Bioinformatics tools for the analysis of plant-associated bacterial genomes

El desarrollo de las plataformas de secuenciación de alto rendimiento han supuesto una extraordinaria disminución en tiempo y costes, lo que ha permitido a los expertos disponer fácilmente de las secuencias genómicas de los organismos con que trabajan. El campo de la fitobacteriología no es una excepción, y en la actualidad existe una colección prominente de genomas de bacterias asociadas a plantas en repositorios públicos. En lo que respecta al complejo Pseudomonas syringae, se dispone de más de 50 genomas correspondientes a sendas cepas, aunque sólo de 3 de ellos se conoce la secuencia completa: P. syringae pv. tomato DC3000, patógena de tomate, P. syringae pv. syringae B728a y P. syringae pv. phaseolicola 1448A, patógenas de judía. Recientemente se ha determinado el genoma completo de la cepa P. syringae pv. syringae UMAF0158, agente causal de la necrosis apical del mango (Cazorla et al., 1998). Dado que distintas cepas de P. syringae provocan distintas enfermedades en un amplio rango de huéspedes, el primer objetivo de esta Tesis Doctoral ha sido el análisis bioinformático del genoma de UMAF0158, haciendo énfasis en factores bacterianos potencialmente implicados en su capacidad para infectar plantas de mango. El genoma consta de un cromosoma de 5.8 Mb y un plásmido de 63 Kb, y presenta una alta similitud (91% de las secuencias codificantes predichas) respecto al genoma de B728a. De entre los determinantes genéticos diferenciales que podrían explicar su interacción con mango, destacan el operon mbo de síntesis de mangotoxina (Carrión et al., 2012), un clúster potencialmente implicado en la producción de celulosa, dos sistemas de secreción diferentes de tipos III y VI (T3SS y T6SS, respectivamente) y un repertorio particular de efectores del T3SS. El genoma de UMAF0158 constituye el primero completo que se obtiene de una P. syringae que afecta a plantas leñosas, y este estudio sienta las bases para posteriores análisis experimentales, que permitirán esclarecer los mecanismos bacterianos que explican la capacidad de este patógeno para infectar mango. Por otro lado, recientemente se ha obtenido el genoma completo de la cepa endofita de olivo Pseudomonas fluorescens PICF7, probada como agente de biocontrol contra la verticilosis, una enfermedad vegetal provocada por el hongo Verticillium dahliae Kleb. (Mercado-Blanco et al., 2004; Prieto y Mercado-Blanco, 2008). El genoma de PICF7 está formado por un cromosoma circular de 6.1 Mb, cuyo análisis bioinformático reveló genes potencialmente implicados en la asociación de dicha cepa con plantas de olivo, como los codificantes de un T3SS y dos T6SS, sideróforos, enzimas detoxificadoras y compuestos volátiles. La identificación de estos factores ayudará a direccionar posteriores estudios funcionales que permitan describir los mecanismos moleculares implicados en el estilo de vida endofítico de PICF7, así como su capacidad de biocontrol. En paralelo, se han desarrollado dos herramientas bioinformáticas para el análisis de genomas bacterianos en el contexto de las interacciones planta-bacteria. La primera de ellas, llamada T346Hunter, es una aplicación web que permite, dado un genoma bacteriano, identificar genes implicados en la síntesis de los componentes estructurales de los sistemas de secreción T3SS, T4SS y T6SS. La herramienta presenta los resultados mediante un documento HTML intuitivo y fácilmente interpretable, mediante el que el usuario puede “navegar” por las diferentes regiones detectadas y visualizar la localización genómica de los distintos componentes que éstas contienen. Se implementó a su vez una segunda aplicación web, llamada PIFAR (Plant-bacteria Interaction FActors Resource), consistente en un repositorio público de determinantes genéticos bacterianos implicados en interacciones planta-bacteria. Para ello, se realizó una búsqueda pormenorizada en la bibliografía científica con objeto de identificar aquellos productos génicos descritos experimentalmente como implicados en asociaciones bacterianas con plantas huésped. A través de la interfaz de PIFAR, el usuario puede consultar la base de datos, así como descargarla en diferentes formatos. También se incluye un formulario que permite subir nuevos factores para su eventual inclusión en la base de datos, y dispone de una herramienta de anotación para genomas bacterianos de entrada. Dicha herremienta se ejecutó sobre el conjunto de genomas bacterianos completos disponible en el NCBI en Diciembre de 2014, correspondiente a 3.042 cromosomas y 2.200 plásmidos. Los resultados obtenidos son también accesibles desde la interfaz de PIFAR. Por último, se abarcó el problema de la clasificación de genoma bacterianos. Combinando T346Hunter y PIFAR con el método de aprendizaje automático Random forests (Breiman, 2001), se generó un modelo probabilístico basado en las anotaciones de ambas herramientas sobre una selección de 420 genomas bacterianos. Dicho modelo permite asignar probabilidades de asociación con planta a secuencias de entrada. Su aplicación sobre el conjunto de aproximadamente 9.500 genomas bacterianos almacenados en el NCBI en Diciembre de 2014 ha revelado potenciales asociaciones con plantas de una serie de patógenos bacterianos comúnmente asociados a mamíferos. De entre ellos destacan un conjunto amplio de enterobacterias cuya capacidad para inducir enfermedades en humanos ha sido probada en los últimos años

