Functional and genetic analysis of the colon cancer network

Cancer is a complex disease that has proven to be difficult to understand on the single-gene level. For this reason a functional elucidation needs to take interactions among genes on a systems-level into account. In this study, we infer a colon cancer network from a large-scale gene expression data set by using the method BC3Net. We provide a structural and a functional analysis of this network and also connect its molecular interaction structure with the chromosomal locations of the genes enabling the definition of cis- and trans-interactions. Furthermore, we investigate the interaction of genes that can be found in close neighborhoods on the chromosomes to gain insight into regulatory mechanisms. To our knowledge this is the first study analyzing the genome-scale colon cancer network.

Prognoses and improvement for head and neck cancers diagnosed in Europe in early 2000s: The EUROCARE-5 a population-based study.

BACKGROUND: Head and neck (H&N) cancers are a heterogeneous group of malignancies, affecting various sites, with different prognoses. The aims of this study are to analyse survival for patients with H&N cancers in relation to tumour location, to assess the change in survival between European countries, and to investigate whether survival improved over time.
METHODS: We analysed about 250,000 H&N cancer cases from 86 cancer registries (CRs). Relative survival (RS) was estimated by sex, age, country and stage. We described survival time trends over 1999-2007, using the period approach. Model based survival estimates of relative excess risks (RERs) of death were also provided by country, after adjusting for sex, age and sub-site.
RESULTS: Five-year RS was the poorest for hypopharynx (25%) and the highest for larynx (59%). Outcome was significantly better in female than in male patients. In Europe, age-standardised 5-year survival remained stable from 1999-2001 to 2005-2007 for laryngeal cancer, while it increased for all the other H&N cancers. Five-year age-standardised RS was low in Eastern countries, 47% for larynx and 28% for all the other H&N cancers combined, and high in Ireland and the United Kingdom (UK), and Northern Europe (62% and 46%). Adjustment for sub-site narrowed the difference between countries. Fifty-four percent of patients was diagnosed at advanced stage (regional or metastatic). Five-year RS for localised cases ranged between 42% (hypopharynx) and 74% (larynx).
CONCLUSIONS: This study shows survival progresses during the study period. However, slightly more than half of patients were diagnosed with regional or metastatic disease at diagnosis. Early diagnosis and timely start of treatment are crucial to reduce the European gap to further improve H&N cancers outcome.

Simulation of economic benefits achieved by water quality improvement for recreational and professional users, within the SPICOSSA SSA (SPICOSSA System Approach) 11 - Guadiana estuary ecosystem sic

Dissertação de Mestrado, Gestão da Água e da Costa, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2010

Marine foundation species shifting ranges and genetic baselines

This thesis revealed the most importance factors shaping the distribution, abundance and genetic diversity of four marine foundation species. Environmental conditions, particularly sea temperatures, nutrient availability and ocean waves, played a primary role in shaping the spatial distribution and abundance of populations, acting on scales varying from tens of meters to hundreds of kilometres. Furthermore, the use of Species Distribution Models (SDMs) with biological records of occurrence and high-resolution oceanographic data, allowed predicting species distributions across time. This approach highlighted the role of climate change, particularly when extreme temperatures prevailed during glacial and interglacial periods. These results, when combined with mtDNA and microsatellite genetic variation of populations allowed inferring for the influence of past range dynamics in the genetic diversity and structure of populations. For instance, the Last Glacial Maximum produced important shifts in species ranges, leaving obvious signatures of higher genetic diversities in regions where populations persisted (i.e., refugia). However, it was found that a species’ genetic pool is shaped by regions of persistence, adjacent to others experiencing expansions and contractions. Contradicting expectations, refugia seem to play a minor role on the re(colonization) process of previously eroded populations. In addition, the available habitat area for expanding populations and the inherent mechanisms of species dispersal in occupying available habitats were also found to be fundamental in shaping the distributions of genetic diversity. However, results suggest that the high levels of genetic diversity in some populations do not rule out that they may have experienced strong genetic erosion in the past, a process here named shifting genetic baselines. Furthermore, this thesis predicted an ongoing retraction at the rear edges and extinctions of unique genetic lineages, which will impoverish the global gene pool, strongly shifting the genetic baselines in the future.

Radiological protection and nuclear engineering studies in multi-MW target systems

Tese de doutoramento, Física, Universidade de Lisboa, Faculdade de Ciências, 2014

Bacteriophage lytic enzymes and their engineering towards improved antibacterial efficacy

Tese de doutoramento, Farmácia (Microbiologia), Universidade de Lisboa, Faculdade de Farmácia, 2015