Molecular pedigree reconstruction and estimation of evolutionary parameters in a wild Atlantic salmon river system with incomplete sampling: a power analysis

Background: Pedigree reconstruction using genetic analysis provides a useful means to estimate fundamental population biology parameters relating to population demography, trait heritability and individual fitness when combined with other sources of data. However, there remain limitations to pedigree reconstruction in wild populations, particularly in systems where parent-offspring relationships cannot be directly observed, there is incomplete sampling of individuals, or molecular parentage inference relies on low quality DNA from archived material. While much can still be inferred from incomplete or sparse pedigrees, it is crucial to evaluate the quality and power of available genetic information a priori to testing specific biological hypotheses. Here, we used microsatellite markers to reconstruct a multi-generation pedigree of wild Atlantic salmon (Salmo salar L.) using archived scale samples collected with a total trapping system within a river over a 10 year period. Using a simulation-based approach, we determined the optimal microsatellite marker number for accurate parentage assignment, and evaluated the power of the resulting partial pedigree to investigate important evolutionary and quantitative genetic characteristics of salmon in the system.

Results: We show that at least 20 microsatellites (ave. 12 alleles/locus) are required to maximise parentage assignment and to improve the power to estimate reproductive success and heritability in this study system. We also show that 1.5 fold differences can be detected between groups simulated to have differing reproductive success, and that it is possible to detect moderate heritability values for continuous traits (h(2) similar to 0.40) with more than 80% power when using 28 moderately to highly polymorphic markers.

Conclusion: The methodologies and work flow described provide a robust approach for evaluating archived samples for pedigree-based research, even where only a proportion of the total population is sampled. The results demonstrate the feasibility of pedigree-based studies to address challenging ecological and evolutionary questions in free-living populations, where genealogies can be traced only using molecular tools, and that significant increases in pedigree assignment power can be achieved by using higher numbers of markers.

Quantum Chromatic Numbers via Operator Systems

We define several new types of quantum chromatic numbers of a graph and characterize them in terms of operator system tensor products. We establish inequalities between these chromatic numbers and other parameters of graphs studied in the literature and exhibit a link between them and non-signalling correlation boxes.

Diabetes in the young - a global view and worldwide estimates of numbers of children with type 1 diabetes

This paper describes the methodology, results and limitations of the 2013 International Diabetes Federation (IDF) Atlas (6th edition) estimates of the worldwide numbers of prevalent cases of type 1 diabetes in children (<15 years). The majority of relevant information in the published literature is in the form of incidence rates derived from registers of newly diagnosed cases. Studies were graded on quality criteria and, if no information was available in the published literature, extrapolation was used to assign a country the rate from an adjacent country with similar characteristics. Prevalence rates were then derived from these incidence rates and applied to United Nations 2012 Revision population estimates for 2013 for each country to obtain estimates of the number of prevalent cases. Data availability was highest for the countries in Europe (76%) and lowest for the countries in sub-Saharan Africa (8%). The prevalence estimates indicate that there are almost 500,000 children aged under 15 years with type 1 diabetes worldwide, the largest numbers being in Europe (129,000) and North America (108,700). Countries with the highest estimated numbers of new cases annually were the United States (13,000), India (10,900) and Brazil (5000). Compared with the prevalence estimates made in previous editions of the IDF Diabetes Atlas, the numbers have increased in most of the IDF Regions, often reflecting the incidence rate increases that have been well-documented in many countries. Monogenic diabetes is increasingly being recognised among those with clinical features of type 1 or type 2 diabetes as genetic studies become available, but population-based data on incidence and prevalence show wide variation due to lack of standardisation in the studies. Similarly, studies on type 2 diabetes in childhood suggest increased incidence and prevalence in many countries, especially in Indigenous peoples and ethnic minorities, but detailed population-based studies remain limited.

