A short motif in Drosophila SECIS Binding Protein 2 provides differential binding affinity to SECIS RNA hairpins

Selenoproteins contain the amino acid selenocysteine which is encoded by a UGA Sec codon. Recoding UGA Sec requires a complex mechanism, comprising the cis-acting SECIS RNA hairpin in the 3′UTR of selenoprotein mRNAs, and trans-acting factors. Among these, the SECIS Binding Protein 2 (SBP2) is central to the mechanism. SBP2 has been so far functionally characterized only in rats and humans. In this work, we report the characterization of the Drosophila melanogaster SBP2 (dSBP2). Despite its shorter length, it retained the same selenoprotein synthesis-promoting capabilities as the mammalian counterpart. However, a major difference resides in the SECIS recognition pattern: while human SBP2 (hSBP2) binds the distinct form 1 and 2 SECIS RNAs with similar affinities, dSBP2 exhibits high affinity toward form 2 only. In addition, we report the identification of a K (lysine)-rich domain in all SBP2s, essential for SECIS and 60S ribosomal subunit binding, differing from the well-characterized L7Ae RNA-binding domain. Swapping only five amino acids between dSBP2 and hSBP2 in the K-rich domain conferred reversed SECIS-binding properties to the proteins, thus unveiling an important sequence for form 1 binding.

FGF signaling controls caudal hindbrain specification through Ras-ERK1/2 pathway

Background: During early steps of embryonic development the hindbrain undergoes a regionalization process along the anterior-posterior (AP) axis that leads to a metameric organization in a series of rhombomeres (r). Refinement of the AP identities within the hindbrain requires the establishment of local signaling centers, which emit signals that pattern territories in their vicinity. Previous results demonstrated that the transcription factor vHnf1 confers caudal identity to the hindbrain inducing Krox20 in r5 and MafB/Kreisler in r5 and r6, through FGF signaling [1].Results: We show that in the chick hindbrain, Fgf3 is transcriptionally activated as early as 30 min after mvHnf1 electroporation, suggesting that it is a direct target of this transcription factor. We also analyzed the expression profiles of FGF activity readouts, such as MKP3 and Pea3, and showed that both are expressed within the hindbrain at early stages of embryonic development. In addition, MKP3 is induced upon overexpression of mFgf3 or mvHnf1 in the hindbrain, confirming vHnf1 is upstream FGF signaling. Finally, we addressed the question of which of the FGF-responding intracellular pathways were active and involved in the regulation of Krox20 and MafB in the hindbrain. While Ras-ERK1/2 activity is necessary for MKP3, Krox20 and MafB induction, PI3K-Akt is not involved in that process.Conclusion: Based on these observations we propose that vHnf1 acts directly through FGF3, and promotes caudal hindbrain identity by activating MafB and Krox20 via the Ras-ERK1/2 intracellular pathway.

OSIRISv1.2: a named entity recognition system for sequence variants of genes in biomedical literature

Background: Single Nucleotide Polymorphisms, among other type of sequence variants, constitute key elements in genetic epidemiology and pharmacogenomics. While sequence data about genetic variation is found at databases such as dbSNP, clues about the functional and phenotypic consequences of the variations are generally found in biomedical literature. The identification of the relevant documents and the extraction of the information from them are hampered by the large size of literature databases and the lack of widely accepted standard notation for biomedical entities. Thus, automatic systems for the identification of citations of allelic variants of genes in biomedical texts are required. Results: Our group has previously reported the development of OSIRIS, a system aimed at the retrieval of literature about allelic variants of genes http://ibi.imim.es/osirisform.html. Here we describe the development of a new version of OSIRIS (OSIRISv1.2, http://ibi.imim.es/OSIRISv1.2.html webcite) which incorporates a new entity recognition module and is built on top of a local mirror of the MEDLINE collection and HgenetInfoDB: a database that collects data on human gene sequence variations. The new entity recognition module is based on a pattern-based search algorithm for the identification of variation terms in the texts and their mapping to dbSNP identifiers. The performance of OSIRISv1.2 was evaluated on a manually annotated corpus, resulting in 99% precision, 82% recall, and an F-score of 0.89. As an example, the application of the system for collecting literature citations for the allelic variants of genes related to the diseases intracranial aneurysm and breast cancer is presented. Conclusion: OSIRISv1.2 can be used to link literature references to dbSNP database entries with high accuracy, and therefore is suitable for collecting current knowledge on gene sequence variations and supporting the functional annotation of variation databases. The application of OSIRISv1.2 in combination with controlled vocabularies like MeSH provides a way to identify associations of biomedical interest, such as those that relate SNPs with diseases.

