Quantitative NME microscopy of iron transport in methanogenic aggregates

Transport of micronutrients (iron, cobalt, nickel, etc.) within biofilms matrixes such as methanogenic granules is of high importance, because these are either essential or toxic for the microorganisms living inside the biofilm. The present study demonstrates quantitative measurements of metal transport inside these biofilms using T1 weighted 3D RARE. It is shown that iron(II)-EDTA diffusion within the granule is independent of direction or the inner structure of the granules. Assuming position dependence of the spin-lattice relaxivity, Fick’s law for diffusion in a sphere can be applied to simulate the diffusion within the methanogenic granules under investigation. A relatively low diffusion coefficient of 2.5*10-11 m2·s-1 was obtained for iron diffusion within the methanogenic granul

Psychometric properties of the Disordered Eating Attitude Scale for adult men

OBJECTIVE: To evaluate psychometric properties of the Disordered Eating Attitude Scale (DEAS) for men. METHODS: Two hundred and twenty-eight undergraduate male students (18-39 years old) answered the DEAS, originally developed and validated for women. Internal consistency was evaluated by Cronbach's Alpha; convergent validity by comparing DEAS and the Eating Attitude (EAT) and Restraint Scale (RS) scores using Pearson's coefficient. Test-retest reliability was evaluated with a subsample (n = 38) in a month interval by means of intraclass correlation coefficient (ICC). Known-groups validity was obtained comparing scores in DEAS among undergraduate students and men with eating disorders (ED) (n = 28). RESULTS: Internal consistency of scale was 0.63. DEAS score correlated with EAT (r = 0.65) and RS (r = 0.51); ICC between test and retest was 0.948. Known-groups analysis differentiated ED patients and undergraduate students (p < 0.001). CONCLUSIONS: The scale presented adequate psychometric properties and could be used in studies with adult men, since the construct is not explored among males. Nevertheless, it is recommended to revise the scale and to develop specific instruments for male public.OBJETIVO: Avaliar as propriedades psicométricas da Escala de Atitudes Alimentares Transtornadas (EAAT) para o sexo masculino. MÉTODOS: Duzentos e vinte e oito universitários (18-39 anos) responderam à EAAT, originalmente desenvolvida e validada para o sexo feminino. A consistência interna foi avaliada pelo Alpha de Cronbach e a validade convergente, por meio do coeficiente de correlação de Pearson comparando os escores da EAAT, do Teste de Atitudes Alimentares (EAT) e da Escala de Restrição (RS). A reprodutibilidade foi avaliada aplicando a escala numa subamostra (n = 38) com um mês de intervalo utilizando o coeficiente de correlação intraclasse (CCI). A validade known-groups foi obtida comparando o escore dos universitários na EAAT com o escore de homens com diagnóstico de transtornos alimentares (TA) (n = 28). RESULTADOS: A consistência interna da escala foi de 0,63. O escore da EAAT foi correlacionado com a EAT (r = 0,65) e RS (r = 0,51), e o CCI entre o teste e o reteste foi de 0,948. A análise known-groups diferenciou pacientes com TA de estudantes universitários (p < 0,001). CONCLUSÕES: A escala apresentou propriedades psicométricas adequadas e pode ser utilizada em estudos com homens adultos - uma vez que o constructo é pouco explorado em homens. Recomenda-se, de qualquer forma, uma revisão da escala e desenvolvimento de instrumentos específicos para o público masculino.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Universidade de São Paulo Faculdade de Saúde Pública Departamento de NutriçãoUniversidade Federal de Juiz de Fora Programa de Pós-Graduação em PsicologiaUniversidade Federal de São Paulo (UNIFESP) Departamento de Saúde, Clínica e InstituiçõesUNIFESP, Depto. de Saúde, Clínica e InstituiçõesSciEL

An XML transfer schema for exchange of genomic and genetic mapping data: implementation as a web service in a Taverna workflow