The paradox of invasion: Reeves’ muntjac deer invade the British Isles from a limited number of founding females

High levels of genetic diversity and high propagule pressure are favoured by conservation biologists as the basis for successful reintroductions and ensuring the persistence of populations. However, invasion ecologists recognize the ‘paradox of invasion’, as successful species introductions may often be characterized by limited numbers of individuals and associated genetic bottlenecks. In the present study, we used a combination of high-resolution nuclear and mitochondrial genetic markers to investigate the invasion history of Reeves' muntjac deer in the British Isles. This invasion has caused severe economic and ecological damage, with secondary spread currently a concern throughout Europe and potentially globally. Microsatellite analysis based on eight loci grouped all 176 introduced individuals studied from across the species' range in the UK into one genetic cluster, and seven mitochondrial D-loop haplotypes were recovered, two of which were present at very low frequency and were related to more common haplotypes. Our results indicate that the entire invasion can be traced to a single founding event involving a low number of females. These findings highlight the fact that even small releases of species may, if ignored, result in irreversible and costly invasion, regardless of initial genetic diversity or continual genetic influx.

Response of soil microbial biomass to 1,2-dichlorobenzene addition in the presence of plant residues

The impact of 1,2-dichlorobenzene on soil microbial biomass in the presence and absence of fresh plant residues (roots) was investigated by assaying total vital bacterial counts, vital fungel hyphal length, total culturable bacterial counts, and culturable fluorescent pseudomonads. Diversity of the fluorescent pseudomonads was investigated using fatty acid methyl ester (FAME) characterization in conjunction with metabolic profiling of the sampled culturable community (Biolog). Mineralization of [¹⁴C]1,2- dichlorobenzene was also assayed. Addition of fresh roots stimulated 1,2- dichlorobenzene mineralization by over 100%, with nearly 20% of the label mineralized in root-amended treatments by the termination of the experiment. Presence of roots also buffered any impacts of 1,2-dichlorobenzene on microbial numbers. In the absence of roots, 1,2-dichlorobenzene greatly stimulated total culturable bacteria and culturable pseudomonads in a concentration-dependent manner. 1,2-Dichlorobenzene, up to concentrations of 50 μg/g soil dry weight had little or no deleterious effects on microbial counts. The phenotypic diversity of the fluorescent pseudomonad population was unaffected by the treatments, even though fluorescent pseudomonad numbers were greatly stimulated by both roots and 1,2-dichlorobenzene. The presence of roots had no detectable impact on the bacterial community composition. No phenotypic shifts in the natural population were required to benefit from the presence of roots and 1,2-dichlorobenzene. The metabolic capacity of the culturable bacterial community was altered in the presence of roots but not in the presence of 1,2-dichlorobenzene. It is argued that the increased microbial biomass and shifts in metabolic capacity of the microbial biomass are responsible for enhanced degradation of 1,2-dichlorobenzene in the presence of decaying plant roots.

Identification of Dynamics of Surface Suction Over an Airfoil at Low Reynolds Numbers

This paper deals with identification of dynamics in suction control of airfoils for low Reynolds number regimes (8 x 10^4 - 5 x 10^5). In particular, the dynamics of interest is the map that relates suction pressure and surface pressure. Identification of such dynamics is of use to a variety of active control applications including suction control in small/medium wind turbines which operate in these Reynolds number regimes. Prior research has largely focused on higher Reynolds number regimes, creating a need for such a study. Towards identifying the said dynamic relations, experiments were conducted on NACA0012 airfoil in a wind tunnel. The dynamic relation between suction and surface pressure was identified as an overdamped second order system.

Novel monoclonal antibody and peptide binders for Mycobacterium avium subsp. paratuberculosis and their application for magnetic separation

The generation of novel Mycobacterium avium subsp. paratuberculosis (MAP)-specific monoclonal antibodies and phage-display derived peptide binders, along with their application for the magnetic separation (MS) of MAP cells, is described. Our aim was to achieve even greater MAP capture capability than is possible with peptide-mediated magnetic separation (PMS) using a 50:50 mix of biotinylated-aMp3 and biotinylated-aMptD peptide-coated beads. Gamma-irradiated whole MAP cells and ethanol extracted antigens (EEA) from these cells were used to elicit an immune response and as phage-display biopanning targets. A range of novel binders was obtained and coated onto paramagnetic beads, both individually and in various combinations, for MS evaluation. IS900 PCR was employed after MS to provide quick results. Capture sensitivity was assessed using a range of MAP concentrations after which the most promising beads were tested for their specificity for MAP, by performing MS followed by culture using 10 other Mycobacterium species. Magnetic beads coated with the biotinylated EEA402 peptide demonstrated a greater level of MAP capture than the current PMS method, even when low numbers of MAP (<10 cfu/ml) were present; however these beads also captured a range of other mycobacteria and so lacked capture specificity. Magnetic beads coated with monoclonal antibodies 6G11 and 15D10 (used as a 50:50 mix or as dually coated beads) also demonstrated improved MAP capture relative to the current PMS method, but with little cross-reactivity to other Mycobacterium spp. Therefore, two new MS protocols are suggested, the application of which would be dependent upon the required endpoint. Biotinylated EEA402-coated beads could potentially be used with a MAP-specific PCR to ensure detection specificity, while beads coated with 6G11 and 15D10 monoclonal antibodies could be used with culture or the phage amplification assay.

