Desarrollo y utilización de herramientas bioinformáticas en el estudio de datos de secuenciación masiva: Análisis genómicos en arácnidos.

Encontramos una gran cantidad de información genómica en bases de datos para numerosos organismos pero existe un sesgo hacia ciertos grupos taxonómicos por el interés económico, social o sanitario. Los avances y el abaratamiento de los costes de las tecnologías de secuenciación masiva han permitido aplicar estas técnicas en organismos no modelo pero aun así no resulta rutinario el poder generar recursos genómicos de buena calidad. Las arañas, grupo de estudio de esta tesis doctoral, son organismos no modelo infrarrepresentados en las bases de datos. La disponibilidad de un nuevo genoma favorecería el conocimiento de importantes aspectos como la presencia del veneno, seda o la adaptación a los procesos de terrestralización y la evolución del sistema quimiosensorial. Los objetivos principales de esta tesis doctoral son el desarrollar herramientas bioinformáticas y generar recursos genómicos en organismos no modelo, especialmente en arácnidos. Hemos implementado la herramienta DOMINO, para la búsqueda e identificación de marcadores moleculares en organismos no modelo mediante datos de secuenciación masiva. Permite generar marcadores a diferentes rangos taxonómicos que pueden ser empleados de forma directa, amplificados por PCR o empleados en el desarrollo de regiones para métodos de captura de secuencia. Hemos validado el software mediante simulaciones computacionales y datos empíricos para ajustar, configurar los parámetros y maximizar su sensibilidad y precisión. Además, hemos desarrollado una interfaz gráfica que permite el acceso a usuarios menos familiarizados con los entornos de programación. También hemos generado un ensamblaje genómico de un representante del género de arañas Dysdera, combinando diferentes librerías de secuenciación. Mediante diferentes estadísticas descriptivas determinamos la calidad y continuidad del ensamblaje y lo anotamos estructural y funcionalmente mediante predicciones ab initio y evidencias de bases de datos y de ARN. Obtuvimos un ensamblaje genómico con N50 de 38 kb, que no podía ser mejorado por la complejidad del genoma que incluía un alto número de repeticiones, aunque la calidad del genoma en cuanto a la integridad de los genes era bastante buena. Por tanto, hemos generado un recurso genómico muy útil no sólo para el análisis de características específicas del género pero también de otros arácnidos o artrópodos.There is a vast amount of information indexed in genomic databases from multiple species of organisms but there is a bias against some taxonomic groups for their relevance at social, sanitary and economical level. The progress and the reduction of sequencing technologies have allowed the implementation of these techniques in non-model organisms but still, it is neither straightforward nor cheap to obtain high quality genomic resources. Spiders, main group of interest of this thesis, are non-model organisms underrepresented in genomic databases. The availability of a new genome would shed light into relevant biological traits such as the presence of venom, silk or the adaptation to terrestrial ecosystems and the chemosensory system. The main objectives of this thesis are to develop bioinformatics methods and to generate genomic resources for non-model organisms, specifically, spiders. We have developed the tool DOMINO for the development of molecular markers in non-model organisms from next generation sequencing data. This tool allows identifying markers at different taxonomic ranges that could be employed directly, amplified using PCR in other related samples or for the generation of sequence capture strategies. We have validated the software using computer simulations and empirical data to adjust, configure and maximize its precision and sensitivity. Also, we have generated a graphical user interface to improve the usability of the software among those users with limited expertise in programming languages. We have also developed a genomic assembly of a representative spider of the genus Dysdera by combining multiple sequencing technologies. Using several descriptive statistics we determined the quality and completeness of the assembly and conducted the structural and functional annotation by ab initio and evidence-based predictions. We obtained a genome with a N50 of 38 kb, that it could not be improved because the complexity of the genome that include a high proportion of repetitive regions, nevertheless the quality of genome in terms of gene completeness was fairly good. Globally we have generated a very useful genomic resource not only for conducting studies of specific biological or evolutionary characteristics in this genus but also for other arachnids or arthropods

Diseño e implementación de 4 cursos (SPOC) para la obtención de la competencia académica de los profesores de religión en educación infantil y primaria (DECA)

Memoria ID2019/073. Ayudas de la Universidad de Salamanca para la innovación docente, curso 2019-2020

Gene Duplications in the Genomes of Staphylococci and Enterococci

Gene duplications are a feature of bacterial genomes. In the present work we analyze the extent of gene duplications in the genomes of three microorganisms that belong to the Firmicutes phylum and that are etiologic agents of several nosocomial infections: Staphylococcus aureus, Enterococcus faecium, and Enterococcus faecalis. In all three groups, there is an irregular distribution of duplications in the genomes of the strains analyzed. Whereas in some of the strains duplications are scarce, hundreds of duplications are present in others. In all three species, mobile DNA accounts for a large percentage of the duplicated genes: phage DNA in S. aureus, and plasmid DNA in the enterococci. Duplicates also include core genes. In all three species, a reduced group of genes is duplicated in all strains analyzed. Duplication of the deoC and rpmG genes is a hallmark of S. aureus genomes. Duplication of the gene encoding the PTS IIB subunit is detected in all enterococci genomes. In E. faecalis it is remarkable that the genomes of some strains encode duplicates of the prgB and prgU genes. They belong to the prgABCU cluster, which responds to the presence of the peptide pheromone cCF10 by expressing the surface adhesins PrgA, PrgB, and PrgC

3′IsomiR Species Composition Affects Reliable Quantification of miRNA/isomiR Variants by Poly(A) RT-qPCR: Impact on Small RNA-Seq Profiling Validation

