EGASP: the human ENCODE Genome Annotation Assessment Project.

BACKGROUND: We present the results of EGASP, a community experiment to assess the state-of-the-art in genome annotation within the ENCODE regions, which span 1% of the human genome sequence. The experiment had two major goals: the assessment of the accuracy of computational methods to predict protein coding genes; and the overall assessment of the completeness of the current human genome annotations as represented in the ENCODE regions. For the computational prediction assessment, eighteen groups contributed gene predictions. We evaluated these submissions against each other based on a 'reference set' of annotations generated as part of the GENCODE project. These annotations were not available to the prediction groups prior to the submission deadline, so that their predictions were blind and an external advisory committee could perform a fair assessment. RESULTS: The best methods had at least one gene transcript correctly predicted for close to 70% of the annotated genes. Nevertheless, the multiple transcript accuracy, taking into account alternative splicing, reached only approximately 40% to 50% accuracy. At the coding nucleotide level, the best programs reached an accuracy of 90% in both sensitivity and specificity. Programs relying on mRNA and protein sequences were the most accurate in reproducing the manually curated annotations. Experimental validation shows that only a very small percentage (3.2%) of the selected 221 computationally predicted exons outside of the existing annotation could be verified. CONCLUSION: This is the first such experiment in human DNA, and we have followed the standards established in a similar experiment, GASP1, in Drosophila melanogaster. We believe the results presented here contribute to the value of ongoing large-scale annotation projects and should guide further experimental methods when being scaled up to the entire human genome sequence.

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.

EGASP: the human ENCODE Genome Annotation Assessment Project

Background: Non-long terminal repeat (non-LTR) retrotransposons have contributed to shaping the structure and function of genomes. In silico and experimental approaches have been used to identify the non-LTR elements of the urochordate Ciona intestinalis. Knowledge of the types and abundance of non-LTR elements in urochordates is a key step in understanding their contribution to the structure and function of vertebrate genomes. Results: Consensus elements phylogenetically related to the I, LINE1, LINE2, LOA and R2 elements of the 14 eukaryotic non-LTR clades are described from C. intestinalis. The ascidian elements showed conservation of both the reverse transcriptase coding sequence and the overall structural organization seen in each clade. The apurinic/apyrimidinic endonuclease and nucleic-acid-binding domains encoded upstream of the reverse transcriptase, and the RNase H and the restriction enzyme-like endonuclease motifs encoded downstream of the reverse transcriptase were identified in the corresponding Ciona families. Conclusions: The genome of C. intestinalis harbors representatives of at least five clades of non-LTR retrotransposons. The copy number per haploid genome of each element is low, less than 100, far below the values reported for vertebrate counterparts but within the range for protostomes. Genomic and sequence analysis shows that the ascidian non-LTR elements are unmethylated and flanked by genomic segments with a gene density lower than average for the genome. The analysis provides valuable data for understanding the evolution of early chordate genomes and enlarges the view on the distribution of the non-LTR retrotransposons in eukaryotes.

Vaginal hysterectomy with the autosuture stapler

Our objective was to assess the applicability of hysterectomy by the vaginal route completely performed with Autosuture staples. Between January 1992 and September 1993, 5 vaginal hysterectomies using Autosuture staplers were performed by the authors. Five vaginal hysterectomies matched for age, parity, and uterine size performed by the same surgeons using reabsorbable sutures during the same period were used as case controls. No febrile morbidity, cuff infections, thrombophlebitis, bladder injury, or hemorrhage complications were observed in the 10 women who entered the study. In summary, vaginal hysterectomy can be performed with Autosutures easily, probably faster with experience, and with less oozing from the operative field, thus providing a safe procedure.

Posterior vaginal wall repair with synthetic absorbable mesh: A new technique for and old procedure

The objective of this study was to assess the applicability of posterior wall repair with a synthetic absorbable mesh. Between January and September 1996, five posterior repairs using absorbable synthetic meshes were performed. Five posterior wall repairs in patients matched for age, parity, and rectocele degree were performed according to usual procedures during the same period, and were used as controls. No febrile morbidity, cuff or posterior vaginal wall infections, thrombophlebitis, rectal injury, or hemorrhagic complications were observed in the 10 women who entered the study. In summary, posterior wall repair can be easily performed with an absorbable soft tissue patch, theoretically preserving sexual activity, and probably offers better functional results with longer experience, thus providing a safe and useful procedure in sexually active women.

