial DNA (mtDNA) variation (i.e. haplogroups) has been analyzed in regards to a number of multifactorial diseases. The statistical power of a case-control study determines the a priori probability to reject the null hypothesis of homogeneity between cases and controlsThe research leading to these results has received funding from the “Ministerio de Ciencia e Innovación” (SAF2008-02971) and from the Plan Galego IDT, Xunta de Galicia (EM 2012/045) given to A.S.S

SPSmart: adapting population based SNP genotype databases for fast and comprehensive web access

Background: In the last five years large online resources of human variability have appeared, notably HapMap, Perlegen and the CEPH foundation. These databases of genotypes with population information act as catalogues of human diversity, and are widely used as reference sources for population genetics studies. Although many useful conclusions may be extracted by querying databases individually, the lack of flexibility for combining data from within and between each database does not allow the calculation of key population variability statistics. Results: We have developed a novel tool for accessing and combining large-scale genomic databases of single nucleotide polymorphisms (SNPs) in widespread use in human population genetics: SPSmart (SNPs for Population Studies). A fast pipeline creates and maintains a data mart from the most commonly accessed databases of genotypes containing population information: data is mined, summarized into the standard statistical reference indices, and stored into a relational database that currently handles as many as 4 × 109 genotypes and that can be easily extended to new database initiatives. We have also built a web interface to the data mart that allows the browsing of underlying data indexed by population and the combining of populations, allowing intuitive and straightforward comparison of population groups. All the information served is optimized for web display, and most of the computations are already pre-processed in the data mart to speed up the data browsing and any computational treatment requested. Conclusion: In practice, SPSmart allows populations to be combined into user-defined groups, while multiple databases can be accessed and compared in a few simple steps from a single query. It performs the queries rapidly and gives straightforward graphical summaries of SNP population variability through visual inspection of allele frequencies outlined in standard pie-chart format. In addition, full numerical description of the data is output in statistical results panels that include common population genetics metrics such as heterozygosity, Fst and In.The grants from the Xunta de Galicia (PGIDIT06PXIB208079PR) and Fundación de Investigación Médica Mutua Madrileña awarded to AS partially supported this projectS