Structural and Functional Insights from the Metagenome of an Acidic Hot Spring Microbial Planktonic Community in the Colombian Andes

A taxonomic and annotated functional description of microbial life was deduced from 53 Mb of metagenomic sequence retrieved from a planktonic fraction of the Neotropical high Andean (3,973 meters above sea level) acidic hot spring El Coquito (EC). A classification of unassembled metagenomic reads using different databases showed a high proportion of Gammaproteobacteria and Alphaproteobacteria (in total read affiliation), and through taxonomic affiliation of 16S rRNA gene fragments we observed the presence of Proteobacteria, micro-algae chloroplast and Firmicutes. Reads mapped against the genomes Acidiphilium cryptum JF-5, Legionella pneumophila str. Corby and Acidithiobacillus caldus revealed the presence of transposase-like sequences, potentially involved in horizontal gene transfer. Functional annotation and hierarchical comparison with different datasets obtained by pyrosequencing in different ecosystems showed that the microbial community also contained extensive DNA repair systems, possibly to cope with ultraviolet radiation at such high altitudes. Analysis of genes involved in the nitrogen cycle indicated the presence of dissimilatory nitrate reduction to N2 (narGHI, nirS, norBCDQ and nosZ), associated with Proteobacteria-like sequences. Genes involved in the sulfur cycle (cysDN, cysNC and aprA) indicated adenylsulfate and sulfite production that were affiliated to several bacterial species. In summary, metagenomic sequence data provided insight regarding the structure and possible functions of this hot spring microbial community, describing some groups potentially involved in the nitrogen and sulfur cycling in this environment. Citation: Jimenez DJ, Andreote FD, Chaves D, Montana JS, Osorio-Forero C, et al. (2012) Structural and Functional Insights from the Metagenome of an Acidic Hot Spring Microbial Planktonic Community in the Colombian Andes. PLoS ONE 7(12): e52069. doi:10.1371/journal.pone.0052069

Describing the Situational Contexts of Sweetened Product Consumption in a Middle Eastern Canadian Community: Application of a Mixed Method Design

Little is known about the situational contexts in which individuals consume processed sources of dietary sugars. This study aimed to describe the situational contexts associated with the consumption of sweetened food and drink products in a Catholic Middle Eastern Canadian community. A two-stage exploratory sequential mixed-method design was employed with a rationale of triangulation. In stage 1 (n = 62), items and themes describing the situational contexts of sweetened food and drink product consumption were identified from semi-structured interviews and were used to develop the content for the Situational Context Instrument for Sweetened Product Consumption (SCISPC). Face validity, readability and cultural relevance of the instrument were assessed. In stage 2 (n = 192), a cross-sectional study was conducted and exploratory factor analysis was used to examine the structure of themes that emerged from the qualitative analysis as a means of furthering construct validation. The SCISPC reliability and predictive validity on the daily consumption of sweetened products were also assessed. In stage 1, six themes and 40-items describing the situational contexts of sweetened product consumption emerged from the qualitative analysis and were used to construct the first draft of the SCISPC. In stage 2, factor analysis enabled the clarification and/or expansion of the instrument's initial thematic structure. The revised SCISPC has seven factors and 31 items describing the situational contexts of sweetened product consumption. Initial validation of the instrument indicated it has excellent internal consistency and adequate test-retest reliability. Two factors of the SCISPC had predictive validity for the daily consumption of total sugar from sweetened products (Snacking and Energy demands) while the other factors (Socialization, Indulgence, Constraints, Visual Stimuli and Emotional needs) were rather associated to occasional consumption of these products.

