Microsatellite standardization and evaluation of genotyping error in a large multi-partner research programme for conservation of Atlantic salmon (Salmo salar L.).

Microsatellite genotyping is a common DNA characterization technique in population, ecological and evolutionary genetics research. Since different alleles are sized relative to internal size-standards, different laboratories must calibrate and standardize allelic designations when exchanging data. This interchange of microsatellite data can often prove problematic. Here, 16 microsatellite loci were calibrated and standardized for the Atlantic salmon, Salmo salar, across 12 laboratories. Although inconsistencies were observed, particularly due to differences between migration of DNA fragments and actual allelic size ('size shifts'), inter-laboratory calibration was successful. Standardization also allowed an assessment of the degree and partitioning of genotyping error. Notably, the global allelic error rate was reduced from 0.05 ± 0.01 prior to calibration to 0.01 ± 0.002 post-calibration. Most errors were found to occur during analysis (i.e. when size-calling alleles; the mean proportion of all errors that were analytical errors across loci was 0.58 after calibration). No evidence was found of an association between the degree of error and allelic size range of a locus, number of alleles, nor repeat type, nor was there evidence that genotyping errors were more prevalent when a laboratory analyzed samples outside of the usual geographic area they encounter. The microsatellite calibration between laboratories presented here will be especially important for genetic assignment of marine-caught Atlantic salmon, enabling analysis of marine mortality, a major factor in the observed declines of this highly valued species.

Genetic Evidence Implicates the Immune System and Cholesterol Metabolism in the Aetiology of Alzheimer's Disease

Background: Late Onset Alzheimer's disease (LOAD) is the leading cause of dementia. Recent large genome-wide association studies (GWAS) identified the first strongly supported LOAD susceptibility genes since the discovery of the involvement of APOE in the early 1990s. We have now exploited these GWAS datasets to uncover key LOAD pathophysiological processes. Methodology: We applied a recently developed tool for mining GWAS data for biologically meaningful information to a LOAD GWAS dataset. The principal findings were then tested in an independent GWAS dataset.

Common variants at ABCA7, MS4A6A/MS4A4E, EPHA1, CD33 and CD2AP are associated with Alzheimer's disease

We sought to identify new susceptibility loci for Alzheimer's disease through a staged association study (GERAD+) and by testing suggestive loci reported by the Alzheimer's Disease Genetic Consortium (ADGC) in a companion paper. We undertook a combined analysis of four genome-wide association datasets (stage 1) and identified ten newly associated variants with P = 1 × 10(-5). We tested these variants for association in an independent sample (stage 2). Three SNPs at two loci replicated and showed evidence for association in a further sample (stage 3). Meta-analyses of all data provided compelling evidence that ABCA7 (rs3764650, meta P = 4.5 × 10(-17); including ADGC data, meta P = 5.0 × 10(-21)) and the MS4A gene cluster (rs610932, meta P = 1.8 × 10(-14); including ADGC data, meta P = 1.2 × 10(-16)) are new Alzheimer's disease susceptibility loci. We also found independent evidence for association for three loci reported by the ADGC, which, when combined, showed genome-wide significance: CD2AP (GERAD+, P = 8.0 × 10(-4); including ADGC data, meta P = 8.6 × 10(-9)), CD33 (GERAD+, P = 2.2 × 10(-4); including ADGC data, meta P = 1.6 × 10(-9)) and EPHA1 (GERAD+, P = 3.4 × 10(-4); including ADGC data, meta P = 6.0 × 10(-10)).

The Role of Variation at AβPP, PSEN1, PSEN2, and MAPT in Late Onset Alzheimer's Disease

Rare mutations in AßPP, PSEN1, and PSEN2 cause uncommon early onset forms of Alzheimer's disease (AD), and common variants in MAPT are associated with risk of other neurodegenerative disorders. We sought to establish whether common genetic variation in these genes confer risk to the common form of AD which occurs later in life (>65 years). We therefore tested single-nucleotide polymorphisms at these loci for association with late-onset AD (LOAD) in a large case-control sample consisting of 3,940 cases and 13,373 controls. Single-marker analysis did not identify any variants that reached genome-wide significance, a result which is supported by other recent genome-wide association studies. However, we did observe a significant association at the MAPT locus using a gene-wide approach (p = 0.009). We also observed suggestive association between AD and the marker rs9468, which defines the H1 haplotype, an extended haplotype that spans the MAPT gene and has previously been implicated in other neurodegenerative disorders including Parkinson's disease, progressive supranuclear palsy, and corticobasal degeneration. In summary common variants at AßPP, PSEN1, and PSEN2 and MAPT are unlikely to make strong contributions to susceptibility for LOAD. However, the gene-wide effect observed at MAPT indicates a possible contribution to disease risk which requires further study.

