Phenol-Explorer 3.0: a major update of the Phenol-Explorer database to incorporate data on the effects of food processing on polyphenol content

Polyphenols are a major class of bioactive phytochemicals whose consumption may play a role in the prevention of a number of chronic diseases such as cardiovascular diseases, type II diabetes and cancers. Phenol-Explorer, launched in 2009, is the only freely available web-based database on the content of polyphenols in food and their in vivo metabolism and pharmacokinetics. Here we report the third release of the database (Phenol-Explorer 3.0), which adds data on the effects of food processing on polyphenol contents in foods. Data on >100 foods, covering 161 polyphenols or groups of polyphenols before and after processing, were collected from 129 peer-reviewed publications and entered into new tables linked to the existing relational design. The effect of processing on polyphenol content is expressed in the form of retention factor coefficients, or the proportion of a given polyphenol retained after processing, adjusted for change in water content. The result is the first database on the effects of food processing on polyphenol content and, following the model initially defined for Phenol-Explorer, all data may be traced back to original sources. The new update will allow polyphenol scientists to more accurately estimate polyphenol exposure from dietary surveys. Database URL: http://www.phenol-explorer.eu

Study of tergal glands morphogenesis through an integrative analysis of genomic data

About 50% of living species are holometabolan insects. Therefore, unraveling the ori- gin of insect metamorphosis from the hemimetabolan (gradual metamorphosis) to the holometabolan (sudden metamorphosis at the end of the life cycle) mode is equivalent to explaining how all this biodiversity originated. One of the problems with studying the evolution from hemimetaboly to holometaboly is that most information is available only in holometabolan species. Within the hemimetabolan group, our model, the cock- roach Blattella germanica, is the most studied species. However, given that the study of adult morphogenesis at organismic level is still complex, we focused on the study of the tergal gland (TG) as a minimal model of metamorphosis. The TG is formed in tergites 7 and 8 (T7-8) in the last days of the last nymphal instar (nymph 6). The comparative study of four T7-T8 transcriptomes provided us with crucial keys of TG formation, but also essential information about the mechanisms and circuitry that allows the shift from nymphal to adult morphogenesis.

Integrating quantitative proteomics and metabolomics in a cellular model of diabetic retinopathy

Diabetic retinopathy is the leading cause of visual loss in individuals under the age of 55. Most investigations into the pathogenesis of diabetic retinopathy have been concentrated on the neural retina since this is where clinical lesions are manifested. Recently, however, various abnormalities in the structural and secretory functions of retinal pigment epithelium that are essential for neuroretina survival, have been found in diabetic retinopathy. In this context, here we study the effect of hyperglycemic and hypoxic conditions on the metabolism of a human retinal pigment epithelial cell line (ARPE-19) by integrating quantitative proteomics using tandem mass tagging (TMT), untargeted metabolomics using MS and NMR, and 13C-glucose isotopic labeling for metabolic tracking. We observed a remarkable metabolic diversification under our simulated in vitro hyperglycemic conditions of diabetes, characterized increased flux through polyol pathways and inhibition of the Krebs cycle and oxidative phosphorylation. Importantly, under low oxygen supply RPE cells seem to consume rapidly glycogen storages and stimulate anaerobic glycolysis. Our results therefore pave the way to future scenarios involving new therapeutic strategies addressed to modulating RPE metabolic impairment, with the aim of regulating structural and secretory alterations of RPE. Finally, this study shows the importance of tackling biomedical problems by integrating metabolomic and proteomics results.

