Hidden biosphere in an oxygen-deficient Atlantic open ocean eddy: future implications of ocean deoxygenation on primary production in the eastern tropical North Atlantic

The eastern tropical North Atlantic (ETNA) is characterized by a highly productive coastal upwelling system and a moderate oxygen minimum zone with lowest open ocean oxygen (O2) concentrations of around 40 μmol kg−1. Only recently, the discovery of re-occurring mesoscale eddies with sometimes close to anoxic O2 concentrations (<1 μmol kg−1) and located just below the mixed layer challenged our understanding of O2 distribution and biogeochemical processes in this area. Here, we present the first metagenomic dataset from a deoxygenated anticyclonic modewater eddy in the open waters of the ETNA. In the eddy, we observed a significantly lower bacterial diversity compared to surrounding waters, along with a significant community shift. We detected enhanced primary productivity in the surface layer of the eddy indicated by elevated chlorophyll concentrations and increased carbon uptake rates up to three times as high as in surrounding waters. Carbon uptake below the euphotic zone correlated to the presence of a specific high-light ecotype of Prochlorococcus, which is usually underrepresented in the ETNA. Our combined data indicate that high primary production in the eddy fuels export production and the presence of a specific microbial community responsible for enhanced respiration at shallow depths, below the mixed layer base. Progressively decreasing O2 concentrations in the eddy were found to promote transcription of the key gene for denitrification, nirS, in the O2-depleted core waters. This process is usually absent from the open ETNA waters. In the light of future ocean deoxygenation our results show exemplarily that even distinct events of anoxia have the potential to alter microbial community structures and with that critically impact primary productivity and biogeochemical processes of oceanic water bodies

Grey and white matter correlates of recent and remote autobiographical memory retrieval:Insights from the dementias

The capacity to remember self-referential past events relies on the integrity of a distributed neural network. Controversy exists, however, regarding the involvement of specific brain structures for the retrieval of recently experienced versus more distant events. Here, we explored how characteristic patterns of atrophy in neurodegenerative disorders differentially disrupt remote versus recent autobiographical memory. Eleven behavioural-variant frontotemporal dementia, 10 semantic dementia, 15 Alzheimer's disease patients and 14 healthy older Controls completed the Autobiographical Interview. All patient groups displayed significant remote memory impairments relative to Controls. Similarly, recent period retrieval was significantly compromised in behavioural-variant frontotemporal dementia and Alzheimer's disease, yet semantic dementia patients scored in line with Controls. Voxel-based morphometry and diffusion tensor imaging analyses, for all participants combined, were conducted to investigate grey and white matter correlates of remote and recent autobiographical memory retrieval. Neural correlates common to both recent and remote time periods were identified, including the hippocampus, medial prefrontal, and frontopolar cortices, and the forceps minor and left hippocampal portion of the cingulum bundle. Regions exclusively implicated in each time period were also identified. The integrity of the anterior temporal cortices was related to the retrieval of remote memories, whereas the posterior cingulate cortex emerged as a structure significantly associated with recent autobiographical memory retrieval. This study represents the first investigation of the grey and white matter correlates of remote and recent autobiographical memory retrieval in neurodegenerative disorders. Our findings demonstrate the importance of core brain structures, including the medial prefrontal cortex and hippocampus, irrespective of time period, and point towards the contribution of discrete regions in mediating successful retrieval of distant versus recently experienced events

Challenges in integrating Escherichia coli molecular biology data

One key challenge in Systems Biology is to provide mechanisms to collect and integrate the necessary data to be able to meet multiple analysis requirements. Typically, biological contents are scattered over multiple data sources and there is no easy way of comparing heterogeneous data contents. This work discusses ongoing standardisation and interoperability efforts and exposes integration challenges for the model organism Escherichia coli K-12. The goal is to analyse the major obstacles faced by integration processes, suggest ways to systematically identify them, and whenever possible, propose solutions or means to assistmanual curation. Integration of gene, protein and compound data was evaluated by performing comparisons over EcoCyc, KEGG, BRENDA, ChEBI, Entrez Gene and UniProt contents. Cross-links, a number of standard nomenclatures and name information supported the comparisons. Except for the gene integration scenario, in no other scenario an element of integration performed well enough to support the process by itself. Indeed, both the integration of enzyme and compound records imply considerable curation. Results evidenced that, even for a well-studied model organism, source contents are still far from being as standardized as it would be desired and metadata varies considerably from source to source. Before designing any data integration pipeline, researchers should decide on the sources that best fit the purpose of analysis and be aware of existing conflicts/inconsistencies to be able to intervene in their resolution. Moreover, they should be aware of the limits of automatic integration such that they can define the extent of necessary manual curation for each application.Portuguese FCT funded MIT-Portugal Program in Bioengineering (MIT-Pt/BS-BB/0082/2008); PhD grant from FCT (ref. SFRH/BD/22863/2005) to S.