Electron-impact excitation of Li to high principal quantum numbers

The time-dependent close-coupling method is used to calculate electron-impact excitation cross sections for the Li(2s)--{\textgreater}Li(nl) and Li(2p)--{\textgreater}Li(nl) transitions at incident energies just above the ionization threshold. The implementation of the time-dependent close-coupling method on a nonuniform lattice allows the study of continuum-coupling effects in excitations to high principal quantum number, i.e., n{\textless}=10. Good agreement is found with R-matrix with pseudostates calculations, which also include continuum-coupling effects, for excitations to low principal quantum number, i.e., n{\textless}=4. Poor agreement is found with standard distorted-wave calculations for excitations to all principal quantum numbers, with differences still at the 50% level for n=10. We are able to give guidance as to the accuracy expected in the n3 extrapolation of nonperturbative close-coupling calculations of low n cross sections and rate coefficients.

Programa "Escola Segura": Contributo para a avaliação dos impactos do programa "Escola Segura" no Concelho de Portalegre

O trabalho que a seguir se apresenta incide sobre o tema Programa “Escola Segura”, mais especificamente sobre a avaliação/caracterização dos impactos do Programa “Escola Segura” no concelho de Portalegre. Este trabalho de investigação tinha, fundamentalmente, cinco grandes objetivos: - Conhecer o Programa “Escola Segura”; - Caracterizar o Programa “Escola Segura” no concelho de Portalegre; - Caracterizar a parceria no território entre a Escola e o Programa “Escola Segura”; - Verificar qual a articulação entre a Escola e o Programa “Escola Segura”; - Idênticas as relações existentes entre agentes do Programa “Escola Segura”, professores e alunos. Encontra-se dividido em duas partes. Na primeira parte, designada por “Enquadramento Teórico” serão revistas algumas das conceptualizações teóricas, as quais se encontram organizadas por três capítulos distintos: “Relação Educativa”, “Disciplina” e “Enquadramento Legal”. De salientar que neste último se inclui o Despacho Conjunto n. ° 105-A/20051, o qual estabelece o conceito, objetivos, âmbitos e estrutura do Programa “Escola Segura”, e, como tal, é desenvolvido de forma mais aprofundada, visto ser o motor, bem como o assunto principal desta investigação. A estrutura da segunda parte deste trabalho, designada por “Investigação”, assenta na existência de três capítulos: “Enquadramento Metodológico”, “Análise e Interpretação de Dados” e “Considerações Finais”. Após discutidos os principais resultados, são também apresentadas algumas recomendações e sugestões. A metodologia deste estado apresenta duas dimensões: - Uma pequena dimensão quantitativa, que caracteriza a realidade objeto de estudo (caracterização dos diferentes estabelecimentos de ensino, pertencentes ao mesmo Agrupamento, quanto ao número de alunos e professores); - Uma forte dimensão qualitativa, que tem como objetivo evidenciar a opinião, que os diferentes atores possuem do Programa “Escola Segura” (análise e interpretação de entrevistas semi-directivas e de textos). Como instrumentos de recolha de dados evidenciam-se dois: - Entrevistas semi-directivas, elaboradas de acordo com os procedimentos indicados em ESTRELA (1990), destinadas aos docentes e agentes do Programa “Escola Segura”; - Ficha de trabalho, elaborada por nós, dirigida aos alunos, que consistia na construção de um texto sobre o Programa “Escola Segura”. A recolha de informação, nomeadamente a obtida por meio de entrevistas semi-diretivas, de forma a permitir um tratamento/análise mais claro e objetivo, foi trabalhada através de grelhas de análise, por categorias. Esta análise de conteúdo foi feita de acordo com os procedimentos indicados por BARDIN (1977). Os resultados obtidos permitem constatar que o Programa “Escola Segura” se desenvolve de formas distintas, de acordo com o meio em que os estabelecimentos de ensino estão inseridos (rural ou urbano), apesar de assentar na mesma filosofia. Sendo que parte desta situação transcende, de alguma forma, os próprios agentes destacados para o Programa em estudo. /ABSTRACT - “Escola Segura” programe Thefollowing work considers the "Escola Segura" programe, specifying on it’s evaluation/characterization in the city of Portalegre. This work of investigation had, fundamentally, five major goals: - Knowing the “Escola Segura ” program; - Characterizing the “Escola Segura ” program in Portalegre; - Characterizing the partnership between the School and the “Escola Segura" program - Verifying the articulation between the School and the “Escola Segura ” Program - Identifying existing relationships between agents of the “Escola Segura” program, teachers and students. In order to do this, we divided this work in two parts: in the first part, designated by "Enquadramento Teórico ", some of the theoretical concepts are reviewed in three different chapters: “Relação Educativa”, “Disciplina” and “Enquadramento Legal ". In the last we included the Despacho Conjunto n.