Genetic conectivity patterns in Holothuria Mammata considering different spatial scales

Dissertação de Mestrado, Biologia Marinha, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2015As a consequence of the world population growth, the demand for sea food resources is increasing. Consequently, worldwide fisheries transition from depleted finfish resources to alternative invertebrates species created a massive industry. Sea cucumber stocks have been overfished in Indo-Pacific Oceans as result of lack of effective management, non-regulated fisheries and an increasing demand from Oriental countries. The “beche de mer” demands have induced expansion of their fisheries worldwide and have resulted in catches of new target species from the Mediterranean Sea and NE Atlantic Ocean. With high commercial value and fragile life-history traits, sea cucumbers are particularly vulnerable to commercial fisheries, especially when there are no scientific knowledge to support their effective management. This study aims to fill in some of the gap in scientific data about sea cucumber populations, namely Holothuria mammata. It was assessed the genetic diversity and structure, connectivity and effective population size with novel polymorphic molecular markers (microsatellites). This analysis was done in several spatial scales and considering oceanographic patterns. Some morphometric traits were also analysed, such as the distribution of length and weight classes. The results showed that Holothuria mammata has globally high genetic diversity, higher genetic connectivity between Atlantic populations and genetic differentiation between Atlantic/Mediterranean and eastern/western Mediterranean basins. Effective population sizes were smaller in the Atlantic, showing some mutationdrift disequilibrium. Oceanographic patterns were strongly correlated with the genetic differentiation patterns. Atlantic populations presented bigger individuals (i.e. length and weight) than Mediterranean ones, clearly associated with environmental conditions, and ecology features. Biometric data and genetic analysis allowed us to establish the three potential stocks inhabiting the geographic area and improve the biological knowledge of this new target species. This information will be useful to suggest the first recommendations to its effective fishery management, and future comparisons in order to assess the fishery effects either at genetic and/or morphometric level

Collagen Type IV-Related Nephropathies in Portugal: Pathogenic COL4A5 Mutations and Clinical Characterization of 22 Families

Alport syndrome (AS) is caused by pathogenic mutations in the genes encoding α3, α4 or α5 chains of collagen IV (COL4A3/COL4A4/COL4A5), resulting in hematuria, chronic renal failure (CRF), sensorineural hearing loss (SNHL) and ocular abnormalities. Mutations in the X-linked COL4A5 gene have been identified in 85% of the families (XLAS). In this study, 22 of 60 probands (37%) of unrelated Portuguese families, with clinical diagnosis of AS and no evidence of autosomal inheritance, had pathogenic COL4A5 mutations detected by Sanger sequencing and/or multiplex-ligation probe amplification, of which 12 (57%) are novel. Males had more severe and earlier renal and extrarenal complications, but microscopic hematuria was a constant finding irrespective of gender. Nonsense and splice site mutations, as well as small and large deletions, were associated with younger age of onset of SNHL in males, and with higher risk of CRF and SNHL in females. Pathogenic COL4A3 or COL4A4 mutations were subsequently identified in more than half of the families without a pathogenic mutation in COL4A5. The lower than expected prevalence of XLAS in Portuguese families warrants the use of next-generation sequencing for simultaneous COL4A3/COL4A4/COL4A5 analysis, as first-tier approach to the genetic diagnosis of collagen type IV-related nephropathies.info:eu-repo/semantics/publishedVersio