Parsing parallel evolution:Ecological divergence and differential gene expression in the adaptive radiations of thick-lipped Midas cichlid fishes from Nicaragua

The study of parallel evolution facilitates the discovery of common rules of diversification. Here, we examine the repeated evolution of thick lips in Midas cichlid fishes (the Amphilophus citrinellus species complex) - from two Great Lakes and two crater lakes in Nicaragua - to assess whether similar changes in ecology, phenotypic trophic traits and gene expression accompany parallel trait evolution. Using next-generation sequencing technology, we characterize transcriptome-wide differential gene expression in the lips of wild-caught sympatric thick- and thin-lipped cichlids from all four instances of repeated thick-lip evolution. Six genes (apolipoprotein D, myelin-associated glycoprotein precursor, four-and-a-half LIM domain protein 2, calpain-9, GTPase IMAP family member 8-like and one hypothetical protein) are significantly underexpressed in the thick-lipped morph across all four lakes. However, other aspects of lips' gene expression in sympatric morphs differ in a lake-specific pattern, including the magnitude of differentially expressed genes (97-510). Generally, fewer genes are differentially expressed among morphs in the younger crater lakes than in those from the older Great Lakes. Body shape, lower pharyngeal jaw size and shape, and stable isotopes (dC and dN) differ between all sympatric morphs, with the greatest differentiation in the Great Lake Nicaragua. Some ecological traits evolve in parallel (those related to foraging ecology; e.g. lip size, body and head shape) but others, somewhat surprisingly, do not (those related to diet and food processing; e.g. jaw size and shape, stable isotopes). Taken together, this case of parallelism among thick- and thin-lipped cichlids shows a mosaic pattern of parallel and nonparallel evolution. © 2012 Blackwell Publishing Ltd.

A Low Radar Cross Section Dipole Antenna Simulation

This paper reports a new method for reducing theRadar Cross-Section (RCS) of a metal backed dipole antenna. Numerical simulations are used to show that when the Perfect Electrical Conductor (PEC) is replaced by a carefully designedFrequency Selective Surface (FSS), the electromagnetic performanceof the antenna is similar in band, but the RCS of the structure is significantly lower out of band. The design of the FSSand the return loss, radiation patterns and RCS are presentedfor an antenna which operates at a center frequency of 4 GHzand the results are compared with a conventional metal backed arrangement

Genomic Resources Notes Accepted 1 June 2015 - 31 July 2015

This article documents the public availability of (i) microbiomes in diet and gut of larvae from the dipteran Dilophus febrilis using massive parallel sequencing, (ii) SNP and SSR discovery and characterization in the transcriptome of the Atlantic mackerel (Scomber scombrus, L) and (iii) assembled transcriptome for an endangered, endemic Iberian cyprinid fish (Squalius pyrenaicus).

QUALITY EVALUATION OF 'SUNBURST' CHERRIES HARVESTED AT DIFFERENT RIPENESS STAGES .

The sweet cherry ‘Sunburst’ is highly appreciated by consumers due to its organoleptic traits. Regional producers tend to harvest cherries sooner in order to increase their profits. With the aim of understanding the consequences of this we have tested the effect of different ripeness stages at the moment of harvesting on fruit quality. Quality parameters tested included external colour (L*, a*, b*), fruit texture, total soluble solids (TSS), and titratable acidity (TA). To evaluate nutritional quality total antioxidant activity was measured too. Once again, and in agreement with results obtained in previous studies, we conclude that there is no advantage in picking less ripe cherries.

EFFECT OF DIFFERENT STORAGE CONDITIONS ON NUTRITIONAL AND QUALITY PARAMETERS OF 'SWEETHEART' CHERRY.