Internet como fuente generadora de contenidos especializados

La plena vigencia de la Web 2.0, así como los tímidos inicios de la Web semántica, propician una excelente oportunidad para el Periodismo especializado. En una sociedad intercomunicada en la que todo aquel que disponga de las herramientas básicas puede convertirse en emisor de contenidos digitales, el papel mediador del periodista debe ser reforzado con el de selector y guía del mapa informativo que ofrece Internet. Con este ánimo se publica el presente texto que recoge las aportaciones de docentes e investigadores del ámbito científico del Periodismo especializado. A sus reflexiones, análisis y críticas han añadido gran cantidad de cuadros y tablas cuya finalidad didáctica no es otra que la de poner un poco de orden en el caos informativo de la red.

Biana: a software framework for compiling biological interactions and analyzing networks

Background: The analysis and usage of biological data is hindered by the spread of information across multiple repositories and the difficulties posed by different nomenclature systems and storage formats. In particular, there is an important need for data unification in the study and use of protein-protein interactions. Without good integration strategies, it is difficult to analyze the whole set of available data and its properties.Results: We introduce BIANA (Biologic Interactions and Network Analysis), a tool for biological information integration and network management. BIANA is a Python framework designed to achieve two major goals: i) the integration of multiple sources of biological information, including biological entities and their relationships, and ii) the management of biological information as a network where entities are nodes and relationships are edges. Moreover, BIANA uses properties of proteins and genes to infer latent biomolecular relationships by transferring edges to entities sharing similar properties. BIANA is also provided as a plugin for Cytoscape, which allows users to visualize and interactively manage the data. A web interface to BIANA providing basic functionalities is also available. The software can be downloaded under GNU GPL license from http://sbi.imim.es/web/BIANA.php.Conclusions: BIANA's approach to data unification solves many of the nomenclature issues common to systems dealing with biological data. BIANA can easily be extended to handle new specific data repositories and new specific data types. The unification protocol allows BIANA to be a flexible tool suitable for different user requirements: non-expert users can use a suggested unification protocol while expert users can define their own specific unification rules.

La Utilización de la plataforma Weibo por periodistas chinos en los asuntos públicos en China

Esta investigación se concentra en la plataforma Weibo, que está introduciendo nuevas formas de redacción de noticias y distribución de informaciones en China. Se trata de un servicio de microblogging chino, parecido al Twitter pero adaptado a los usuarios chinos. Siendo una herramienta de web 2.0, Weibo ha cambiado el trabajo cotidiano de los periodistas chinos. En el presente estudio se elabora análisis de contenido cuantitativo y cualitativo con fin de explorar la forma de utilización por los periodistas chinos en los asuntos públicos.

Consumo y convergencia mediática de la prensa local en Cataluña

Los nuevos hábitos de consumo de medios en el marco de la convergencia digital están propiciando un cambio en las estrategias de los medios de comunicación. Mientras unos usuarios siguen prefiriendo la radio, la televisión y la prensa tradicional para informarse otros participan de la experiencia digital en internet (blogs, redes sociales...) y dispositivos móviles, etc. En este panorama es complicado precisar dónde nace y termina el contenido o hasta qué punto es la participación del usuario quien (re) construye la información; así los contenidos mutan y se diluyen en varios soportes. En este contexto, la prensa local también vive las consecuencias del nuevo paradigma y asume los retos del reacomodo del sector ante la nueva realidad. Esta comunicación presenta las conclusiones del estudio cualitativo con entrevistas en profundidad a los responsables de medios locales en Cataluña sobre sus usuarios, contenidos y soportes en el marco de la convergencia digital.