º 105-A/2005, which establishes the concept, objectives, ambits and structures of the previously mentioned program. As such, it was developed more extensively, for this seems to be the engine as well as the main subject of this investigation. The structure of the second part of this work, designated by "Investigação", also consists of three chapters: “Enquadramento Metodológico", “Análise e interpretação de dados" and "Considerações finais”. Finally, after discussing the main results, we will state recommendations and suggestions. The methodology of this study has two dimensions: - A small quantitative dimension, that characterizes the reality that is the study object (characterization of different schools belonging to the same Scholl Groups, in terms of numbers of students and teachers); - A strong qualitative dimension, with the purpose of stating the opinion that the different actors possess of the “Escola Segura” program (analysis and interpretation of semi-directive interviews and texts). We will focus on two instruments of data sampling: - Semi-directive interviews, elaborated in agreement with the suitable procedures in STAR (1990), destinated to teachers and agents of the “Escola Segura” Program; - A work sheet directed to the students, that we developed, which consisted in elaborating a text about the aforementioned program. Data sampling, obtained through semi-directive interviews in order to allow a clearer and more objective treatment and analysis, was developed through analysis sheets divided into categories. This content analysis was made in agreement with the suitable procedures by BARDIN (1977). The obtained results allow to verify that the “Escola Segura” program develops in distinct ways, according to which environment schools are inserted in (rural or urban), even though it is based on the same philosophy. Part of this situation even transcends, in a way, the indicated agents for the studied program

Combined disaggregation of agricultural land uses, livestock numbers and crops' production: an entropy approach

This paper presents several combined agricultural data disaggregation models in order to recover the farms' land uses, the livestock numbers and main crops' productions. The proposed approach estimates incomplete information at disaggregated level through entropy, using an information prior, and generating information for a combined calculation use of data in the estimation of other variables. The models were applied to the region of Algarve, to some rural pilot areas (Salir-Ameixial-Cachopo and Alcoutim) for livestock data, since this data in some Algarve's inland areas is needed for a European forest fire prevention project, and to the agrarian zones in a more complex framework. The results are promising. They were validated, in cross reference to real data, having proven to be valid and reliable. The total error was small and a considerable level of information heterogeneity was recovered. The total error was about 27,9% for the counties' land uses and 21% for the agrarian zones, and for the livestock it was also acceptable. The level of heterogeneity recovered was always higher than 50%, revealing some improvements regarding previous studies.

Long-term seasonal changes in the abundance of Dendrodoris nudibranchs: a five-year survey

Dissertação de mestrado, Biologia Marinha, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2015

Aprendizagem dos números reais : um estudo com alunos do 9.º ano

Relatório da Prática de Ensino Supervisionada, Ensino de Matemática, Universidade de Lisboa, 2013

Neuro-glia-vascular alterations by common neonatal clinical conditions

Tese de doutoramento, Farmácia (Biologia Celular e Molecular), Universidade de Lisboa, Faculdade de Farmácia, 2014