Spatial and Temporal Variation of Archaeal, Bacterial and Fungal Communities in Agricultural Soils

Background: Soil microbial communities are in constant change at many different temporal and spatial scales. However, the importance of these changes to the turnover of the soil microbial communities has been rarely studied simultaneously in space and time. Methodology/Principal Findings: In this study, we explored the temporal and spatial responses of soil bacterial, archaeal and fungal beta-diversities to abiotic parameters. Taking into account data from a 3-year sampling period, we analyzed the abundances and community structures of Archaea, Bacteria and Fungi along with key soil chemical parameters. We questioned how these abiotic variables influence the turnover of bacterial, archaeal and fungal communities and how they impact the long-term patterns of changes of the aforementioned soil communities. Interestingly, we found that the bacterial and fungal b-diversities are quite stable over time, whereas archaeal diversity showed significantly higher fluctuations. These fluctuations were reflected in temporal turnover caused by soil management through addition of N-fertilizers. Conclusions: Our study showed that management practices applied to agricultural soils might not significantly affect the bacterial and fungal communities, but cause slow and long-term changes in the abundance and structure of the archaeal community. Moreover, the results suggest that, to different extents, abiotic and biotic factors determine the community assembly of archaeal, bacterial and fungal communities.

Research Blogging: Indexing and Registering the Change in Science 2.0

Increasing public interest in science information in a digital and 2.0 science era promotes a dramatically, rapid and deep change in science itself. The emergence and expansion of new technologies and internet-based tools is leading to new means to improve scientific methodology and communication, assessment, promotion and certification. It allows methods of acquisition, manipulation and storage, generating vast quantities of data that can further facilitate the research process. It also improves access to scientific results through information sharing and discussion. Content previously restricted only to specialists is now available to a wider audience. This context requires new management systems to make scientific knowledge more accessible and useable, including new measures to evaluate the reach of scientific information. The new science and research quality measures are strongly related to the new online technologies and services based in social media. Tools such as blogs, social bookmarks and online reference managers, Twitter and others offer alternative, transparent and more comprehensive information about the active interest, usage and reach of scientific publications. Another of these new filters is the Research Blogging platform, which was created in 2007 and now has over 1,230 active blogs, with over 26,960 entries posted about peer-reviewed research on subjects ranging from Anthropology to Zoology. This study takes a closer look at RB, in order to get insights into its contribution to the rapidly changing landscape of scientific communication.

DIGITAL LIBRARIES AND LEARNING OBJECTS REPOSITORIES

Discusses the technological changes that affects learning organizations as well as the human, technical, legal and sustainable aspects regarding learning objects repositories creation, maintenance and use. It presents concepts of information objects and learning objects, the functional requirements needed to their storage at Learning Management Systems. The role of Metadata is reviewed concerning learning objects creation and retrieval, followed by considerations about learning object repositories models, community participation/collaborative strategies and potential derived metrics/indicators. As a result of this desktop research, it can be said that not only technical competencies are critical to any learning objects repository implementation, but it urges that an engaged community of interest be establish as a key to support a learning object repository project. On that matter, researchers are applying Activity Theory (Vygostky, Luria y Leontiev) in order to seek joint perceptions and actions involving learning objects repository users, curators and managers, perceived as critical assets to a successful proposal.

Evolution of Body Elongation in Gymnophthalmid Lizards: Relationships with Climate

The evolution of elongated body shapes in vertebrates has intrigued biologists for decades and is particularly recurrent among squamates. Several aspects might explain how the environment influences the evolution of body elongation, but climate needs to be incorporated in this scenario to evaluate how it contributes to morphological evolution. Climatic parameters include temperature and precipitation, two variables that likely influence environmental characteristics, including soil texture and substrate coverage, which may define the selective pressures acting during the evolution of morphology. Due to development of geographic information system (GIS) techniques, these variables can now be included in evolutionary biology studies and were used in the present study to test for associations between variation in body shape and climate in the tropical lizard family Gymnophthalmidae. We first investigated how the morphological traits that define body shape are correlated in these lizards and then tested for associations between a descriptor of body elongation and climate. Our analyses revealed that the evolution of body elongation in Gymnophthalmidae involved concomitant changes in different morphological traits: trunk elongation was coupled with limb shortening and a reduction in body diameter, and the gradual variation along this axis was illustrated by less-elongated morphologies exhibiting shorter trunks and longer limbs. The variation identified in Gymnophthalmidae body shape was associated with climate, with the species from more arid environments usually being more elongated. Aridity is associated with high temperatures and low precipitation, which affect additional environmental features, including the habitat structure. This feature may influence the evolution of body shape because contrasting environments likely impose distinct demands for organismal performance in several activities, such as locomotion and thermoregulation. The present study establishes a connection between morphology and a broader natural component, climate, and introduces new questions about the spatial distribution of morphological variation among squamates.