Abstract The sweet cherry ‘Sweetheart’, although having a short shelf life, is highly appreciated by consumers due to its organoleptic characteristics. Different storage methods were tested to study the maintenance of quality during a period of 27 days: 1) cold (air at 1°C and 95% relative humidity) (CC), 2) cold and polypropylene film bags (1°C and 95% relative humidity) (MA) and 3) cold and controlled atmosphere (1°C, 95% RH, 10% CO2 and 8% O2) (CA). Quality parameters tested included external colour (L*, a*, b*), total soluble solids (TSS), and titratable acidity (TA). To evaluate nutritional quality anthocyanins, total antioxidant activity, and total phenolics were measured. Results allow us to say that phenolic compounds were relatively stable and similar during storage in CC and MA. Cherries stored under CA conditions presented lowest concentrations of phenolic compounds. Phenolic compounds, total anthocyanins and antioxidant activity were inversely correlated with values of colour coordinates. Considering all the evaluations done during this work it is unquestionable that fruits stored in controlled atmosphere conditions had significantly different quality.

SHORT-TERM EFFECTS OF SALINITY ON SOME PHYSIOLOGICAL PARAMETERS OF YOUNG OLIVE TREES OF ARBEQUINA, COBRANÇOSA AND GALEGA VARIETIES

SHORT-TERM EFFECTS OF SALINITY ON SOME PHYSIOLOGICAL PARAMETERS OF YOUNG OLIVE TREES OF ARBEQUINA, COBRANÇOSA AND GALEGA VARIETIES Ana Elisa Rato1,4, Renato Coelho1, Margarida Vaz1, Teresa Carola2, Dália Barbosa2, Nádia Silva1, José dos Santos2, Lourenço Machado2, João Godinho2, Luzia Ruas2, Margarida Barradas2, Hernani Pereira2, Sara Porfírio4 1 ICAAM, Universidade de Évora, Apartado 94, 7002-554 Évora, Portugal 2 Master students, Universidade de Évora, Apartado 94, 7002-554 Évora, Portugal 3 Ph.D. student, Universidade de Évora, Apartado 94, 7002-554 Évora, Portugal 4 aerato@uevora.pt Due to the desertification in some regions, the interest in plant’s tolerance to salinity has been increasing, as this response is determining for plant survival in stress conditions. This work reports the investigation of tolerance to salt in two year-old olive trees (Olea europaea L.) of three varieties, Arbequina, Cobrançosa and Galega vulgar. Plants were grown in 10 L plastic pots containing approximately 9 Kg of a sandy granitic soil, on a greenhouse. For 3 months (from the beginning of February to the end of April 2012), they were subjected to three levels of salinity in the irrigation water, 0 mM, 80 mM and 200 mM NaCl (6 plants per salinity level in a total of 18 plants of each variety),. Stomatal conductance (gs) and relative leaf chlorophyll content were assessed on each plant in February, March and April. Mid-day leaf water potential () and soil salinity were measured at the end of the experiment (April). On average, concerning all treatments and dates of determination, stomatal conductance of Arbequina and Galega vulgar was quite similar, around 40 mmol m-2 s-1, but Cobrançosa had a value of gs 36% higher, almost 50% higher (61 mmol m-2 s-1) when compared with the controls (0 mM salt) of the other two varieties. In percentage of controls, there was little difference in gs between varieties and between salinities during February and March. In contrast, in April, after about 90 days of exposure to salt, there was a clear decrease in gs with salt irrigation, proportional to salt concentration. Compared with controls, plants irrigated with 200 mM salt showed around 80% (Arbequina) or 85% (Cobrançosa and Galega vulgar) decrease in gs. Chlorophyll content of leaves showed less than 5% difference between varieties on the average of all treatments and dates of determination. During the course of this experiment, the salinity levels used did not show any relevant effect on chlorophyll content. Overall, at the end of the experimental period (April), leaf water potential () at midday was significantly higher in Cobrançosa (-1,4 MPa) than in Galega vulgar (-1,7 MPa) or Arbequina (-1,8 MPa), and salt decreased  of control plants (-1,25 MPa) by an average 30% (with 80 mM) and 65% (with 200 mM). At the end of the experiment, salinity in the soil irrigated with 0 mM, 80 mM or 200 mM NaCl was, on average of all varieties, 0,2 mS, 1,0 mS or 2,0 mS, respectively. Soil salinity was quite similar in Arbequina and Galega vulgar but about 35% lower in the pots of Cobrançosa, on average of all salt-irrigation levels. Plants of Cobrançosa had higher stomatal conductance, however they showed higher water potential and lower salinity in the soil. These apparently contradictory results seem to suggest that Cobrançosa responds to salt differently from the other two varieties. This issue needs further investigation.