Islands of euchromatin-like sequence and expressed polymorphic sequences within the short arm of human chromosome 21.

The goals of the human genome project did not include sequencing of the heterochromatic regions. We describe here an initial sequence of 1.1 Mb of the short arm of human chromosome 21 (HSA21p), estimated to be 10% of 21p. This region contains extensive euchromatic-like sequence and includes on average one transcript every 100 kb. These transcripts show multiple inter- and intrachromosomal copies, and extensive copy number and sequence variability. The sequencing of the "heterochromatic" regions of the human genome is likely to reveal many additional functional elements and provide important evolutionary information.

Impacto de inseticidas sobre parasitóides da traça-das-crucíferas em repolho, no Distrito Federal

Este trabalho teve como objetivo identificar os parasitóides da Plutella xylostella(L.) presentes em áreas de cultivo do Distrito Federal, tratadas ou não com inseticidas, onde larvas do inseto foram coletadas. Foram identificados quatro parasitóides: Apantelessp. (Braconidae), Oomyzus sokolowiskii (Kurdjumov) (Eulophidae), Diadegmasp. (Ichneumonidae) e Actiasp. (Tachinidae). Onível de parasitismo nas áreas não tratadas com inseticidas variou de 5% a 94%, enquanto em áreas tratadas variou de 11% a 87%. A maior parte das larvas de traça-das-crucíferas foram encontradas nas cabeças de repolho ou na parte inferior das folhas da saia das plantas. Esta distribuição de larvas sobre as plantas deve permitir que estas escapem do contato com o inseticida, e, conseqüentemente, os parasitóides podem sobreviver nas plantas tratadas.

GSVA: gene set variation analysis for microarray and RNA-seq data

Gene set enrichment (GSE) analysis is a popular framework for condensing information from gene expression profiles into a pathway or signature summary. The strengths of this approach over single gene analysis include noise and dimension reduction, as well as greater biological interpretability. As molecular profiling experiments move beyond simple case-control studies, robust and flexible GSE methodologies are needed that can model pathway activity within highly heterogeneous data sets. To address this challenge, we introduce Gene Set Variation Analysis (GSVA), a GSE method that estimates variation of pathway activity over a sample population in an unsupervised manner. We demonstrate the robustness of GSVA in a comparison with current state of the art sample-wise enrichment methods. Further, we provide examples of its utility in differential pathway activity and survival analysis. Lastly, we show how GSVA works analogously with data from both microarray and RNA-seq experiments. GSVA provides increased power to detect subtle pathway activity changes over a sample population in comparison to corresponding methods. While GSE methods are generally regarded as end points of a bioinformatic analysis, GSVA constitutes a starting point to build pathway-centric models of biology. Moreover, GSVA contributes to the current need of GSE methods for RNA-seq data. GSVA is an open source software package for R which forms part of the Bioconductor project and can be downloaded at http://www.bioconductor.org.

El joc d'esquena del davanter centre al futbol, és més eficaç jugant de cara o girant-se?

Segons Castelo (1999, 2009) i Ardá i Casal (2003) la fase ofensiva del futbol es divideix en la fase de progressió, en la qual es busca progressar a porteria, i en la fase de manteniment o emergència, en la qual s’assegura la possessió de la pilota. L’objectiu és analitzar si quan el davanter centre rep la pilota d’esquena a porteria, es manté amb més eficàcia la possessió jugant en progressió o en emergència durant els 5” posteriors a la recepció de la pilota per part del davanter. L’estudi és Descriptiu d’Observació Directa, en aquest s’observen i s’analitzen, a través de vídeos, 10 partits de la fase de grups de la fase final de la Eurocopa 2012, en concret els partits són dels grups A i B. Els resultats confirmen la hipòtesi inicial, ja que es manté amb més eficàcia la pilota quan aquesta es juga en emergència (71%) que no pas en progressió (54%).