Effect of pH and nanoclay content on the morphology and physicochemicalproperties of soy protein/montmorillonite nanocomposite obtained byextrusion

The present work attempts to clarify the influence of montmorillonite nanoclay content and pH on the me-chanical properties of extruded soy protein nanocomposites. The mechanical behaviour is dominated by theformation of positive synergies between protein and nanoclay above a nanoclay concentration threshold.Moreover, the presence of nanoclay can improve water uptake. The pH also exerts a strong influence on me-chanical and water absorption properties, although montmorillonite tend to reduce this effect.Eventually, this study put forward the feasibility of using a combination of soy protein and montmorillonite toobtain potentially attractive biodegradable nanocomposite materials, processed by means of a simple and easilyscalable twin-screw extruder.Junta de Andalucía (project TEP-6134)Ministerio de Economía y Competitividad (CTQ2015-71164-P

Absorptive capacity from foreign direct investment in Spanish manufacturing firms

This paper deals with the determinants of absorptive capacity from foreign direct investment (FDI) spillovers. We study how firm behavior, capabilities, and structure drive absorptive capacity such as research and development (R&D) activities and expenditures, R&D results, internal organization of innovation, external relationships of innovation, human-capital quality, family management, business complexity, and market concentration. Our results enhance and complement previous evidence of the determinants of absorptive capacity, particularly with different approaches to innovative activities as mediators of the capability

Temporal response to drought stress in several Prunus rootstocks and wild species

Prunus species are important crops in temperate regions. In these regions, drought periods are predicted to occur more frequently due to climate change. In this sense, to reduce the impact of climate warming, obtaining new tolerant/resistant cultivars and rootstocks is a mandatory goal in Prunus breeding. Therefore, the current study assembled three Prunus species including almond, (P. dulcis Mill D.A. Webb), apricot (P. armeniaca L.) and peach (P. persica L.) to model the temporal effects of drought. A hybrid peach × almond and a wild almond-relative species Prunus webbii were also included in the study. Physiological traits associated with photosynthetic activity, leaf water status, and chlorophyll content were assessed under three watering treatments. Results showed that effects of time, genotype, and treatment interact significantly in all traits. In addition, results confirmed that P. webbii have a greater tolerance to drought than commercial rootstocks. However, “Real Fino” apricot showed the fastest recovery after re-irrigation while being one of the most affected cultivars. In addition, from the better response to these watering treatments by the almond genotypes, two different trends were observed after re-irrigation treatment that clearly differentiate the response of the almond cultivar “Garrigue” from the rest of Prunus genotypes. A better characterization of the short-term drought response in Prunus, an accurate and more efficient evaluation of the genotype effect was obtained from the use of mixed models considering appropriate variance–covariance structures. Although the advantages of these approaches are rarely used in Prunus breeding, these methodologies should be undertaken in the future by breeders to increase efficiency in developing new breeding materials.info:eu-repo/semantics/publishedVersio

Relaciones interorganizativas, estrategia de conocimiento e innovación en los clusters de turismo cultural

