Browsing by Issue Date, starting with "2019-01-10"
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- Assembly and annotation of the sardine (Sardina pilchardus) transcriptomePublication . Garcia, Carlos Miguel Estevens Vieira Rolo; Power, Deborah; Louro, BrunoThe European sardine (Sardina pilchardus) is a fish of high cultural and economic importance in Portugal and current stock assessment studies report an alarming stock biomass decrease due to overfishing and/or environmental change. For better management of the sardine fisheries, there is an urgent need to understand the causal factors leading to the historically low level of the sardine stock in Portuguese waters. Important biological questions such as population diversity level, structure and migrations can be tackled with the development and usage of genomic tools. The ability to answer such important biological questions will be valuable and can be integrated into stock assessment data modelling and aid data-based policy making for better biological resource management. Eleven tissues were sequenced and curated to assemble the transcriptome. Through the comparison of different approaches, the best seemed to go through a quality control step with Trim Galore and a de novo assembly. A post-assembly quality control with Transrate seemed to be better when assembling a group of different tissues rather than one specific ones. The assembly with reads from all the tissues studied contained 170,478 contigs and had an N50 value of 486. Before this project almost no genomic/genetics resources existed to assist biological studies of the sardine and the species genome and transcriptome are cornerstone resources needed to translate applied scientific genetic data into management measures. In this project, a reference transcriptome of the sardine was assembled and functionally annotated.
- Avaliação de alunos com currículo específico individual: práticas pedagógicas no 2º ciclo do ensino básicoPublication . Roque, Maria Teresa de Almeida dos Santos; Guerreiro, AntónioO estudo centra-se na problemática da avaliação de alunos com necessidades educativas especiais (NEE) do 2.ºciclo no ensino básico, mais concretamente dos alunos com currículo específico individual (CEI), tendo como objetivo principal a reflexão sobre a importância de encontrar estratégias que facilitem as aprendizagens de crianças com NEE. Pretendeu-se assim, identificar o processo de avaliação de alunos com CEI e aprofundar o conhecimento sobre as práticas de avaliação desses alunos e como estas permitem adequar estratégias e optar por decisões curriculares promovendo a eficácia da educação especial. A pesquisa bibliográfica teve como finalidade fundamentar as conceções implícitas, bem como realçar os conceitos de avaliação, inclusão/diferenciação/flexibilidade e necessidades educativas especiais. O estudo seguiu uma metodologia descritiva e qualitativa centrada no paradigma interpretativo, realizando um estudo de caso de dois alunos com CEI, incluídos na mesma turma, integrando seis professores do 2.º ciclo do mesmo conselho de turma. O trabalho de campo decorreu entre setembro de 2017 a maio de 2018, num agrupamento de escolas do distrito de Faro. Os instrumentos de recolha de dados passaram pelas entrevistas semiestruturadas, conversas informais e análise documental. Os dados recolhidos foram objeto de análise de conteúdo tendo por referência um sistema de categorias surgidos dos discursos dos professores entrevistados. A análise dos resultados obtidos permite-nos estudar opiniões e reflexões dos professores que revelaram ter dificuldades na concretização da inclusão, falta de tempo e falta de apoio para operacionalizar a inclusão dos alunos com CEI. As conclusões apontam para a necessidade de realçar o contributo que a avaliação tem para o sucesso dos alunos e para a reestruturação do CEI e para o papel dos professores no desenvolvimento de práticas de avaliação formativas que contribuem para as aprendizagens dos alunos com NEE e CEI, onde as relações interpessoais, o reforço positivo e a autoestima são primordiais para facilitar o desenvolvimento e as aprendizagens destas crianças.
- Identifying novel genes associated with breast cancer susceptibility using differential allelic expression ratiosPublication . Martins, Catarina Pinto; Maia, Ana Teresa; Xavier, JoanaBreast Cancer (BC) is the most common cancer among women worldwide. However, the current knowledge of BC susceptibility only accounts for half of the familial cases. The few functional studies performed for genome-wide association studies (GWAS) loci revealed a role for cis-regulatory variation, suggesting that risk variants may be acting by regulating gene expression levels. Therefore, we hypothesise that the most efficient approach to tackle BC missing heritability is to focus susceptibility studies on variants with greater cis-regulatory potential. Hereby, we present an innovative approach to genetic association studies, using a quantifiable readout of the effect of cis-regulatory variants — differential allelic expression (DAE). To identify candidate risk genes for our study, we selected Single Nucleotide Polymorphisms (SNPs) weakly associated with BC risk in GWAS and in the iCOGS consortium and identified their proxy SNPs. The resulting 591 candidate risk variants were located in 92 different genes, of which 41 had evidence of being cisregulated in a DAE study of normal breast tissue. The clinical impact of these genes was assessed, for a diverse list of clinical variables (differential expression analysis, FDR ⩽ 1% and absolute fold-change ⩾1.5). A final list of 18 risk candidates cis-regulated and with clinical impact genes was identified. OCIAD1 and GRHL2 genes were selected to perform case-control association studies using DAE values. DAE of OCIAD1 was significantly associated with BC risk (p-value=0.002 and 0.008, in two independent experiments using blood samples), while DAE of GRHL2 needs further validation of association (pvalue= 0.014 and 0.096, in two independent experiments in breast tissue). This project proved that association studies using DAE as a quantifiable variable, together with the whole pipeline used to select the candidate genes, is an efficient approach to detect novel risk genes for BC