SARS-CoV-2 introductions and early dynamics of the epidemic in Portugal

Genomic surveillance of SARS-CoV-2 in Portugal was rapidly implemented by the National Institute of Health in the early stages of the COVID-19 epidemic, in collaboration with more than 50 laboratories distributed nationwide. Methods By applying recent phylodynamic models that allow integration of individual-based travel history, we reconstructed and characterized the spatio-temporal dynamics of SARSCoV-2 introductions and early dissemination in Portugal. Results We detected at least 277 independent SARS-CoV-2 introductions, mostly from European countries (namely the United Kingdom, Spain, France, Italy, and Switzerland), which were consistent with the countries with the highest connectivity with Portugal. Although most introductions were estimated to have occurred during early March 2020, it is likely that SARS-CoV-2 was silently circulating in Portugal throughout February, before the first cases were confirmed. Conclusions Here we conclude that the earlier implementation of measures could have minimized the number of introductions and subsequent virus expansion in Portugal. This study lays the foundation for genomic epidemiology of SARS-CoV-2 in Portugal, and highlights the need for systematic and geographically-representative genomic surveillance.We gratefully acknowledge to Sara Hill and Nuno Faria (University of Oxford) and Joshua Quick and Nick Loman (University of Birmingham) for kindly providing us with the initial sets of Artic Network primers for NGS; Rafael Mamede (MRamirez team, IMM, Lisbon) for developing and sharing a bioinformatics script for sequence curation (https://github.com/rfm-targa/BioinfUtils); Philippe Lemey (KU Leuven) for providing guidance on the implementation of the phylodynamic models; Joshua L. Cherry (National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health) for providing guidance with the subsampling strategies; and all authors, originating and submitting laboratories who have contributed genome data on GISAID (https://www.gisaid.org/) on which part of this research is based. The opinions expressed in this article are those of the authors and do not reflect the view of the National Institutes of Health, the Department of Health and Human Services, or the United States government. This study is co-funded by Fundação para a Ciência e Tecnologia and Agência de Investigação Clínica e Inovação Biomédica (234_596874175) on behalf of the Research 4 COVID-19 call. Some infrastructural resources used in this study come from the GenomePT project (POCI-01-0145-FEDER-022184), supported by COMPETE 2020 - Operational Programme for Competitiveness and Internationalisation (POCI), Lisboa Portugal Regional Operational Programme (Lisboa2020), Algarve Portugal Regional Operational Programme (CRESC Algarve2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF), and by Fundação para a Ciência e a Tecnologia (FCT).info:eu-repo/semantics/publishedVersio

Elementos facilitadores de um percurso urbano numa malha consolidada

Desde o início das civilizações que as aldeias, vilas, cidades ou qualquer outro tipo de aglomerado habitacional, fazia recurso ao uso de vias mais curtas, acessos rápidos e menos cansativos entre pontos de comum interesse. Estes percursos, muitas vezes, surgem do nada, inadvertidamente, despropositadamente, de maneira muito espontânea e sem que se saiba em concreto qual foi a sua origem. Estas situações sucedem com muita frequência nos caminhos de pé posto que por norma resultam num verdadeiro percurso de êxito, por possuírem caraterísticas suficientemente fiéis ao que seria um percurso ideal para os habitantes. Porém a evolução do meio urbano e a necessidade de urbanizar estes percursos, aos quais é suposto manter ao máximo a sua identidade, após o seu redesenho com recurso a estratégias de planeamento, torna-se em determinadas zonas, indispensável o recurso a meios mecânicos facilitadores de percurso. Em Lisboa, no Chiado, e no Algarve, em Albufeira, mais propriamente na praia do Peneco, os nossos casos de estudo, a escolha foi baseada nas caraterísticas topográficas e na consolidação urbana, uma vez que a morfologia do seu relevo é por excelência favorável para encontrar, analisar e comparar soluções que fizeram recurso a elementos facilitadores de um percurso urbano. Vamos abordar casos concretos e aprofundar a nossa pesquisa, realçando que, de certa forma, temos um tema pouco explorado, porém de muita importância quando aplicado no estudo do território urbano.From the beginning of civilizations that villages, towns, cities or any other type of housing, recourse to the use of shorter roads, quick access and less tiresome between points of common interest. These shortcuts often come out of nowhere, inadvertently, unintentionally, very spontaneously and without knowing in concrete what their origin was. These situations happen very frequently in footpaths, since they usually result in a true success, because they have characteristics sufficiently faithful to what would be an ideal course for the inhabitants. But the evolution of the urban environment and the need to urbanize these routes, which are supposed to keep their identity to the maximum, after their redesign using the techniques of urban planning becomes, the use of mechanical means facilitating the course becomes indispensable in certain zones. In Lisbon, at Chiado and in Algarve, at Albufeira more precisely on the beach of Peneco, our case studies, the choice was based on the topographic characteristics and urban consolidation, since the morphology of its relief is par excellence favorable to find, analyze and compare solutions that made use of elements that facilitate an urban route. We will address concrete cases and deepen our research, noting that in a certain way we have a little explored topic, but of great importance when applied in the study of urban territory.Orientação: João Filipe Ribeiro Borges da Cunh

Intrusion and anomaly detection for the next-generation of industrial automation and control systems