Stochastic population growth in spatially heterogeneous environments

Classical ecological theory predicts that environmental stochasticity increases extinction risk by reducing the average per-capita growth rate of populations. To understand the interactive effects of environmental stochasticity, spatial heterogeneity, and dispersal on population growth, we study the following model for population abundances in $n$ patches: the conditional law of $X_{t+dt}$ given $X_t=x$ is such that when $dt$ is small the conditional mean of $X_{t+dt}^i-X_t^i$ is approximately $[x^i\mu_i+\sum_j(x^j D_{ji}-x^i D_{ij})]dt$, where $X_t^i$ and $\mu_i$ are the abundance and per capita growth rate in the $i$-th patch respectivly, and $D_{ij}$ is the dispersal rate from the $i$-th to the $j$-th patch, and the conditional covariance of $X_{t+dt}^i-X_t^i$ and $X_{t+dt}^j-X_t^j$ is approximately $x^i x^j \sigma_{ij}dt$. We show for such a spatially extended population that if $S_t=(X_t^1+...+X_t^n)$ is the total population abundance, then $Y_t=X_t/S_t$, the vector of patch proportions, converges in law to a random vector $Y_\infty$ as $t\to\infty$, and the stochastic growth rate $\lim_{t\to\infty}t^{-1}\log S_t$ equals the space-time average per-capita growth rate \sum_i\mu_i\E[Y_\infty^i] experienced by the population minus half of the space-time average temporal variation \E[\sum_{i,j}\sigma_{ij}Y_\infty^i Y_\infty^j] experienced by the population. We derive analytic results for the law of $Y_\infty$, find which choice of the dispersal mechanism $D$ produces an optimal stochastic growth rate for a freely dispersing population, and investigate the effect on the stochastic growth rate of constraints on dispersal rates. Our results provide fundamental insights into "ideal free" movement in the face of uncertainty, the persistence of coupled sink populations, the evolution of dispersal rates, and the single large or several small (SLOSS) debate in conservation biology.Comment: 47 pages, 4 figure

Contrasting prefrontal cortex contributions to episodic memory dysfunction in behavioural variant frontotemporal dementia and alzheimer's disease

Recent evidence has questioned the integrity of episodic memory in behavioural variant frontotemporal dementia (bvFTD), where recall performance is impaired to the same extent as in Alzheimer's disease (AD). While these deficits appear to be mediated by divergent patterns of brain atrophy, there is evidence to suggest that certain prefrontal regions are implicated across both patient groups. In this study we sought to further elucidate the dorsolateral (DLPFC) and ventromedial (VMPFC) prefrontal contributions to episodic memory impairment in bvFTD and AD. Performance on episodic memory tasks and neuropsychological measures typically tapping into either DLPFC or VMPFC functions was assessed in 22 bvFTD, 32 AD patients and 35 age- and education-matched controls. Behaviourally, patient groups did not differ on measures of episodic memory recall or DLPFC-mediated executive functions. BvFTD patients were significantly more impaired on measures of VMPFC-mediated executive functions. Composite measures of the recall, DLPFC and VMPFC task scores were covaried against the T1 MRI scans of all participants to identify regions of atrophy correlating with performance on these tasks. Imaging analysis showed that impaired recall performance is associated with divergent patterns of PFC atrophy in bvFTD and AD. Whereas in bvFTD, PFC atrophy covariates for recall encompassed both DLPFC and VMPFC regions, only the DLPFC was implicated in AD. Our results suggest that episodic memory deficits in bvFTD and AD are underpinned by divergent prefrontal mechanisms. Moreover, we argue that these differences are not adequately captured by existing neuropsychological measures

Growth and energy and protein intake of preterm newborns in the first year of gestation-corrected age

