Rhodopsin gene polymorphism associated with divergent light environments in atlantic cod

The spectral sensitivity of visual pigments in vertebrate eyes is optimized for specific light conditions. One of such pigments, rhodopsin (RH1), mediates dim-light vision. Amino acid replacements at tuning sites may alter spectral sensitivity, providing a mechanism to adapt to ambient light conditions and depth of habitat in fish. Here we present a first investigation of RH1 gene polymorphism among two ecotypes of Atlantic cod in Icelandic waters, which experience divergent light environments throughout the year due to alternative foraging behaviour. We identified one synonymous single nucleotide polymorphism (SNP) in the RH1 protein coding region and one in the 3' untranslated region (3'-UTR) that are strongly divergent between these two ecotypes. Moreover, these polymorphisms coincided with the well-known panthophysin (Pan I) polymorphism that differentiates coastal and frontal (migratory) populations of Atlantic cod. While the RH1 SNPs do not provide direct inference for a specific molecular mechanism, their association with this dim-sensitive pigment indicates the involvement of the visual system in local adaptation of Atlantic cod.

The prevalence of refractive errors among adults in the United States, Western Europe, and Australia.

OBJECTIVE:

To estimate the prevalence of refractive errors in persons 40 years and older.

METHODS:

Counts of persons with phakic eyes with and without spherical equivalent refractive error in the worse eye of +3 diopters (D) or greater, -1 D or less, and -5 D or less were obtained from population-based eye surveys in strata of gender, race/ethnicity, and 5-year age intervals. Pooled age-, gender-, and race/ethnicity-specific rates for each refractive error were applied to the corresponding stratum-specific US, Western European, and Australian populations (years 2000 and projected 2020).

RESULTS:

Six studies provided data from 29 281 persons. In the US, Western European, and Australian year 2000 populations 40 years or older, the estimated crude prevalence for hyperopia of +3 D or greater was 9.9%, 11.6%, and 5.8%, respectively (11.8 million, 21.6 million, and 0.47 million persons). For myopia of -1 D or less, the estimated crude prevalence was 25.4%, 26.6%, and 16.4% (30.4 million, 49.6 million, and 1.3 million persons), respectively, of whom 4.5%, 4.6%, and 2.8% (5.3 million, 8.5 million, and 0.23 million persons), respectively, had myopia of -5 D or less. Projected prevalence rates in 2020 were similar.

CONCLUSIONS:

Refractive errors affect approximately one third of persons 40 years or older in the United States and Western Europe, and one fifth of Australians in this age group.

Validating the use of intrinsic markers in body feathers to identify inter‑individual differences in non‑breeding areas of northern fulmars

Many wildlife studies use chemical analyses to explore spatio-temporal variation in diet, migratory patterns and contaminant exposure. Intrinsic markers are particularly valuable for studying non-breeding marine predators, when direct methods of investigation are rarely feasible. However, any inferences regarding foraging ecology are dependent upon the time scale over which tissues such as feathers are formed. In this study, we validate the use of body feathers for studying non-breeding foraging patterns in a pelagic seabird, the northern fulmar. Analysis of carcasses of successfully breeding adult fulmars indicated that body feathers moulted between September and March, whereas analyses of carcasses and activity patterns suggested that wing feather and tail feather moult occurred during more restricted periods (September to October and September to January, respectively). By randomly sampling relevant body feathers, average values for individual birds were shown to be consistent. We also integrated chemical analyses of body feather with geolocation tracking data to demonstrate that analyses of δ13C and δ15N values successfully assigned 88 % of birds to one of two broad wintering regions used by breeding adult fulmars from a Scottish study colony. These data provide strong support for the use of body feathers as a tool for exploring non-breeding foraging patterns and diet in wide-ranging, pelagic seabirds.

A comparison of endoscopy versus pathology sizing of colorectal adenomas and potential implications for surveillance colonoscopy

