New insights into alternative splicing using microarray technology

Tese de doutoramento, Ciências Biomédicas (Ciências Morfológicas), Universidade de Lisboa, Faculdade de Medicina, 2010Disponível no documentoFundação para a Ciência e a Tecnologia (SFRH/ BD/22825/2005

Prática de ensino supervisionada em educação pré-escolar: a relevância da interação adulto-criança no processo de aprendizagem e desenvolvimento

O presente relatório, realizado no âmbito das unidades curriculares de Prática de Ensino Supervisionada I e II em Creche e Jardim-de-infância, visa compreender a relevância da interação adulto-criança no processo de aprendizagem e desenvolvimento e de como esta influência a qualidade do ambiente educativo. Para descrever a relevância desta interação utilizaram-se diferentes referenciais como, o Modelo High-Scope cujo enfoque é aprendizagem pela ação, a Teoria de Aprendizagem e Desenvolvimento de Lev-Vygotsky que evidencia que a criança se desenvolve através da interação com o meio e com a sociedade, o Manual DQP cujos instrumentos permitem avaliar e melhorar os contextos educativos e as Orientações Curriculares para a Educação Pré-Escolar fundamental enquanto apoio para os educadores nas decisões sobre a sua ação educativa. Numa metodologia de investigação-ação e com o suporte dos referenciais mencionados procurei superar dificuldades, potenciar ambientes educativos de qualidade e melhorar o meu processo de construção e formação profissional; #### Abstract Teaching Practice in Pre-school Education – The Importance of Adult-Child Interaction in the Process of Learning and Development This report, conducted in the context of curricular units Teaching Practice I and II ‘creche’ and pre-school, aims to understand the importance of adult-child interaction in learning and development and how this influences the quality of educational environment. To describe the relevance of this interaction we used different references such as the High-Scope Model which focuses on action learning, the Theory of Learning and Development Lev Vygotsky, which shows that the child develops through interaction with the environment and with society, the Manual DQP whose instruments to assess and improve the educational contexts and Curriculum Guidelines for Pre-School Education as fundamental support for educators in decisions about their educational. A methodology of action research and the support of the references mentioned searched overcome difficulties, enhance quality educational environments and improve my build process and training

Núcleo Museológico Urbano da Bela Vista. Diagnóstico e Propostas para a Elaboração de um Programa Museológico

O presente trabalho de projeto, dedicado ao Núcleo Museológico Urbano da Bela Vista, em Setúbal, foca-se essencialmente em duas questões: a elaboração de um diagnóstico à situação atual da instituição em causa e a construção de uma proposta a partir da qual seja possível a criação de um regulamento para o projeto e um decorrente programa museológico. Uma breve contextualização e caracterização do Bairro da Bela Vista, em Setúbal, permitem-nos compreender os motivos que levaram, em primeiro lugar, à criação do NMU e à sua instalação naquele que é, sem dúvida, o bairro mais desacreditado da cidade. Motivações à parte, a realidade sobre o funcionamento do Núcleo Museológico fica aquém das expectativas e o diagnóstico aqui realizado, apoiado maioritariamente nas informações fornecidas diretamente pela divisão da Câmara Municipal de Setúbal, responsável pela sua gestão, mostranos que há ainda muito trabalho a fazer para que o NMU possa cumprir os seus objetivos. No sentido de contribuir para que o Núcleo Museológico Urbano possa vir um dia a atingir todo o seu potencial, e com base naquilo que me foi possível observar enquanto fui realizando o diagnóstico a esta instituição, escrevi uma proposta, da qual constam vários pontos que considero serem indispensáveis e que poderão vir a integrar o regulamento e o decorrente programa museológico do NMU. É importante salientar também que, embora o principal objetivo deste trabalho seja contribuir para a criação de um documento que possa vir a servir como instrumento de trabalho que facilite o desempenho das funções diárias do Núcleo Museológico Urbano, pretendo ao mesmo tempo chamar a atenção para a existência deste equipamento na cidade e para a urgência de tomar as medidas necessárias para que não continue a passar despercebido.The present project, dedicated to the Urban Museum Center of Bela Vista in Setúbal, focuses on elaborating a diagnosis of this institution’s current situation and on creating a proposal plan for the museum. A brief contextualization and characterization of the Bela Vista borough allows to understand the reasons for creating and installing the Center in one of the most infamous neighborhoods in the city. Reasons aside, the reality of the Urban Museum Center’s performance is well below expectations and the diagnosis here presented, mostly based on information provided by the Setubal City Council’s division responsible for its management, shows us that there is still a lot of work to be done before the Center is able to reach its goals. In order to contribute toward aiding the Urban Museum Center reaching its full potential, and based on what I could observe while working on the diagnosis of this institution, I wrote a proposal that addresses a few points that I consider indispensable and can one day integrate a plan for this museum. It is important to keep in mind that, although the main goal of this project is to contribute to the creation of a document that may, in the future, serve as a tool to facilitate the Center’s daily workload, it also intends to draw attention to the existence of the Urban Museum Center and the urgent measures needed to keep it from being unnoticed

