Desarrollo de técnicas bioinformáticas para el análisis de datos de secuenciación masiva en sistemática y genómica evolutiva: Aplicación en el análisis del sistema quimiosensorial en artrópodos

[spa] Las tecnologías de secuenciación de próxima generación (NGS) proporcionan datos potentes para investigar cuestiones biológicas y evolutivas fundamentales, como estudios relacionados con la genómica evolutiva de la adaptación y la filogenética. Actualmente, es posible llevar a cabo proyectos genómicos complejos analizando genomas completos y / o transcriptomas, incluso de organismos no modelo. En esta tesis, hemos realizado dos estudios complementarios utilizando datos NGS. En primer lugar, hemos analizado el transcriptoma (RNAseq) de los principales órganos quimiosensoriales del quelicerado Macrothele calpeiana, Walckenaer, 1805, la única araña protegida en Europa, para investigar el origen y la evolución del sistema quimiosensorial (SQ) en los artrópodos. El SQ es un proceso fisiológico esencial para la supervivencia de los organismos, y está involucrado en procesos biológicos vitales, como la detección de alimentos, parejas o depredadores y sitios de ovoposición. Este sistema, está relativamente bien caracterizado en hexápodos, pero existen pocos estudios en otros linajes de artrópodos. El análisis de nuestro transcriptoma permitió detectar algunos genes expresados en los supuestos órganos quimiosensoriales de los quelicerados, como cinco NPC2 y dos IR. Además, también detectamos 29 tránscritos adicionales después de incluir en los perfiles de HMM nuevos miembros del SQ de genomas de artrópodos recientemente disponibles, como algunos genes de las familias de los SNMP, ENaC, TRP, GR y una OBP-like. Desafortunadamente, muchos de ellos eran fragmentos parciales. En segundo lugar, también hemos desarrollado algunas herramientas bioinformáticas para analizar datos de RNAseq y desarrollar marcadores moleculares. Los investigadores interesados en la aplicación biológica de datos NGS pueden carecer de la experiencia bioinformática requerida para el tratamiento de la gran cantidad de datos generados. En este contexto, principalmente, es necesario el desarrollo de herramientas fáciles de usar para realizar todos los procesos relacionados con el procesamiento básico de datos NGS y la integración de utilidades para realizar análisis posteriores. En esta tesis, hemos desarrollado dos herramientas bioinformáticas con interfaz gráfica, que permite realizar todos los procesos comunes del procesamiento de datos NGS y algunos de los principales análisis posteriores: i) TRUFA (TRanscriptome User-Friendly Analysis), que permite analizar datos RNAseq de organismos que no modelos, incluyendo la anotación funcional y el análisis de expresión génica diferencial; y ii) DOMINO (Development Of Molecular markers In Non-model Organisms), que permite identificar y seleccionar marcadores moleculares apropiados para análisis de biología evolutiva. Estas herramientas han sido validadas utilizando simulaciones por ordenador y datos experimentales, principalmente de arañas.[eng] The Next Generation Sequencing (NGS) technologies are providing powerful data to investigate fundamental biological and evolutionary questions including phylogenetic and adaptive genomic topics. Currently, it is possible to carry out complex genomic projects analyzing the complete genomes and/or transcriptomes even in non-model organisms. In this thesis, we have performed two complementary studies using NGS data. Firstly, we have analyzed the transcriptome (RNAseq) of the main chemosensory organs of the chelicerate Macrothele calpeiana, Walckenaer, 1805, the only spider protected in Europe, to investigate the origin and evolution of the Chemosensory System (CS) in arthropods. The CS is an essential physiological process for the survival of organisms, and it is involved in vital biological processes, such as the detection of food, partners or predators and oviposition sites. This system, which has it relatively well characterized in hexapods, is completely unknown in other arthropod lineages. Our transcriptome analysis allowed to detect some genes expressed in the putative chemosensory organs of chelicerates, such as five NPC2s and two IRs. Furthermore, we detected 29 additional transcripts after including new CS members from recently available genomes in the HMM profiles, such as the SNMPs, ENaCs, TRPs, GRs and one OBP-like. Unfortunately, many of them were partial fragments. Secondly, we have also developed some bioinformatics tools to analyze RNAseq data, and to develop molecular markers. Researchers interested in the biological application of NGS data may lack the bioinformatic expertise required for the treatment of the large amount of data generated. In this context, the development of user-friendly tools for common data processing and the integration of utilities to perform downstream analysis is mostly needed. In this thesis, we have developed two bioinformatics tools with an easy to use graphical interface to perform all the basics processes of the NGS data processing: i) TRUFA (TRanscriptome User-Friendly Analysis), that allows analyzing RNAseq data from non-model organisms, including the functional annotation and differential gene expression analysis; and ii) DOMINO (Development of Molecular markers in Non-model Organisms), which allows identifying and selecting molecular markers appropriated for evolutionary biology analysis. These tools have been validated using computer simulations and experimental data, mainly from spiders

A General Asymmetric Formal Synthesis of Aza-Baylis–Hillman Type Products under Bifunctional Catalysis

