3,187 research outputs found
DIVULGAÇÃO DE CIÊNCIA E TECNOLOGIA – ESPAÇO COPPE MIGUEL DE SIMONI
No full textBarbosa, Caroline A.D1(M); Costa, Rodolfo J.D.S2(M); Oliveira, Raphael G.D3(M); Santos, Ellen O.D4(M); Soares, Anderson.E5 (M); Souza, Erick.A6(M); Barreto, Luana C7(M); Couceiro, João V.S8(M); Veloso, Emanoelle M.R9(M); Peixoto, Alessandro J.10 (O)1Instituto de Física, UFRJ ; 2Instituto de Física, UFRJ ; 3Instituto de Física, UFRJ ; 4Instituto de Psicologia, UFRJ; 5Engenharia Elétrica, Poli/UFRJ; 6Instituto de Física, UFRJ; 7Faculdade de Arquitetura e Urbanismo, UFRJ ; 8 Instituto de Biologia, UFRJ; 9Faculdade de Letras, UFRJ ; 10 Este trabalho visa apresentar o Espaço COPPE Miguel de Simoni Tecnologia e Desenvolvimento Humano, apresentando seus métodos pedagógicos, bem como os resultados obtidos pelo projeto. O Espaço tem como objetivo expor e abordar a importância da ciência na sociedade, com propostas apresentadas por meio de salas com experimentos interativos e de montagem de experimentos em oficinas interativas. O Espaço visa apresentar ao jovem o mundo acadêmico, seus desafios e possibilidades, um dos objetivos também é despertar no aluno o interesse pela pesquisa científica, através da exibição de resultados de sucesso, elaborados na COPPE. No Espaço COPPE são abordados conceitos científicos e sociais. Máquinas, experimentos e atividades mostram, na prática, conceitos e sua importância para a sociedade de forma interativa, além da elaboração de oficinas em que os alunos, com auxilio dos monitores, participam da montagem de experimento relacionado com seu cotidiano. Através das reações dos visitantes às apresentações, é possível observar como o Espaço pode atuar na complementação do ensino formal, possibilitando que o aluno compreenda fenômenos que fazem parte de seu cotidiano. A maioria dos visitantes do espaço é proveniente da rede pública do estado do Rio de Janeiro. Esse ano, o Espaço COPPE já recebeu cerca de 578 alunos, de idade entre 13 e 19 anos, e 37 professores que promovem a oferta de conhecimento científico, podendo ser decisiva para despertar o interesse pela ciência. Uma média de 94% dos visitantes avalia com nota máxima a exposição. Neste ano, o Espaço COPPE participou da Semana Nacional de Museus e participará novamente na Reunião Anual da Sociedade Brasileira para o Progresso da Ciência. No ano passado esses eventos renderam um acréscimo de aproximadamente 1500 pessoas em seu atendimento anual. O Espaço ainda vai inaugurar este ano novos nichos com os seguintes temas e pesquisas: Energia, Meio Ambiente e Mudanças Climáticas, Biocombustíveis de Segunda Geração, MagLev Cobra, Oceanos e Projeto Azul, Usina de Ondas, Recifes Artificiais, Lixo na Baía de Guanabara, Cidades Sustentáveis, Projeto Iguaçu, Química dos Plásticos, Construções Sustentáveis, Cooperativas Populares, O CERN, Nanotecnologia, Minerais, Fotônica, Petróleo, Contribuições do Passado, Desafios do Pré-sal, Ciência/Tecnologia/Arte, Sistema de Análise de Obras de Arte e Arqueometria, Saúde e Esporte, Remo, Micropartículas, Biofármacos; Realidade Virtual e Robótica
A bioinformatic and computational approach to regulation of genome function: integrated analysis of genome organization, promoter sequences and gene expression.