Eugenol como anestésico para a tilápia-do-nilo

O objetivo deste trabalho foi avaliar o eugenol como anestésico para a tilápia-do-nilo. Para a concentração ideal, foram avaliados seis tratamentos (50, 75, 100, 150, 200 e 250 mg L-1), com dez peixes por tratamento, anestesiados individualmente, acompanhados durante a indução e recuperação. A toxicidade foi estimada pela submissão de 210 peixes a 7 concentrações de eugenol (50, 75, 100, 150, 200, 250, 300 mg L-1), durante 600 s e, para a margem de segurança, 120 peixes foram submetidos a 75 mg L-1 durante cinco intervalos de tempo (600, 1.200, 1.800 e 2.400 s). As concentrações eficientes foram 50 e 75 mg L-1. Os valores de toxicidade letal (CL), aos 600 s, foram: CL01, 81,97 mg L-1; CL50, 184,26 mg L-1; e CL99, 286,55 mg L-1; e os tempos de concentrações letais (TCL) foram: TCL01, 566,97 s; TCL50, 1.611,66 s; e TCL99, 2.656,34 s. Concluiu-se que 75 mg L-1 são suficientes para a anestesia profunda de curta duração, com margem de segurança de 484,27 s, e 50 mg L-1 para longos períodos (600 s). A maior concentração terapêutica do eugenol custa R$ 0,065 por litro de água. A eutanásia pode ser realizada com 286,55 mg L-1 durante 600 s.

Divergência genética entre acessos açucarados e não açucarados de mandioca

O objetivo deste trabalho foi estimar a divergência genética entre acessos de mandioca açucarados e não açucarados, por meio de marcadores moleculares, caracteres quantitativos e qualitativos, bem como determinar a correlação entre essas estimativas. Foram utilizados quatro acessos de mandioca açucarados e quatro não açucarados, com duas variedades locais e duas comerciais. Os acessos foram avaliados em campo, em laboratório, com marcadores RAPD, quanto a 12 caracteres quantitativos e 33 morfológicos. Foram estimadas as matrizes de dissimilaridade/distância genética entre os acessos, por meio dos caracteres qualitativos e quantitativos e da significância da correlação entre as matrizes. A divergência genética entre os acessos foi elevada e os acessos açucarados foram diferenciados das variedades não açucaradas locais e comerciais. As distâncias estimadas, por meio de marcadores moleculares e caracteres qualitativos, evidenciaram elevada associação entre si e associação moderada com a estimada por meio de caracteres quantitativos.

Tandem chimerism as a means to increase protein complexity in the human genome.

The "one-gene, one-protein" rule, coined by Beadle and Tatum, has been fundamental to molecular biology. The rule implies that the genetic complexity of an organism depends essentially on its gene number. The discovery, however, that alternative gene splicing and transcription are widespread phenomena dramatically altered our understanding of the genetic complexity of higher eukaryotic organisms; in these, a limited number of genes may potentially encode a much larger number of proteins. Here we investigate yet another phenomenon that may contribute to generate additional protein diversity. Indeed, by relying on both computational and experimental analysis, we estimate that at least 4%-5% of the tandem gene pairs in the human genome can be eventually transcribed into a single RNA sequence encoding a putative chimeric protein. While the functional significance of most of these chimeric transcripts remains to be determined, we provide strong evidence that this phenomenon does not correspond to mere technical artifacts and that it is a common mechanism with the potential of generating hundreds of additional proteins in the human genome.

Braquiterapia de alta taxa de dose no tratamento do carcinoma da próstata: análise da toxicidade aguda e do comportamento bioquímico

OBJETIVO: Analisar a resposta bioquímica nas variáveis volume prostático, valor do antígeno prostático específico (PSA), escores de Gleason, estádio, risco da doença e hormonioterapia. MATERIAIS E MÉTODOS: No período de fevereiro de 1998 a julho de 2001, 46 pacientes com câncer de próstata foram tratados com radioterapia, numa combinação de teleterapia e braquiterapia de alta taxa de dose (BATD). A idade variou de 51 a 79 anos (média de 66,4 anos). O estádio T1c foi o mais freqüente: 30 (65%). O escore de Gleason era abaixo de 7 em 78% dos pacientes. O PSA variou de 3,4 a 33,3, estando abaixo de 10 em 39% das vezes. O volume prostático médio foi de 32,3 cc. Um total de 28% dos pacientes recebeu hormonioterapia. A dose de teleterapia variou de 45 a 50,4 Gy, associada a quatro frações de BATD de 4 Gy. RESULTADOS: O seguimento variou de 6 a 43 meses. Quatro pacientes perderam seguimento e quatro morreram (um por doença). Dos 39 pacientes analisados, 76% apresentaram PSA menor que 1,5. Nenhuma das variáveis analisadas foi estatisticamente significante (p > 0,05) com relação ao controle bioquímico. CONCLUSÃO: A utilização de BATD foi eficiente no tratamento do câncer de próstata e, neste estudo, as variáveis consideradas como fatores prognósticos não interferiram no controle bioquímico.