This is the peer reviewed version of the following article: Chemistry A European Journal 24.13 (2018): 3117-3121, which has been published in final form at https://doi.org/10.1002/chem.201705218. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived VersionsWeinheim A new organocatalytic strategy for the synthesis of enantioenriched aza-Baylis–Hillman type products via a frustrated vinylogous reaction is presented. This process proceeds under mild conditions with good yields, completed Z/E selectivity and excellent enantioselectivities. Moreover, easy derivatizations of the final products led to important building blocks of organic synthesis such as 1,3-aminoalcohols and Lewis base catalystsFinancial support from the Spanish Government (CTQ2015-64561-R), the European Research Council (ERC-CG, contract number: 647550), is also gratefully acknowledge

Assessment on proximate composition, dietary fiber, phytic acid and protein hydrolysis of germinated Ecuatorian brown rice

Germinated brown rice (GBR) is considered healthier than brown rice (BR) but its nutritive value has been hardly studied. Since nutritive quality of GBR depends on genetic diversity and germination conditions, six Ecuadorian BR varieties were germinated at 28 and 34 ºC for 48 and 96 h in darkness and proximate composition, dietary fiber fractions, phytic acid content as well as degree of protein hydrolysis and peptide content were studied. Protein, lipids, ash and available carbohydrate ranged 7.3-10.4%, 2.0-4.0%, 0.8-1.5% and 71.6 to 84.0%, respectively, in GBR seedlings. Total dietary fiber increased during germination (6.1-13.6%), with a large proportion of insoluble fraction, and phytic acid was reduced noticeably. In general, protein hydrolysis occurred during germination was more accused at 28 ºC for 48 h. These results suggest that GBR can be consumed directly as nutritive staple food for a large population worldwide contributing to their nutritional requirements.This work was partly funded by AGL2010-16310 Project from the Ministry of Economy and Competitiveness (MINECO, Spain).Peer Reviewe

Comorbilidad entre trastornos de conducta y depresión mayor en la adolescencia: prevalencia, teorías explicativas y estatus nosológico

This theoretical study examines the main findings and researches regarding the comorbidity between conduct disorder and major depression in adolescence. On the one hand, it is argued that high prevalence of comorbidity imply common risk factors (biological, cognitive- emotional and socio-cultural) and a causal relationship between these mental illness, usually conduct disorder preceding major depression. On the other hand, independent nosological status of this comorbidity» is advocated on the basis of several external criteria (e.g. response to treatment, course into adulthood and psychopathological profile), which distinguish this mixed clinical entity from conduct disorder and major depression, especially the latter category. These findings are discussed concerning the classification of «depressive conduct disorder» within current diagnosis reference manuals

Lisa through the canvas

[Resumen] Lisa a través del lienzo es una appserie de animación infantil dirigida a niños y niñas de 8 y 9 años. El objetivo del proyecto es acercar a los niños al mundo de la historia del arte de una forma amena, a través de los episodios de la serie, de 6 minutos de duración. Además, el proyecto cuenta con una aplicación para dispositivos móviles que actúa como soporte principal y ofrece contenidos adicionales educativos para que los niños aprendan más sobre el mundo del arte.[Resumo] Lisa a través do lenzo é unha appserie de animación infantil dirixida a nenos e nenas de 8 e 9 anos. O obxectivo do proxecto é acercar aos nenos ao mundo da historia do arte dunha forma amena, a través dos episodios da serie, de 6 minutos de duración. Ademáis, o proxecto conta cunha aplicación para dispositivos móbiles que actúa como soporte principal e ofrece contidos adicionais educativos para que os nenos aprendan máis sobre o mundo do arte.[Abstract] Lisa through the canvas is an animation appseries meant for 8 and 9 years old children. The objective of this project is bring the kids to the History of Art world in a enjoyable way, through the episodes of the series, which are 6 minutes long. Moreover, the project counts with an app for mobile devices that features aditional educative content so the kids can learn more about art.Traballo fin de grao (UDC.COM). Comunicación audiovisual. Curso 2018/201

White cabbage fermentation improves ascorbigen content, antioxidant and nitric oxide production inhibitory activity in LPS-induced macrophages

Consumption of foods rich in dietary antioxidants and anti-inflammatory compounds is becoming a key strategy to lower oxidative stress and inflammation. The objective of this work was to study the effect of fermentation and starter culture on ascorbigen (ABG) and vitamin C content, as well as antioxidant and anti-inflammatory properties of white cabbage (Brassica oleracea var. capitata cv. Megaton). Lactobacillus plantarum CECT 748 (LP), Leuconostoc mesenteroides CECT 219 (LM) or a mixed culture of both strains at 1:1 ratio (LPM) were used as starter cultures in sauerkraut manufacture. Microbiological and sensorial quality of sauerkraut was also examined. White cabbage fermentation increased (P < 0.05) ABG content (up to 12-fold), oxygen radical absorbance capacity (ORAC) values (up to 2-fold) and NO production inhibitory potency (up to 2.6-fold). Vitamin C content slightly decreased (P < 0.05) up to 1.4-fold during fermentation. LM sauerkraut showed the highest (P < 0.05) ABG concentration (204.8 μmol/100 g d.w.), ORAC values (164.0 μmol Trolox/g d.w.) and NO inhibitory potency (IC50 = 60.8 μg extract/mL). The microbiological quality of LM, LP and LPM sauerkrauts was satisfactory. Experimental sauerkrauts showed higher overall acceptability (P < 0.05) compared to commercial products. Consequently, selection of starter culture is of great importance in the manufacture of sauerkraut with improved content of bioactive compounds and health-promoting potential. © 2011 Elsevier Ltd.This work was supported by the Spanish Commission of Science and Technology (CICYT), Project number AGL2007-62044. E. P. is indebted to a JAE-doc grant funded by CSIC.Peer Reviewe