No full textAlthough much is known about gene expression regulation in both Prokaryotes and Eukaryotes, this complex and fascinating mechanism still remains to be fully elucidated. The relatively recent advent of high-throughput techniques for studying transcription has made available an invaluable amount of data that can be used for genome-wide analysis using bioinformatics approaches. These computational methods have now become an integrative part of biological research. The different topics of this thesis are related to the development and application of computational methodologies to better understand the basis of genomic gene expression regulation at different levels. A first level of investigation regarded the relationships among chromosomal structure, expression profile and functional characteristics, focusing on genomic organization and structure. For this task, REEF (REgionally Enriched Features) software has been developed, designed to identify genomic regions enriched in specific features, such as a class or group of genes homogeneous for expression and/or functional characteristics. REEF can be used to detect density variations of specific features along the genome sequence, for example genomic regions with significant enrichment of genes which are co-expressed, differentially expressed, or related to particular molecular functions. Local feature enrichment is calculated using test statistic based on the hypergeometric distribution applied genome-wide by sliding windows and false discovery rate is used for controlling multiplicity. REEF has been applied to the study of genomic distribution of tissue-specific genes and to the analysis of gene differentially expressed when comparing different myeloid cell lines. These analyses identified clusters of tissue-specific genes in the human genome and positional enrichment of hemopoietic functional module-related genes. The second level of investigation regarded gene expression regulation at promoter level. Unknown transcription factor binding sites might be detected by searching for shared sequence elements in upstream regulatory regions of genes with common biological function and/or similar expression profile. In fact, genes with similar expression are frequently co-regulated and genes with related function are often similarly expressed. New methodologies for the identification of regulatory motifs in human promoters were developed and tested. Since a drawback of this approach is the exceedingly high number of results, the use of biological knowledge both before and after application of automated pattern discovery allowed the definition of a “sheltered environment” enhancing the specificity of the computational analysis. COOP (Clustering of Overlapping Patterns) software for the extraction of sequence motifs was developed and used to analyze genomic sequences of 1 Kb upstream of 91 retina specific genes, identifying a set of putative regulative motifs, frequently occurring in retina promoter sequences. Most of them are localized in the proximal portion of promoters and tend to be less variable in central region than in lateral regions and some of them are similar to known regulatory sequences. The performances of COOP were further evaluated by simulation approaches and by applying it to a standard positive control dataset, proposed by Tompa and colleagues for systematic evaluation and comparison of pattern discovery software. A webtool for the prediction of functional elements in promoter sequences, MOST (MOtif Searching web Tool), has been applied to different datasets under various testing conditions in order to study the influence of specific search parameters on results. Two groups of promoter sequences containing known regulatory signals were used as positive control datasets: the public yeast benchmark dataset of Tompa and colleagues and a custom produced dataset of 37 human promoter sequences, subgroups of which contained some instances of one of nine different signals. The testing of performances of the method on different benchmark datasets gave quite positive results.
Taking the concepts behind COOP to a new level, a more rigorous methodology was developed for the identification of surprising and putatively regulatory motifs, by comparing their frequency in promoters sequences of co-expressed genes with that in a background set of sequences, representative of the whole set of human gene promoters. Promoter sequences are divided in overlapping regions, considered independently, for identifying positional bias in the arrangement of transcription factors binding sites along promoters. Due to the genome-wide characteristics of this approach, a new webtool for the automatic identification and retrieval of a high number of promoters in the human genome was also developed. This motif discovery methodology has been adopted to investigate structure of promoters of genes crucial during myeloid differentiation
REEF: searching REgionally Enriched Features in genomes
No full textAbstract Background In Eukaryotic genomes, different features including genes are not uniformly distributed. The integration of annotation information and genomic position of functional DNA elements in the Eukaryotic genomes opened the way to test novel hypotheses of higher order genome organization and regulation of expression. Results REEF is a new tool, aimed at identifying genomic regions enriched in specific features, such as a class or group of genes homogeneous for expression and/or functional characteristics. The method for the calculation of local feature enrichment uses test statistic based on the Hypergeometric Distribution applied genome-wide by using a sliding window approach and adopting the False Discovery Rate for controlling multiplicity. REEF software, source code and documentation are freely available at http://telethon.bio.unipd.it/bioinfo/reef/. Conclusion REEF can aid to shed light on the role of organization of specific genomic regions in the determination of their functional role.</p
A imagem de Alessandro Baricco no Brasil
No full textDissertação (mestrado) - Universidade Federal de Santa Catarina, Centro de Comunicação e Expressão, Programa de Pós-Graduação em Estudos da Tradução, Florianópolis, 2013.Com a intenção de delinear o modo pelo qual o escritor italiano Alessandro Baricco se inseriu no sistema literário brasileiro e os caminhos percorridos pelos seus livros traduzidos, esta dissertação dá voz às experiências tradutórias de seus tradutores. A inserção de Bariccono Brasil tem seu início em 1997, através de uma proposição da Profa. Dra. Roberta Barni à editora Iluminuras da tradução de Oceano Mare. A partir daí, outras sete obras foram publicadas no Brasil, sendo três delas traduzidas por Roberta Barni e as outras quatro por quatro tradutores diferentes. De um lado, considera-se o tradutor como figura principal namediação entre culturas, e, de outro, se analisa a realidade desta figuradentro do sistema literário, sua invisibilidade, seus limites e o exercíciode sua profissão. A pesquisa conta, ainda, com críticas e resenhas referentes ao autor italiano publicadas em jornais consagrados no Brasil, considerando estas como parte constituinte da imagem de Baricco refletida em território nacional. Abstract : Intending to delineate the way the Italian writer Alessandro Baricco has been inserted in the Brazilian literary system and the paths his translated books have followed, this thesis gives voice to the translating experiences of his translators. Baricco's insertion in Brazil began in 1997, through a personal project of Dr. Roberta Barni, with her translation of Oceano Mare. Since then, seven other of his works have been published in Brazil, three of which were translated by Roberta Barni and the other four by four different translators. On the one hand,the translator is considered as the main figure in mediation betweencultures and, on the other, this figure's reality is analyzed within theliterary system: its invisibility, its limits and its professional practice. Criticisms and reviews of this Italian author published in well established Brazilian newspapers are also considered, with the understanding that they are part of Baricco's image reflected here
La maturità di Alessandro Fei del Barbiere, in bilico tra Maniera e Riforma
No full textThis article studies the mature career of the Florentine painter Alessandro Fei del Barbiere (1537-1592), beginning with the rediscovery of the 'Ascension' altarpiece formerly in the Albizi Chapel in the destroyed church of San Pier Maggiore, Florence. Studying this painting and others recorded in 1584 by the biographer Raffaello Borghini, such as the two altarpieces for Santa Maria delle Grazie and the Madonna dell'Umiltà in Pistoia, the author reconstructs a body of works showing how in the 1580s Fei gradually went beyond the archaic style of his apprenticeship - he had been trained by Ridolfo del Ghirlandaio and Pierfrancesco Foschi, but was also marked by the Maniera of Vasari - evolving towards naturalism in both mimesis and pictorial handling. In Florence, his development partly parallels that of Santi di Tito and his circle, but Fei was also influenced by a probable sojourn during the early part of that decade in Rome, where he could have been inspired by Girolamo Muziano and the painters working for Pope Gregory XIII. Among other proposals, the author suggests that the artist was responsible for decorating the chancel of Fiesole Cathedral (c. 1584-1589), which consisted of an altarpiece, only rarely discussed by scholars, and a cycle of frescoes hitherto attributed to Nicodemo Ferrucci
MAGIA2: from miRNA and genes expression data integrative analysis to microRNA-transcription factor mixed regulatory circuits (2012 update).
