Browsing by Issue Date, starting with "2015-12-11"
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- Analysis of the translatome by ribosome profiling in colorectal cancerPublication . Silva, JoanaColorectal cancer (CRC) is a serious health problem due to its high incidence and mortality rates despite the major advances in cancer therapeutic approaches [1]. CRC carcinogenesis progression is based in a continuous accumulation of genetic alterations that leads to variations in the overall gene expression profiles [2]. This creates the need for deep analysis of cancer gene expression patterns and, thus, a more reliable understanding of the human proteome to disclose the molecular and cellular pathways as well as the regulatory mechanisms involved in cancer progression [2-4]. Genome wide analyses of gene expression have so far focused on the abundance of mRNA species as measured either by microarray or, more recently, by RNA deep sequencing [5,6]. However, neither approach provides information on protein synthesis, an important end point of gene expression [5,7]. Ribosome profiling is an emerging technique that uses deep sequencing to monitor in vivo translation and provide global and quantitative measurements of translation [7,8]. It can also reveal unexpected complexity in translation, including the presence of ribosomes outside of classical protein-coding regions of the transcriptome [5]. In this approach, translation is profiled by nuclease footprinting of ribosomes on RNA templates and high-throughput sequencing in order to determine the precise positions of ribosomes on a transcript and its overall density [8]. Ribosome profiling studies have been performed in cancer cell lines, where they showed an increase in overall protein identification and new proteins not yet annotated that possibly were originated from N-terminal extensions or upstream open reading frames (uORFs) [9-12]. The main goal of this project is to determine the changes between the translatome of CRC and normal colorectal cells and the role of such alterations in the tumorigenesis process of CRC cells. For this purpose, we will perform ribosome profiling in normal (NCM460) and CRC (HCT116) cell lines. Bioinformatics and gene ontology analysis of the translated mRNAs will elucidate the main cellular pathways through which the corresponding proteins are involved in CRC progression. Then, we will dissect which of these proteins can interfere and induce cell survival of CRC cells. Furthermore, we aim to analyze the potential contribution of translatable short alternative ORFs (AltORFs) and/or the corresponding peptides towards CRC progression. This information will be crucial to the development of new therapeutic strategies for CRC.
- The impact of indoor air quality and contaminants on respiratory health of older people living in long-term care residences in PortoPublication . Mendes, Ana; Papoila, Ana Luísa; Carreiro-Martins, Pedro; Bonassi, Stefano; Caires, Iolanda; Palmeiro, Teresa; Aguiar, Lívia; Pereira, Cristiana; Neves, Paula; Mendes, Diana; Botelho, Maria Amália Silveira; Neuparth, Nuno; Teixeira, João PauloBackground: persons who are 65 years or older often spend an important part of their lives indoors thus adverse indoor climate might influence their health status. Objective: to evaluate the influence of indoor air quality and contaminants on older people’s respiratory health. Design: cross-sectional study. Setting: 21 long-term care residences (LTC) in the city of Porto, Portugal. Subjects: older people living in LTC with ≥65 years old. Methods: the Portuguese version of BOLD questionnaire was administered by an interviewer to older residents able to participate (n = 143). Indoor air contaminants (IAC) were measured twice, during winter and summer in 135 areas. Mixed effects logistic regression models were used to study the association between the health questionnaire results and the monitored IAC, adjusted for age, smoking habits, gender and number of years living in the LTC. Results: cough (23%) and sputum (12%) were the major respiratory symptoms, and allergic rhinitis (18%) the main selfreported illness. Overall particulate matter up to 2.5 micrometres in size median concentration was above the reference levels both in winter and summer seasons. Peak values of particulate matter up to 10 micrometres in size (PM10), total volatile organic compounds, carbon dioxide, bacteria and fungi exceeded the reference levels. Older people exposed to PM10 above the reference levels demonstrated higher odds of allergic rhinitis (OR = 2.9, 95% CI: 1.1–7.2). Conclusion: high levels of PM10 were associated with 3-fold odds of allergic rhinitis. No association was found between indoor air chemical and biological contaminants and respiratory symptoms.