Rhodolith Beds Are Major CaCO3 Bio-Factories in the Tropical South West Atlantic

Rhodoliths are nodules of non-geniculate coralline algae that occur in shallow waters (<150 m depth) subjected to episodic disturbance. Rhodolith beds stand with kelp beds, seagrass meadows, and coralline algal reefs as one of the world's four largest macrophyte-dominated benthic communities. Geographic distribution of rhodolith beds is discontinuous, with large concentrations off Japan, Australia and the Gulf of California, as well as in the Mediterranean, North Atlantic, eastern Caribbean and Brazil. Although there are major gaps in terms of seabed habitat mapping, the largest rhodolith beds are purported to occur off Brazil, where these communities are recorded across a wide latitudinal range (2 degrees N - 27 degrees S). To quantify their extent, we carried out an inter-reefal seabed habitat survey on the Abrolhos Shelf (16 degrees 50' - 19 degrees 45'S) off eastern Brazil, and confirmed the most expansive and contiguous rhodolith bed in the world, covering about 20,900 km(2). Distribution, extent, composition and structure of this bed were assessed with side scan sonar, remotely operated vehicles, and SCUBA. The mean rate of CaCO3 production was estimated from in situ growth assays at 1.07 kg m(-2) yr(-1), with a total production rate of 0.025 Gt yr(-1), comparable to those of the world's largest biogenic CaCO3 deposits. These gigantic rhodolith beds, of areal extent equivalent to the Great Barrier Reef, Australia, are a critical, yet poorly understood component of the tropical South Atlantic Ocean. Based on the relatively high vulnerability of coralline algae to ocean acidification, these beds are likely to experience a profound restructuring in the coming decades.

Potential Drug-Drug Interactions in Prescriptions to Patients over 45 Years of Age in Primary Care, Southern Brazil

Background: Few cross-sectional studies involving adults and elderly patients with major DDIs have been conducted in the primary care setting. The study aimed to investigate the prevalence of potential drug-drug interactions (DDIs) in patients treated in primary care. Methodology/Principal Findings: A cross-sectional study involving patients aged 45 years or older was conducted at 25 Basic Health Units in the city of Maringa (southern Brazil) from May to December 2010. The data were collected from prescriptions at the pharmacy of the health unit at the time of the delivery of medication to the patient. After delivery, the researcher checked the electronic medical records of the patient. A total of 827 patients were investigated (mean age: 64.1; mean number of medications: 4.4). DDIs were identified in the Micromedex (R) database. The prevalence of potential DDIs and major DDIs was 63.0% and 12.1%, respectively. In both the univariate and multivariate analyses, the number of drugs prescribed was significantly associated with potential DDIs, with an increasing risk from three to five drugs (OR = 4.74; 95% CI: 2.90-7.73) to six or more drugs (OR = 23.03; 95% CI: 10.42-50.91). Forty drugs accounted for 122 pairs of major DDIs, the most frequent of which involved simvastatin (23.8%), captopril/enalapril (16.4%) and fluoxetine (16.4%). Conclusions/Significance: This is the first large-scale study on primary care carried out in Latin America. Based on the findings, the estimated prevalence of potential DDIs was high, whereas clinically significant DDIs occurred in a smaller proportion. Exposing patients to a greater number of prescription drugs, especially three or more, proved to be a significant predictor of DDIs. Prescribers should be more aware of potential DDIs. Future studies should assess potential DDIs in primary care over a longer period of time.

