Prominent use of distal 5’ transcription start sites and discovery of a large number of additional exons in ENCODE regions

This report presents systematic empirical annotation of transcript products from 399 annotated protein-coding loci across the 1% of the human genome targeted by the Encyclopedia of DNA elements (ENCODE) pilot project using a combination of 5' rapid amplification of cDNA ends (RACE) and high-density resolution tiling arrays. We identified previously unannotated and often tissue- or cell-line-specific transcribed fragments (RACEfrags), both 5' distal to the annotated 5' terminus and internal to the annotated gene bounds for the vast majority (81.5%) of the tested genes. Half of the distal RACEfrags span large segments of genomic sequences away from the main portion of the coding transcript and often overlap with the upstream-annotated gene(s). Notably, at least 20% of the resultant novel transcripts have changes in their open reading frames (ORFs), most of them fusing ORFs of adjacent transcripts. A significant fraction of distal RACEfrags show expression levels comparable to those of known exons of the same locus, suggesting that they are not part of very minority splice forms. These results have significant implications concerning (1) our current understanding of the architecture of protein-coding genes; (2) our views on locations of regulatory regions in the genome; and (3) the interpretation of sequence polymorphisms mapping to regions hitherto considered to be "noncoding," ultimately relating to the identification of disease-related sequence alterations.

GENCODE: producing a reference annotation for ENCODE

Background: The GENCODE consortium was formed to identify and map all protein-coding genes within the ENCODE regions. This was achieved by a combination of initial manualannotation by the HAVANA team, experimental validation by the GENCODE consortium and a refinement of the annotation based on these experimental results.Results: The GENCODE gene features are divided into eight different categories of which onlythe first two (known and novel coding sequence) are confidently predicted to be protein-codinggenes. 5’ rapid amplification of cDNA ends (RACE) and RT-PCR were used to experimentallyverify the initial annotation. Of the 420 coding loci tested, 229 RACE products have beensequenced. They supported 5’ extensions of 30 loci and new splice variants in 50 loci. In addition,46 loci without evidence for a coding sequence were validated, consisting of 31 novel and 15putative transcripts. We assessed the comprehensiveness of the GENCODE annotation byattempting to validate all the predicted exon boundaries outside the GENCODE annotation. Outof 1,215 tested in a subset of the ENCODE regions, 14 novel exon pairs were validated, only twoof them in intergenic regions.Conclusions: In total, 487 loci, of which 434 are coding, have been annotated as part of theGENCODE reference set available from the UCSC browser. Comparison of GENCODEannotation with RefSeq and ENSEMBL show only 40% of GENCODE exons are contained withinthe two sets, which is a reflection of the high number of alternative splice forms with uniqueexons annotated. Over 50% of coding loci have been experimentally verified by 5’ RACE forEGASP and the GENCODE collaboration is continuing to refine its annotation of 1% humangenome with the aid of experimental validation.

Gene finding in the chicken genome

Background: Despite the continuous production of genome sequence for a number of organisms,reliable, comprehensive, and cost effective gene prediction remains problematic. This is particularlytrue for genomes for which there is not a large collection of known gene sequences, such as therecently published chicken genome. We used the chicken sequence to test comparative andhomology-based gene-finding methods followed by experimental validation as an effective genomeannotation method.Results: We performed experimental evaluation by RT-PCR of three different computational genefinders, Ensembl, SGP2 and TWINSCAN, applied to the chicken genome. A Venn diagram wascomputed and each component of it was evaluated. The results showed that de novo comparativemethods can identify up to about 700 chicken genes with no previous evidence of expression, andcan correctly extend about 40% of homology-based predictions at the 5' end.Conclusions: De novo comparative gene prediction followed by experimental verification iseffective at enhancing the annotation of the newly sequenced genomes provided by standardhomology-based methods.

Educar en periodismo de datos :estudio de casos y propuestas de inclusión curricular

Des de l'arribada d'internet i les TIC, el periodista ha vist evolucionar les seves competències i habilitats de forma molt ràpida. Avui el periodista té una nova oportunitat per apropar-se a la ciutadania i superar les mancances tecnològiques i els reptes financers que sofreix la professió. Una vegada més la formació del periodista és essencial. En aquesta investigació s'elaborarà una proposta de perfil del periodista de dades amb el fi de descriure las seves habilitats i competències. A través d'un estudi de cas d'universitats del món que ensenyen el periodisme de dades, es realitzarà una proposta d'inclusió curricular

Set obres sobre retòrica i persuasió

El comentari crític de set obres sobre retòrica i persuasió, publicades recentment, ofereix una visió de diverses perspectives teòriques i també de les aplicacions a situacions comunicatives específiques. Les obres són El arte de hablar , de José Antonio Hernández Guerrero i María del Carmen García Tejera; Retórica , de Giambattista Vico, editada per primera vegada en castellà; 40 jocs per parlar català , de Jacqueline Jacquet, Sílvia Casulleras, Núria Mirabet; Acròbates de l'emoció , d'Amadeu Viana; Tres finestres obertes al món de la comunicació , de Ricard Morant i Miquel Peñarroya; El lenguaje de la negociación , de Joan Mulholland; i Tècniques de negociació i resolució de conflictes , de Carles Mendieta i Suñé.