Finding and characterizing Partially Methylated Domains in human haematopoietic cells

DNA cytosine methylation has been demonstrated to be a central epigenetic modification that has essential roles in a myriad of cellular processes. Some examples of these include gene regulation, DNA-protein interactions, cellular differentiation, X-inactivation, maintenance of genome integrity by suppressing transposable elements and viruses, embryogenesis, genomic imprinting and tumourigenesis. This list is increasingly growing thanks to recent advances in genome-wide technologies, like Whole Genome Bisulfite Sequencing (WGBS-Seq). The development of this technology in research has allowed the identification of new features of the DNA methylation landscape that was not possible using previous technologies, like Partially Methylated Domains (PMDs). PMDs have been found in several cell lines, as well as in both healthy and cancer primary samples. They have been described as regions with high variability in methylation levels across individual CpG sites and intermediate methylation levels on average with respect to the genome. Here, we performed an extensive search of PMDs in a big dataset of different haematopoietic primary cells from both myeloid and lymphoid lineages. We found and characterized significant PMDs in plasma B cells, confirming that PMDs are a phenomenon that is restricted to certain differentiated cells. Additionally, we found loci aberrantly hypomethylated in a myeloma sample which overlapped with plasma B cell PMDs. Genome-wide comparison of the myeloma and plasma B cell sample revealed that this is probably also the case for other loci.

Estudi d'alternatives de gestió de la fracció orgànica generada al municipi de l'Esquirol

L'entrada en vigor de la Directiva 1999/31/CE limita l'entrada de residus biodegradables a l'abocador i promou la gestió d'aquests residus per altres vies. El compostatge és una alternativa a la deposició en abocador que respecta el cicle natural de la matèria. A Catalunya, aquesta tècnica s'ha vist potenciada pels plans de gestió de residus PRECAT201 i PINFRECAT202. L'objecte d'aquest estudi és avaluar l'eficiència de la recollida selectiva al municipi de l'Esquirol; i comparar i avaluar diferents alternatives de gestió de la FORM3 dins i fora del municipi. La metodologia de l'estudi ha consistit en analitzar les dades de la recollida selectiva de l'ARC4, tant del municipi de l'Esquirol com de la resta de municipis del Collsacabra, i calcular els costos econòmics de la gestió de la FORM en el supòsit de tractament mitjançant l'autocompostatge, una planta de compostatge a petita escala o el tractament en una planta de compostatge convencional. Els resultats de l'estudi indiquen que la recollida selectiva del municipi de l'Esquirol obté uns valors per sobre dels objectius del PROGREMIC5, amb l'excepció de la FORM. Per tal de millorar la qualitat i la quantitat de la FORM recollida, l'estudi proposa en una primera fase: implantar el sistema de recollida selectiva porta a porta d'aquesta fracció i de la fracció resta; i en una segona fase: tractar la FORM en una petita planta de compostatge amb el sistema de sitges amb ventilació forçada.

Disseny i implementació d'un sistema de control del grau de satisfacció dels clients dels serveis de restauració

Diseño de un sistema de control de la satisfacción a partir de las valoraciones a distintas empresas de restauración emitidas por clientes, inspectores y recopiladas de otras aplicaciones externas, que calcula una puntuación mensual a partir de una fórmula matemática que puede ir variando. Permite realizar consultas estadísticas relacionadas con las distintas valoraciones emitidas y las puntuaciones mensuales.

Identification of molecular subtypes and gene expression patterns of breast cancer analysing RNA-seq data

Breast cancer is the most common diagnosed cancer and the leading cause of cancer death among females worldwide. It is considered a highly heterogeneous disease and it must be classified into more homogeneous groups. Hence, the purpose of this study was to classify breast tumors based on variations in gene expression patterns derived from RNA sequencing by using different class discovery methods. 42 breast tumors paired-samples were sequenced by Illumine Genome Analyzer and the data was analyzed and prepared by TopHat2 and htseq-count. As reported previously, breast cancer could be grouped into five main groups known as basal epithelial-like group, HER2 group, normal breast-like group and two Luminal groups with a distinctive expression profile. Classifying breast tumor samples by using PAM50 method, the most common subtype was Luminal B and was significantly associated with ESR1 and ERBB2 high expression. Luminal A subtype had ESR1 and SLC39A6 significant high expression, whereas HER2 subtype had a high expression of ERBB2 and CNNE1 genes and low luminal epithelial gene expression. Basal-like and normal-like subtypes were associated with low expression of ESR1, PgR and HER2, and had significant high expression of cytokeratins 5 and 17. Our results were similar compared with TGCA breast cancer data results and with known studies related with breast cancer classification. Classifying breast tumors could add significant prognostic and predictive information to standard parameters, and moreover, identify marker genes for each subtype to find a better therapy for patients with breast cancer.