The paper aims to identify the knowledge strategy (KS) developed by the firms belonging to tourism cluster according to their inter-organizational relationships and hence to analyse the impact on innovation. The empirical study is conducted on a sample of 215 firms located in UNESCO World Heritage Cities in Spain (WHCS). The methodology is based on both factor analysis and conglomerates analysis. The findings show that firms with high levels of both bonding and bridging capital carry out activities of exploration and also exploration of knowledge through an ambidextrous strategy. On the contrary, firms with scarceness of links (low levels of bonding and bringing capital) perform few activities of knowledge exploration and exploitation. On the other hand, firms that have high levels of bonding or bridging capital generally implement a punctuated equilibrium strategy. Finally, we prove that firms with an ambidexterity KS exhibit better innovation performance.El objetivo del trabajo consiste en identificar la estrategia de conocimiento seguida por las empresas pertenecientes a un clúster turístico en función de relaciones interorganizativas y determinar su impacto en la innovación. El estudio empírico se realiza sobre una muestra de 215 empresas localizadas en las Ciudades Patrimonio de la Humanidad de España. La metodología está basada en análisis factorial y de conglomerados. Los resultados indican que aquellas empresas que poseen elevados niveles de "bonding" y "bridging" capital desarrollan actividades tanto de explotación como de exploración de conocimiento a través de una estrategia ambidiestra. Por el contrario, las empresas con escasos vínculos (bajos niveles de "bonding" y "bridging" capital) desarrollan escasas actividades de explotación y exploración de conocimiento. Por otro lado, las empresas que tienen altos niveles de "bonding" o "bridging" capital llevan a cabo una estrategia de equilibrio puntuado. Finalmente, comprobamos que las empresas que desarrollan una estrategia de conocimiento ambidiestra presentan mayor nivel de innovación.Ministerio de Economía y Competitivida

Substrate recognition and catalysis by LytB, a pneumococcal peptidoglycan hydrolase involved in virulence

17 p.-7 fig.-2 tab. Rico-Lastres, Palma et al.Streptococcus pneumoniae is a major cause of life-threatening diseases worldwide. Here we provide an in-depth functional characterization of LytB, the peptidoglycan hydrolase responsible for physical separation of daughter cells. Identified herein as an N-acetylglucosaminidase, LytB is involved also in colonization and invasion of the nasopharynx, biofilm formation and evasion of host immunity as previously demonstrated. We have shown that LytB cleaves the GlcNAc-β-(1,4)-MurNAc glycosidic bond of peptidoglycan building units. The hydrolysis occurs at sites with fully acetylated GlcNAc moieties, with preference for uncross-linked muropeptides. The necessity of GlcN acetylation and the presence of a single acidic moiety (Glu585) essential for catalysis strongly suggest a substrate-assisted mechanism with anchimeric assistance of the acetamido group of GlcNAc moieties. Additionally, modelling of the catalytic region bound to a hexasaccharide tripentapeptide provided insights into substrate-binding subsites and peptidoglycan recognition. Besides, cell-wall digestion products and solubilisation rates might indicate a tight control of LytB activity to prevent unrestrained breakdown of the cell wall. Choline-independent localization at the poles of the cell, mediated by the choline-binding domain, peptidoglycan modification, and choline-mediated (lipo) teichoic-acid attachment contribute to the high selectivity of LytB. Moreover, so far unknown chitin hydrolase and glycosyltransferase activities were detected using GlcNAc oligomers as substrate.Research was funded by grants from the Ministerio de Ciencia e Innovación (MICINN) and the Ministerio de Economía y Competitividad (MINECO) to P. García (SAF2009-10824 and SAF2012-39444-C02-01) and M. Menéndez (BFU2009-10052 and BFU2012-36825), the Consejería de Educación de la Comunidad de Madrid (S2010/BMD/2457) to M. Menéndez. The work in the United Kingdom and the US was supported by grants from the BBSRC (BB/G015902/1) to W. Vollmer and from the National Institutes of Health (GM61629) to S. Mobashery. Additional funding was provided by the CIBER de Enfermedades Respiratorias (CIBERES), an initiative of the Instituto de Salud Carlos III (ISCIII). Palma Rico-Lastres and Roberto Díez-Martínez were the recipients of fellowships from the MICINN (FPI program).Peer reviewe

Latent Profiles of Burnout, Self-Esteem and Depressive Symptomatology among Teachers

Burnout is a reality in the teaching profession. Specifically, teaching staff usually have higher burnout rates. The present study aims to analyze the different burnout profiles and to verify if there were differences between burnout profiles in depressive symptomatology and in the self-esteem of the teachers at school. The total number of participants was 210 teachers from 30 to 65 years. The first scale was the Maslach burnout inventory, the second scale was the Self-Rating depression scale and the third scale was the Rosenberg Self-Esteem Scale . The latent class analysis identified three burnout profiles: the first group with a high level of emotional exhaustion, low personal accomplishment and depersonalization (high burnout); the second group with low emotional exhaustion, low depersonalization and high personal accomplishment (low burnout) and the third group with low depersonalization, low emotional exhaustion and low personal accomplishment (moderate burnout). The results revealed that there were differences in depressive symptomatology (group 1 obtained higher scores than group 2 and group 3) and self-esteem (group 2 obtained higher scores than group 1). The psychological balance and health of teachers depend on preventing the factors that have been associated with this syndrome