Mutual Information Rate and Bounds for It

The amount of information exchanged per unit of time between two nodes in a dynamical network or between two data sets is a powerful concept for analysing complex systems. This quantity, known as the mutual information rate (MIR), is calculated from the mutual information, which is rigorously defined only for random systems. Moreover, the definition of mutual information is based on probabilities of significant events. This work offers a simple alternative way to calculate the MIR in dynamical (deterministic) networks or between two time series (not fully deterministic), and to calculate its upper and lower bounds without having to calculate probabilities, but rather in terms of well known and well defined quantities in dynamical systems. As possible applications of our bounds, we study the relationship between synchronisation and the exchange of information in a system of two coupled maps and in experimental networks of coupled oscillators.

Three-feature model to reproduce the topology of citation networks and the effects from authors' visibility on their h-index

Various factors are believed to govern the selection of references in citation networks, but a precise, quantitative determination of their importance has remained elusive. In this paper, we show that three factors can account for the referencing pattern of citation networks for two topics, namely "graphenes" and "complex networks", thus allowing one to reproduce the topological features of the networks built with papers being the nodes and the edges established by citations. The most relevant factor was content similarity, while the other two - in-degree (i.e. citation counts) and age of publication - had varying importance depending on the topic studied. This dependence indicates that additional factors could play a role. Indeed, by intuition one should expect the reputation (or visibility) of authors and/or institutions to affect the referencing pattern, and this is only indirectly considered via the in-degree that should correlate with such reputation. Because information on reputation is not readily available, we simulated its effect on artificial citation networks considering two communities with distinct fitness (visibility) parameters. One community was assumed to have twice the fitness value of the other, which amounts to a double probability for a paper being cited. While the h-index for authors in the community with larger fitness evolved with time with slightly higher values than for the control network (no fitness considered), a drastic effect was noted for the community with smaller fitness. (C) 2012 Elsevier Ltd. All rights reserved.

Taxonomic and Functional Microbial Signatures of the Endemic Marine Sponge Arenosclera brasiliensis

The endemic marine sponge Arenosclera brasiliensis (Porifera, Demospongiae, Haplosclerida) is a known source of secondary metabolites such as arenosclerins A-C. In the present study, we established the composition of the A. brasiliensis microbiome and the metabolic pathways associated with this community. We used 454 shotgun pyrosequencing to generate approximately 640,000 high-quality sponge-derived sequences (similar to 150 Mb). Clustering analysis including sponge, seawater and twenty-three other metagenomes derived from marine animal microbiomes shows that A. brasiliensis contains a specific microbiome. Fourteen bacterial phyla (including Proteobacteria, Cyanobacteria, Actinobacteria, Bacteroidetes, Firmicutes and Cloroflexi) were consistently found in the A. brasiliensis metagenomes. The A. brasiliensis microbiome is enriched for Betaproteobacteria (e.g., Burkholderia) and Gammaproteobacteria (e.g., Pseudomonas and Alteromonas) compared with the surrounding planktonic microbial communities. Functional analysis based on Rapid Annotation using Subsystem Technology (RAST) indicated that the A. brasiliensis microbiome is enriched for sequences associated with membrane transport and one-carbon metabolism. In addition, there was an overrepresentation of sequences associated with aerobic and anaerobic metabolism as well as the synthesis and degradation of secondary metabolites. This study represents the first analysis of sponge-associated microbial communities via shotgun pyrosequencing, a strategy commonly applied in similar analyses in other marine invertebrate hosts, such as corals and algae. We demonstrate that A. brasiliensis has a unique microbiome that is distinct from that of the surrounding planktonic microbes and from other marine organisms, indicating a species-specific microbiome.

Preserving Iron Gall Ink Objects in Collections in South and Central America and the Caribbean, Part 1: Assessing Preservation Needs of Ink-Corroded Materials

Most museums, libraries, and archives throughout the world have to deal with paper damaged by iron gall ink. For more than a decade international research has been devoted to the topic in an attempt to provide practical treatments for objects and formulate guidelines for the preservation of iron gall ink collections. A working group of conservators in South and Central America and the Caribbean have developed a program to disseminate research findings, collect data about the condition of iron gall ink collections in their countries and identify imminent training needs. The goal of this project is to combine the latest research with existing and acceptable conservation practices and share information about risk management, proper housing, examination and treatment of iron gall ink inscribed artefacts-at risk. Communications among colleagues were established to learn more about the current resources available in collections from various countries.