Notes de notes

Desenvolupament d'una aplicació que permeti gestionar l'avaluació de l'alumnat d'una escola de música. L'objectiu de l'aplicació és facilitar l'exercici d'avaluació contínua del procés d'ensenyament/aprenentatge.

Construction and validation of a scoring system for the selection of high-quality data in a Spanish population primary care database (SIDIAP)

Background Computerised databases of primary care clinical records are widely used for epidemiological research. In Catalonia, the InformationSystem for the Development of Research in Primary Care (SIDIAP) aims to promote the development of research based on high-quality validated data from primary care electronic medical records. Objective The purpose of this study is to create and validate a scoring system (Registry Quality Score, RQS) that will enable all primary care practices (PCPs) to be selected as providers of researchusable data based on the completeness of their registers. Methods Diseases that were likely to be representative of common diagnoses seen in primary care were selected for RQS calculations. The observed/ expected cases ratio was calculated for each disease. Once we had obtained an estimated value for this ratio for each of the selected conditions we added up the ratios calculated for each condition to obtain a final RQS. Rate comparisons between observed and published prevalences of diseases not included in the RQS calculations (atrial fibrillation, diabetes, obesity, schizophrenia, stroke, urinary incontinenceand Crohn’s disease) were used to set the RQS cutoff which will enable researchers to select PCPs with research-usable data. Results Apart from Crohn’s disease, all prevalences were the same as those published from the RQS fourth quintile (60th percentile) onwards. This RQS cut-off provided a total population of 1 936 443 (39.6% of the total SIDIAP population). Conclusions SIDIAP is highly representative of the population of Catalonia in terms of geographical, age and sex distributions. We report the usefulness of rate comparison as a valid method to establish research-usable data within primary care electronic medical records

Effet de la RNase HI sur l’expression génique et sur le surenroulement de l’ADN chez Escherichia coli

Les R-loops générés durant la transcription sont impliqués dans de nombreuse fonctions incluant la réplication, la recombinaison et l’expression génique tant chez les procaryotes que chez les eucaryotes. Plusieurs études ont montré qu’un excès de supertours négatifs et des séquences riches en bases G induisent la formation de R-loops. Jusqu’à maintenant, nos résultats nous ont permis d’établir un lien direct entre les topoisomérases, le niveau de surenroulement et la formation de R-loops. Cependant, le rôle physiologique des R-loops est encore largement inconnu. Dans le premier article, une étude détaillée du double mutant topA rnhA a montré qu’une déplétion de RNase HI induit une réponse cellulaire qui empêche la gyrase d’introduire des supertours. Il s’agit ici, de la plus forte évidence supportant les rôles majeurs de la RNase HI dans la régulation du surenroulement de l’ADN. Nos résultats ont également montré que les R-loops pouvaient inhiber l’expression génique. Cependant, les mécanismes exacts sont encore mal connus. L’accumulation d’ARNs courts au détriment d’ARNs pleine longueur peut être causée soit par des blocages durant l’élongation de la transcription soit par la dégradation des ARNs pleine longueur. Dans le deuxième article, nous montrons que l’hypersurenroulement négatif peut mener à la formation de R-loops non-spécifiques (indépendants de la séquence nucléotidique). La présence de ces derniers, engendre une dégradation massive des ARNs et ultimement à la formation de protéines tronquées. En conclusion, ces études montrent l’évidence d’un lien étroit entre la RNase HI, la formation des R-loops, la topologie de l’ADN et l’expression génique. De plus, elles attestent de la présence d’un nouvel inhibiteur de gyrase ou d’un mécanisme encore inconnu capable de réguler son activité. Cette surprenante découverte est élémentaire sachant que de nombreux antibiotiques ciblent la gyrase. Finalement, ces études pourront servir également de base à des recherches similaires chez les cellules eucaryotes.