QUALITY OF 'SWEETHEART' CHERRY UNDER DIFFERENT STORAGE CONDITIONS

Abstract: In Portalegre, Portugal, sweet cherry production is very important to the region’s economic sustainability. The sweet cherry ‘Sweetheart’ has exhibited short shelf life in spite of being highly appreciated by consumers due to its organoleptic characteristics. In this trial, we evaluated fruit quality of ‘Sweetheart’ stored under different storage conditions: 1) cold conditions (1ºC and high humidity 95%), 2) cold conditions and polypropylene film bags (MA), and 3) controlled atmosphere (CA) (1°C, 95% humidity, 10% CO2 and 8% O2). Fruit physical and chemical parameters were evaluated after 0, 6, 13, 20 and 27 days of cold storage. Quality parameters tested included weight loss, external colour (L* a* b*), visual assessment of the epidermis, epidermis and mesocarp penetration test, soluble solids content (SSC), and titratable acidity (TA). We also performed sensory analyses. The results for textural properties, colour coordinates and sensory analysis suggest that ‘Sweetheart’ fruit can be stored under cold conditions, 1°C, 95% humidity, for up to 21 days without significant loss of quality. Controlled atmosphere maintained tissue turgidity during storage; however, this was not noticed by the panelists, who consistently classified fruits stored under CA conditions with lower overall ratings than fruits under cold conditions with or without film bags.

On lattices from combinatorial game theory modularity and a representation theorem: Finite case

We show that a self-generated set of combinatorial games, S, may not be hereditarily closed but, strong self-generation and hereditary closure are equivalent in the universe of short games. In [13], the question “Is there a set which will give an on-distributive but modular lattice?” appears. A useful necessary condition for the existence of a finite non-distributive modular L(S) is proved. We show the existence of S such that L(S) is modular and not distributive, exhibiting the first known example. More, we prove a Representation Theorem with Games that allows the generation of all finite lattices in game context. Finally, a computational tool for drawing lattices of games is presented.

Cartografia da oferta educativa e formativa destinada à população adulta do concelho de Vendas Novas na última década (2000 a 2010)

A presente dissertação constitui-se num estudo desenvolvido na área da educação de adultos, tendo como questão central: qual a oferta educativa e formativa certificada dirigida à população adulta do concelho de Vendas Novas, no período de 2000 a 2010? Procurámos dar resposta a esta questão, reflectindo sobre os conceitos relativos à Educação e Aprendizagem ao Longo da Vida e traçando uma breve retrospectiva das políticas educativas que nortearam este sector da educação. Atendendo à natureza do objecto em estudo, seguiu-se uma metodologia qualitativa, tendo a recolha de dados recaído sobre documentos oficiais produzidos por instâncias locais e regionais. Para a sua análise e interpretação, recorreu-se à técnica de análise de conteúdo, com o objectivo de destacar o seu conteúdo, quer evidente, quer latente. Os resultados emanados deste estudo permitiram-nos concluir efectivamente que as ofertas formativas colocadas ao dispor da população do concelho de Vendas Novas, durante a década de 2000 – 2010, foram muito diversificadas e procuraram, não só dar resposta às necessidades de formação/qualificação diagnosticadas, mas também dar cumprimento às orientações políticas nacionais e internacionais, em matéria de educação de adultos; ABSTRACT:This dissertation is the result of a study carries out in the area of adult education, having as central concern the mapping of the certified educational and training offer for adults in the county of Vendas Novas, in the period between 2000 and 2010. We tried to answer this question, reflecting on the concepts relating to education and lifelong learning and plotting a brief review of educational policies that guided this sector of education. Due to the nature of the subject under study, was followed a qualitative methodology, and data collection has relied on official documents produced by local and regional authorities. For the analysis and interpretation of data, we used the technique of content analysis, in order to highlight its content, either obvious or latent. The results emanating from this study allowed us to conclude that the provision of educational and training offer made available to the population of the county of Vendas Novas, during the decade 2000 - 2010, was very diverse and sought to address not only the training / qualification needs diagnosed, but also to comply with the national and international guidelines, in the field of adult education.

Relatório de Avaliação Externa do Agrupamento de Escolas de Almodôvar

O presente relatório expressa os resultados da avaliação externa do Agrupamento de Escolas de Almodôvar, realizada pela equipa de avaliação, na sequência da visita efetuada entre 19 e 22 de janeiro de 2015. As conclusões decorrem da análise dos documentos fundamentais do Agrupamento, em especial da sua autoavaliação, dos indicadores de sucesso académico dos alunos, das respostas aos questionários de satisfação da comunidade e da realização de entrevistas.