Ofertas de trabalho na Web para os profissionais brasileiros da informação-documentação: análise das competências e habilidades exigidas pelas empresas e instituições

Analisam-se as características de ofertas de emprego do setor da Informação-Documentação. A mostra foi obtida de anúncios na Internet, feitos por empresas e instituições privadas brasileiras, durante o ano de 2010. A atividade foi realizada no âmbito de pesquisa maior, que tem como objetivo geral construir uma taxonomia que classifique e hierarquize as competências e conhecimentos exigidos pelas empresas, bem como as características dos postos oferecidos. Extraiu-se a informação de 200 ofertas de emprego obtidas nos portais Catho e Portal do bibliotecário. Cada entrada foi mantida em seu contexto de incidência e com a expressão original. Os termos obtidos passaram por um processo de normalização. A análise busca classificar e valorar as atividades, conhecimentos e tarefas mais solicitados, bem como as aptidões, competências e habilidades, além das incidências das unidades e dos profissionais de informação.

FGFR4 Profile as a Prognostic Marker in Squamous Cell Carcinoma of the Mouth and Oropharynx

Background: Fibroblast growth factor receptor 4 (FGFR4) is a member of a receptor tyrosine kinase family of enzymes involved in cell cycle control and proliferation. A common single nucleotide polymorphism (SNP) Gly388Arg variant has been associated with increased tumor cell motility and progression of breast cancer, head and neck cancer and soft tissue sarcomas. The present study evaluated the prognostic significance of FGFR4 in oral and oropharynx carcinomas, finding an association of FGFR4 expression and Gly388Arg genotype with tumor onset and prognosis. Patients and Methods: DNA from peripheral blood of 122 patients with oral and oropharyngeal squamous cell carcinomas was used to determine FGFR4 genotype by PCR-RFLP. Protein expression was assessed by immunohistochemistry (IHC) on paraffin-embedded tissue microarrays. Results: Presence of allele Arg388 was associated with lymphatic embolization and with disease related premature death. In addition, FGFR4 low expression was related with lymph node positivity and premature relapse of disease, as well as disease related death. Conclusion: Our results propose FGFR4 profile, measured by the Gly388Arg genotype and expression, as a novel marker of prognosis in squamous cell carcinoma of the mouth and oropharynx.

Evolutionary Diversification of Banded Tube-Dwelling Anemones (Cnidaria; Ceriantharia; Isarachnanthus) in the Atlantic Ocean

The use of molecular data for species delimitation in Anthozoa is still a very delicate issue. This is probably due to the low genetic variation found among the molecular markers (primarily mitochondrial) commonly used for Anthozoa. Ceriantharia is an anthozoan group that has not been tested for genetic divergence at the species level. Recently, all three Atlantic species described for the genus Isarachnanthus of Atlantic Ocean, were deemed synonyms based on morphological simmilarities of only one species: Isarachnanthus maderensis. Here, we aimed to verify whether genetic relationships (using COI, 16S, ITS1 and ITS2 molecular markers) confirmed morphological affinities among members of Isarachnanthus from different regions across the Atlantic Ocean. Results from four DNA markers were completely congruent and revealed that two different species exist in the Atlantic Ocean. The low identification success and substantial overlap between intra and interspecific COI distances render the Anthozoa unsuitable for DNA barcoding, which is not true for Ceriantharia. In addition, genetic divergence within and between Ceriantharia species is more similar to that found in Medusozoa (Hydrozoa and Scyphozoa) than Anthozoa and Porifera that have divergence rates similar to typical metazoans. The two genetic species could also be separated based on micromorphological characteristics of their cnidomes. Using a specimen of Isarachnanthus bandanensis from Pacific Ocean as an outgroup, it was possible to estimate the minimum date of divergence between the clades. The cladogenesis event that formed the species of the Atlantic Ocean is estimated to have occured around 8.5 million years ago (Miocene) and several possible speciation scenarios are discussed.