Background and AimsTo compare endoscopy and pathology sizing in a large population-based series of colorectal adenomas and to evaluate the implications for patient stratification into surveillance colonoscopy.MethodsEndoscopy and pathology sizes available from intact adenomas removed at colonoscopies performed as part of the Northern Ireland Bowel Cancer Screening Programme, from 2010 to 2015, were included in this study. Chi-squared tests were applied to compare size categories in relation to clinicopathological parameters and colonoscopy surveillance strata according to current American Gastroenterology Association and British Society of Gastroenterology guidelines.ResultsA total of 2521 adenomas from 1467 individuals were included. There was a trend toward larger endoscopy than pathology sizing in 4 of the 5 study centers, but overall sizing concordance was good. Significantly greater clustering with sizing to the nearest 5 mm was evident in endoscopy versus pathology sizing (30% vs 19%, p<0.001), which may result in lower accuracy. Applying a 10-mm cut-off relevant to guidelines on risk stratification, 7.3% of all adenomas and 28.3% of those 8 to 12 mm in size had discordant endoscopy and pathology size categorization. Depending upon which guidelines are applied, 4.8% to 9.1% of individuals had differing risk stratification for surveillance recommendations, with the use of pathology sizing resulting in marginally fewer recommended surveillance colonoscopies.ConclusionsChoice of pathology or endoscopy approaches to determine adenoma size will potentially influence surveillance colonoscopy follow-up in 4.8% to 9.1% of individuals. Pathology sizing appears more accurate than endoscopy sizing, and preferential use of pathology size would result in a small, but clinically important, decreased burden on surveillance colonoscopy demand. Careful endoscopy sizing is required for adenomas removed piecemeal.

Ecotoxicological tests using Chironomus riparius

Os sistemas aquáticos naturais podem estar sujeitos frequentemente a entrada de tóxicos, quer seja através da lixiviação dos campos agrícolas ou da descarga por parte de unidades industriais. Avaliar o impacto potencial destes contaminantes nos sistemas aquáticos é muito importante, porque pode promover consequências sérias no balanço ecológico dos ecossistemas. Os efeitos de níveis sub-letais destes tóxicos nas populações aquáticas são detectados, em muitos casos, somente após diversas gerações, dependendo da espécie e do contaminante. O comportamento animal é considerado como sendo a primeira linha de defesa perante estímulos ambientais, e pode ser uma representação de alterações fisiológicas no organismo, sendo portanto um indicador excelente de alterações ambientais. O desenvolvimento dos sistemas de aviso prévio que integram parâmetros comportamentais pode ajudar a prever mais rapidamente possíveis alterações ao nível das populações naturais, do que a utilização de testes ecotoxicológicos padrão com a mesma finalidade. O conhecimento acerca de possíveis implicações devido a alterações comportamentais, em organismos bentónicos e em populações do campo sujeitas a tóxicos, é ainda escasso. Sabendo isto, neste estudo pretendeu-se investigar como o comportamento de Chironomus riparius – usando um biomonitor em tempo real – e outros parâmetros tais como crescimento, emergência de adultos, bioacumulação e biomarcadores, são afectados pela exposição a imidacloprid e ao mercúrio, que foram seleccionados como contaminantes. Os resultados demonstraram que a exposição às concentrações sub-letais de imidacloprid afecta o crescimento e o comportamento dos quironomídeos e que estes organismos podem recuperar de uma exposição curta ao insecticida. O comportamento que corresponde à ventilação de C. riparius revelou-se como um parâmetro mais sensível do que a locomoção e do que as respostas bioquímicas, quando as larvas foram sujeitas ao imidacloprid. Larvas de C. riparius expostas a concentrações sub-letais de mercúrio apresentaram uma tendência de diminuição de actividade comportamental, em testes com concentrações crescentes do tóxico; o crescimento das larvas foi também prejudicado, e as taxas de emergência de adultos e o tempo de desenvolvimento apresentaram retardamento. Estes organismos podem bioacumular rapidamente o mercúrio em condições de não alimentação e apresentam uma lenta depuração deste metal. Estes efeitos podem, em último caso, conduzir a prováveis repercussões ao nível da população e das comunidades. As reduções em actividades comportamentais, mesmo em concentrações baixas, podem diminuir a quantidade de tempo gasta na procura de alimento, produzindo efeitos aos níveis morfo-fisiológicos, e assim afectar severamente o desempenho dos quironomídeos no ambiente. O uso destes factores comportamentais como um parâmetro ecotoxicológico sub-letal relevante ao nível da toxicologia aumentará a versatilidade dos testes, permitindo uma resposta comportamental mensurável e quantitativa ao nível do organismo, utilizando uma avaliação não destrutiva, e assim certificando que esta aproximação pode ser usada em testes ecotoxicológicos futuros.