- Transcriptomic screen for DIS3 and DIS3L1 exosome subunits associated functional networks in colorectal cancerPublication . Costa, Paulo; Romão, Luísa; Gama-Carvalho, MargaridaThe final step of cytoplasmic mRNA degradation proceeds in either a 5’-3’ direction, catalyzed by XRN1, or in a 3’-5’ direction catalyzed by the exosome. In yeast, DIS3/Rrp44 protein is the catalytic subunit of the exosome. In humans, there are three known paralogues of this enzyme: DIS3, DIS3L1, and DIS3L2. Important findings over the last years have shed a new light onto the.mechanistic details of RNA degradation by these exoribonucleases. In addition, it has been shown that they are involved in growth, mitotic control and important human diseases, including cancer. For example, DIS3L2 inactivation was associated with mitotic abnormalities and altered expression of mitotic checkpoint proteins (Astuti et al., 2012). In another study, DIS3 was found to be highly expressed in colorectal cancer (CRC), suggesting an oncogenic function (Camps et al., 2013). A major challenge in systems biology is to reveal the cellular networks that give rise to specific phenotypes (Lan et al., 2013). In this project, we aim to analyze how DIS3 and DIS3L1 regulate the human transcriptome, and how their functional interactions modulate the transcriptional reprogramming of colorectal cancer cells. We will perform an extensive characterization of the DIS3 and DIS3L1 mRNA targets, using DIS3 and DIS3L1 knockdown and microarray analysis, in normal colorectal cells, and in different CRC cell lines, in the presence and absence of stress stimuli, such as hypoxia. Differential expression and gene set enrichment analyses of collected data will elucidate new cellular pathways regulated by DIS3 and DIS3L1 and/or by their targets, as well as how they can be involved in CRC. In addition, this analysis may reveal novel functional networks through which the RNA exosome modulates the eukaryotic transcriptome.
- GERIA - Qualidade do Ar Interior: Principais ResultadosPublication . Cano, ManuelaApresentação dos principais resultados do projeto GERIA. GERIA tem com objetivo: obter dados sobre a qualidade do ambiente interior em lares - Equipamentos Residenciais para Pessoas Idosas (ERPI) - de modo a estudar a sua relação com a ventilação dos locais e a saúde/qualidade de vida dos utentes.
- Avaliação da resistência a antibióticos em estirpes de cianobactérias isoladas de ambientes hídricosPublication . Oliveira, Micaela; Dias, Elsa; Dias, Deodália[PT] Os ambientes hídricos constituem veículos para a emergência e disseminação da resistência a antibióticos. As cianobactérias encontram-se amplamente distribuidas nestes ambientes, estando frequentemente expostas a antibióticos, bactérias resistentes e genes de resistência. Contudo, o seu papel no resistoma hídrico nunca foi investigado. Este trabalho pretendeu avaliar a susceptibilidade de oito estirpes de Microcystis aeruginosa, oito estirpes de Planktothrix agardhii e oito estirpes de Planktothrix mougeotii a diferentes antibióticos (amoxicilina, ceftazidima, ceftriaxona, canamicina, gentamicina, tetraciclina, ácido nalidíxico, norfloxacina e trimetoprim). Para tal, foi utilizado um procedimento baseado no método standard Broth Microdilution para bactérias, no qual as cianobactérias foram expostas a diluições sucessivas de cada antibiótico em meio Z8 (0,0015 mg/L – 1,6 mg/L) e mantidas numa câmara de culturas sob ciclos de 14 horas de luz – com uma intensidade de 16 ± 4 μEm-2 s-1 – e 10 horas de escuro, a uma temperatura de 20 ± 1ºC. O crescimento celular foi seguido durante 14 dias (observação macroscópica, microscópica e leitura da DO450nm) e as concentrações inibitórias mínimas de cada antibiótico (CIMs) foram calculadas para cada estirpe. Nenhuma das estirpes foi susceptível a qualquer das concentrações de ácido nalidíxico e de trimetoprim testadas. Adicionalmente, as estirpes de M. aeruginosa apresentaram uma susceptibilidade reduzida à tetraciclina, as estirpes de P. agardhii apresentaram uma susceptibilidade reduzida à norfloxacina e as estirpes de P. mougeotii não foram susceptíveis à amoxicilina nem à norfloxacina e apresentaram uma susceptibilidade reduzida à tetraciclina. Foi também pesquisada a presença de genes e de integrões associados à resistência a antibióticos nas cianobactérias em estudo por PCR e posterior sequenciação dos produtos obtidos. Foram encontrados genes de resistência à estreptomicina numa estirpe de M. aeruginosa, em três estirpes de P. agardhii e em quatro estirpes de P. mougeotii; genes de resistência às sulfonamidas em quatro estirpes de M. aeruginosa, em três estirpes de P. agardhii e em cinco estirpes de P. mougeotii; integrões de classe 1 em duas estirpes de M. aeruginosa, em três estirpes de P. agardhii e em três estirpes de P. mougeotii. Adicionalmente, o gene qacE foi encontrado numa estirpe de M. aeruginosa e numa estirpe de P. agardhii. Os resultados obtidos sugerem que as cianobactérias apresentam resistência intrínseca a alguns antibióticos e que, de acordo com o seu local de origem, podem apresentar resistência adquirida a outros. Assim, tudo indica que, de facto, as cianobactérias desempenham um papel importante no resistoma hídrico.