Macroelements and Trace Elements Content in Brine-Canned Mackerel (Scomber colias) Subjected to High-Pressure Processing and Frozen Storage

This study analysed the effect of prior high-pressure processing (HPP; 200–600 MPa, 2 min), freezing (−30 °C, 48 h), and frozen storage (−18 °C, 6 months) on the macroelement and trace element content in brine-canned mackerel (Scomber colias). Most elements (Na, Ca, Ba, Mn, Fe, Cu, Cd, Sn, As, S, and Se) showed an increased (p < 0.05) presence in mackerel muscle canned after freezing. A content increase (p < 0.05) was also observed for Na and Sn if prior frozen storage was also applied; on the contrary, Ca, Ba, Mn, Fe, Cd, S, and Se showed a content decrease (p < 0.05) as a result of such storage. Freezing, frozen storage, and canning led to lower values (p < 0.05) in canned fish for K, Mg, Pb, and P. Prior HPP led to relevant content decreases (p < 0.05) for K, Mg, Ca, Ba, Mn, Fe, Pb, and P contents in fish canned after the freezing step; HPP provoked additional decreases (p < 0.05) in Ca, Ba, and Mn levels in samples corresponding to 6-month frozen storage. On the contrary, prior HPP led to marked increases (p < 0.05) for Cd, S, and Se contents in all canned samples. Content changes are explained on the basis of modifications of other constituents and liquor losses from muscleThis study was supported by the Spanish “Consejo Superior de Investigaciones Científicas (CSIC)” (Research Project 2017-70E032)S

On the performance of deep learning models for time series classification in streaming

Processing data streams arriving at high speed requires the development of models that can provide fast and accurate predictions. Although deep neural networks are the state-of-the-art for many machine learning tasks, their performance in real-time data streaming scenarios is a research area that has not yet been fully addressed. Nevertheless, there have been recent efforts to adapt complex deep learning models for streaming tasks by reducing their processing rate. The design of the asynchronous dual-pipeline deep learning framework allows to predict over incoming instances and update the model simultaneously using two separate layers. The aim of this work is to assess the performance of different types of deep architectures for data streaming classification using this framework. We evaluate models such as multi-layer perceptrons, recurrent, convolutional and temporal convolutional neural networks over several time-series datasets that are simulated as streams. The obtained results indicate that convolutional architectures achieve a higher performance in terms of accuracy and efficiency.Ministerio de Economía y Competitividad TIN2017-88209-C2-2-RJunta de Andalucía US-1263341Junta de Andalucía P18-RT-277

A comparative study of supervised machine learning algorithms for the prediction of long-range chromatin interactions

The role of three-dimensional genome organization as a critical regulator of gene expression has become increasingly clear over the last decade. Most of our understanding of this association comes from the study of long range chromatin interaction maps provided by Chromatin Conformation Capture-based techniques, which have greatly improved in recent years. Since these procedures are experimentally laborious and expensive, in silico prediction has emerged as an alternative strategy to generate virtual maps in cell types and conditions for which experimental data of chromatin interactions is not available. Several methods have been based on predictive models trained on one-dimensional (1D) sequencing features, yielding promising results. However, different approaches vary both in the way they model chromatin interactions and in the machine learning-based strategy they rely on, making it challenging to carry out performance comparison of existing methods. In this study, we use publicly available 1D sequencing signals to model cohesin-mediated chromatin interactions in two human cell lines and evaluate the prediction performance of six popular machine learning algorithms: decision trees, random forests, gradient boosting, support vector machines, multi-layer perceptron and deep learning. Our approach accurately predicts long-range interactions and reveals that gradient boosting significantly outperforms the other five methods, yielding accuracies of about 95%. We show that chromatin features in close genomic proximity to the anchors cover most of the predictive information, as has been previously reported. Moreover, we demonstrate that gradient boosting models trained with different subsets of chromatin features, unlike the other methods tested, are able to produce accurate predictions. In this regard, and besides architectural proteins, transcription factors are shown to be highly informative. Our study provides a framework for the systematic prediction of long-range chromatin interactions, identifies gradient boosting as the best suited algorithm for this task and highlights cell-type specific binding of transcription factors at the anchors as important determinants of chromatin wiring mediated by cohesin.This research was funded by grant TIN2015-64776-C3-2-R from the Spanish Government and the European Regional Development FundPeer reviewe