No full textiWhale: a computational pipeline based on Docker and SCons for detection and annotation of somatic variants in cancer WES data
No full textWhole exome sequencing (WES) is a powerful approach for discovering sequence variants in cancer cells but its time effectiveness is limited by the complexity and issues of WES data analysis. Here we present iWhale, a customizable pipeline based on Docker and SCons, reliably detecting somatic variants by three complementary callers (MuTect2, Strelka2 and VarScan2). The results are combined to obtain a single variant call format file for each sample and variants are annotated by integrating a wide range of information extracted from several reference databases, ultimately allowing variant and gene prioritization according to different criteria. iWhale allows users to conduct a complex series of WES analyses with a powerful yet customizable and easy-to-use tool, running on most operating systems (macOs, GNU/Linux and Windows). iWhale code is freely available at https://github.com/alexcoppe/iWhale and the docker image is downloadable from https://hub.docker.com/r/alexcoppe/iwhale
Impact of probe annotation on the integration of miRNA-mRNA expression profiles for miRNA target detection.
No full textMicroRNAs (miRNAs) are small non-coding RNAs that mediate gene expression at the post-transcriptional and translational levels by an imperfect binding to target mRNA 3'UTR regions. While the ab-initio computational prediction of miRNA-mRNA interactions still poses significant challenges, it is possible to overcome some of its limitations by carefully integrating into the analysis the paired expression profiles of miRNAs and mRNAs. In this work, we show how the choice of a proper probe annotation for microarray platforms is an essential requirement to achieve good sensitivity in the identification of miRNA-mRNA interactions. We compare the results obtained from the analysis of the same expression profiles using both gene and transcript based custom CDFs that we have developed for a number of different annotations (ENSEMBL, RefSeq, AceView). In all cases, transcript-based annotations clearly improve the effectiveness of data integration and thus provide a more reliable confirmation of computationally predicted miRNA-mRNA interactions
Transcriptome sequencing and de novo annotation of the critically endangered Adriatic sturgeon
No full textBackground: Sturgeons are a group of Condrostean fish with very high evolutionary, economical and conservation interest. The eggs of these living fossils represent one of the most high prized foods of animal origin. The intense fishing pressure on wild stocks to harvest caviar has caused in the last decades a dramatic decline of their distribution and abundance leading the International Union for Conservation of Nature to list them as the more endangered group of species. As a direct consequence, world-wide efforts have been made to develop sturgeon aquaculture programmes for caviar production. In this context, the characterization of the genes involved in sex determination could provide relevant information for the selective farming of the more profitable females.
Results: The 454 sequencing of two cDNA libraries from the gonads and brain of one male and one female full-sib A. naccarii, yielded 182,066 and 167,776 reads respectively, which, after strict quality control, were iterative assembled into more than 55,000 high quality ESTs. The average per-base coverage reached by assembling the two libraries was 4X. The multi-step annotation process resulted in 16% successfully annotated sequences with GO terms. We screened the transcriptome for 32 sex-related genes and highlighted 7 genes that are potentially specifically expressed, 5 in male and 2 in females, at the first life stage at which sex is histologically identifiable. In addition we identified 21,791 putative EST-linked SNPs and 5,295 SSRs.
Conclusions: This study represents the first large massive release of sturgeon transcriptome information that we organized into the public database AnaccariiBase, which is freely available at http://compgen.bio.unipd.it/anaccariibase/. This transcriptomic data represents an important source of information for further studies on sturgeon species. The hundreds of putative EST-linked molecular makers discovered in this study will be invaluable for sturgeon reintroduction and breeding programs
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