Directorio de expertos en el tratamiento de la información (EXIT). Análisis de uso

Descripción y características del Directorio EXIT (Expertos en el tratamiento de la información), puesto en marcha oficialmente en junio de 2005. A los dos años (julio de 2007) se ha evaluado y analizado su funcionamiento, implantación, visibilidad y aceptación por parte de la comunidad profesional de bibliotecarios, documentalistas, archiveros y especialistas en información a la que sirve, y en especial su uso. Técnicamente, EXIT está considerado un directorio estado-del-arte a nivel mundial, siendo además un genuino producto de la web 2.0 ya que son los propios interesados los que rellenan y mantienen al día sus fichas, bajo la supervisión de sus creadores-gestores y de un Comité Evaluador internacional.

Evaluación de DocuMenea, sistema de promoción social de noticias de biblioteconomía y documentación.

Uno de los servicios más populares de la Web 2.0 son las plataformas de promoción social de noticias. En el entorno hispanoamericano quizá el más conocido sea Menéame; utilizando su código abierto se creó DocuMenea con las mismas características pero circunscrito exclusivamente al ámbito de la Biblioteconomía y Documentación. En este trabajo se presenta una evaluación de este servicio desde su creación en noviembre del año 2006 hasta diciembre de 2008. Como resultados se obtiene que se envió un total de 2.166 noticias de las que 1.610 fueron publicadas. El servicio cuenta con 582 usuarios con una participación desigual ya el 74% nunca ha enviado ninguna noticia y el 91% no ha votado en ninguna ocasión. Temáticamente se identificaron cuatro ejes: Google, bibliotecas, redes sociales/web 2.0 y el libro. Finalmente se obtuvo el ranking de fuentes cuyas tres primeras posiciones la obtuvieron diarios de información general.

Sobre la sociedad red

Crónica del curso ¿Sociedad red: Cambios sociales, organizaciones y ciudadanos¿ (Barcelona, octubre 2008). Los temas tratados fueron el estado de desarrollo de la sociedad red, organizaciones, ciudadanía, comunicación e innovación.

Smed454 dataset: unravelling the transcriptome of Schmidtea mediterranea

Background: Freshwater planarians are an attractive model for regeneration and stem cell research and have become a promising tool in the field of regenerative medicine. With the availability of a sequenced planarian genome, the recent application of modern genetic and high-throughput tools has resulted in revitalized interest in these animals, long known for their amazing regenerative capabilities, which enable them to regrow even a new head after decapitation. However, a detailed description of the planarian transcriptome is essential for future investigation into regenerative processes using planarians as a model system. Results: In order to complement and improve existing gene annotations, we used a 454 pyrosequencing approach to analyze the transcriptome of the planarian species Schmidtea mediterranea Altogether, 598,435 454-sequencing reads, with an average length of 327 bp, were assembled together with the ~10,000 sequences of the S. mediterranea UniGene set using different similarity cutoffs. The assembly was then mapped onto the current genome data. Remarkably, our Smed454 dataset contains more than 3 million novel transcribed nucleotides sequenced for the first time. A descriptive analysis of planarian splice sites was conducted on those Smed454 contigs that mapped univocally to the current genome assembly. Sequence analysis allowed us to identify genes encoding putative proteins with defined structural properties, such as transmembrane domains. Moreover, we annotated the Smed454 dataset using Gene Ontology, and identified putative homologues of several gene families that may play a key role during regeneration, such as neurotransmitter and hormone receptors, homeobox-containing genes, and genes related to eye function. Conclusions: We report the first planarian transcript dataset, Smed454, as an open resource tool that can be accessed via a web interface. Smed454 contains significant novel sequence information about most expressed genes of S. mediterranea. Analysis of the annotated data promises to contribute to identification of gene families poorly characterized at a functional level. The Smed454 transcriptome data will assist in the molecular characterization of S. mediterranea as a model organism, which will be useful to a broad scientific community.