Desafios de uma newsmagazine na era digital: o caso da Revista Sábado

Este relatório de estágio resulta de uma experiência de três meses na revista Sábado e visa aferir quais as principais diferenças entre a cobertura jornalística que a revista faz, em acontecimentos especiais na sua versão em papel e no seu domínio online. Para isso, selecionaram-se dois casos portugueses, – um previsível e outro imprevisível – considerados os mais relevantes durante o período de estágio: as eleições autárquicas de 2017 e os incêndios de outubro do mesmo ano que os de Pedrógão Grande. Foi aplicada uma metodologia de investigação mista, conjugando uma análise de conteúdo com 11 entrevistas semiestruturadas a jornalistas, editores e diretores da revista. Conclui-se que o digital é mais imediato, serve a necessidade de uma constante atualização no caso de acontecimentos especiais, ao passo que, na revista, são publicados artigos mais pensados, cuidados e que permitem ao leitor uma contextualização do assunto. Além disso, considera-se que a Sábado não aproveita ainda todas as potencialidades já existentes no meio digital, principalmente no que respeita à interatividade, multimedialidade e hipertextualidade.This internship report aims assess the main differences between the journalistic coverage that Sábado does, in special events, in its paper version and in its online domain. For this, two cases were selected – a predictable and an unpredictable - considered the most relevant during the internship period, the municipal elections of 2017 and the October fires of the same year as those of Pedrógão Grande. A mixed methodology of research was applied, combining a content analysis with 11 semi-structured interviews to journalists, editors and directors of the magazine. It is concluded that digital is more immediate, it serves the need for constant updating in the case of special events, whereas in the magazine, articles are published in a more thoughtful and caring way and that allow the reader a contextualization of the subject. In addition, it is considered that Sábado does not take advantage of all the potential already existing in the digital environment, especially in terms of interactivity, multimedia and hypertextuality

Concerted Regulation of Glycosylation Factors Sustains Tissue Identity and Function

Funding Information: This work was financed by national funds from Fundação para a Ciência e Tecnologia (FCT), in the scope of the project UIDP/04378/2020 and UIDB/04378/2020 of the Research Unit on Applied Molecular Biosciences—UCIBIO and the project LA/P/0140/2020 of the Associate Laboratory Institute for Health and Bioeconomy—i4HB. Moreover, this research was funded by: PTDC/MED-ONC/28660/2017 from Fundação para a Ciência e Tecnologia (FCT) to A.R.G. A.R.G is recipient of Researcher Grant CEECIND/02699/2017 from FCT. R.F. is recipient of a research grant (SFRH/BD/124326/2016) from FCT, Portugal; European Union’s Horizon 2020 research and innovation program under the EJP RD COFUND-EJP N° 825575, EJPRD/0001/2020. This work had also the support of INCD funded by FCT and FEDER under the project 22153-01/SAICT/2016. The Genotype-Tissue Expression (GTEx) Project was supported by the Common Fund of the Office of the Director of the National Institutes of Health, and by NCI, NHGRI, NHLBI, NIDA, NIMH, and NINDS. Publisher Copyright: © 2022 by the authors.Glycosylation is a fundamental cellular process affecting human development and health. Complex machinery establishes the glycan structures whose heterogeneity provides greater structural diversity than other post-translational modifications. Although known to present spatial and temporal diversity, the evolution of glycosylation and its role at the tissue-specific level is poorly understood. In this study, we combined genome and transcriptome profiles of healthy and diseased tissues to uncover novel insights into the complex role of glycosylation in humans. We constructed a catalogue of human glycosylation factors, including transferases, hydrolases and other genes directly involved in glycosylation. These were categorized as involved in N-, O- and lipid-linked glycosylation, glypiation, and glycosaminoglycan synthesis. Our data showed that these glycosylation factors constitute an ancient family of genes, where evolutionary constraints suppressed large gene duplications, except for genes involved in O-linked and lipid glycosylation. The transcriptome profiles of 30 healthy human tissues revealed tissue-specific expression patterns preserved across mammals. In addition, clusters of tightly co-expressed genes suggest a glycosylation code underlying tissue identity. Interestingly, several glycosylation factors showed tissue-specific profiles varying with age, suggesting a role in ageing-related disorders. In cancer, our analysis revealed that glycosylation factors are highly perturbed, at the genome and transcriptome levels, with a strong predominance of copy number alterations. Moreover, glycosylation factor dysregulation was associated with distinct cellular compositions of the tumor microenvironment, reinforcing the impact of glycosylation in modulating the immune system. Overall, this work provides genome-wide evidence that the glycosylation machinery is tightly regulated in healthy tissues and impaired in ageing and tumorigenesis, unveiling novel potential roles as prognostic biomarkers or therapeutic targets.publishersversionpublishe