Mitochondrial dysfunction increases oxidative stress and decreases chronological life span in fission yeast

Background: Oxidative stress is a probable cause of aging and associated diseases. Reactive oxygen species (ROS) originate mainly from endogenous sources, namely the mitochondria. Methodology/Principal Findings: We analyzed the effect of aerobic metabolism on oxidative damage in Schizosaccharomyces pombe by global mapping of those genes that are required for growth on both respiratory-proficient media and hydrogen-peroxide-containing fermentable media. Out of a collection of approximately 2700 haploid yeast deletion mutants, 51 were sensitive to both conditions and 19 of these were related to mitochondrial function. Twelve deletion mutants lacked components of the electron transport chain. The growth defects of these mutants can be alleviated by the addition of antioxidants, which points to intrinsic oxidative stress as the origin of the phenotypes observed. These respiration-deficient mutants display elevated steady-state levels of ROS, probably due to enhanced electron leakage from their defective transport chains, which compromises the viability of chronologically-aged cells. Conclusion/Significance: Individual mitochondrial dysfunctions have often been described as the cause of diseases or aging, and our global characterization emphasizes the primacy of oxidative stress in the etiology of such processes.

Sea state effect on the sea surface emissivity at L-band

In May 1999, the European Space Agency (ESA) selected the Earth Explorer Opportunity Soil Moisture and Ocean Salinity (SMOS) mission to obtain global and frequent soil moisture and ocean salinity maps. SMOS' single payload is the Microwave Imaging Radiometer by Aperture Synthesis (MIRAS), an L-band two-dimensional aperture synthesis radiometer with multiangular observation capabilities. At L-band, the brightness temperature sensitivity to the sea surface salinity (SSS) is low, approximately 0.5 K/psu at 20/spl deg/C, decreasing to 0.25 K/psu at 0/spl deg/C, comparable to that to the wind speed /spl sim/0.2 K/(m/s) at nadir. However, at a given time, the sea state does not depend only on local winds, but on the local wind history and the presence of waves traveling from far distances. The Wind and Salinity Experiment (WISE) 2000 and 2001 campaigns were sponsored by ESA to determine the impact of oceanographic and atmospheric variables on the L-band brightness temperature at vertical and horizontal polarizations. This paper presents the results of the analysis of three nonstationary sea state conditions: growing and decreasing sea, and the presence of swell. Measured sea surface spectra are compared with the theoretical ones, computed using the instantaneous wind speed. Differences can be minimized using an "effective wind speed" that makes the theoretical spectrum best match the measured one. The impact on the predicted brightness temperatures is then assessed using the small slope approximation/small perturbation method (SSA/SPM).

Aplicación de algunos modelos de series temporales al mercado de la electricidad en España

Hoy día, todo el mundo tiene un ojo puesto en el Mercado Eléctrico en nuestro país. No existe duda alguna sobre la importancia que tiene el comportamiento de la demanda eléctrica. Una de las peculiaridades de la electricidad que producimos, es que hoy por hoy, no existen aún métodos lo suficientemente efectivos para almacenarla, al menos en grandes cantidades. Por consiguiente, la cantidad demandada y la ofertada/producida deben casar de manera casi perfecta. Debido a estas razones, es bastante interesante tratar de predecir el comportamiento futuro de la demanda, estudiando una posible tendencia y/o estacionalidad. Profundizando más en los datos históricos de las demandas; es relativamente sencillo descubrir la gran influencia que la temperatura ambiente, laboralidad o la actividad económica tienen sobre la respuesta de la demanda. Una vez teniendo todo esto claro, podemos decidir cuál es el mejor método para aplicarlo en este tipo de series temporales. Para este fin, los métodos de análisis más comunes han sido presentados y explicados, poniendo de relieve sus principales características, así como sus aplicaciones. Los métodos en los que se ha centrado este proyecto son en los modelos de alisado y medias móviles. Por último, se ha buscado una relación entre la demanda eléctrica peninsular y el precio final que pagamos por la luz.