Aplicación de gestión y web para un criadero-residencia canino.

El objetivo de este proyecto es implementar un sitio Web i un programa gestor de datos para el criadero/residencia canino De La Serranía (Madrid). Gracias al desarrollo de esta aplicación y del sitio Web se conseguirá que el cliente suprima el uso de todo el papel utilizado anteriormente para guardar la información relativa a clientes, animales y entradas a la residencia, podrá controlar la ocupación de la residencia y generar automáticamente las facturas, crear automáticamente árboles genealógicos de todos los ejemplares registrados, mejorar el rendimiento del criadero gracias a la opción que controla los datos de cría de cada animal: fecha de monta, fecha de parto, resultados de cada parto, etc. y controlar los gastos y ganancias de la empresa

Desarrollo de una geoplataforma cibertaxonómica europea

Desde hace unos años se han tomado iniciativas muy importantes para facilitar la inserción de información biológica georeferenciada en bases de datos accesibles al público en general, mediante estándares para el intercambio de información en la red (TDWG; http://www.tdwg.org/). La iniciativa mundial más importante orientada a la digitalización y difusión de datos sobre la diversidad biológica es GBIF (http://www.gbif.org/) la cual ha logrado compilar más de 180 millones de registros provenientes de más de 500 colecciones repartidas por todo el mundo. Sin embargo, desafortunadamente, la calidad y representatividad espacial y taxonómica de esta información impide su utilización generalizada con fines aplicados. Desde el MNCN (CSIC), estamos comenzando a desarrollar una serie de herramientas dentro del proyecto EDIT (http://www.e-taxonomy.eu/) a fin de proporcionar aplicaciones capaces de visualizar y evaluar la calidad de la información biológica georeferenciada a la comunidad de taxónomos europea. El desarrollo creciente de técnicas de modelización capaces de extrapolar la distribución de los organismos a partir de datos fragmentarios, requiere de aplicaciones que permitan un estudio previo de la información de partida para: i) estimar las unidades espaciales con inventarios relativamente fiables, ii) representar su ubicación y iii) localizar espacialmente el conjunto mínimo de unidades espaciales que garantice una cobertura ambiental adecuada de los datos a modelizar. La ausencia de aplicaciones web asequibles y de fácil manejo ha motivado el desarrollo de este proyecto. Hasta el presente esta disponible una plataforma para descarga libre de capas de información geográfica -unidades espaciales y variables ambientales-, y una herramienta de visualización basada en la librería javascript de MapBuilder, que toma datos de PostGIS a través del servidor de mapas GeoServer (http://edit.csic.es). En un futuro cercano pretendemos aprovechar la posibilidad que nos proporciona PostGIS para realizar el análisis espacial (punto-en-polígono) “al vuelo”, plasmándose dichos resultados en la generación de mapas temáticos

Serveis Tècnics de Recerca. Unitat d'Assessorament Estadístic

La Unitat d’Assessorament Estadístic es va crear el passat mes de març i es va incorporar als Serveis Tècnics de Recerca. La seva creació respon a la necessitat cada vegada més gran que hi ha a la Universitat de Girona d’una gestió i interpretació eficaç dels resultats que proporcionen les bases de dades. També era una necessitat per a institucions i empreses del territori, perquè a Girona no hi havia cap servei d’aquestes característiques

Intervenciones con cuidadores de familiares mayores dependientes : una revisi??n

Resumen tomado de la publicaci??n. Resumen tambi??n en ingl??s