TRUFA: A user-friendly web server for de novo RNA-seq analysis using cluster computing.

Application of next-generation sequencing (NGS) methods for transcriptome analysis (RNA-seq) has become increasingly accessible in recent years and are of great interest to many biological disciplines including, eg, evolutionary biology, ecology, biomedicine, and computational biology. Although virtually any research group can now obtain RNA-seq data, only a few have the bioinformatics knowledge and computation facilities required for transcriptome analysis. Here, we present TRUFA (TRanscriptome User-Friendly Analysis), an open informatics platform offering a web-based interface that generates the outputs commonly used in de novo RNA-seq analysis and comparative transcriptomics. TRUFA provides a comprehensive service that allows performing dynamically raw read cleaning, transcript assembly, annotation, and expression quantification. Due to the computationally intensive nature of such analyses, TRUFA is highly parallelized and benefits from accessing high-performance computing resources. The complete TRUFA pipeline was validated using four previously published transcriptomic data sets. TRUFA's results for the example datasets showed globally similar results when comparing with the original studies, and performed particularly better when analyzing the green tea dataset. The platform permits analyzing RNA-seq data in a fast, robust, and user-friendly manner. Accounts on TRUFA are provided freely upon request at https://trufa.ifca.es

Estudio de la pseudotuberculosis ovina en los animales remitidos al servicio de clínica de rumiantes en el periodo 2014-2017

La pseudotuberculosis o linfadenitis caseosa (LC) es una enfermedad infecciosa, contagiosa, de curso crónico y no siempre detectable a simple vista. Está causada por Corynebacterium pseudotuberculosis. El cuadro clínico y lesional de la LC se corresponden con dos tipos de presentaciones: la superficial, afectando a linfonodos subcutáneos, y la visceral, afectando a órganos y linfonodos internos. El presente trabajo muestra los resultados obtenidos en el Servicio Clínico de Rumiantes de la Facultad de Veterinaria de Zaragoza desde el año 2014 hasta el año 2017, comprobados con necropsia y análisis microbiológico de las muestras tomadas. Sobre un total de 160 animales se observó la presencia de LC en el 31,9% (51) de los casos. La forma visceral fue observada con mayor frecuencia, estando presente en el 70,6% (36) de las ocasiones, mientras que la presentación superficial se observó en el 21,6% (11) y ambas en el 7,8% (4) de las ocasiones. En el 24,4% (39) solo presentaba lesión en un órgano y/o linfonodo, siendo el pulmón y el parénquima mamario las localizaciones más afectadas con un 5,6% (9) y un 5% (8) respectivamente. Los resultados obtenidos obligan a considerar la existencia de una posible infravaloración del diagnóstico de la enfermedad a nivel de campo, lo que repercutiría a la hora de valorar las causas de desvieje de un rebaño, así como las pérdidas generadas por esta patología en el matadero, como consecuencia de los decomisos

Comparative analysis of tissue-specific transcriptomes in the funnel-web spider Macrothele calpeiana (Araneae, Hexathelidae)

Altres ajuts: Beatriu de Pinós (Generalitat de Catalunya, 2010BP-A 00438 i 2010BP-B 00175)The funnel-web spider Macrothele calpeiana is a charismatic Mygalomorph with a great interest in basic, applied and translational research. Nevertheless, current scarcity of genomic and transcriptomic data of this species clearly limits the research in this non-model organism. To overcome this limitation, we launched the first tissue-specific enriched RNA-seq analysis in this species using a subtractive hybridization approach, with two main objectives, to characterize the specific transcriptome of the putative chemosensory appendages (palps and first pair of legs), and to provide a new set of DNA markers for further phylogenetic studies. We have characterized the set of transcripts specifically expressed in putative chemosensory tissues of this species, much of them showing features shared by chemosensory system genes. Among specific candidates, we have identified some members of the iGluR and NPC2 families. Moreover, we have demonstrated the utility of these newly generated data as molecular markers by inferring the phylogenetic position M. calpeina in the phylogenetic tree of Mygalomorphs. Our results provide novel resources for researchers interested in spider molecular biology and systematics, which can help to expand our knowledge on the evolutionary processes underlying fundamental biological questions, as species invasion or biodiversity origin and maintenance