The next-generation of Industrial Automation and Control Systems (IACS) and Supervisory Control and Data Acquisition (SCADA) systems pose numerous challenges in terms of cybersecurity monitoring. We have been witnessing the convergence of OT/IT networks, combined with massively distributed metering and control scenarios such as smart grids. Larger and geographically widespread attack surfaces, and inherently more data to analyse, will become the norm. Despite several advances in recent years, domain-specific security tools have been facing the challenges of trying to catch up with all the existing security flaws from the past, while also accounting for the specific needs of the next-generation of IACS. Moreover, the aggregation of multiple techniques and sources of information into a comprehensive approach has not been explored in depth. Such a holistic perspective is paramount since it enables a global and enhanced analysis enabled by the usage, combination and aggregation of the outputs from multiple sources and techniques. This paper starts by providing a review of the more recent anomaly detection techniques for SCADA systems, focused on both theoretical machine learning approaches and complete frameworks. Afterwards, it proposes a complete framework for an Intrusion and Anomaly Detection System (IADS) composed of specific detection probes, an event processing layer and a core anomaly detection component, amongst others. Finally, the paper presents an evaluation of the framework within a large-scale hybrid testbed, and a comparison of different anomaly detection scenarios based on various machine learning techniques.info:eu-repo/semantics/publishedVersio

A New Signal of Tropicalization in the Northeast Atlantic: The Spread of the Spotfin Burrfish Chilomycterus reticulatus in Madeira Archipelago and Its Invasion Risk

Current trends in the global climate facilitate the displacement of numerous marine species from their native distribution ranges to higher latitudes when facing warming conditions. In this work, we analyzed occurrences of a circumtropical reef fish, the spotfin burrfish, Chilomycterus reticulatus (Linnaeus, 1958), in the Madeira Archipelago (NE Atlantic) between 1898 and 2021. In addition to available data sources, we performed an online survey to assess the distribution and presence of this species in the Madeira Archipelago, along with other relevant information, such as size class and year of the first sighting. In total, 28 valid participants responded to the online survey, georeferencing 119 C. reticulatus sightings and confirming its presence in all archipelago islands. The invasiveness of the species was screened using the Aquatic Species Invasiveness Screening Kit. Five assessments rated the fish as being of medium risk of establishing a local population and becoming invasive. Current temperature trends might have facilitated multiple sightings of this thermophilic species in the Madeira Archipelago. The present study indicates an increase in C. reticulatus sightings in the region. This underlines the need for updated comprehensive information on species diversity and distribution to support informed management and decisions. The spread of yet another thermophilic species in Madeiran waters provides further evidence of an ongoing tropicalization, emphasizing the need for monitoring programs and the potential of citizen science in complementing such programs

Primeira avaliação dos impactos da pandemia COVID-19 sobre pesca recreativa marinha global

In late 2019, an outbreak caused by a novel coronavirus started in China (Graham and Baric, 2020; Hu et al., 2020; Maxmen, 2021). A global pandemic was declared in March 2020, as COVID-19, the disease caused by the coronavirus (World Health Organization, 2020b), escalated outside China (World Health Organization, 2020a). In mid-2021, when vaccination campaigns began to show positive effects on the control of the disease in several countries (Kaur and Gupta, 2020), the COVID-19 pandemic caused millions of deaths and hundreds of millions of infections (Dong et al., 2020). To fight the pandemic, governments reacted with measures designed to contain the spread of the virus, especially through measures aimed to reduce social interactions, including lockdowns (Wilder-Smith and Freedman, 2020), travel restrictions (Chinazzi et al., 2020), and limiting people’s access to non-essential activities (Storr et al., 2021). Humanity suffered a notable impact as a result of the pandemic, including losses of jobs and an abrupt disruption in global demand of goods and services (Barua, 2020; McKibbin and Fernando, 2020; Nicola et al., 2020). The pandemic further degraded the quality of life of the most vulnerable people, particularly those with mental health problems (Brooks et al., 2020), victims of domestic violence (Usher et al., 2020), children (Singh et al., 2020), or indigenous populations (Lane, 2020). As a result, an increase in economic inequality and worldwide poverty is expected, especially in developing countries (World Bank, 2020), and a peak in the suicide rate (Kawohl and Nordt, 2020). On the other hand, global reduction of human activities has had some positive effects on the global environment, especially for air and water quality (Rutz et al., 2020), and noise reduction (Zambrano-Monserrate et al., 2020). Marine ecosystems for example experienced less impacts derived from commercial fishing due to disruptions in large markets such as the United States (White et al., 2021a) or the European Union (Prellezo and Carvahlo, 2020; Coll et al., 2021).info:eu-repo/semantics/publishedVersio

MISTIC SEAS II: Designing and implementing pilot monitoring programmes for cetaceans in Macaronesian waters

Poster.-- World Marine Mammal Conference, Barcelona, 9-12 December 2019Peer reviewe