Small RNA-sequencing (small RNA-seq) has revealed the presence of small RNA-naturally occurring variants such as microRNA (miRNA) isoforms or isomiRs. Due to their small size and the sequence similarity among miRNA isoforms, their validation by RT-qPCR is challenging. We previously identified two miR-31-5p isomiRs-the canonical and a 3 ' isomiR variant (3 ' G addition)-which were differentially expressed between individuals with azoospermia of different origin. Here, we sought to determine the discriminatory capacity between these two closely-related miRNA isoforms of three alternative poly(A) based-RT-qPCR strategies in both synthetic and real biological context. We found that these poly(A) RT-qPCR strategies exhibit a significant cross-reactivity between these miR-31-5p isomiRs which differ by a single nucleotide, compromising the reliable quantification of individual miRNA isoforms. Fortunately, in the biological context, given that the two miRNA variants show changes in the same direction, RT-qPCR results were consistent with the findings of small RNA-seq study. We suggest that miRNA selection for RT-qPCR validation should be performed with care, prioritizing those canonical miRNAs that, in small RNA-seq, show parallel/homogeneous expression behavior with their most prevalent isomiRs, to avoid confounding RT-qPCR-based results. This is suggested as the current best strategy for robust biomarker selection to develop clinically useful tests

Experimental Feeding and Growth of Turbot (Scophthalmus maximus L.) from 0.5 To 2.7 Kg in Galicia (NW Spain)

Two groups of turbot, Scophthalmus maximus L., of 0.5 and 1.2 kg initial mean weight were fed a semimoist diet containing fish, fish meal and vitamin-mineral complex. The trial was carried out in tanks of 16 cubic meters, for aperiod of a year. Resul ts on feed conversion index and growth in weight are give

A new generation of task-parallel algorithms for matrix inversion in many-threaded CPUs

We take advantage of the new tasking features in OpenMP to propose advanced task-parallel algorithms for the inversion of dense matrices via Gauss-Jordan elimination. Our algorithms perform a partitioning of the matrix operand into two levels of tasks: The matrix is first divided vertically, by column blocks (or panels), in order to accommodate the standard partial pivoting scheme that ensures the numerical stability of the method. In addition, depending on the particular kernel to be applied, each panel is partitioned either horizontally by row blocks (tiles) or vertically by µ-panels (of columns), in order to extract sufficient task parallelism to feed a many-threaded general purpose processor (CPU). The results of the experimental evaluation show the performance benefits of the advanced tasking algorithms on an Intel Xeon Gold processor with 20 cores.This research was sponsored by projects RTI2018-093684-B-I00 and TIN2017-82972-R of Ministerio de Ciencia, Innovación y Universidades; project S2018/TCS-4423 of Comunidad de Madrid; and project PR65/19-22445 of Universidad Complutense de Madrid.Peer ReviewedPostprint (author's final draft

Programming parallel dense matrix factorizations and inversion for new-generation NUMA architectures

We propose a methodology to address the programmability issues derived from the emergence of new-generation shared-memory NUMA architectures. For this purpose, we employ dense matrix factorizations and matrix inversion (DMFI) as a use case, and we target two modern architectures (AMD Rome and Huawei Kunpeng 920) that exhibit configurable NUMA topologies. Our methodology pursues performance portability across different NUMA configurations by proposing multi-domain implementations for DMFI plus a hybrid task- and loop-level parallelization that configures multi-threaded executions to fix core-to-data binding, exploiting locality at the expense of minor code modifications. In addition, we introduce a generalization of the multi-domain implementations for DMFI that offers support for virtually any NUMA topology in present and future architectures. Our experimentation on the two target architectures for three representative dense linear algebra operations validates the proposal, reveals insights on the necessity of adapting both the codes and their execution to improve data access locality, and reports performance across architectures and inter- and intra-socket NUMA configurations competitive with state-of-the-art message-passing implementations, maintaining the ease of development usually associated with shared-memory programming.This research was sponsored by project PID2019-107255GB of Ministerio de Ciencia, Innovación y Universidades; project S2018/TCS-4423 of Comunidad de Madrid; project 2017-SGR-1414 of the Generalitat de Catalunya and the Madrid Government under the Multiannual Agreement with UCM in the line Program to Stimulate Research for Young Doctors in the context of the V PRICIT, project PR65/19-22445. This project has also received funding from the European High-Performance Computing Joint Undertaking (JU) under grant agreement No 955558. The JU receives support from the European Union’s Horizon 2020 research and innovation programme, and Spain, Germany, France, Italy, Poland, Switzerland, Norway. The work is also supported by grants PID2020-113656RB-C22 and PID2021-126576NB-I00 of MCIN/AEI/10.13039/501100011033 and by ERDF A way of making Europe.Peer ReviewedPostprint (published version

Dispositivo de rotación de tubos de resonancia magnética nuclear

Número de publicación: ES2522718 A1 (17.11.2014) También publicado como: ES2522718 B1 (12.11.2015) Número de Solicitud: Consulta de Expedientes OEPM (C.E.O.) P201400655 (24.07.2014)La invención un dispositivo especialmente diseñado para llevar a cabo la agitación de un tubo de resonancia magnética nuclear (RMN) que comprende: un soporte (2) al que está fijado un motor (3) eléctrico de eje horizontal; un adaptador (4) de tubos (100) de resonancia magnética nuclear fijado al eje del motor (3) eléctrico; un sensor Hall (5) dispuesto para detectar una posición inicial de dicho eje; un medio (6) de procesamiento conectado al motor (3) eléctrico y al sensor Hall (5); un módulo (7) de comunicaciones para llevar a cabo la programación del medio (6) de procesamiento; y una interfaz (8) de control y visualización conectada al medio (5) de procesamiento para operar el dispositivo (1) y visualizar datos acerca de su funcionamiento.Universidad de Almerí