Ribosome profiling reveals the rhythmic liver translatome and circadian clock regulation by upstream open reading frames.

Mammalian gene expression displays widespread circadian oscillations. Rhythmic transcription underlies the core clock mechanism, but it cannot explain numerous observations made at the level of protein rhythmicity. We have used ribosome profiling in mouse liver to measure the translation of mRNAs into protein around the clock and at high temporal and nucleotide resolution. We discovered, transcriptome-wide, extensive rhythms in ribosome occupancy and identified a core set of approximately 150 mRNAs subject to particularly robust daily changes in translation efficiency. Cycling proteins produced from nonoscillating transcripts revealed thus-far-unknown rhythmic regulation associated with specific pathways (notably in iron metabolism, through the rhythmic translation of transcripts containing iron responsive elements), and indicated feedback to the rhythmic transcriptome through novel rhythmic transcription factors. Moreover, estimates of relative levels of core clock protein biosynthesis that we deduced from the data explained known features of the circadian clock better than did mRNA expression alone. Finally, we identified uORF translation as a novel regulatory mechanism within the clock circuitry. Consistent with the occurrence of translated uORFs in several core clock transcripts, loss-of-function of Denr, a known regulator of reinitiation after uORF usage and of ribosome recycling, led to circadian period shortening in cells. In summary, our data offer a framework for understanding the dynamics of translational regulation, circadian gene expression, and metabolic control in a solid mammalian organ.

Anàlisi de la incidència del sistema de joc en la creació de situacions de superioritat numèrica en el futbol amb el juvenil “A” del Futbol Club Barcelona

El present treball es centra en l’estudi de les situacions de superioritat numèrica generades al llarg de la temporada 2013-2014 de l’equip Juvenil A del Futbol Club Barcelona. L’objectiu principal d’aquest treball és esbrinar quina incidència té el sistema de joc 1-4-3-3 en la creació d’aquestes situacions ofensives en el joc de l’equip. Per tal d’enregistrar múltiples situacions de joc i diferenciar la seva complexitat, s’han establert tres variables d’estudi: la zona del camp on es crea la superioritat numèrica (dividint el camp en 12 zones), el tipus de superioritat produïda (2 contra 1, 3 contra 1, 3 contra 2, 4 contra 2 i 4 contra 3), i la freqüència d’interacció dels jugadors en les situacions de superioritat en relació al networking (jugadors que intervenen en les situacions de superioritat per tal de poder establir relacions entre posicions del sistema de joc 1-4-3-3). El mètode utilitzat és notacional (ja que s’enregistra la freqüència en què succeeix un fenomen a partir d’unes taules creades especialment per l’enregistrament de dades), on fent ús de la proposta de Gréhaigne (2001) s’analitzen 8 partits al llarg de la temporada 2013-2014. Els resultats obtinguts mostren que es produeixen més superioritats a les zones 4 i 6 (20,37% respectivament), seguides de les zones 7 (14,81%) i 5 (13,89%). El major tipus de superioritat ha estat el 2 contra 1 (48,15%) seguit del 3 contra 2 (39,81%). La interacció més freqüent entre jugadors en les situacions de 2 contra 1 ha estat: lateral dret i central dret (26,92%) i lateral esquerre i central esquerre (21,15%). En les situacions de tres jugadors (3 contra 1) ha estat: entre el central dret, central esquerre i el pivot (28,57%) i entre el central dret, el lateral dret i el pivot (28,75%). En les situacions de 3 contra 2: lateral dret, l’interior dret i l’extrem dret (18,60%) i entre el central esquerre, el lateral esquerre i l’interior esquerre (18,60%). Pel que fa a les situacions de 4 contra 2 no se n’ha produït cap, i les de 4 contra 3 hi ha una igualtat entre diverses posicions(16,67%), però no s’observen dades molt significatives en quan a la intervenció, excepte la posició del pivot que intervé en gairebé totes. Aquestes dades, s’assimilen al que diuen Sans i Frattarola (2009) sobre el fet que en la zona d’inici es creen més situacions de superioritat que en la zona de progressió i finalització. També Castelo (1999) aporta un estudi sobre els percentatges d’aportacions ofensives dels jugadors en funció de l’espai i la demarcació, però tot i que en aquest cas no ho compara amb situacions de superioritat numèrica, les dades extretes son interessants per la comparativa amb l’estudi que es presenta.