Browsing by Issue Date, starting with "2019-03-21"
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- Effects of positive airway pressure therapy on red blood cells in patients with obstructive sleep apneaPublication . Coelho-Valentim, Cristina; Vaz, Fátima; Barbara, Cristina; Penque, DeborahIntroduction: Obstructive Sleep Apnea (OSA) syndrome is characterized by recurrent arousals from sleep and intermittent hypoxemia. We recently demonstrated that OSA can cause alterations in the red blood cells (RBC) proteome that may be associated with OSA outcomes. Here we intend to investigate whether the positive airway pressure (PAP) treatment can revert/modulate these proteome alterations.
- Departamento de Genética Humana do INSA - Grupo de Investigação em Toxicologia Genética: material de apoio a visitaPublication . Louro, Henriqueta; Silva, Maria JoãoApresentação do Departamento de Genética Humana. Conceitos e metodologias básicas utilizadas em toxicologia genética. Nanotoxicologia.
- Nanopore sequencing in human genetic studies: application to structural variant detectionPublication . Silva, Catarina; Vieira, LuísBackground: Nanopore sequencing is a recent technology which allows direct real-time sequencing of DNA or RNA molecules and production of read lengths as long as the size of the original fragments. It is based on the application of an ionic current to move DNA strands through an array of nanopores embedded in an electrically-resistant membrane. An ASIC chip placed below this membrane is responsible for recording signal changes in the nanopore, which are then translated into a specific base sequence. Although major improvements have been made in the genomic short-read sequencing technologies, structural variants (SV) detection still stands as a challenge. The characteristics of nanopore sequencing make it well suited for whole genome sequencing and as a preferential tool to identify SV, namely those associated with tumours. In this work we present a complete workflow to detect SV in tumour samples using nanopore sequencing. Methods: We used a test tumour sample to prepare DNA libraries using the rapid sequencing kit (Oxford Nanopore Technologies-ONT) and sequenced those in a single R9.4 flow cell on the MinION device (ONT). We implemented a pipeline for SV detection using multiple bioinformatics tools: MinKNOW software (ONT) (run set up and data acquisition), Albacore pipeline (ONT) (basecalling), LAST aligner (mapping) and Picky (SV detection and analysis). Results: The use of the rapid sequencing kit allowed a fast preparation of sequencing libraries when compared with standard library preparation procedures. The MinION generated a total of 2.34 Gb of DNA. The highest number of reads were obtained during the first 8-10h of the sequencing run. Overall, 87.8% of reads had a quality (Q) value >7 (quality threshold) and 54.2% had a Q value >10. The longest read obtained had 74369 bases and the mean read length was of 4508 bases. All reads with a length >50 kb had Q values >= 7. A total of 3470 SV were identified, including deletions, duplications, translocations, insertions and inversions. Conclusions: Long-read sequencing technology is becoming an important tool as it poses itself as a powerful complementary method that suppresses the inherent limitations of other technologies. Nanopore sequencing is a fast and sensitive approach of great potential for human genomics research and for use in a clinical perspective, namely in the detection of SV in the human genome. A critical issue in nanopore sequencing is DNA quality and integrity because longer size reads make it easier to detect large SV.
- Functional effects of differentially expressed microRNAs in alveolar epithelial cells exposed to MWCNT-7 or crocidolitePublication . Ventura, Célia; Vieira, Luís; Silva, Catarina; Sousa-Uva, Antonio; Silva, Maria JoãoBackground and Aims Multi-walled carbon nanotubes (MWCNT) are widely used engineered nanomaterials in industrial and biomedical applications, but their inhalation may induce pulmonary adverse effects. Moreover, the MWCNT-7 (Mitsui-7) has been classified as possibly carcinogenic to humans. Nevertheless, MWCNT-7 molecular modes of action are poorly understood and there are no biomarkers of exposure or effect for occupational monitoring. Recently, several pulmonary diseases, including lung cancer, have been associated with alterations in microRNA expression. These changes are potentially useful to detect or evaluate disease progression and to understand the molecular effects induced by the disease or toxicant. In this study, we describe a set of differentially expressed microRNAs (DE miRNAs) in A549 epithelial alveolar cells, following exposure to an occupationally relevant dose of MWCNT-7 or crocidolite. The functional pathways and ontology terms enriched with genes targeted by DE miRNAs were identified. Moreover, an interaction network of DE miRNAs-target cancer genes was constructed.