Pain expressiveness and altruistic behavior

Predictions which invoke evolutionary mechanisms ar e hard to test. Agent-based modeling in artificial life offers a way to simulate behaviors and interac tions in specific physical or social environments o ver many generations. The outcomes have implications fo r understanding adaptive value of behaviors in context. Pain-related behavior in animals is communicated to other animals that might protect or help, or might exploit or predate. An agent-based model simulated the effects of displaying or not displaying pain (expresser/non-expresser strategies) when injured, and of helping, ignoring or exploiting another in pain (altruistic/non-altruistic/selfish strategies) . Agents modeled in MATLAB interacted at random while foraging (gaining energy); random injury inte rrupted foraging for a fixed time unless help from an altruistic agent, who paid an energy cost, speeded recovery. Environmental and social conditions also varied, and each model ran for 10,000 iterations. Findings were meaningful in that, in general, conti ngencies evident from experimental work with a variety of mammals, over a few interactions, were r eplicated in the agent-based model after selection pressure over many generations. More energy-demandi ng expression of pain reduced its frequency in successive generations, and increasing injury frequ ency resulted in fewer expressers and altruists. Allowing exploitation of injured agents decreased e xpression of pain to near zero, but altruists remained. Decreasing costs or increasing benefits o f helping hardly changed its frequency, while increasing interaction rate between injured agents and helpers diminished the benefits to both. Agent- based modeling allows simulation of complex behavio urs and environmental pressures over evolutionary time.

Feed-backs between genetic structure and perturbation-driven decline in seagrass (Posidonia oceanica) meadows

We explored the relationships between perturbation-driven population decline and genetic/genotypic structure in the clonal seagrass Posidonia oceanica, subject to intensive meadow regression around four Mediterranean fish-farms, using seven specific microsatellites. Two meadows were randomly sampled (40 shoots) within 1,600 m2 at each site: the “impacted” station, 5–200 m from fish cages, and the “control” station, around 1,000 m downstream further away (considered a proxy of the pre-impact genetic structure at the site). Clonal richness (R), Simpson genotypic diversity (D*) and clonal sub-range (CR) were highly variable among sites. Nevertheless, the maximum distance at which clonal dispersal was detected, indicated by CR, was higher at impacted stations than at the respective control station (paired t-test: P < 0.05, N = 4). The mean number of alleles (Â) and the presence of rare alleles ( r) decreased at impacted stations (paired t-test: P < 0.05, and P < 0.02, respectively, N = 4). At a given perturbation level (quantified by the organic and nutrient loads), shoot mortality at the impacted stations significantly decreased with CR at control stations (R 2 = 0.86, P < 0.05). Seagrass mortality also increased with  (R 2 = 0.81, P < 0.10), R (R 2 = 0.96, P < 0.05) and D* (R 2 = 0.99, P < 0.01) at the control stations, probably because of the negative correlation between those parameters and CR. Therefore, the effects of clonal size structure on meadow resistance could play an important role on meadow survival. Large genotypes of P. oceanica meadows thus seem to resist better to fish farm-derived impacts than little ones. Clonal integration, foraging advantage or other size-related fitness traits could account for this effect.

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

Activity, distribution and microhabitat use by the imperilled mira chub Squalius Torgalensis

Tese de doutoramento, Biologia (Ecologia), Universidade de Lisboa, Faculdade de Ciências, 2014

O repertório cerâmico da sala nº 1(Vidigueira), na sequência Neolítico final e Calcolítico do Alentejo Médio

O trabalho aqui proposto tem como objectivo central, a realização de análises ao conjunto dos recipientes cerâmicos pertencentes ao povoado da Sala nº1. Repertório esse, que se baseou no acervo retirado do sítio arqueológico Sala nº1, intervencionado pelo Professor Victor S. Gonçalves (1988, 1989 e 1995). As análises e descrições efectuadas foram sempre norteadas para a tentativa de estabelecer uma sequência de formas que se pudesse verificar quanto à sua normalização e frequência nos contextos presentes ao povoado da Sala nº1. Traduzindo nessa realidade, a diacronia transversal entre os estratos arqueológicos pertencentes ao Neolítico final e os estratos pertencentes ao Calcolítico. Tendo sempre como parâmetros de análise, as metodologias e critérios descritivos dos recipientes cerâmicos, presentes nos trabalhos publicados sobre as realidades cronológicas semelhantes no Sul de Portugal. O próprio conjunto de recipientes cerâmicos aqui analisado foi submetido a essas metodologias, com fim de obter primordialmente as formas e as tipologias a que pertencem. Nesse sentido procurei criar um quadro de referência local e regional, e posteriormente coloca-lo num enquadramento geral do Neolítico final e início do Calcolítico do Alentejo Médio, tentando verificar as similitudes nos quadros tipológicos existentes, como os estabelecidos por Carlos Tavares da Silva e Joaquina Soares. Sendo este um estudo que abrange um tempo cronológico de praticamente 1500 anos, premiei através da amplitude dos contornos que moldaram esta análise, algumas perspectivas possíveis. Quer ao nível das tipologias, quer ao nível das estratégias de ocupação do território, aplicáveis para o espaço e o tempo em análise. Verificando a realidade escassa nos contextos alentejanos (publicados), em que a cultura material se integra numa estratigrafia e cronologias com uma diacronia semelhante à do povoado da Sala nº1. Tentei integrar este povoado num estudo que não sendo comparativo, tivesse essa componente em relação às tipologias e formas cerâmicas identificadas. Procurou-se dar enfase à realidade artefactual das taças carenadas, e à sua possível evolução para formas mais adaptáveis ao uso e consumo quotidiano das comunidades contemporâneas das fases Calcolíticas do povoado.