Dynamic transitions in RNA polymerase II density profiles during transcription termination

Eukaryotic protein-coding genes are transcribed by RNA polymerase II (RNAPII) through a cycle composed of three main phases: initiation, elongation, and termination. Recent studies using chromatin immunoprecipitation coupled to high-throughput sequencing suggest that the density of RNAPII molecules is higher at the 3′-end relative to the gene body. Here we show that this view is biased due to averaging density profiles for "metagene" analysis. Indeed, the majority of genes exhibit little, if any, detectable accumulation of polymerases during transcription termination. Compared with genes with no enrichment, genes that accumulate RNAPII at the 3′-end are shorter, more frequently contain the canonical polyadenylation [poly(A)] signal AATAAA and G-rich motifs in the downstream sequence element, and have higher levels of expression. In 1% to 4% of actively transcribing genes, the RNAPII enriched at the 3′-end is phosphorylated on Ser5, and we provide evidence suggesting that these genes have their promoter and terminator regions juxtaposed. We also found a striking correlation between RNAPII accumulation and nucleosome organization, suggesting that the presence of nucleosomes after the poly(A) site induces pausing of polymerases, leading to their accumulation. Yet we further observe that nucleosome occupancy at the 3′-end of genes is dynamic and correlates with RNAPII density. Taken together, our results provide novel insight to transcription termination, a fundamental process that remains one of the least understood stages of the transcription cycle.info:eu-repo/semantics/publishedVersio

RNA polymerase II phosphorylated on CTD serine 5 interacts with the spliceosome during co-transcriptional splicing

© 2018 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).The highly intronic nature of protein coding genes in mammals necessitates a co-transcriptional splicing mechanism as revealed by mNET-seq analysis. Immunoprecipitation of MNase-digested chromatin with antibodies against RNA polymerase II (Pol II) shows that active spliceosomes (both snRNA and proteins) are complexed to Pol II S5P CTD during elongation and co-transcriptional splicing. Notably, elongating Pol II-spliceosome complexes form strong interactions with nascent transcripts, resulting in footprints of approximately 60 nucleotides. Also, splicing intermediates formed by cleavage at the 5' splice site are associated with nearly all spliced exons. These spliceosome-bound intermediates are frequently ligated to upstream exons, implying a sequential, constitutive, and U12-dependent splicing process. Finally, lack of detectable spliced products connected to the Pol II active site in human HeLa or murine lymphoid cells suggests that splicing does not occur immediately following 3' splice site synthesis. Our results imply that most mammalian splicing requires exon definition for completion.This work was supported by funding to N.J.P. (Wellcome Trust Investigator Award [107928/Z/15/Z] and ERC Advanced [339270] grants) and to M.C.-F. (Fundação Ciência e Tecnologia, Portugal; grant PTDC/BEX-BCM/5899/2014).info:eu-repo/semantics/publishedVersio

Genetic predisposition for aggressive behaviour related with dopamine and serotonin pathways : an overview

Abstract in proceedings of the Fourth International Congress of CiiEM: Health, Well-Being and Ageing in the 21st Century, held at Egas Moniz’ University Campus in Monte de Caparica, Almada, from 3–5 June 2019.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.info:eu-repo/semantics/publishedVersio

The genetic susceptibility linking preterm birth and periodontal disease : a review

Abstract in proceedings of the Fourth International Congress of CiiEM: Health, Well-Being and Ageing in the 21st Century, held at Egas Moniz’ University Campus in Monte de Caparica, Almada, from 3–5 June 2019.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.info:eu-repo/semantics/publishedVersio

Mammalian NET-Seq reveals genome-wide nascent transcription coupled to RNA processing

© Copyright © 2015 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/)Transcription is a highly dynamic process. Consequently, we have developed native elongating transcript sequencing technology for mammalian chromatin (mNET-seq), which generates single-nucleotide resolution, nascent transcription profiles. Nascent RNA was detected in the active site of RNA polymerase II (Pol II) along with associated RNA processing intermediates. In particular, we detected 5'splice site cleavage by the spliceosome, showing that cleaved upstream exon transcripts are associated with Pol II CTD phosphorylated on the serine 5 position (S5P), which is accumulated over downstream exons. Also, depletion of termination factors substantially reduces Pol II pausing at gene ends, leading to termination defects. Notably, termination factors play an additional promoter role by restricting non-productive RNA synthesis in a Pol II CTD S2P-specific manner. Our results suggest that CTD phosphorylation patterns established for yeast transcription are significantly different in mammals. Taken together, mNET-seq provides dynamic and detailed snapshots of the complex events underlying transcription in mammals.This work was supported by funding to N.J.P. (Wellcome Trust Programme [091805/Z/10/Z] and ERC Advanced [339270] Grants) and to M.C.-F. (Fundação Ciência e Tecnologia, Portugal).info:eu-repo/semantics/publishedVersio