CONTEXT: There are few longitudinal studies that analyze the growth and nutritional status parameters of children born prematurely. OBJECTIVE: To evaluate the growth and dietary intake of preterm newborns in the first year of gestation-corrected age. DESIGN: Prospective clinical study. SETTING: Tertiary care hospital. PATIENTS: 19 children (7 male) who were born prematurely, with birth weight between 1000g and 2000g, which was adequate for the gestational age. PROCEDURES: At 3, 6, 9 and 12 months of gestation-corrected age, children were evaluated in relation to weight, height and cephalic perimeter, using the National Center for Health Statistics as the standard reference, and the Rozalez-Lopez and Frisancho standards for brachial perimeter and triceps and subscapular skinfolds. The calculated dietary intake was compared to the Recommended Dietary Allowances. MAIN MEASUREMENTS: The Z score was calculated for the weight/age, height/age and weight/height relationships, and the percentiles of the perimeters and skinfolds were considered. Dietary intake records were made using the 24-hour Dietary Recall and the Food Frequency Intake Questionnaire methods. The Virtual Nutri software was used to calculate energy and protein intake. RESULTS: The weight/age, height/age and weight/height relationships and the brachial perimeter and triceps skinfold were statistically greater in the first semester in relation to the second. The cephalic perimeter remained above the 50th percentile for the ages studied and there was no difference in the subscapular skinfold between the first and second semesters, remaining below the 50th percentile. The calorie and protein intake, although statistically lower in the first than in the second semester, always remained above the recommended. CONCLUSIONS: The pace of growth is greater in the first semester than in the second, not reaching the standard expected for full-term newborns, with the exception of the cephalic perimeter, which remains adequate. Calorie/protein intake shows an inverse relationship with growth speed, remaining above the recommended for full-term newborns, although with difficulty in depositing subcutaneous fat, in spite of the high caloric intake.CONTEXTO: Atualmente há estudos longitudinais limitados que definem parâmetros de crescimento e estado nutricional de crianças nascidas prematuras. OBJETIVO: Avaliar o crescimento e a ingestão dietética em recém-nascidos pré-termo no primeiro ano de idade corrigida. TIPO DE ESTUDO: Estudo clínico prospectivo. LOCAL: Hospital de cuidados terciários. PACIENTES: 19 crianças (sete do sexo masculino) nascidas prematuras, adequadas para a idade gestacional, com peso de nascimento entre 1.000 g e 2.000 g, acompanhadas aos 3, 6, 9 e 12 meses de idade corrigida. PROCEDIMENTOS: Aos 3, 6, 9 e 12 meses de idade corrigida, as crianças foram avaliadas quanto ao peso, estatura e perímetros utilizando-se, como padrão de referência, o National Center of Health Statistics e quanto à circunferência braquial e às dobras cutâneas triciptal e subescapular, utilizando-se o padrão de Ronalez-Lopez e de Frisancho. A ingestão dietética calculada foi comparada às Recommended Dietary Allowances. RESULTADOS: As relações peso/idade, estatura/idade, peso/estatura, circunferência braquial e dobra cutânea do tríceps foram estatisticamente maiores no primeiro semestre em relação ao segundo. O perímetro cefálico manteve-se acima do percentil 50 nas idades estudadas e a dobra cutânea subescapular não mostrou diferença entre o primeiro e o segundo semestres, mantendo-se abaixo do percentil 50. A ingestão de calorias e proteínas, apesar de estatisticamente menor no primeiro do que no segundo semestre, permaneceu sempre maior do que o recomendado. CONCLUSÕES: O ritmo de crescimento mostra maior velocidade no primeiro semestre do que no segundo, não atingindo o padrão esperado para os recém-nascidos a termo, com exceção do perímetro cefálico, que se mantém adequado. A ingestão de calorias/proteínas mostra relação inversa com o ritmo de crescimento, permanecendo acima do recomendado para nascidos a termo, havendo, porém, dificuldade de deposição de gordura subcutânea, apesar da alta ingestão calórica.Universidade PaulistaUniversidade Federal de São Paulo (UNIFESP) Escola Paulista de MedicinaUNIFESP, EPMSciEL

Concepções de agricultores ecológicos do Paraná sobre alimentação saudável.

OBJETIVO: Descrever as concepções de agricultores ecológicos sobre alimentação saudável. MÉTODOS: Estudo com abordagem qualitativa. Entre janeiro e fevereiro de 2007, foram realizadas entrevistas em profundidade com o apoio de um roteiro com 11 mulheres e um homem residentes em comunidade agrícola de Rio Branco do Sul, PR, selecionados aleatoriamente dentre as 20 famílias de agricultores ecológicos desse município. RESULTADOS: Três categorias de análise foram identificadas: "tomada de consciência da alimentação saudável", "capacidade de compra" e "terra saudável". O significado da alimentação saudável para as mulheres agricultoras envolve a ideia de que os alimentos devem ser naturais, sem agrotóxicos nem produtos químicos industrializados. Cotidianamente o consumo de frutas, verduras e legumes somado ao básico feijão, arroz e carne deve ser abundante e a composição do prato deve visar à prevenção de obesidade e doenças crônico-degenerativas. O cuidado com os recursos naturais para garantir a produção de alimentos saudáveis, a segurança alimentar, a sustentabilidade do meio ambiente e a vida futura do planeta integram o conceito de alimentação saudável. CONCLUSÕES: O conhecimento, a autocrítica e o discernimento acompanharam as concepções em relação à alimentação saudável