Impacto da iluminação natural e artificial na disponibilidade de macro-invertebrados bentónicos para as aves limícolas

Tese de mestrado em Ecologia Marinha, apresentada à Universidade de Lisboa, através da Faculdade de Ciências, 2015

Reading Maud’s remains: Tennyson, geological processes, and palaeontological reconstructions

As Tennyson's “little Hamlet ,” Maud (1855) posits a speaker who, like Hamlet, confronts the ignominious fate of dead remains. Maud's speaker contemplates such remains as bone, hair, shell, and he experiences his world as one composed of hard inorganic matter, such things as rocks, gems, flint, stone, coal, and gold. While Maud's imagery of “stones, and hard substances” has been read as signifying the speaker's desire “unnaturally to harden himself into insensibility” (Killham 231, 235), I argue that these substances benefit from being read in the context of Tennyson's wider understanding of geological processes. Along with highlighting these materials, the text's imagery focuses on processes of fossilisation, while Maud's characters appear to be in the grip of an insidious petrification. Despite the preoccupation with geological materials and processes, the poem has received little critical attention in these terms. Dennis R. Dean, for example, whose Tennyson and Geology (1985) is still the most rigorous study of the sources of Tennyson's knowledge of geology, does not detect a geological register in the poem, arguing that by the time Tennyson began to write Maud, he was “relatively at ease with the geological world” (Dean 21). I argue, however, that Maud reveals that Tennyson was anything but “at ease” with geology. While In Memoriam (1851) wrestles with religious doubt that is both initiated, and, to some extent, alleviated by geological theories, it finally affirms the transcendence of spirit over matter. Maud, conversely, gravitates towards the ground, concerning itself with the corporal remains of life and with the agents of change that operate on all matter. Influenced by his reading of geology, and particularly Charles Lyell's provocative writings on the embedding and fossilisation of organic material in strata in his Principles of Geology (1830–33) volume 2, Tennyson's poem probes the taphonomic processes that result in the incorporation of dead remains and even living flesh into the geological system.

Re-evaluation of a reported increased micronucleus frequency in lymphocytes of workers occupationally exposed to formaldehyde

A replicate evaluation of increased micronucleus (MN) frequencies in peripheral lymphocytes of workers occupationally exposed to formaldehyde (FA) was undertaken to verify the observed effect and to determine scoring variability. May–Grünwald–Giemsa-stained slides were obtained from a previously performed cytokinesis-block micronucleus test (CBMNT) with 56 workers in anatomy and pathology laboratories and 85 controls. The first evaluation by one scorer (scorer 1) had led to a highly significant difference between workers and controls (3.96 vs 0.81 MN per 1000 cells). The slides were coded before re-evaluation and the code was broken after the complete re-evaluation of the study. A total of 1000 binucleated cells (BNC) were analysed per subject and the frequency of MN (in ‰) was determined. Slides were distributed equally and randomly between two scorers, so that the scorers had no knowledge of the exposure status. Scorer 2 (32 exposed, 36 controls) measured increased MN frequencies in exposed workers (9.88 vs 6.81). Statistical analysis with the two-sample Wilcoxon test indicated that this difference was not significant (p = 0.17). Scorer 3 (20 exposed, 46 controls) obtained a similar result, but slightly higher values for the comparison of exposed and controls (19.0 vs 12.89; p = 0.089). Combining the results of the two scorers (13.38 vs 10.22), a significant difference between exposed and controls (p = 0.028) was obtained when the stratified Wilcoxon test with the scorers as strata was applied. Interestingly, the re-evaluation of the slides led to clearly higher MN frequencies for exposed and controls compared with the first evaluation. Bland–Altman plots indicated that the agreement between the measurements of the different scorers was very poor, as shown by mean differences of 5.9 between scorer 1 and scorer 2 and 13.0 between scorer 1 and scorer 3. Calculation of the intra-class correlation coefficient (ICC) revealed that all scorer comparisons in this study were far from acceptable for the reliability of this assay. Possible implications for the use of the CBMNT in human biomonitoring studies are discussed.

A linguagem do espaço em Henry James: a fase madura

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Sei whale (Balaenoptera borealis) ecology and management in the North Atlantic

Tese de Doutoramento em Ciências do Mar, especialidade em Ecologia Marinha.