Smed454 dataset: unravelling the transcriptome of Schmidtea mediterranea

Background Freshwater planarians are an attractive model for regeneration and stem cell research and have become a promising tool in the field of regenerative medicine. With the availability of a sequenced planarian genome, the recent application of modern genetic and high-throughput tools has resulted in revitalized interest in these animals, long known for their amazing regenerative capabilities, which enable them to regrow even a new head after decapitation. However, a detailed description of the planarian transcriptome is essential for future investigation into regenerative processes using planarians as a model system. Results In order to complement and improve existing gene annotations, we used a 454 pyrosequencing approach to analyze the transcriptome of the planarian species Schmidtea mediterranea Altogether, 598,435 454-sequencing reads, with an average length of 327 bp, were assembled together with the ~10,000 sequences of the S. mediterranea UniGene set using different similarity cutoffs. The assembly was then mapped onto the current genome data. Remarkably, our Smed454 dataset contains more than 3 million novel transcribed nucleotides sequenced for the first time. A descriptive analysis of planarian splice sites was conducted on those Smed454 contigs that mapped univocally to the current genome assembly. Sequence analysis allowed us to identify genes encoding putative proteins with defined structural properties, such as transmembrane domains. Moreover, we annotated the Smed454 dataset using Gene Ontology, and identified putative homologues of several gene families that may play a key role during regeneration, such as neurotransmitter and hormone receptors, homeobox-containing genes, and genes related to eye function. Conclusions We report the first planarian transcript dataset, Smed454, as an open resource tool that can be accessed via a web interface. Smed454 contains significant novel sequence information about most expressed genes of S. mediterranea. Analysis of the annotated data promises to contribute to identification of gene families poorly characterized at a functional level. The Smed454 transcriptome data will assist in the molecular characterization of S. mediterranea as a model organism, which will be useful to a broad scientific community.

LibraryThing: la catalogació a l'abast de tothom

En aquest article es presenta l'eina web de catalogació de llibres LibraryThing, creada per Tim Spalding l'any 2005, que s'emmarca en l'anomenat Web 2.0 gràcies a les opcions que ofereix com a instrument social. Se'n descriuen l'origen i l'abast actual, les característiques que la diferencien d'altres eines semblants, les principals opcions de personalització i el procés de creació d'una biblioteca. Malgrat que ha estat concebut com una eina no professional, moltes biblioteques petites l'han adoptat, atès que és molt fàcil d'emprar. Això ha portat Tim Spalding i el seu equip a oferir versions per a organitzacions i un producte pensat especialment per compartir la informació deLibraryThing amb les biblioteques: LibraryThing for libraries.

Autorregulación de aprendizajes en educación superior mediante la escritura de blogs

La importancia de mecanismos de regulación de los propios aprendizajes por parte de los estudiantes, así como de la calidad de la retroalimentación y de la evaluación formativa por parte de los profesores está en las agendas internacionales de la calidad de la enseñanza superior. El uso de herramientas de lectura, escritura e interacción web 2.0 se enmarca claramente en ese propósito general. El artículo ofrece resultados de una investigación-acción interuniversitaria sobre la evaluación de competencias con blogs. Más concretamente, presenta tres escenarios formativos en los que el blog se utiliza como herramienta de evaluación reflexiva; indaga el grado en que el alumnado se hace consciente de su proceso de aprendizaje, cómo lo evidencia y cómo lo autorregula; y, finalmente, analiza el tipo de feed-back utilizado por el profesorado. Se presentan resultados del análisis documental tanto de las producciones llevadas a cabo en los blogs como del feed-back facilitado por el profesorado. Los resultados muestran el peso que tiene la calidad del feed-back que facilita el profesorado en el proceso de acompañamiento de construcción de competencias.

LinkedOpenData, el futur de la catalogació

Introducció al LOD. Evolució tecnològica de la última dècada i repàs dels principals conceptes relacionats fins a arribar a la web semàntica i les dades enllaçables en obert. Evolució en l'àmbit bibliotecari i els catàlegs: tendències encaminades cap a la millora de l’accés, el web 2.0 i l’accés a la informació a text complet. Per què i com participar en el moviment LOD. Iniciatives en el món bibliotecari: Què s’està fent a nivell internacional en el món dels catàlegs i la catalogació?. Com seran doncs els catàlegs del futur, i finalment, com es concreta a la pràctica.