<p>Abstract</p> <p>Background</p> <p>Genomic analysis, particularly for less well-characterized organisms, is greatly assisted by performing comparative analyses between different types of genome maps and across species boundaries. Various providers publish a plethora of on-line resources collating genome mapping data from a multitude of species. Datasources range in scale and scope from small bespoke resources for particular organisms, through larger web-resources containing data from multiple species, to large-scale bioinformatics resources providing access to data derived from genome projects for model and non-model organisms. The heterogeneity of information held in these resources reflects both the technologies used to generate the data and the target users of each resource. Currently there is no common information exchange standard or protocol to enable access and integration of these disparate resources. Consequently data integration and comparison must be performed in an <it>ad hoc </it>manner.</p> <p>Results</p> <p>We have developed a simple generic XML schema (GenomicMappingData.xsd – GMD) to allow export and exchange of mapping data in a common lightweight XML document format. This schema represents the various types of data objects commonly described across mapping datasources and provides a mechanism for recording relationships between data objects. The schema is sufficiently generic to allow representation of any map type (for example genetic linkage maps, radiation hybrid maps, sequence maps and physical maps). It also provides mechanisms for recording data provenance and for cross referencing external datasources (including for example ENSEMBL, PubMed and Genbank.). The schema is extensible via the inclusion of additional datatypes, which can be achieved by importing further schemas, e.g. a schema defining relationship types. We have built demonstration web services that export data from our ArkDB database according to the GMD schema, facilitating the integration of data retrieval into Taverna workflows.</p> <p>Conclusion</p> <p>The data exchange standard we present here provides a useful generic format for transfer and integration of genomic and genetic mapping data. The extensibility of our schema allows for inclusion of additional data and provides a mechanism for typing mapping objects via third party standards. Web services retrieving GMD-compliant mapping data demonstrate that use of this exchange standard provides a practical mechanism for achieving data integration, by facilitating syntactically and semantically-controlled access to the data.</p

Purple sulfur bacteria fix N-2 via molybdenum-nitrogenase in a low molybdenum Proterozoic ocean analogue

Biological N-2 fixation was key to the expansion of life on early Earth. The N-2-fixing microorganisms and the nitrogenase type used in the Proterozoic are unknown, although it has been proposed that the canonical molybdenum-nitrogenase was not used due to low molybdenum availability. We investigate N-2 fixation in Lake Cadagno, an analogue system to the sulfidic Proterozoic continental margins, using a combination of biogeochemical, molecular and single cell techniques. In Lake Cadagno, purple sulfur bacteria (PSB) are responsible for high N-2 fixation rates, to our knowledge providing the first direct evidence for PSB in situ N-2 fixation. Surprisingly, no alternative nitrogenases are detectable, and N-2 fixation is exclusively catalyzed by molybdenum-nitrogenase. Our results show that molybdenum-nitrogenase is functional at low molybdenum conditions in situ and that in contrast to previous beliefs, PSB may have driven N-2 fixation in the Proterozoic ocean. N-2 fixation was key to the expansion of life on Earth, but which organisms fixed N-2 and if Mo-nitrogenase was functional in the low Mo early ocean is unknown. Here, the authors show that purple sulfur bacteria fix N-2 using Mo-nitrogenase in a Proterozoic ocean analogue, despite low Mo conditions

PHI-base update: additions to the pathogen–host interaction database

The pathogen–host interaction database (PHI-base) is a web-accessible database that catalogues experimentally verified pathogenicity, virulence and effector genes from bacterial, fungal and Oomycete pathogens, which infect human, animal, plant, insect, fish and fungal hosts. Plant endophytes are also included. PHI-base is therefore an invaluable resource for the discovery of genes in medically and agronomically important pathogens, which may be potential targets for chemical intervention. The database is freely accessible to both academic and non-academic users. This publication describes recent additions to the database and both current and future applications. The number of fields that characterize PHI-base entries has almost doubled. Important additional fields deal with new experimental methods, strain information, pathogenicity islands and external references that link the database to external resources, for example, gene ontology terms and Locus IDs. Another important addition is the inclusion of anti-infectives and their target genes that makes it possible to predict the compounds, that may interact with newly identified virulence factors. In parallel, the curation process has been improved and now involves several external experts. On the technical side, several new search tools have been provided and the database is also now distributed in XML format. PHI-base is available at: http://www.phi-base.org/

MPHASYS: a mouse phenotype analysis system

<p>Abstract</p> <p>Background</p> <p>Systematic, high-throughput studies of mouse phenotypes have been hampered by the inability to analyze individual animal data from a multitude of sources in an integrated manner. Studies generally make comparisons at the level of genotype or treatment thereby excluding associations that may be subtle or involve compound phenotypes. Additionally, the lack of integrated, standardized ontologies and methodologies for data exchange has inhibited scientific collaboration and discovery.</p> <p>Results</p> <p>Here we introduce a Mouse Phenotype Analysis System (MPHASYS), a platform for integrating data generated by studies of mouse models of human biology and disease such as aging and cancer. This computational platform is designed to provide a standardized methodology for working with animal data; a framework for data entry, analysis and sharing; and ontologies and methodologies for ensuring accurate data capture. We describe the tools that currently comprise MPHASYS, primarily ones related to mouse pathology, and outline its use in a study of individual animal-specific patterns of multiple pathology in mice harboring a specific germline mutation in the DNA repair and transcription-specific gene Xpd.</p> <p>Conclusion</p> <p>MPHASYS is a system for analyzing multiple data types from individual animals. It provides a framework for developing data analysis applications, and tools for collecting and distributing high-quality data. The software is platform independent and freely available under an open-source license <abbrgrp><abbr bid="B1">1</abbr></abbrgrp>.</p

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